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PortEco Microarray Pipeline

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Title/Dataset Description Reference Platform GEO Accession ArrayExpress Accession Data loaded Curation completed Notes category/subcat date started geneprofile wdk zscore finished

public

Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions

no publication

Affymetrix GeneChip E.coli Genome 2.0 Array

E-MEXP-3800

loaded 07/16/13

JD

E-MEXP-3800.idf.txt
E-MEXP-3800.sdrf.txt

needs c1-4

Media comparisons/Culturing history

03/20/13

public

Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress

no publication

Affymetrix GeneChip E.coli Genome 2.0 Array

E-MEXP-3799

loaded 07/16/13

JD

E-MEXP-3799.idf.txt
E-MEXP-3799.sdrf.txt

needs c1-4

Media comparisons/H2O2

03/20/13

public

Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor

no publication

Affymetrix E. coli Genome 2.0 Array

GSE43325

E-GEOD-43325

loaded 07/15/13

JD

E-GEOD-43325.idf.txt
E-GEOD-43325.sdrf.txt

needs c1-c4; new organism? O55:H7

Quorum sensing/virulence

03/21/13

public

Nitric oxide effect in Escherichia coli O157:H7 EDL933

no publication

Affymetrix E. coli Genome 2.0 Array

GSE29076

E-GEOD-29076

loaded 07/16/13

JD

E-GEOD-29076.idf.txt
E-GEOD-29076.sdrf.txt

needs c1-4

Nitric oxide/transcription profiling

03/21/13

public

Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism

PMID:23292772
jbact

Affymetrix E. coli Genome 2.0 Array

GSE42702

E-GEOD-427020

loaded 06/06/13

C1-C4 Complete AMS

JD: no cel files and only norm intensity values E-GEOD-42702.idf.txt
E-GEOD-42702.sdrf.txt

needs c1-4

Stress response/Parkinson's disease

03/21/13

public

Fucose sensing regulates bacterial intestinal colonization

PMID:23160491 nature

Affymetrix E. coli Genome 2.0 Array

GSE34991

E-GEOD-34991

loaded 6/27/13

JD

E-GEOD-34991.idf.txt
E-GEOD-34991.sdrf.txt

needs c1-4

Fucose sensing/colonization

03/21/13

public

Global transcriptional responses to the bacteriocin colicin M in Escherichia coli

PMID:23421615 BMCMicro

Affymetrix E. coli Genome 2.0 Array

GSE37026

E-GEOD-37026

loaded 7/01/13

JD

E-GEOD-37026.idf.txt
E-GEOD-37026.sdrf.txt

needs c1-4

colicins/transcription profiling

03/21/13

public

Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli

PMID:23222720
jbact

Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]

E-MTAB-1347

loaded 07/02/13

JD

E-MTAB-1347.idf.txt
E-MTAB-1347.sdrf.txt

ready to load?

Two-component systems/transcript profiling

03/24/13

public

Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)

PMID:23071782
plosone

Affymetrix E. coli Genome 2.0 Array

GSE21820

E-GEOD-21820

loaded 06/06/13

C1-C4 Complete AMS

JD

E-GEOD-21820.idf.txt
E-GEOD-21820.sdrf.txt

needs c1-4

Starvation/Phosphate

03/21/13

public

Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence

PMID:23163871
FEMS_IMM

Affymetrix E. coli Genome 2.0 Array

GSE22285

E-GEOD-22285

loaded 07/02/13

JD

E-GEOD-22285.idf.txt
E-GEOD-22285.sdrf.txt

needs c1-4

Virulence/Host factors

03/21/13

public

Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure

PMID:23183978
AEM

Affymetrix E. coli Genome 2.0 Array

GSM999249

E-GEOD-40693

loaded 5/16/13

C1-4 done, AMS

05/15/13 DAS sent idf, sdrf to JD

JD E-GEOD-40693.idf.txt
E-GEOD-40693.sdrf.txt

needs c1-4

Antimicrobial agent/transcription profiling

03/21/13

+

+ Cinnamaldehyde

+

complete 5/17/13

public

Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression

PMID:23472115
plosone

Affymetrix E. coli Genome 2.0 Array

GSE40648

E-GEOD-40648

loaded 6/25/13

JD

E-GEOD-40648.idf.txt
E-GEOD-40648.sdrf.txt

microgravity/transcript profiling

03/22/13

public

Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli

PMID:22869698
pnas

Affymetrix E. coli Genome 2.0 Array

GSM540098

E-GEOD-21652

loaded 07/10/13

JD

E-GEOD-21652.idf.txt
E-GEOD-21652.sdrf.txt

needs c3-4

Biotechnology/Transcript profiling

03/22/13

public

Global transcriptional response of E. coli to the presence and absence of bile salts

no publication

Affymetrix E. coli Genome 2.0 Array

GSE20380

E-GEOD-20380

loaded 07/15/13

JD

E-GEOD-20380.idf.txt
E-GEOD-20380.sdrf.txt

ready to load?

