In [6]:
from ome import base,settings
In [7]:
base.engine
Out[7]:
Engine(postgresql://:@localhost:5432/ome)
In [8]:
settings.data_directory
Out[8]:
'/Users/sfederow/ome_data/'
In [9]:
session = base.Session()
session.query(base.Genome).all()
Out[9]:
[Genome (#1) PRJNA43747 Saccharomyces cerevisiae S288c,
Genome (#26422) PRJNA57779 Escherichia coli str. K-12 substr. MG1655]
In [10]:
from ome import components
#components.
In [11]:
session.query(components.Gene).filter_by(name = 'gapA').all()
Out[11]:
[Gene: (b1779, gapA) 1860794-1861790 (+)]
In [12]:
gapA = session.query(components.Gene).filter_by(name = 'gapA').one()
In [13]:
gapA.protein
Out[13]:
[Protein (#43313, enzyme; Energy metabolism, carbon: Glycolysis)]
In [14]:
gapA.groups
Out[14]:
[]
In [10]:
from om.components import *
session.query(Protein).filter(Protein.long_name.ilike('groE%')).all()
Out[10]:
[Protein (#3904, GroEL, chaperone Hsp60, peptide-dependent ATPase, heat shock protein),
Protein (#3903, GroES, chaperone binds to Hsp60 in pres. Mg-ATP, suppressing its ATPase activity)]
In [11]:
GroE = session.query(Protein).filter(Protein.long_name.ilike('groE%')).first()
In [12]:
GroE.gene
Out[12]:
Gene: (b4143, groL) 4369047-4370694 (+)
In [13]:
GroE.parent
Out[13]:
[Complex (#4700): GroEL-GroES chaperonin complex]
In [15]:
GroE.parent[0].children
Out[15]:
[Protein (#3903, GroES, chaperone binds to Hsp60 in pres. Mg-ATP, suppressing its ATPase activity),
Protein (#3904, GroEL, chaperone Hsp60, peptide-dependent ATPase, heat shock protein)]
In [16]:
PdhR = session.query(Protein).filter(Protein.long_name.ilike('PdhR%')).first()
PdhR.parent
Out[16]:
[Complex (#4894): PdhR-pyruvate]
In [17]:
PdhR.parent[0].children
Out[17]:
[Protein (#108, PdhR DNA-binding transcriptional dual regulator)]
In [18]:
session.query(Complex).limit(20).all()
Out[18]:
[Complex (#4146): transcription termination factor Rho,
Complex (#4147): CcmCDE protoheme IX reservoir complex,
Complex (#4148): pyruvate dehydrogenase,
Complex (#4149): soluble NADH dehydrogenase fragment,
Complex (#4150): <i>N</i>-acetylneuraminate mutarotase,
Complex (#4151): fused diaminohydroxyphosphoribosylaminopyrimidine deaminase / 5-amino-6-(5-phosphoribosylamino)uracil reductase,
Complex (#4152): branched-chain amino-acid aminotransferase,
Complex (#4153): molybdate ABC transporter,
Complex (#4154): MazE-MazF antitoxin/toxin complex and DNA-binding transcriptional repressor,
Complex (#4155): MazF toxin of the MazF-MazE toxin-antitoxin system that exhibits ribonuclease activity,
Complex (#4156): MazE antitoxin of the MazF-MazE toxin-antitoxin system,
Complex (#4157): galactofuranose / galactopyranose ABC transporter,
Complex (#4158): fused glutathionylspermidine amidase / glutathionylspermidine synthetase,
Complex (#4159): aliphatic sulfonate ABC transporter,
Complex (#4160): AcrEF-TolC multidrug efflux transport system,
Complex (#4161): TolC outer membrane channel,
Complex (#4162): 23S rRNA m<sup>3</sup>Ψ1915 methyltransferase,
Complex (#4163): predicted rRNA methyltransferase,
Complex (#4164): HipAB toxin/antitoxin complex and DNA-binding transcriptional repressor,
Complex (#4165): HipB antitoxin and DNA-binding transcriptional repressor]
In [31]:
session.query(Complex).filter(Complex.long_name.ilike('HipAB%')).first().children
Out[31]:
[Protein (#1417, phosphorylated serine/threonine kinase HipA),
Complex (#4165): HipB antitoxin and DNA-binding transcriptional repressor]
In [32]:
session.query(TU).limit(10).all()
Out[32]:
[TU (#10228, sdhCDAB-sucABCD),
TU (#10229, rcsC),
TU (#10230, znuCB),
TU (#10231, yjeFE-amiB-mutL-miaA-hfq-hflXKC),
TU (#10232, gsk),
TU (#10233, guaC),
TU (#10234, fsaA),
TU (#10235, hdfR),
TU (#10236, lpp),
TU (#10237, pdhR-aceEF-lpdA)]
In [33]:
pdhR_aceEF_lpdA = session.query(TU).filter(TU.name.ilike('pdhR%')).first()
In [34]:
pdhR_aceEF_lpdA.genes
Out[34]:
[Gene: (b0113, pdhR) 122091-122856 (+),
Gene: (b0114, aceE) 123016-125680 (+),
Gene: (b0115, aceF) 125694-127587 (+),
Gene: (b0116, lpd) 127911-129336 (+)]
In [35]:
pdhR_aceEF_lpdA.genome_region.leftpos
Out[35]:
122034
In [36]:
session.query(DnaBindingSite).limit(10).all()
Out[36]:
[DNA (#4966, BS0-2550) 786853-786853 +,
DNA (#4967, BS0-1342) 3681627-3681627 +,
DNA (#4968, BS00207) 4630726-4630726 +,
DNA (#4969, BS0-8130) 1102827-1102827 +,
DNA (#4970, BS0-8133) 2585498-2585514 +,
DNA (#4971, BS0-8134) 2585468-2585480 +,
DNA (#4972, BS0-8135) 2585435-2585453 +,
DNA (#4973, BS0-8136) 2151929-2151943 +,
DNA (#4974, BS0-8137) 3037213-3037213 +,
DNA (#4975, BS0-8138) 3865415-3865431 +]
In [38]:
from sqlalchemy import func
session.query(func.distinct(components.Component.type)).all()
Out[38]:
[(u'complex'), (u'binding_site'), (u'tu'), (u'protein'), (u'component')]
In [39]:
session.query(Metabolite).all()
Out[39]:
[]
In [40]:
from om import data
In [ ]:
data.
Pretty much everything is a dataset.
Every dataset has a strain, an environment, a type, and a datasource.
In [41]:
session.query(data.DataSet).all()
Out[41]:
[ChIPExperiment (#1, ChIPExo-RpoD_wt_fructose_NH4Cl_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#2, ChIPExo-RpoD_wt_fructose_NH4Cl_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#3, ChIPExo-RpoD_wt_fructose_NH4Cl_O2_3_anti-rpod): ChIPExo RpoD 3,
ChIPExperiment (#4, ChIPExo-RpoD_wt_glucose_NH4Cl_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#5, ChIPExo-RpoD_wt_glucose_NH4Cl_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#6, ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#7, ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#8, ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_3_anti-rpod): ChIPExo RpoD 3,
ChIPExperiment (#9, ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_2_anti-myc): ChIPExo ArcA 2,
ChIPExperiment (#10, ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_3_anti-myc): ChIPExo ArcA 3,
ChIPExperiment (#11, ChIPExo-Crp_Ar3_glycerol_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#12, ChIPExo-Crp_Ar3_glycerol_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#13, ChIPExo-Crp_Ar3_glycerol_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#14, ChIPExo-Crp_Crp8myc_fructose_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#15, ChIPExo-Crp_Crp8myc_fructose_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#16, ChIPExo-Crp_Crp8myc_glucose_NH4Cl_O2_1_anti-myc): ChIPExo Crp 1,
ChIPExperiment (#17, ChIPExo-Crp_Crp8myc_glucose_NH4Cl_O2_2_anti-myc): ChIPExo Crp 2,
ChIPExperiment (#18, ChIPExo-Crp_Crp8myc_glycerol_NH4Cl_O2_1_anti-myc): ChIPExo Crp 1,
ChIPExperiment (#19, ChIPExo-Crp_Crp8myc_glycerol_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#20, ChIPExo-Crp_Crp8myc_glycerol_NH4Cl_O2_2_anti-myc): ChIPExo Crp 2,
ChIPExperiment (#21, ChIPExo-Crp_Crp8myc_glycerol_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#22, ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#23, ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#24, ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#25, ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#26, ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#27, ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#28, ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#29, ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#30, ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#31, ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#32, ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#33, ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#34, ChIPExo-Crp_wt_fructose_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#35, ChIPExo-Crp_wt_fructose_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#36, ChIPExo-Crp_wt_fructose_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#37, ChIPExo-Crp_wt_fructose_NH4Cl_O2_4_anti-crp): ChIPExo Crp 4,
ChIPExperiment (#38, ChIPExo-Crp_wt_fructose_NH4Cl_O2_5_anti-crp): ChIPExo Crp 5,
ChIPExperiment (#39, ChIPExo-Crp_wt_glucose_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#40, ChIPExo-Crp_wt_glucose_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#41, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#42, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp_rif): ChIPExo Crp 1,
ChIPExperiment (#43, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#44, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp_rif): ChIPExo Crp 2,
ChIPExperiment (#45, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#46, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp_rif): ChIPExo Crp 3,
ChIPExperiment (#47, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_4_anti-crp): ChIPExo Crp 4,
ChIPExperiment (#48, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_5_anti-crp): ChIPExo Crp 5,
ChIPExperiment (#49, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_6_anti-crp): ChIPExo Crp 6,
ChIPExperiment (#50, ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_2_anti-myc): ChIPExo Fnr 2,
ChIPExperiment (#51, ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_3_anti-myc): ChIPExo Fnr 3,
ChIPExperiment (#52, ChIPExo-RpoA_wt_glucose_NH4Cl_O2_1_anti-rpoA): ChIPExo RpoA 1,
ChIPExperiment (#53, ChIPExo-RpoA_wt_glucose_NH4Cl_O2_2_anti-rpoA): ChIPExo RpoA 2,
ChIPExperiment (#54, ChIPExo-Fur_Fur8myc_glucose_NH4Cl_O2_1_anti-myc_dpd): ChIPExo Fur 1,
ChIPExperiment (#55, ChIPExo-Fur_Fur8myc_glucose_NH4Cl_O2_1_anti-myc_FeCl2): ChIPExo Fur 1,
ChIPExperiment (#56, ChIPExo-Fur_Fur8myc_glucose_NH4Cl_O2_2_anti-myc_dpd): ChIPExo Fur 2,
ChIPExperiment (#57, ChIPExo-Fur_Fur8myc_glucose_NH4Cl_O2_2_anti-myc_FeCl2): ChIPExo Fur 2,
ChIPExperiment (#58, ChIPExo-Nac_Nac8myc_glucose_cytidine_O2_1_anti-myc): ChIPExo Nac 1,
ChIPExperiment (#59, ChIPExo-Nac_Nac8myc_glucose_cytidine_O2_2_anti-myc): ChIPExo Nac 2,
ChIPExperiment (#60, ChIPExo-Nac_Nac8myc_glucose_cytosine_O2_1_anti-myc): ChIPExo Nac 1,
ChIPExperiment (#61, ChIPExo-Nac_Nac8myc_glucose_cytosine_O2_2_anti-myc): ChIPExo Nac 2,
ChIPExperiment (#62, ChIPExo-Nac_Nac8myc_glucose_glutamine_O2_1_anti-myc): ChIPExo Nac 1,
ChIPExperiment (#63, ChIPExo-Nac_Nac8myc_glucose_glutamine_O2_2_anti-myc): ChIPExo Nac 2,
ChIPExperiment (#64, ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_1_anti-myc): ChIPExo Nac 1,
ChIPExperiment (#65, ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_2_anti-myc): ChIPExo Nac 2,
ChIPExperiment (#66, ChIPExo-NtrC_NtrC8myc_glucose_cytidine_O2_1_anti-myc): ChIPExo NtrC 1,
ChIPExperiment (#67, ChIPExo-NtrC_NtrC8myc_glucose_cytidine_O2_2_anti-myc): ChIPExo NtrC 2,
ChIPExperiment (#68, ChIPExo-NtrC_NtrC8myc_glucose_cytosine_O2_1_anti-myc): ChIPExo NtrC 1,
ChIPExperiment (#69, ChIPExo-NtrC_NtrC8myc_glucose_cytosine_O2_2_anti-myc): ChIPExo NtrC 2,
ChIPExperiment (#70, ChIPExo-NtrC_NtrC8myc_glucose_glutamine_O2_1_anti-myc): ChIPExo NtrC 1,
ChIPExperiment (#71, ChIPExo-NtrC_NtrC8myc_glucose_glutamine_O2_2_anti-myc): ChIPExo NtrC 2,
ChIPExperiment (#72, ChIPExo-NtrC_NtrC8myc_glucose_NH4Cl_O2_1_anti-myc): ChIPExo NtrC 1,
ChIPExperiment (#73, ChIPExo-NtrC_NtrC8myc_glucose_NH4Cl_O2_2_anti-myc): ChIPExo NtrC 2,
ChIPExperiment (#74, ChIPExo-RpoD_wt_glucose_cytidine_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#75, ChIPExo-RpoD_wt_glucose_cytidine_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#76, ChIPExo-RpoD_wt_glucose_cytosine_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#77, ChIPExo-RpoD_wt_glucose_cytosine_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#78, ChIPExo-RpoD_wt_glucose_glutamine_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#79, ChIPExo-RpoD_wt_glucose_glutamine_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#80, ChIPExo-RpoD_wt_glucose_NH4Cl_O2_1_anti-rpod_nitrogenstudy): ChIPExo RpoD 1,
ChIPExperiment (#81, ChIPExo-RpoD_wt_glucose_NH4Cl_O2_2_anti-rpod_nitrogenstudy): ChIPExo RpoD 2,
ChIPExperiment (#82, ChIPExo-RpoN_wt_glucose_cytidine_O2_1_anti-rpon): ChIPExo RpoN 1,
ChIPExperiment (#83, ChIPExo-RpoN_wt_glucose_cytidine_O2_2_anti-rpon): ChIPExo RpoN 2,
ChIPExperiment (#84, ChIPExo-RpoN_wt_glucose_cytosine_O2_1_anti-rpon): ChIPExo RpoN 1,
ChIPExperiment (#85, ChIPExo-RpoN_wt_glucose_cytosine_O2_2_anti-rpon): ChIPExo RpoN 2,
ChIPExperiment (#86, ChIPExo-RpoN_wt_glucose_glutamine_O2_1_anti-rpon): ChIPExo RpoN 1,
ChIPExperiment (#87, ChIPExo-RpoN_wt_glucose_glutamine_O2_2_anti-rpon): ChIPExo RpoN 2,
ChIPExperiment (#88, ChIPExo-RpoN_wt_glucose_NH4Cl_O2_1_anti-rpon): ChIPExo RpoN 1,
ChIPExperiment (#89, ChIPExo-RpoN_wt_glucose_NH4Cl_O2_1_anti-rpon_nitrogenstudy): ChIPExo RpoN 1,
ChIPExperiment (#90, ChIPExo-RpoN_wt_glucose_NH4Cl_O2_2_anti-rpon): ChIPExo RpoN 2,
ChIPExperiment (#91, ChIPExo-RpoN_wt_glucose_NH4Cl_O2_2_anti-rpon_nitrogenstudy): ChIPExo RpoN 2,
ChIPExperiment (#92, ChIPExo-RpoS_wt_glucose_NH4Cl_O2_1_anti-rpos): ChIPExo RpoS 1,
ChIPExperiment (#93, ChIPExo-RpoS_wt_glucose_NH4Cl_O2_2_anti-rpos): ChIPExo RpoS 2,
ChIPExperiment (#94, ChIPchip-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_1_anti-myc): ChIPchip ArcA 1,
ChIPExperiment (#95, ChIPchip-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_2_anti-myc): ChIPchip ArcA 2,
ChIPExperiment (#96, ChIPchip-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_3_anti-myc): ChIPchip ArcA 3,
ChIPExperiment (#97, ChIPchip-ArcA_ArcA8myc_glucose_NH4Cl_NO3_1_anti-myc): ChIPchip ArcA 1,
ChIPExperiment (#98, ChIPchip-ArcA_ArcA8myc_glucose_NH4Cl_NO3_2_anti-myc): ChIPchip ArcA 2,
ChIPExperiment (#99, ChIPchip-ArcA_ArcA8myc_glucose_NH4Cl_NO3_3_anti-myc): ChIPchip ArcA 3,
ChIPExperiment (#100, ChIPchip-ArgR_ArgR8myc_glucose_NH4Cl_O2_1_anti-myc): ChIPchip ArgR 1,
ChIPExperiment (#101, ChIPchip-ArgR_ArgR8myc_glucose_NH4Cl_O2_2_anti-myc): ChIPchip ArgR 2,
ChIPExperiment (#102, ChIPchip-Cra_Cra8myc_acetate_NH4Cl_O2_1_anti-myc): ChIPchip Cra 1,
ChIPExperiment (#103, ChIPchip-Cra_Cra8myc_acetate_NH4Cl_O2_2_anti-myc): ChIPchip Cra 2,
ChIPExperiment (#104, ChIPchip-Cra_Cra8myc_acetate_NH4Cl_O2_3_anti-myc): ChIPchip Cra 3,
ChIPExperiment (#105, ChIPchip-Cra_Cra8myc_glucose_NH4Cl_anaerobic_1_anti-myc): ChIPchip Cra 1,
ChIPExperiment (#106, ChIPchip-Cra_Cra8myc_glucose_NH4Cl_anaerobic_2_anti-myc): ChIPchip Cra 2,
ChIPExperiment (#107, ChIPchip-Cra_Cra8myc_glucose_NH4Cl_anaerobic_3_anti-myc): ChIPchip Cra 3,
ChIPExperiment (#108, ChIPchip-Cra_Cra8myc_glucose_NH4Cl_O2_1_anti-myc): ChIPchip Cra 1,
ChIPExperiment (#109, ChIPchip-Cra_Cra8myc_glucose_NH4Cl_O2_2_anti-myc): ChIPchip Cra 2,
ChIPExperiment (#110, ChIPchip-Cra_Cra8myc_glucose_NH4Cl_O2_3_anti-myc): ChIPchip Cra 3,
ChIPExperiment (#111, ChIPchip-Crp_Crp8myc_acetate_NH4Cl_O2_2_anti-myc): ChIPchip Crp 2,
ChIPExperiment (#112, ChIPchip-Crp_Crp8myc_acetate_NH4Cl_O2_3_anti-myc): ChIPchip Crp 3,
ChIPExperiment (#113, ChIPchip-Crp_Crp8myc_fructose_NH4Cl_O2_1_anti-myc): ChIPchip Crp 1,
ChIPExperiment (#114, ChIPchip-Crp_Crp8myc_fructose_NH4Cl_O2_2_anti-myc): ChIPchip Crp 2,
ChIPExperiment (#115, ChIPchip-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_1_anti-myc): ChIPchip Fnr 1,
ChIPExperiment (#116, ChIPchip-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_2_anti-myc): ChIPchip Fnr 2,
ChIPExperiment (#117, ChIPchip-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_3_anti-myc): ChIPchip Fnr 3,
ChIPExperiment (#118, ChIPchip-Fnr_Fnr8myc_glucose_NH4Cl_NO3_1_anti-myc): ChIPchip Fnr 1,
ChIPExperiment (#119, ChIPchip-Fnr_Fnr8myc_glucose_NH4Cl_NO3_2_anti-myc): ChIPchip Fnr 2,
ChIPExperiment (#120, ChIPchip-Fnr_Fnr8myc_glucose_NH4Cl_NO3_3_anti-myc): ChIPchip Fnr 3,
ChIPExperiment (#121, ChIPchip-Lrp_Lrp8myc_glucose_NH4Cl_O2_1_anti-myc): ChIPchip Lrp 1,
ChIPExperiment (#122, ChIPchip-Lrp_Lrp8myc_glucose_NH4Cl_O2_2_anti-myc): ChIPchip Lrp 2,
ChIPExperiment (#123, ChIPchip-Lrp_Lrp8myc_glucose_NH4Cl_O2_3_anti-myc): ChIPchip Lrp 3,
ChIPExperiment (#124, ChIPchip-PurR_PurR8myc_glucose_NH4Cl_O2_1_anti-myc): ChIPchip PurR 1,
ChIPExperiment (#125, ChIPchip-PurR_PurR8myc_glucose_NH4Cl_O2_2_anti-myc): ChIPchip PurR 2,
RNASeqExperiment (#126, RNAseq_Ar3_glycerol_NH4Cl_O2_1): 1,
RNASeqExperiment (#127, RNAseq_Ar3_glycerol_NH4Cl_O2_2): 2,
RNASeqExperiment (#128, RNAseq_Ar3_glycerol_NH4Cl_O2_3): 3,
RNASeqExperiment (#129, RNAseq_delAr1_glycerol_NH4Cl_O2_1): 1,
RNASeqExperiment (#130, RNAseq_delAr1_glycerol_NH4Cl_O2_2): 2,
RNASeqExperiment (#131, RNAseq_delAr1_glycerol_NH4Cl_O2_3): 3,
RNASeqExperiment (#132, RNAseq_delAr1delAr2_glycerol_NH4Cl_O2_1): 1,
RNASeqExperiment (#133, RNAseq_delAr1delAr2_glycerol_NH4Cl_O2_2): 2,
RNASeqExperiment (#134, RNAseq_delAr1delAr2_glycerol_NH4Cl_O2_3): 3,
RNASeqExperiment (#135, RNAseq_delAr2_glycerol_NH4Cl_O2_1): 1,
RNASeqExperiment (#136, RNAseq_delAr2_glycerol_NH4Cl_O2_3): 3,
RNASeqExperiment (#137, RNAseq_delta-crp_fructose_NH4Cl_O2_1): 1,
RNASeqExperiment (#138, RNAseq_delta-crp_fructose_NH4Cl_O2_2): 2,
RNASeqExperiment (#139, RNAseq_delta-crp_fructose_NH4Cl_O2_3): 3,
RNASeqExperiment (#140, RNAseq_delta-crp_glucose_NH4Cl_O2_1): 1,
RNASeqExperiment (#141, RNAseq_delta-crp_glucose_NH4Cl_O2_2): 2,
RNASeqExperiment (#142, RNAseq_delta-crp_glucose_NH4Cl_O2_3): 3,
RNASeqExperiment (#143, RNAseq_delta-crp_glycerol_NH4Cl_O2_1): 1,
RNASeqExperiment (#144, RNAseq_delta-crp_glycerol_NH4Cl_O2_2): 2,
RNASeqExperiment (#145, RNAseq_delta-crp_glycerol_NH4Cl_O2_3): 3,
RNASeqExperiment (#146, RNAseq_wt_fructose_NH4Cl_O2_1): 1,
RNASeqExperiment (#147, RNAseq_wt_fructose_NH4Cl_O2_2): 2,
RNASeqExperiment (#148, RNAseq_wt_glucose_NH4Cl_O2_1): 1,
RNASeqExperiment (#149, RNAseq_wt_glucose_NH4Cl_O2_2): 2,
RNASeqExperiment (#150, RNAseq_wt_glycerol_NH4Cl_O2_1): 1,
RNASeqExperiment (#151, RNAseq_wt_glycerol_NH4Cl_O2_2): 2,
RNASeqExperiment (#152, RNAseq_delAr2_glycerol_NH4Cl_O2_2): 2,
RNASeqExperiment (#153, RNAseq_bw25113_acetate_NH4Cl_O2_1_thiamine): 1,
RNASeqExperiment (#154, RNAseq_bw25113_acetate_NH4Cl_O2_2_thiamine): 2,
RNASeqExperiment (#155, RNAseq_bw25113_fumarate_NH4Cl_O2_1_thiamine): 1,
RNASeqExperiment (#156, RNAseq_bw25113_fumarate_NH4Cl_O2_2_thiamine): 2,
RNASeqExperiment (#157, RNAseq_bw25113_glucose_NH4Cl_O2_1_thiamine): 1,
RNASeqExperiment (#158, RNAseq_bw25113_glucose_NH4Cl_O2_2_thiamine): 2,
RNASeqExperiment (#159, RNAseq_bw25113_pyruvate_NH4Cl_O2_1_thiamine): 1,
RNASeqExperiment (#160, RNAseq_bw25113_pyruvate_NH4Cl_O2_2_thiamine): 2,
RNASeqExperiment (#161, RNAseq_delta-fur_glucose_NH4Cl_O2_1_dpd): 1,
RNASeqExperiment (#162, RNAseq_delta-fur_glucose_NH4Cl_O2_1_FeCl2): 1,
RNASeqExperiment (#163, RNAseq_delta-fur_glucose_NH4Cl_O2_2_dpd): 2,
RNASeqExperiment (#164, RNAseq_delta-fur_glucose_NH4Cl_O2_2_FeCl2): 2,
RNASeqExperiment (#165, RNAseq_wt_glucose_cytidine_O2_1): 1,
RNASeqExperiment (#166, RNAseq_wt_glucose_cytidine_O2_2): 2,
RNASeqExperiment (#167, RNAseq_wt_glucose_cytosine_O2_1): 1,
RNASeqExperiment (#168, RNAseq_wt_glucose_cytosine_O2_2): 2,
RNASeqExperiment (#169, RNAseq_wt_glucose_glutamine_O2_1): 1,
RNASeqExperiment (#170, RNAseq_wt_glucose_glutamine_O2_2): 2,
RNASeqExperiment (#171, RNAseq_wt_glucose_NH4Cl_O2_1_dpd): 1,
RNASeqExperiment (#172, RNAseq_wt_glucose_NH4Cl_O2_1_FeCl2): 1,
RNASeqExperiment (#173, RNAseq_wt_glucose_NH4Cl_O2_2_dpd): 2,
RNASeqExperiment (#174, RNAseq_wt_glucose_NH4Cl_O2_2_FeCl2): 2,
RNASeqExperiment (#175, RNAseq_wt_glucose_NH4Cl_O2_3): 3,
RNASeqExperiment (#176, RNAseq_wt_glucose_NH4Cl_O2_4): 4,
Array Experiment (#177, affyexp_delta-arcA_glucose_NH4Cl_anaerobic_1_asv2): asv2 1,
Array Experiment (#178, affyexp_delta-arcA_glucose_NH4Cl_anaerobic_2_asv2): asv2 2,
Array Experiment (#179, affyexp_delta-arcA_glucose_NH4Cl_anaerobic_3_asv2): asv2 3,
Array Experiment (#180, affyexp_delta-arcA_glucose_NH4Cl_O2_1_asv2): asv2 1,
Array Experiment (#181, affyexp_delta-arcA_glucose_NH4Cl_O2_2_asv2): asv2 2,
Array Experiment (#182, affyexp_delta-arcA_glucose_NH4Cl_O2_3_asv2): asv2 3,
Array Experiment (#183, affyexp_delta-arcAfnr_glucose_NH4Cl_anaerobic_1_asv2): asv2 1,
Array Experiment (#184, affyexp_delta-arcAfnr_glucose_NH4Cl_anaerobic_2_asv2): asv2 2,
Array Experiment (#185, affyexp_delta-arcAfnr_glucose_NH4Cl_anaerobic_3_asv2): asv2 3,
Array Experiment (#186, affyexp_delta-arcAfnr_glucose_NH4Cl_O2_1_asv2): asv2 1,
Array Experiment (#187, affyexp_delta-arcAfnr_glucose_NH4Cl_O2_2_asv2): asv2 2,
Array Experiment (#188, affyexp_delta-arcAfnr_glucose_NH4Cl_O2_3_asv2): asv2 3,
Array Experiment (#189, affyexp_delta-fnr_glucose_NH4Cl_anaerobic_1_asv2): asv2 1,
Array Experiment (#190, affyexp_delta-fnr_glucose_NH4Cl_anaerobic_2_asv2): asv2 2,
Array Experiment (#191, affyexp_delta-fnr_glucose_NH4Cl_anaerobic_3_asv2): asv2 3,
Array Experiment (#192, affyexp_delta-fnr_glucose_NH4Cl_O2_1_asv2): asv2 1,
Array Experiment (#193, affyexp_delta-fnr_glucose_NH4Cl_O2_2_asv2): asv2 2,
Array Experiment (#194, affyexp_delta-fnr_glucose_NH4Cl_O2_3_asv2): asv2 3,
Array Experiment (#195, affyexp_delta-narL_glucose_NH4Cl_anaerobic_1_asv2): asv2 1,
Array Experiment (#196, affyexp_delta-narL_glucose_NH4Cl_anaerobic_2_asv2): asv2 2,
Array Experiment (#197, affyexp_delta-narL_glucose_NH4Cl_anaerobic_3_asv2): asv2 3,
Array Experiment (#198, affyexp_delta-narL_glucose_NH4Cl_NO3_1_asv2): asv2 1,
Array Experiment (#199, affyexp_delta-narL_glucose_NH4Cl_NO3_2_asv2): asv2 2,
Array Experiment (#200, affyexp_delta-narL_glucose_NH4Cl_NO3_3_asv2): asv2 3,
Array Experiment (#201, affyexp_delta-narLnarP_glucose_NH4Cl_anaerobic_1_asv2): asv2 1,
Array Experiment (#202, affyexp_delta-narLnarP_glucose_NH4Cl_anaerobic_2_asv2): asv2 2,
Array Experiment (#203, affyexp_delta-narLnarP_glucose_NH4Cl_anaerobic_3_asv2): asv2 3,
Array Experiment (#204, affyexp_delta-narLnarP_glucose_NH4Cl_NO3_1_asv2): asv2 1,
Array Experiment (#205, affyexp_delta-narLnarP_glucose_NH4Cl_NO3_2_asv2): asv2 2,
Array Experiment (#206, affyexp_delta-narLnarP_glucose_NH4Cl_NO3_3_asv2): asv2 3,
Array Experiment (#207, affyexp_delta-narP_glucose_NH4Cl_anaerobic_1_asv2): asv2 1,
Array Experiment (#208, affyexp_delta-narP_glucose_NH4Cl_anaerobic_2_asv2): asv2 2,
Array Experiment (#209, affyexp_delta-narP_glucose_NH4Cl_anaerobic_3_asv2): asv2 3,
Array Experiment (#210, affyexp_delta-narP_glucose_NH4Cl_NO3_2_asv2): asv2 2,
Array Experiment (#211, affyexp_delta-narP_glucose_NH4Cl_NO3_3_asv2): asv2 3,
Array Experiment (#212, affyexp_wt_glucose_NH4Cl_anaerobic_1_asv2): asv2 1,
Array Experiment (#213, affyexp_wt_glucose_NH4Cl_anaerobic_2_asv2): asv2 2,
Array Experiment (#214, affyexp_wt_glucose_NH4Cl_anaerobic_3_asv2): asv2 3,
Array Experiment (#215, affyexp_wt_glucose_NH4Cl_anaerobic_4_asv2): asv2 4,
Array Experiment (#216, affyexp_wt_glucose_NH4Cl_anaerobic_5_asv2): asv2 5,
Array Experiment (#217, affyexp_wt_glucose_NH4Cl_anaerobic_6_asv2): asv2 6,
Array Experiment (#218, affyexp_wt_glucose_NH4Cl_NO3_1_asv2): asv2 1,
Array Experiment (#219, affyexp_wt_glucose_NH4Cl_NO3_2_asv2): asv2 2,
Array Experiment (#220, affyexp_wt_glucose_NH4Cl_NO3_3_asv2): asv2 3,
Array Experiment (#221, affyexp_wt_glucose_NH4Cl_O2_1_asv2): asv2 1,
Array Experiment (#222, affyexp_wt_glucose_NH4Cl_O2_2_asv2): asv2 2,
Array Experiment (#223, affyexp_wt_glucose_NH4Cl_O2_3_asv2): asv2 3,
Array Experiment (#224, affyexp_delta-arcA_glucose_NH4Cl_NO3_1_ec2): ec2 1,
Array Experiment (#225, affyexp_delta-arcA_glucose_NH4Cl_NO3_2_ec2): ec2 2,
Array Experiment (#226, affyexp_delta-arcA_glucose_NH4Cl_NO3_3_ec2): ec2 3,
Array Experiment (#227, affyexp_delta-cra_acetate_NH4Cl_O2_1_ec2): ec2 1,
Array Experiment (#228, affyexp_delta-cra_acetate_NH4Cl_O2_2_ec2): ec2 2,
Array Experiment (#229, affyexp_delta-cra_acetate_NH4Cl_O2_3_ec2): ec2 3,
Array Experiment (#230, affyexp_delta-cra_glucose_NH4Cl_anaerobic_1_ec2): ec2 1,
Array Experiment (#231, affyexp_delta-cra_glucose_NH4Cl_anaerobic_2_ec2): ec2 2,
Array Experiment (#232, affyexp_delta-cra_glucose_NH4Cl_anaerobic_3_ec2): ec2 3,
Array Experiment (#233, affyexp_delta-cra_glucose_NH4Cl_O2_1_ec2): ec2 1,
Array Experiment (#234, affyexp_delta-cra_glucose_NH4Cl_O2_2_ec2): ec2 2,
Array Experiment (#235, affyexp_delta-cra_glucose_NH4Cl_O2_3_ec2): ec2 3,
Array Experiment (#236, affyexp_delta-crp_fructose_NH4Cl_O2_1_ec2): ec2 1,
Array Experiment (#237, affyexp_delta-crp_fructose_NH4Cl_O2_2_ec2): ec2 2,
Array Experiment (#238, affyexp_delta-crp_fructose_NH4Cl_O2_3_ec2): ec2 3,
Array Experiment (#239, affyexp_delta-crp_glucose_NH4Cl_O2_1_ec2): ec2 1,
Array Experiment (#240, affyexp_delta-crp_glucose_NH4Cl_O2_2_ec2): ec2 2,
Array Experiment (#241, affyexp_delta-crp_glucose_NH4Cl_O2_3_ec2): ec2 3,
Array Experiment (#242, affyexp_delta-fnr_glucose_NH4Cl_NO3_1_ec2): ec2 1,
Array Experiment (#243, affyexp_delta-fnr_glucose_NH4Cl_NO3_2_ec2): ec2 2,
Array Experiment (#244, affyexp_delta-fnr_glucose_NH4Cl_NO3_3_ec2): ec2 3,
Array Experiment (#245, affyexp_delta-lrp_glucose_leucine_O2_1_ec2): ec2 1,
Array Experiment (#246, affyexp_delta-lrp_glucose_leucine_O2_2_ec2): ec2 2,
Array Experiment (#247, affyexp_delta-lrp_glucose_leucine_O2_3_ec2): ec2 3,
Array Experiment (#248, affyexp_delta-lrp_glucose_NH4Cl_O2_1_ec2): ec2 1,
Array Experiment (#249, affyexp_delta-lrp_glucose_NH4Cl_O2_2_ec2): ec2 2,
Array Experiment (#250, affyexp_delta-lrp_glucose_NH4Cl_O2_3_ec2): ec2 3,
Array Experiment (#251, affyexp_delta-purR_glucose_adenine_O2_1_ec2): ec2 1,
Array Experiment (#252, affyexp_delta-purR_glucose_adenine_O2_2_ec2): ec2 2,
Array Experiment (#253, affyexp_delta-purR_glucose_NH4Cl_O2_1_ec2): ec2 1,
Array Experiment (#254, affyexp_delta-purR_glucose_NH4Cl_O2_2_ec2): ec2 2,
Array Experiment (#255, affyexp_wt_acetate_NH4Cl_O2_1_ec2): ec2 1,
Array Experiment (#256, affyexp_wt_acetate_NH4Cl_O2_2_ec2): ec2 2,
Array Experiment (#257, affyexp_wt_acetate_NH4Cl_O2_3_ec2): ec2 3,
Array Experiment (#258, affyexp_wt_fructose_NH4Cl_O2_1_ec2): ec2 1,
Array Experiment (#259, affyexp_wt_fructose_NH4Cl_O2_2_ec2): ec2 2,
Array Experiment (#260, affyexp_wt_fructose_NH4Cl_O2_3_ec2): ec2 3,
Array Experiment (#261, affyexp_wt_glucose_adenine_O2_1_ec2): ec2 1,
Array Experiment (#262, affyexp_wt_glucose_adenine_O2_2_ec2): ec2 2,
Array Experiment (#263, affyexp_wt_glucose_leucine_O2_1_ec2): ec2 1,
Array Experiment (#264, affyexp_wt_glucose_leucine_O2_2_ec2): ec2 2,
Array Experiment (#265, affyexp_wt_glucose_leucine_O2_3_ec2): ec2 3,
Array Experiment (#266, affyexp_wt_glucose_NH4Cl_anaerobic_1_ec2): ec2 1,
Array Experiment (#267, affyexp_wt_glucose_NH4Cl_anaerobic_2_ec2): ec2 2,
Array Experiment (#268, affyexp_wt_glucose_NH4Cl_anaerobic_3_ec2): ec2 3,
Array Experiment (#269, affyexp_wt_glucose_NH4Cl_NO3_1_ec2): ec2 1,
Array Experiment (#270, affyexp_wt_glucose_NH4Cl_NO3_2_ec2): ec2 2,
Array Experiment (#271, affyexp_wt_glucose_NH4Cl_NO3_3_ec2): ec2 3,
Array Experiment (#272, affyexp_wt_glucose_NH4Cl_O2_1_ec2): ec2 1,
Array Experiment (#273, affyexp_wt_glucose_NH4Cl_O2_2_ec2): ec2 2,
Array Experiment (#274, affyexp_wt_glucose_NH4Cl_O2_3_ec2): ec2 3,
Expression Data (#275): RNAseq_wt_fructose_NH4Cl_O2,
Expression Data (#276): RNAseq_wt_glucose_NH4Cl_O2,
Expression Data (#277): RNAseq_wt_glycerol_NH4Cl_O2,
Expression Data (#278): RNAseq_wt_glucose_NH4Cl_O2_dpd,
Expression Data (#279): RNAseq_wt_glucose_NH4Cl_O2_FeCl2,
Expression Data (#280): RNAseq_wt_glucose_cytidine_O2,
Expression Data (#281): RNAseq_wt_glucose_cytosine_O2,
Expression Data (#282): RNAseq_wt_glucose_glutamine_O2,
Expression Data (#283): RNAseq_Ar3_glycerol_NH4Cl_O2,
Expression Data (#284): RNAseq_delAr1_glycerol_NH4Cl_O2,
Expression Data (#285): RNAseq_delAr1delAr2_glycerol_NH4Cl_O2,
Expression Data (#286): RNAseq_delAr2_glycerol_NH4Cl_O2,
Expression Data (#287): RNAseq_delta-crp_fructose_NH4Cl_O2,
Expression Data (#288): RNAseq_delta-crp_glucose_NH4Cl_O2,
Expression Data (#289): RNAseq_delta-crp_glycerol_NH4Cl_O2,
Expression Data (#290): RNAseq_bw25113_acetate_NH4Cl_O2_thiamine,
Expression Data (#291): RNAseq_bw25113_fumarate_NH4Cl_O2_thiamine,
Expression Data (#293): RNAseq_bw25113_pyruvate_NH4Cl_O2_thiamine,
Expression Data (#295): RNAseq_delta-fur_glucose_NH4Cl_O2_FeCl2,
Expression Data (#298): affyexp_wt_glucose_NH4Cl_anaerobic,
Expression Data (#299): affyexp_wt_glucose_NH4Cl_NO3,
Expression Data (#303): affyexp_delta-crp_fructose_NH4Cl_O2,
Expression Data (#304): affyexp_delta-crp_glucose_NH4Cl_O2,
Expression Data (#305): affyexp_delta-arcA_glucose_NH4Cl_O2,
Expression Data (#306): affyexp_delta-arcA_glucose_NH4Cl_anaerobic,
Expression Data (#307): affyexp_delta-arcA_glucose_NH4Cl_NO3,
Expression Data (#308): affyexp_delta-arcAfnr_glucose_NH4Cl_O2,
Expression Data (#309): affyexp_delta-arcAfnr_glucose_NH4Cl_anaerobic,
Expression Data (#310): affyexp_delta-fnr_glucose_NH4Cl_O2,
Expression Data (#311): affyexp_delta-fnr_glucose_NH4Cl_anaerobic,
Expression Data (#312): affyexp_delta-fnr_glucose_NH4Cl_NO3,
Expression Data (#313): affyexp_delta-narL_glucose_NH4Cl_anaerobic,
Expression Data (#314): affyexp_delta-narL_glucose_NH4Cl_NO3,
Expression Data (#315): affyexp_delta-narLnarP_glucose_NH4Cl_anaerobic,
Expression Data (#316): affyexp_delta-narLnarP_glucose_NH4Cl_NO3,
Expression Data (#317): affyexp_delta-narP_glucose_NH4Cl_anaerobic,
Expression Data (#318): affyexp_delta-narP_glucose_NH4Cl_NO3,
Expression Data (#325): affyexp_delta-purR_glucose_adenine_O2,
ChIP Peak Analysis (#327, ChIPExo-RpoD_wt_glucose_cytidine_O2_anti-rpod_default_peaks): Environment: C:glucose, N:cytidine, e:O2 ,
ChIP Peak Analysis (#329, ChIPExo-Crp_wt_fructose_NH4Cl_O2_anti-crp_default_peaks): Environment: C:fructose, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#330, ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_anti-myc_default_peaks): Environment: C:glucose, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#332, ChIPExo-NtrC_NtrC8myc_glucose_cytosine_O2_anti-myc_default_peaks): Environment: C:glucose, N:cytosine, e:O2 ,
ChIP Peak Analysis (#336, ChIPExo-RpoD_wt_fructose_NH4Cl_O2_anti-rpod_default_peaks): Environment: C:fructose, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#337, ChIPchip-Crp_Crp8myc_fructose_NH4Cl_O2_anti-myc_default_peaks): Environment: C:fructose, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#339, ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_anti-rpod_default_peaks): Environment: C:glycerol, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#340, ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_anti-crp_default_peaks): Environment: C:glycerol, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#341, ChIPExo-Crp_Ar3_glycerol_NH4Cl_O2_anti-crp_default_peaks): Environment: C:glycerol, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#342, ChIPchip-ArcA_ArcA8myc_glucose_NH4Cl_NO3_anti-myc_default_peaks): Environment: C:glucose, N:NH4Cl, e:NO3 ,
ChIP Peak Analysis (#343, ChIPExo-RpoD_wt_glucose_glutamine_O2_anti-rpod_default_peaks): Environment: C:glucose, N:glutamine, e:O2 ,
ChIP Peak Analysis (#345, ChIPExo-RpoN_wt_glucose_NH4Cl_O2_anti-rpon_default_peaks): Environment: C:glucose, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#347, ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_anti-crp_default_peaks): Environment: C:glycerol, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#348, ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_anti-crp_default_peaks): Environment: C:glycerol, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#349, ChIPExo-RpoN_wt_glucose_cytidine_O2_anti-rpon_default_peaks): Environment: C:glucose, N:cytidine, e:O2 ,
ChIP Peak Analysis (#351, ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_anti-myc_default_peaks): Environment: C:glucose, N:NH4Cl, e:anaerobic ,
ChIP Peak Analysis (#355, ChIPchip-Crp_Crp8myc_acetate_NH4Cl_O2_anti-myc_default_peaks): Environment: C:acetate, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#357, ChIPchip-ArgR_ArgR8myc_glucose_NH4Cl_O2_anti-myc_default_peaks): Environment: C:glucose, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#359, ChIPExo-Fur_Fur8myc_glucose_NH4Cl_O2_anti-myc_dpd_default_peaks): Environment: C:glucose, N:NH4Cl, e:O2 dpd,
ChIP Peak Analysis (#361, ChIPExo-RpoS_wt_glucose_NH4Cl_O2_anti-rpos_default_peaks): Environment: C:glucose, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#363, ChIPExo-RpoD_wt_glucose_cytosine_O2_anti-rpod_default_peaks): Environment: C:glucose, N:cytosine, e:O2 ,
ChIP Peak Analysis (#366, ChIPExo-NtrC_NtrC8myc_glucose_cytidine_O2_anti-myc_default_peaks): Environment: C:glucose, N:cytidine, e:O2 ,
ChIP Peak Analysis (#368, ChIPchip-Cra_Cra8myc_acetate_NH4Cl_O2_anti-myc_default_peaks): Environment: C:acetate, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#369, ChIPchip-PurR_PurR8myc_glucose_NH4Cl_O2_anti-myc_default_peaks): Environment: C:glucose, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#372, ChIPExo-RpoN_wt_glucose_cytosine_O2_anti-rpon_default_peaks): Environment: C:glucose, N:cytosine, e:O2 ,
ChIP Peak Analysis (#376, ChIPExo-Crp_Crp8myc_glycerol_NH4Cl_O2_anti-myc_default_peaks): Environment: C:glycerol, N:NH4Cl, e:O2 ,
Expression Data (#292): RNAseq_bw25113_glucose_NH4Cl_O2_thiamine,
Expression Data (#294): RNAseq_delta-fur_glucose_NH4Cl_O2_dpd,
Expression Data (#296): affyexp_wt_fructose_NH4Cl_O2,
Expression Data (#297): affyexp_wt_glucose_NH4Cl_O2,
Expression Data (#300): affyexp_wt_acetate_NH4Cl_O2,
Expression Data (#301): affyexp_wt_glucose_leucine_O2,
Expression Data (#302): affyexp_wt_glucose_adenine_O2,
Expression Data (#319): affyexp_delta-cra_glucose_NH4Cl_O2,
Expression Data (#320): affyexp_delta-cra_glucose_NH4Cl_anaerobic,
Expression Data (#321): affyexp_delta-cra_acetate_NH4Cl_O2,
Expression Data (#322): affyexp_delta-lrp_glucose_NH4Cl_O2,
Expression Data (#323): affyexp_delta-lrp_glucose_leucine_O2,
Expression Data (#324): affyexp_delta-purR_glucose_NH4Cl_O2,
ChIP Peak Analysis (#326, ChIPExo-Crp_wt_glucose_NH4Cl_O2_anti-crp_default_peaks): Environment: C:glucose, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#328, ChIPExo-Nac_Nac8myc_glucose_glutamine_O2_anti-myc_default_peaks): Environment: C:glucose, N:glutamine, e:O2 ,
ChIP Peak Analysis (#331, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_anti-crp_default_peaks): Environment: C:glycerol, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#333, ChIPchip-Cra_Cra8myc_glucose_NH4Cl_O2_anti-myc_default_peaks): Environment: C:glucose, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#334, ChIPchip-Lrp_Lrp8myc_glucose_NH4Cl_O2_anti-myc_default_peaks): Environment: C:glucose, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#335, ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_anti-myc_default_peaks): Environment: C:glucose, N:NH4Cl, e:anaerobic ,
ChIP Peak Analysis (#338, ChIPExo-RpoD_wt_glucose_NH4Cl_O2_anti-rpod_default_peaks): Environment: C:glucose, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#344, ChIPExo-Nac_Nac8myc_glucose_cytidine_O2_anti-myc_default_peaks): Environment: C:glucose, N:cytidine, e:O2 ,
ChIP Peak Analysis (#346, ChIPExo-RpoN_wt_glucose_glutamine_O2_anti-rpon_default_peaks): Environment: C:glucose, N:glutamine, e:O2 ,
ChIP Peak Analysis (#350, ChIPExo-Fur_Fur8myc_glucose_NH4Cl_O2_anti-myc_FeCl2_default_peaks): Environment: C:glucose, N:NH4Cl, e:O2 FeCl2,
ChIP Peak Analysis (#352, ChIPchip-Fnr_Fnr8myc_glucose_NH4Cl_NO3_anti-myc_default_peaks): Environment: C:glucose, N:NH4Cl, e:NO3 ,
ChIP Peak Analysis (#353, ChIPchip-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_anti-myc_default_peaks): Environment: C:glucose, N:NH4Cl, e:anaerobic ,
ChIP Peak Analysis (#354, ChIPExo-NtrC_NtrC8myc_glucose_glutamine_O2_anti-myc_default_peaks): Environment: C:glucose, N:glutamine, e:O2 ,
ChIP Peak Analysis (#356, ChIPExo-RpoA_wt_glucose_NH4Cl_O2_anti-rpoA_default_peaks): Environment: C:glucose, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#358, ChIPExo-Nac_Nac8myc_glucose_cytosine_O2_anti-myc_default_peaks): Environment: C:glucose, N:cytosine, e:O2 ,
ChIP Peak Analysis (#360, ChIPExo-NtrC_NtrC8myc_glucose_NH4Cl_O2_anti-myc_default_peaks): Environment: C:glucose, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#362, ChIPExo-Crp_Crp8myc_fructose_NH4Cl_O2_anti-crp_default_peaks): Environment: C:fructose, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#364, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_anti-crp_rif_default_peaks): Environment: C:glycerol, N:NH4Cl, e:O2 rif,
ChIP Peak Analysis (#365, ChIPExo-Crp_Crp8myc_glycerol_NH4Cl_O2_anti-crp_default_peaks): Environment: C:glycerol, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#367, ChIPExo-RpoN_wt_glucose_NH4Cl_O2_anti-rpon_nitrogenstudy_default_peaks): Environment: C:glucose, N:NH4Cl, e:O2 nitrogenstudy,
ChIP Peak Analysis (#370, ChIPchip-Cra_Cra8myc_glucose_NH4Cl_anaerobic_anti-myc_default_peaks): Environment: C:glucose, N:NH4Cl, e:anaerobic ,
ChIP Peak Analysis (#371, ChIPExo-Crp_Crp8myc_glucose_NH4Cl_O2_anti-myc_default_peaks): Environment: C:glucose, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#373, ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_anti-crp_default_peaks): Environment: C:glycerol, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#374, ChIPchip-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_anti-myc_default_peaks): Environment: C:glucose, N:NH4Cl, e:anaerobic ,
ChIP Peak Analysis (#375, ChIPExo-RpoD_wt_glucose_NH4Cl_O2_anti-rpod_nitrogenstudy_default_peaks): Environment: C:glucose, N:NH4Cl, e:O2 nitrogenstudy,
Differential Expression (#377): RNAseq_bw25113_acetate/fumarate_NH4Cl_O2_thiamine,
Differential Expression (#378): RNAseq_wt_glucose_NH4Cl/cytidine_O2,
Differential Expression (#379): RNAseq_wt_glucose_cytidine/glutamine_O2,
Differential Expression (#380): RNAseq_wt_glucose_cytosine/glutamine_O2,
Differential Expression (#381): RNAseq_wt_glucose_NH4Cl/glutamine_O2,
Differential Expression (#382): RNAseq_delta-crp/wt_fructose_NH4Cl_O2,
Differential Expression (#383): RNAseq_wt_glucose_NH4Cl_O2_supp/FeCl2,
Differential Expression (#384): RNAseq_delta-fur/wt_glucose_NH4Cl_O2_FeCl2,
Differential Expression (#385): RNAseq_delta-fur_glucose_NH4Cl_O2_FeCl2/dpd,
Differential Expression (#386): RNAseq_wt_glucose_cytidine/cytosine_O2,
Differential Expression (#387): RNAseq_wt_glucose_NH4Cl/cytosine_O2,
Differential Expression (#388): RNAseq_bw25113_fumarate/glucose_NH4Cl_O2_thiamine,
Differential Expression (#389): RNAseq_bw25113_acetate/glucose_NH4Cl_O2_thiamine,
Differential Expression (#390): RNAseq_delAr2/wt_glycerol_NH4Cl_O2,
Differential Expression (#391): RNAseq_wt_fructose/glycerol_NH4Cl_O2,
Differential Expression (#392): RNAseq_delAr1/wt_glycerol_NH4Cl_O2,
Differential Expression (#393): RNAseq_delAr1delAr2/wt_glycerol_NH4Cl_O2,
Differential Expression (#394): RNAseq_Ar3/wt_glycerol_NH4Cl_O2,
Differential Expression (#395): RNAseq_wt_glucose/glycerol_NH4Cl_O2,
Differential Expression (#396): RNAseq_delta-crp/wt_glycerol_NH4Cl_O2,
Differential Expression (#397): RNAseq_wt_fructose/glucose_NH4Cl_O2,
Differential Expression (#398): RNAseq_delta-crp/wt_glucose_NH4Cl_O2,
Differential Expression (#399): RNAseq_wt_glucose_NH4Cl_O2_FeCl2/dpd,
Differential Expression (#400): RNAseq_delta-fur/wt_glucose_NH4Cl_O2_dpd,
Differential Expression (#401): RNAseq_wt_glucose_NH4Cl_O2_supp/dpd,
Differential Expression (#402): RNAseq_delta-crp_fructose/glycerol_NH4Cl_O2,
Differential Expression (#403): RNAseq_delta-crp_glucose/glycerol_NH4Cl_O2,
Differential Expression (#404): RNAseq_bw25113_fumarate/pyruvate_NH4Cl_O2_thiamine,
Differential Expression (#405): RNAseq_bw25113_glucose/pyruvate_NH4Cl_O2_thiamine,
Differential Expression (#406): RNAseq_bw25113_acetate/pyruvate_NH4Cl_O2_thiamine,
Differential Expression (#407): RNAseq_delta-crp_fructose/glucose_NH4Cl_O2,
Differential Expression (#408): affyexp_delta-narLnarP_glucose_NH4Cl_NO3/anaerobic,
Differential Expression (#409): affyexp_delta-narLnarP/wt_glucose_NH4Cl_NO3,
Differential Expression (#410): affyexp_delta-purR_glucose_NH4Cl/adenine_O2,
Differential Expression (#411): affyexp_delta-purR/wt_glucose_NH4Cl_O2]
In [42]:
from om.data import *
In [43]:
session.query(Strain).all()
Out[43]:
[Strain: wt,
Strain: ArcA8myc,
Strain: Ar3,
Strain: Crp8myc,
Strain: delAr1,
Strain: delAr1delAr2,
Strain: delAr2,
Strain: delta-crp,
Strain: Fnr8myc,
Strain: Fur8myc,
Strain: Nac8myc,
Strain: NtrC8myc,
Strain: ArgR8myc,
Strain: Cra8myc,
Strain: Lrp8myc,
Strain: PurR8myc,
Strain: bw25113,
Strain: delta-fur,
Strain: delta-arcA,
Strain: delta-arcAfnr,
Strain: delta-fnr,
Strain: delta-narL,
Strain: delta-narLnarP,
Strain: delta-narP,
Strain: delta-cra,
Strain: delta-lrp,
Strain: delta-purR,
Strain: generic]
In [44]:
session.query(Environment).all()
Out[44]:
[Environment: C:fructose, N:NH4Cl, e:O2 ,
Environment: C:glucose, N:NH4Cl, e:O2 ,
Environment: C:glycerol, N:NH4Cl, e:O2 ,
Environment: C:glucose, N:NH4Cl, e:anaerobic ,
Environment: C:glycerol, N:NH4Cl, e:O2 rif,
Environment: C:glucose, N:NH4Cl, e:O2 dpd,
Environment: C:glucose, N:NH4Cl, e:O2 FeCl2,
Environment: C:glucose, N:cytidine, e:O2 ,
Environment: C:glucose, N:cytosine, e:O2 ,
Environment: C:glucose, N:glutamine, e:O2 ,
Environment: C:glucose, N:NH4Cl, e:O2 nitrogenstudy,
Environment: C:glucose, N:NH4Cl, e:NO3 ,
Environment: C:acetate, N:NH4Cl, e:O2 ,
Environment: C:acetate, N:NH4Cl, e:O2 thiamine,
Environment: C:fumarate, N:NH4Cl, e:O2 thiamine,
Environment: C:glucose, N:NH4Cl, e:O2 thiamine,
Environment: C:pyruvate, N:NH4Cl, e:O2 thiamine,
Environment: C:glucose, N:leucine, e:O2 ,
Environment: C:glucose, N:adenine, e:O2 ,
Environment: type:environment, name:generic]
In [45]:
session.query(ChIPExperiment).all()
Out[45]:
[ChIPExperiment (#1, ChIPExo-RpoD_wt_fructose_NH4Cl_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#2, ChIPExo-RpoD_wt_fructose_NH4Cl_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#3, ChIPExo-RpoD_wt_fructose_NH4Cl_O2_3_anti-rpod): ChIPExo RpoD 3,
ChIPExperiment (#4, ChIPExo-RpoD_wt_glucose_NH4Cl_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#5, ChIPExo-RpoD_wt_glucose_NH4Cl_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#6, ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#7, ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#8, ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_3_anti-rpod): ChIPExo RpoD 3,
ChIPExperiment (#9, ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_2_anti-myc): ChIPExo ArcA 2,
ChIPExperiment (#10, ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_3_anti-myc): ChIPExo ArcA 3,
ChIPExperiment (#11, ChIPExo-Crp_Ar3_glycerol_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#12, ChIPExo-Crp_Ar3_glycerol_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#13, ChIPExo-Crp_Ar3_glycerol_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#14, ChIPExo-Crp_Crp8myc_fructose_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#15, ChIPExo-Crp_Crp8myc_fructose_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#16, ChIPExo-Crp_Crp8myc_glucose_NH4Cl_O2_1_anti-myc): ChIPExo Crp 1,
ChIPExperiment (#17, ChIPExo-Crp_Crp8myc_glucose_NH4Cl_O2_2_anti-myc): ChIPExo Crp 2,
ChIPExperiment (#18, ChIPExo-Crp_Crp8myc_glycerol_NH4Cl_O2_1_anti-myc): ChIPExo Crp 1,
ChIPExperiment (#19, ChIPExo-Crp_Crp8myc_glycerol_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#20, ChIPExo-Crp_Crp8myc_glycerol_NH4Cl_O2_2_anti-myc): ChIPExo Crp 2,
ChIPExperiment (#21, ChIPExo-Crp_Crp8myc_glycerol_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#22, ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#23, ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#24, ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#25, ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#26, ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#27, ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#28, ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#29, ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#30, ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#31, ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#32, ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#33, ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#34, ChIPExo-Crp_wt_fructose_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#35, ChIPExo-Crp_wt_fructose_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#36, ChIPExo-Crp_wt_fructose_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#37, ChIPExo-Crp_wt_fructose_NH4Cl_O2_4_anti-crp): ChIPExo Crp 4,
ChIPExperiment (#38, ChIPExo-Crp_wt_fructose_NH4Cl_O2_5_anti-crp): ChIPExo Crp 5,
ChIPExperiment (#39, ChIPExo-Crp_wt_glucose_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#40, ChIPExo-Crp_wt_glucose_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#41, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#42, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp_rif): ChIPExo Crp 1,
ChIPExperiment (#43, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#44, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp_rif): ChIPExo Crp 2,
ChIPExperiment (#45, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#46, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp_rif): ChIPExo Crp 3,
ChIPExperiment (#47, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_4_anti-crp): ChIPExo Crp 4,
ChIPExperiment (#48, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_5_anti-crp): ChIPExo Crp 5,
ChIPExperiment (#49, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_6_anti-crp): ChIPExo Crp 6,
ChIPExperiment (#50, ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_2_anti-myc): ChIPExo Fnr 2,
ChIPExperiment (#51, ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_3_anti-myc): ChIPExo Fnr 3,
ChIPExperiment (#52, ChIPExo-RpoA_wt_glucose_NH4Cl_O2_1_anti-rpoA): ChIPExo RpoA 1,
ChIPExperiment (#53, ChIPExo-RpoA_wt_glucose_NH4Cl_O2_2_anti-rpoA): ChIPExo RpoA 2,
ChIPExperiment (#54, ChIPExo-Fur_Fur8myc_glucose_NH4Cl_O2_1_anti-myc_dpd): ChIPExo Fur 1,
ChIPExperiment (#55, ChIPExo-Fur_Fur8myc_glucose_NH4Cl_O2_1_anti-myc_FeCl2): ChIPExo Fur 1,
ChIPExperiment (#56, ChIPExo-Fur_Fur8myc_glucose_NH4Cl_O2_2_anti-myc_dpd): ChIPExo Fur 2,
ChIPExperiment (#57, ChIPExo-Fur_Fur8myc_glucose_NH4Cl_O2_2_anti-myc_FeCl2): ChIPExo Fur 2,
ChIPExperiment (#58, ChIPExo-Nac_Nac8myc_glucose_cytidine_O2_1_anti-myc): ChIPExo Nac 1,
ChIPExperiment (#59, ChIPExo-Nac_Nac8myc_glucose_cytidine_O2_2_anti-myc): ChIPExo Nac 2,
ChIPExperiment (#60, ChIPExo-Nac_Nac8myc_glucose_cytosine_O2_1_anti-myc): ChIPExo Nac 1,
ChIPExperiment (#61, ChIPExo-Nac_Nac8myc_glucose_cytosine_O2_2_anti-myc): ChIPExo Nac 2,
ChIPExperiment (#62, ChIPExo-Nac_Nac8myc_glucose_glutamine_O2_1_anti-myc): ChIPExo Nac 1,
ChIPExperiment (#63, ChIPExo-Nac_Nac8myc_glucose_glutamine_O2_2_anti-myc): ChIPExo Nac 2,
ChIPExperiment (#64, ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_1_anti-myc): ChIPExo Nac 1,
ChIPExperiment (#65, ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_2_anti-myc): ChIPExo Nac 2,
ChIPExperiment (#66, ChIPExo-NtrC_NtrC8myc_glucose_cytidine_O2_1_anti-myc): ChIPExo NtrC 1,
ChIPExperiment (#67, ChIPExo-NtrC_NtrC8myc_glucose_cytidine_O2_2_anti-myc): ChIPExo NtrC 2,
ChIPExperiment (#68, ChIPExo-NtrC_NtrC8myc_glucose_cytosine_O2_1_anti-myc): ChIPExo NtrC 1,
ChIPExperiment (#69, ChIPExo-NtrC_NtrC8myc_glucose_cytosine_O2_2_anti-myc): ChIPExo NtrC 2,
ChIPExperiment (#70, ChIPExo-NtrC_NtrC8myc_glucose_glutamine_O2_1_anti-myc): ChIPExo NtrC 1,
ChIPExperiment (#71, ChIPExo-NtrC_NtrC8myc_glucose_glutamine_O2_2_anti-myc): ChIPExo NtrC 2,
ChIPExperiment (#72, ChIPExo-NtrC_NtrC8myc_glucose_NH4Cl_O2_1_anti-myc): ChIPExo NtrC 1,
ChIPExperiment (#73, ChIPExo-NtrC_NtrC8myc_glucose_NH4Cl_O2_2_anti-myc): ChIPExo NtrC 2,
ChIPExperiment (#74, ChIPExo-RpoD_wt_glucose_cytidine_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#75, ChIPExo-RpoD_wt_glucose_cytidine_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#76, ChIPExo-RpoD_wt_glucose_cytosine_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#77, ChIPExo-RpoD_wt_glucose_cytosine_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#78, ChIPExo-RpoD_wt_glucose_glutamine_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#79, ChIPExo-RpoD_wt_glucose_glutamine_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#80, ChIPExo-RpoD_wt_glucose_NH4Cl_O2_1_anti-rpod_nitrogenstudy): ChIPExo RpoD 1,
ChIPExperiment (#81, ChIPExo-RpoD_wt_glucose_NH4Cl_O2_2_anti-rpod_nitrogenstudy): ChIPExo RpoD 2,
ChIPExperiment (#82, ChIPExo-RpoN_wt_glucose_cytidine_O2_1_anti-rpon): ChIPExo RpoN 1,
ChIPExperiment (#83, ChIPExo-RpoN_wt_glucose_cytidine_O2_2_anti-rpon): ChIPExo RpoN 2,
ChIPExperiment (#84, ChIPExo-RpoN_wt_glucose_cytosine_O2_1_anti-rpon): ChIPExo RpoN 1,
ChIPExperiment (#85, ChIPExo-RpoN_wt_glucose_cytosine_O2_2_anti-rpon): ChIPExo RpoN 2,
ChIPExperiment (#86, ChIPExo-RpoN_wt_glucose_glutamine_O2_1_anti-rpon): ChIPExo RpoN 1,
ChIPExperiment (#87, ChIPExo-RpoN_wt_glucose_glutamine_O2_2_anti-rpon): ChIPExo RpoN 2,
ChIPExperiment (#88, ChIPExo-RpoN_wt_glucose_NH4Cl_O2_1_anti-rpon): ChIPExo RpoN 1,
ChIPExperiment (#89, ChIPExo-RpoN_wt_glucose_NH4Cl_O2_1_anti-rpon_nitrogenstudy): ChIPExo RpoN 1,
ChIPExperiment (#90, ChIPExo-RpoN_wt_glucose_NH4Cl_O2_2_anti-rpon): ChIPExo RpoN 2,
ChIPExperiment (#91, ChIPExo-RpoN_wt_glucose_NH4Cl_O2_2_anti-rpon_nitrogenstudy): ChIPExo RpoN 2,
ChIPExperiment (#92, ChIPExo-RpoS_wt_glucose_NH4Cl_O2_1_anti-rpos): ChIPExo RpoS 1,
ChIPExperiment (#93, ChIPExo-RpoS_wt_glucose_NH4Cl_O2_2_anti-rpos): ChIPExo RpoS 2,
ChIPExperiment (#94, ChIPchip-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_1_anti-myc): ChIPchip ArcA 1,
ChIPExperiment (#95, ChIPchip-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_2_anti-myc): ChIPchip ArcA 2,
ChIPExperiment (#96, ChIPchip-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_3_anti-myc): ChIPchip ArcA 3,
ChIPExperiment (#97, ChIPchip-ArcA_ArcA8myc_glucose_NH4Cl_NO3_1_anti-myc): ChIPchip ArcA 1,
ChIPExperiment (#98, ChIPchip-ArcA_ArcA8myc_glucose_NH4Cl_NO3_2_anti-myc): ChIPchip ArcA 2,
ChIPExperiment (#99, ChIPchip-ArcA_ArcA8myc_glucose_NH4Cl_NO3_3_anti-myc): ChIPchip ArcA 3,
ChIPExperiment (#100, ChIPchip-ArgR_ArgR8myc_glucose_NH4Cl_O2_1_anti-myc): ChIPchip ArgR 1,
ChIPExperiment (#101, ChIPchip-ArgR_ArgR8myc_glucose_NH4Cl_O2_2_anti-myc): ChIPchip ArgR 2,
ChIPExperiment (#102, ChIPchip-Cra_Cra8myc_acetate_NH4Cl_O2_1_anti-myc): ChIPchip Cra 1,
ChIPExperiment (#103, ChIPchip-Cra_Cra8myc_acetate_NH4Cl_O2_2_anti-myc): ChIPchip Cra 2,
ChIPExperiment (#104, ChIPchip-Cra_Cra8myc_acetate_NH4Cl_O2_3_anti-myc): ChIPchip Cra 3,
ChIPExperiment (#105, ChIPchip-Cra_Cra8myc_glucose_NH4Cl_anaerobic_1_anti-myc): ChIPchip Cra 1,
ChIPExperiment (#106, ChIPchip-Cra_Cra8myc_glucose_NH4Cl_anaerobic_2_anti-myc): ChIPchip Cra 2,
ChIPExperiment (#107, ChIPchip-Cra_Cra8myc_glucose_NH4Cl_anaerobic_3_anti-myc): ChIPchip Cra 3,
ChIPExperiment (#108, ChIPchip-Cra_Cra8myc_glucose_NH4Cl_O2_1_anti-myc): ChIPchip Cra 1,
ChIPExperiment (#109, ChIPchip-Cra_Cra8myc_glucose_NH4Cl_O2_2_anti-myc): ChIPchip Cra 2,
ChIPExperiment (#110, ChIPchip-Cra_Cra8myc_glucose_NH4Cl_O2_3_anti-myc): ChIPchip Cra 3,
ChIPExperiment (#111, ChIPchip-Crp_Crp8myc_acetate_NH4Cl_O2_2_anti-myc): ChIPchip Crp 2,
ChIPExperiment (#112, ChIPchip-Crp_Crp8myc_acetate_NH4Cl_O2_3_anti-myc): ChIPchip Crp 3,
ChIPExperiment (#113, ChIPchip-Crp_Crp8myc_fructose_NH4Cl_O2_1_anti-myc): ChIPchip Crp 1,
ChIPExperiment (#114, ChIPchip-Crp_Crp8myc_fructose_NH4Cl_O2_2_anti-myc): ChIPchip Crp 2,
ChIPExperiment (#115, ChIPchip-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_1_anti-myc): ChIPchip Fnr 1,
ChIPExperiment (#116, ChIPchip-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_2_anti-myc): ChIPchip Fnr 2,
ChIPExperiment (#117, ChIPchip-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_3_anti-myc): ChIPchip Fnr 3,
ChIPExperiment (#118, ChIPchip-Fnr_Fnr8myc_glucose_NH4Cl_NO3_1_anti-myc): ChIPchip Fnr 1,
ChIPExperiment (#119, ChIPchip-Fnr_Fnr8myc_glucose_NH4Cl_NO3_2_anti-myc): ChIPchip Fnr 2,
ChIPExperiment (#120, ChIPchip-Fnr_Fnr8myc_glucose_NH4Cl_NO3_3_anti-myc): ChIPchip Fnr 3,
ChIPExperiment (#121, ChIPchip-Lrp_Lrp8myc_glucose_NH4Cl_O2_1_anti-myc): ChIPchip Lrp 1,
ChIPExperiment (#122, ChIPchip-Lrp_Lrp8myc_glucose_NH4Cl_O2_2_anti-myc): ChIPchip Lrp 2,
ChIPExperiment (#123, ChIPchip-Lrp_Lrp8myc_glucose_NH4Cl_O2_3_anti-myc): ChIPchip Lrp 3,
ChIPExperiment (#124, ChIPchip-PurR_PurR8myc_glucose_NH4Cl_O2_1_anti-myc): ChIPchip PurR 1,
ChIPExperiment (#125, ChIPchip-PurR_PurR8myc_glucose_NH4Cl_O2_2_anti-myc): ChIPchip PurR 2]
In [46]:
print session.query(ChIPExperiment)
SELECT chip_experiment.id AS chip_experiment_id, data_set.id AS data_set_id, data_set.name AS data_set_name, data_set.type AS data_set_type, data_set.replicate AS data_set_replicate, data_set.strain_id AS data_set_strain_id, data_set.environment_id AS data_set_environment_id, data_set.data_source_id AS data_set_data_source_id, chip_experiment.antibody AS chip_experiment_antibody, chip_experiment.protocol_type AS chip_experiment_protocol_type, chip_experiment.target AS chip_experiment_target, chip_experiment.group_name AS chip_experiment_group_name, chip_experiment.normalization_method AS chip_experiment_normalization_method, chip_experiment.normalization_factor AS chip_experiment_normalization_factor
FROM data_set JOIN chip_experiment ON data_set.id = chip_experiment.id
In [47]:
session.query(ChIPExperiment).filter(ChIPExperiment.protocol_type == 'ChIPExo').all()
Out[47]:
[ChIPExperiment (#1, ChIPExo-RpoD_wt_fructose_NH4Cl_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#2, ChIPExo-RpoD_wt_fructose_NH4Cl_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#3, ChIPExo-RpoD_wt_fructose_NH4Cl_O2_3_anti-rpod): ChIPExo RpoD 3,
ChIPExperiment (#4, ChIPExo-RpoD_wt_glucose_NH4Cl_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#5, ChIPExo-RpoD_wt_glucose_NH4Cl_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#6, ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#7, ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#8, ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_3_anti-rpod): ChIPExo RpoD 3,
ChIPExperiment (#9, ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_2_anti-myc): ChIPExo ArcA 2,
ChIPExperiment (#10, ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_3_anti-myc): ChIPExo ArcA 3,
ChIPExperiment (#11, ChIPExo-Crp_Ar3_glycerol_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#12, ChIPExo-Crp_Ar3_glycerol_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#13, ChIPExo-Crp_Ar3_glycerol_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#14, ChIPExo-Crp_Crp8myc_fructose_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#15, ChIPExo-Crp_Crp8myc_fructose_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#16, ChIPExo-Crp_Crp8myc_glucose_NH4Cl_O2_1_anti-myc): ChIPExo Crp 1,
ChIPExperiment (#17, ChIPExo-Crp_Crp8myc_glucose_NH4Cl_O2_2_anti-myc): ChIPExo Crp 2,
ChIPExperiment (#18, ChIPExo-Crp_Crp8myc_glycerol_NH4Cl_O2_1_anti-myc): ChIPExo Crp 1,
ChIPExperiment (#19, ChIPExo-Crp_Crp8myc_glycerol_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#20, ChIPExo-Crp_Crp8myc_glycerol_NH4Cl_O2_2_anti-myc): ChIPExo Crp 2,
ChIPExperiment (#21, ChIPExo-Crp_Crp8myc_glycerol_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#22, ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#23, ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#24, ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#25, ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#26, ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#27, ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#28, ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#29, ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#30, ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#31, ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#32, ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#33, ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#34, ChIPExo-Crp_wt_fructose_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#35, ChIPExo-Crp_wt_fructose_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#36, ChIPExo-Crp_wt_fructose_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#37, ChIPExo-Crp_wt_fructose_NH4Cl_O2_4_anti-crp): ChIPExo Crp 4,
ChIPExperiment (#38, ChIPExo-Crp_wt_fructose_NH4Cl_O2_5_anti-crp): ChIPExo Crp 5,
ChIPExperiment (#39, ChIPExo-Crp_wt_glucose_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#40, ChIPExo-Crp_wt_glucose_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#41, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp): ChIPExo Crp 1,
ChIPExperiment (#42, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp_rif): ChIPExo Crp 1,
ChIPExperiment (#43, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp): ChIPExo Crp 2,
ChIPExperiment (#44, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp_rif): ChIPExo Crp 2,
ChIPExperiment (#45, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp): ChIPExo Crp 3,
ChIPExperiment (#46, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp_rif): ChIPExo Crp 3,
ChIPExperiment (#47, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_4_anti-crp): ChIPExo Crp 4,
ChIPExperiment (#48, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_5_anti-crp): ChIPExo Crp 5,
ChIPExperiment (#49, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_6_anti-crp): ChIPExo Crp 6,
ChIPExperiment (#50, ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_2_anti-myc): ChIPExo Fnr 2,
ChIPExperiment (#51, ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_3_anti-myc): ChIPExo Fnr 3,
ChIPExperiment (#52, ChIPExo-RpoA_wt_glucose_NH4Cl_O2_1_anti-rpoA): ChIPExo RpoA 1,
ChIPExperiment (#53, ChIPExo-RpoA_wt_glucose_NH4Cl_O2_2_anti-rpoA): ChIPExo RpoA 2,
ChIPExperiment (#54, ChIPExo-Fur_Fur8myc_glucose_NH4Cl_O2_1_anti-myc_dpd): ChIPExo Fur 1,
ChIPExperiment (#55, ChIPExo-Fur_Fur8myc_glucose_NH4Cl_O2_1_anti-myc_FeCl2): ChIPExo Fur 1,
ChIPExperiment (#56, ChIPExo-Fur_Fur8myc_glucose_NH4Cl_O2_2_anti-myc_dpd): ChIPExo Fur 2,
ChIPExperiment (#57, ChIPExo-Fur_Fur8myc_glucose_NH4Cl_O2_2_anti-myc_FeCl2): ChIPExo Fur 2,
ChIPExperiment (#58, ChIPExo-Nac_Nac8myc_glucose_cytidine_O2_1_anti-myc): ChIPExo Nac 1,
ChIPExperiment (#59, ChIPExo-Nac_Nac8myc_glucose_cytidine_O2_2_anti-myc): ChIPExo Nac 2,
ChIPExperiment (#60, ChIPExo-Nac_Nac8myc_glucose_cytosine_O2_1_anti-myc): ChIPExo Nac 1,
ChIPExperiment (#61, ChIPExo-Nac_Nac8myc_glucose_cytosine_O2_2_anti-myc): ChIPExo Nac 2,
ChIPExperiment (#62, ChIPExo-Nac_Nac8myc_glucose_glutamine_O2_1_anti-myc): ChIPExo Nac 1,
ChIPExperiment (#63, ChIPExo-Nac_Nac8myc_glucose_glutamine_O2_2_anti-myc): ChIPExo Nac 2,
ChIPExperiment (#64, ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_1_anti-myc): ChIPExo Nac 1,
ChIPExperiment (#65, ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_2_anti-myc): ChIPExo Nac 2,
ChIPExperiment (#66, ChIPExo-NtrC_NtrC8myc_glucose_cytidine_O2_1_anti-myc): ChIPExo NtrC 1,
ChIPExperiment (#67, ChIPExo-NtrC_NtrC8myc_glucose_cytidine_O2_2_anti-myc): ChIPExo NtrC 2,
ChIPExperiment (#68, ChIPExo-NtrC_NtrC8myc_glucose_cytosine_O2_1_anti-myc): ChIPExo NtrC 1,
ChIPExperiment (#69, ChIPExo-NtrC_NtrC8myc_glucose_cytosine_O2_2_anti-myc): ChIPExo NtrC 2,
ChIPExperiment (#70, ChIPExo-NtrC_NtrC8myc_glucose_glutamine_O2_1_anti-myc): ChIPExo NtrC 1,
ChIPExperiment (#71, ChIPExo-NtrC_NtrC8myc_glucose_glutamine_O2_2_anti-myc): ChIPExo NtrC 2,
ChIPExperiment (#72, ChIPExo-NtrC_NtrC8myc_glucose_NH4Cl_O2_1_anti-myc): ChIPExo NtrC 1,
ChIPExperiment (#73, ChIPExo-NtrC_NtrC8myc_glucose_NH4Cl_O2_2_anti-myc): ChIPExo NtrC 2,
ChIPExperiment (#74, ChIPExo-RpoD_wt_glucose_cytidine_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#75, ChIPExo-RpoD_wt_glucose_cytidine_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#76, ChIPExo-RpoD_wt_glucose_cytosine_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#77, ChIPExo-RpoD_wt_glucose_cytosine_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#78, ChIPExo-RpoD_wt_glucose_glutamine_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#79, ChIPExo-RpoD_wt_glucose_glutamine_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#80, ChIPExo-RpoD_wt_glucose_NH4Cl_O2_1_anti-rpod_nitrogenstudy): ChIPExo RpoD 1,
ChIPExperiment (#81, ChIPExo-RpoD_wt_glucose_NH4Cl_O2_2_anti-rpod_nitrogenstudy): ChIPExo RpoD 2,
ChIPExperiment (#82, ChIPExo-RpoN_wt_glucose_cytidine_O2_1_anti-rpon): ChIPExo RpoN 1,
ChIPExperiment (#83, ChIPExo-RpoN_wt_glucose_cytidine_O2_2_anti-rpon): ChIPExo RpoN 2,
ChIPExperiment (#84, ChIPExo-RpoN_wt_glucose_cytosine_O2_1_anti-rpon): ChIPExo RpoN 1,
ChIPExperiment (#85, ChIPExo-RpoN_wt_glucose_cytosine_O2_2_anti-rpon): ChIPExo RpoN 2,
ChIPExperiment (#86, ChIPExo-RpoN_wt_glucose_glutamine_O2_1_anti-rpon): ChIPExo RpoN 1,
ChIPExperiment (#87, ChIPExo-RpoN_wt_glucose_glutamine_O2_2_anti-rpon): ChIPExo RpoN 2,
ChIPExperiment (#88, ChIPExo-RpoN_wt_glucose_NH4Cl_O2_1_anti-rpon): ChIPExo RpoN 1,
ChIPExperiment (#89, ChIPExo-RpoN_wt_glucose_NH4Cl_O2_1_anti-rpon_nitrogenstudy): ChIPExo RpoN 1,
ChIPExperiment (#90, ChIPExo-RpoN_wt_glucose_NH4Cl_O2_2_anti-rpon): ChIPExo RpoN 2,
ChIPExperiment (#91, ChIPExo-RpoN_wt_glucose_NH4Cl_O2_2_anti-rpon_nitrogenstudy): ChIPExo RpoN 2,
ChIPExperiment (#92, ChIPExo-RpoS_wt_glucose_NH4Cl_O2_1_anti-rpos): ChIPExo RpoS 1,
ChIPExperiment (#93, ChIPExo-RpoS_wt_glucose_NH4Cl_O2_2_anti-rpos): ChIPExo RpoS 2]
In [48]:
session.query(ChIPExperiment).filter(and_(ChIPExperiment.protocol_type == 'ChIPExo',
ChIPExperiment.antibody == 'anti-rpod')).all()
Out[48]:
[ChIPExperiment (#1, ChIPExo-RpoD_wt_fructose_NH4Cl_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#2, ChIPExo-RpoD_wt_fructose_NH4Cl_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#3, ChIPExo-RpoD_wt_fructose_NH4Cl_O2_3_anti-rpod): ChIPExo RpoD 3,
ChIPExperiment (#4, ChIPExo-RpoD_wt_glucose_NH4Cl_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#5, ChIPExo-RpoD_wt_glucose_NH4Cl_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#6, ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#7, ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#8, ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_3_anti-rpod): ChIPExo RpoD 3,
ChIPExperiment (#74, ChIPExo-RpoD_wt_glucose_cytidine_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#75, ChIPExo-RpoD_wt_glucose_cytidine_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#76, ChIPExo-RpoD_wt_glucose_cytosine_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#77, ChIPExo-RpoD_wt_glucose_cytosine_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#78, ChIPExo-RpoD_wt_glucose_glutamine_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#79, ChIPExo-RpoD_wt_glucose_glutamine_O2_2_anti-rpod): ChIPExo RpoD 2,
ChIPExperiment (#80, ChIPExo-RpoD_wt_glucose_NH4Cl_O2_1_anti-rpod_nitrogenstudy): ChIPExo RpoD 1,
ChIPExperiment (#81, ChIPExo-RpoD_wt_glucose_NH4Cl_O2_2_anti-rpod_nitrogenstudy): ChIPExo RpoD 2]
In [49]:
session.query(ChIPPeakAnalysis).limit(10).all()
Out[49]:
[ChIP Peak Analysis (#326, ChIPExo-Crp_wt_glucose_NH4Cl_O2_anti-crp_default_peaks): Environment: C:glucose, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#327, ChIPExo-RpoD_wt_glucose_cytidine_O2_anti-rpod_default_peaks): Environment: C:glucose, N:cytidine, e:O2 ,
ChIP Peak Analysis (#328, ChIPExo-Nac_Nac8myc_glucose_glutamine_O2_anti-myc_default_peaks): Environment: C:glucose, N:glutamine, e:O2 ,
ChIP Peak Analysis (#329, ChIPExo-Crp_wt_fructose_NH4Cl_O2_anti-crp_default_peaks): Environment: C:fructose, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#330, ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_anti-myc_default_peaks): Environment: C:glucose, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#331, ChIPExo-Crp_wt_glycerol_NH4Cl_O2_anti-crp_default_peaks): Environment: C:glycerol, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#332, ChIPExo-NtrC_NtrC8myc_glucose_cytosine_O2_anti-myc_default_peaks): Environment: C:glucose, N:cytosine, e:O2 ,
ChIP Peak Analysis (#333, ChIPchip-Cra_Cra8myc_glucose_NH4Cl_O2_anti-myc_default_peaks): Environment: C:glucose, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#334, ChIPchip-Lrp_Lrp8myc_glucose_NH4Cl_O2_anti-myc_default_peaks): Environment: C:glucose, N:NH4Cl, e:O2 ,
ChIP Peak Analysis (#335, ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_anti-myc_default_peaks): Environment: C:glucose, N:NH4Cl, e:anaerobic ]
In [50]:
session.query(ChIPPeakAnalysis).first().children
Out[50]:
[ChIPExperiment (#74, ChIPExo-RpoD_wt_glucose_cytidine_O2_1_anti-rpod): ChIPExo RpoD 1,
ChIPExperiment (#75, ChIPExo-RpoD_wt_glucose_cytidine_O2_2_anti-rpod): ChIPExo RpoD 2]
In [53]:
session.query(ChIPPeakData).filter(ChIPPeakData.data_set_id == 330).limit(20).all()
Out[53]:
[ChIP Peak: 155-356 4626.10 ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_anti-myc_default_peaks,
ChIP Peak: 209-410 1730.90 ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_anti-myc_default_peaks,
ChIP Peak: 83469-83670 1199.10 ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_anti-myc_default_peaks,
ChIP Peak: 83537-83738 2267.40 ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_anti-myc_default_peaks,
ChIP Peak: 83576-83777 1091.80 ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_anti-myc_default_peaks,
ChIP Peak: 83634-83835 1593.70 ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_anti-myc_default_peaks,
ChIP Peak: 169784-169985 8440.30 ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_anti-myc_default_peaks,
ChIP Peak: 169806-170007 4580.70 ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_anti-myc_default_peaks,
ChIP Peak: 188570-188771 5568.00 ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_anti-myc_default_peaks,
ChIP Peak: 228811-229012 3650.60 ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_anti-myc_default_peaks,
ChIP Peak: 228869-229070 3192.40 ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_anti-myc_default_peaks,
ChIP Peak: 236815-237016 1375.90 ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_anti-myc_default_peaks,
ChIP Peak: 236873-237074 2616.50 ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_anti-myc_default_peaks,
ChIP Peak: 236930-237131 1760.50 ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_anti-myc_default_peaks,
ChIP Peak: 261962-262163 1227.30 ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_anti-myc_default_peaks,
ChIP Peak: 262060-262261 1166.70 ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_anti-myc_default_peaks,
ChIP Peak: 357831-358032 4792.30 ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_anti-myc_default_peaks,
ChIP Peak: 357866-358067 1578.70 ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_anti-myc_default_peaks,
ChIP Peak: 365570-365771 477.00 ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_anti-myc_default_peaks,
ChIP Peak: 606512-606713 8871.00 ChIPExo-Nac_Nac8myc_glucose_NH4Cl_O2_anti-myc_default_peaks]
In [54]:
session.query(RNASeqExperiment).all()
Out[54]:
[RNASeqExperiment (#126, RNAseq_Ar3_glycerol_NH4Cl_O2_1): 1,
RNASeqExperiment (#127, RNAseq_Ar3_glycerol_NH4Cl_O2_2): 2,
RNASeqExperiment (#128, RNAseq_Ar3_glycerol_NH4Cl_O2_3): 3,
RNASeqExperiment (#129, RNAseq_delAr1_glycerol_NH4Cl_O2_1): 1,
RNASeqExperiment (#130, RNAseq_delAr1_glycerol_NH4Cl_O2_2): 2,
RNASeqExperiment (#131, RNAseq_delAr1_glycerol_NH4Cl_O2_3): 3,
RNASeqExperiment (#132, RNAseq_delAr1delAr2_glycerol_NH4Cl_O2_1): 1,
RNASeqExperiment (#133, RNAseq_delAr1delAr2_glycerol_NH4Cl_O2_2): 2,
RNASeqExperiment (#134, RNAseq_delAr1delAr2_glycerol_NH4Cl_O2_3): 3,
RNASeqExperiment (#135, RNAseq_delAr2_glycerol_NH4Cl_O2_1): 1,
RNASeqExperiment (#136, RNAseq_delAr2_glycerol_NH4Cl_O2_3): 3,
RNASeqExperiment (#137, RNAseq_delta-crp_fructose_NH4Cl_O2_1): 1,
RNASeqExperiment (#138, RNAseq_delta-crp_fructose_NH4Cl_O2_2): 2,
RNASeqExperiment (#139, RNAseq_delta-crp_fructose_NH4Cl_O2_3): 3,
RNASeqExperiment (#140, RNAseq_delta-crp_glucose_NH4Cl_O2_1): 1,
RNASeqExperiment (#141, RNAseq_delta-crp_glucose_NH4Cl_O2_2): 2,
RNASeqExperiment (#142, RNAseq_delta-crp_glucose_NH4Cl_O2_3): 3,
RNASeqExperiment (#143, RNAseq_delta-crp_glycerol_NH4Cl_O2_1): 1,
RNASeqExperiment (#144, RNAseq_delta-crp_glycerol_NH4Cl_O2_2): 2,
RNASeqExperiment (#145, RNAseq_delta-crp_glycerol_NH4Cl_O2_3): 3,
RNASeqExperiment (#146, RNAseq_wt_fructose_NH4Cl_O2_1): 1,
RNASeqExperiment (#147, RNAseq_wt_fructose_NH4Cl_O2_2): 2,
RNASeqExperiment (#148, RNAseq_wt_glucose_NH4Cl_O2_1): 1,
RNASeqExperiment (#149, RNAseq_wt_glucose_NH4Cl_O2_2): 2,
RNASeqExperiment (#150, RNAseq_wt_glycerol_NH4Cl_O2_1): 1,
RNASeqExperiment (#151, RNAseq_wt_glycerol_NH4Cl_O2_2): 2,
RNASeqExperiment (#152, RNAseq_delAr2_glycerol_NH4Cl_O2_2): 2,
RNASeqExperiment (#153, RNAseq_bw25113_acetate_NH4Cl_O2_1_thiamine): 1,
RNASeqExperiment (#154, RNAseq_bw25113_acetate_NH4Cl_O2_2_thiamine): 2,
RNASeqExperiment (#155, RNAseq_bw25113_fumarate_NH4Cl_O2_1_thiamine): 1,
RNASeqExperiment (#156, RNAseq_bw25113_fumarate_NH4Cl_O2_2_thiamine): 2,
RNASeqExperiment (#157, RNAseq_bw25113_glucose_NH4Cl_O2_1_thiamine): 1,
RNASeqExperiment (#158, RNAseq_bw25113_glucose_NH4Cl_O2_2_thiamine): 2,
RNASeqExperiment (#159, RNAseq_bw25113_pyruvate_NH4Cl_O2_1_thiamine): 1,
RNASeqExperiment (#160, RNAseq_bw25113_pyruvate_NH4Cl_O2_2_thiamine): 2,
RNASeqExperiment (#161, RNAseq_delta-fur_glucose_NH4Cl_O2_1_dpd): 1,
RNASeqExperiment (#162, RNAseq_delta-fur_glucose_NH4Cl_O2_1_FeCl2): 1,
RNASeqExperiment (#163, RNAseq_delta-fur_glucose_NH4Cl_O2_2_dpd): 2,
RNASeqExperiment (#164, RNAseq_delta-fur_glucose_NH4Cl_O2_2_FeCl2): 2,
RNASeqExperiment (#165, RNAseq_wt_glucose_cytidine_O2_1): 1,
RNASeqExperiment (#166, RNAseq_wt_glucose_cytidine_O2_2): 2,
RNASeqExperiment (#167, RNAseq_wt_glucose_cytosine_O2_1): 1,
RNASeqExperiment (#168, RNAseq_wt_glucose_cytosine_O2_2): 2,
RNASeqExperiment (#169, RNAseq_wt_glucose_glutamine_O2_1): 1,
RNASeqExperiment (#170, RNAseq_wt_glucose_glutamine_O2_2): 2,
RNASeqExperiment (#171, RNAseq_wt_glucose_NH4Cl_O2_1_dpd): 1,
RNASeqExperiment (#172, RNAseq_wt_glucose_NH4Cl_O2_1_FeCl2): 1,
RNASeqExperiment (#173, RNAseq_wt_glucose_NH4Cl_O2_2_dpd): 2,
RNASeqExperiment (#174, RNAseq_wt_glucose_NH4Cl_O2_2_FeCl2): 2,
RNASeqExperiment (#175, RNAseq_wt_glucose_NH4Cl_O2_3): 3,
RNASeqExperiment (#176, RNAseq_wt_glucose_NH4Cl_O2_4): 4]
In [55]:
{x['leftpos']:x['value'] for x in query_genome_data([133,134], leftpos=gapA.leftpos, rightpos=gapA.rightpos)}
Out[55]:
{1860794: 2919.0,
1860795: 2949.0,
1860796: 3467.0,
1860797: 3576.0,
1860798: 3565.0,
1860799: 3588.0,
1860800: 3648.0,
1860801: 3759.0,
1860802: 3770.0,
1860803: 3845.0,
1860804: 3863.0,
1860805: 3858.0,
1860806: 3860.0,
1860807: 3869.0,
1860808: 3857.0,
1860809: 3849.0,
1860810: 3840.0,
1860811: 3807.0,
1860812: 3806.0,
1860813: 3769.0,
1860814: 3770.0,
1860815: 3815.0,
1860816: 3874.0,
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Content source: aebrahim/ome
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