bile acids/transcript profiling

03/22/13

public

Expression data from QdNOs treated Escherichia coli

no publication

Affymetrix E. coli Genome 2.0 Array

GSE39607

E-GEOD-39607

loaded 07/15/13

JD

E-GEOD-39607.idf.txt
E-GEOD-39607.sdrf.txt

needs c4

Antimicrobial agent/transcript profiling

03/22/13

public

Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression

PMID:23106382
fmes-micro

Affymetrix E. coli Genome 2.0 Array

GSM760801

E-GEOD-30679

loaded 5/26/13

05/24/13 - DAS

JD

E-GEOD-30679.idf.txt
E-GEOD-30679.sdrf.txt

needs c3-4

diglutathionylspermidine/transcription profiling

03/22/13

+

+

+

complete 05/30/13

public

Antitoxin DinJ influences the general stress response through transcript stabilizer CspE

PMID:22026739
env_microb

Affymetrix E. coli Genome 2.0 Array

GSM761209

E-GEOD-30692

loaded 06/07/13

07/10/13 - DAS

JD

E-GEOD-30692.idf.txt
E-GEOD-30692.sdrf.txt

needs c3

Toxin-antitoxin system/Stress response

03/22/13

+

+

+

complete 07/10/13

public

Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.

PMID:22274708
AMB

Affymetrix E. coli Genome 2.0 Array

GSE30424

E-GEOD-30424

loaded 07/03/13

JD

E-GEOD-30424.idf.txt
E-GEOD-30424.sdrf.txt

ready to load?

biofilm/Indole

03/22/13

public

Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7

PMID:22589288
Bio

Affymetrix E. coli Genome 2.0 Array

GSE34046

E-GEOD-34046

loaded 6/27/13

JD

E-GEOD-34046.idf.txt
E-GEOD-34046.sdrf.txt

ready to load?

virulence/Ethanolamine

03/22/13

public

E-GEOD-21857

loaded (partially, as E-GEOD-21820)

JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen). Capture only expression data: E-GEOD-21820

public

E-TABM-86

public

Protein acetylation in prokaryotes increases stress resistance

PMID:21703240
BBRC

Affymetrix E. coli Genome 2.0 Array

GSE29803

E-GEOD-29803

loaded 07/10/13

JD

E-GEOD-29803.idf.txt
E-GEOD-29803.sdrf.txt

needs c3-4?

Lysine acetylation/stress resistance

03/25/13

public

E-GEOD-40427

public

E-GEOD-33212

public

E-GEOD-42205

public

E-GEOD-40557

public

E-GEOD-39439

public

E-GEOD-35049

public

E-GEOD-35822

public

E-GEOD-41093

public

E-GEOD-41940

public

E-GEOD-41938

public

E-GEOD-26223

public

E-MTAB-996

public

Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields

PMID:22331529

Affymetrix E. coli Genome 2.0 Array

GSE35371

E-GEOD-35371

loaded 6/28/13

JD
E-GEOD-35371.idf.txt
E-GEOD-35371.sdrf.txt
needs c3-c4

Transcript profiling/Magnetic field

02/25/13

public

Evolution of gene expression during long term coexistence in a bacterial evolution experiment

PMID:22645336
PNAS

Affymetrix E. coli Genome 2.0 Array

GSE30639

E-GEOD-30639

loaded 6/27/13

JD
E-GEOD-30639.idf.txt
E-GEOD-30639.sdrf.txt
needs c3-c4

evolution/chemostat

02/26/13

public

Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.

PMID:20886356
mgg

Affymetrix GeneChip E.coli Genome 2.0 Array

E-MEXP-2609

loaded 03/25/13

03/20/13 - DAS

JD
E-MEXP-2609.idf.txt
E-MEXP-2609.sdrf.txt

biofilm/urine

02/26/13

+

+

+

complete (redone 5/9/13)

public

Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase

no publication listed

Affymetrix GeneChip E.coli Genome 2.0 Array

GSE17526

E-GEOD-17526

loaded 5/14/13

3/30/2013 - DAS

JD
E-GEOD-17526.idf.txt
E-GEOD-17526.sdrf.txt

Ethanol shock/rpoS

02/26/13

+

+

+

complete on 5/15/13

public

Expression data from E. coli cells overexpressing GraL for short and long periods of time

PMID:20008510

Affymetrix E. coli Genome 2.0 Array

GSE15406
(GSE15404, GSE15405)

E-GEOD-15406
(E-GEOD-15404, E-GEOD-15405)

loaded 6/28/13

JD
E-GEOD-15406.idf.txt
E-GEOD-15406.sdrf.txt
needs c1-c4

Overexpression/????

02/26/13

public

Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate

PMID:20501031

Affymetrix E. coli Genome 2.0 Array

GSE17519

E-GEOD-17519

loaded 07/11/13

JD
E-GEOD-17519.idf.txt
E-GEOD-17519.sdrf.txt
c1-c4

benzoate/transcript profiling

02/26/13

public

E. coli response to Antimicrobial Arylamides

PMID:21844313

Affymetrix E. coli Genome 2.0 Array

GSE31140

E-GEOD-31140

loaded 03/19/13 re-loaded 04/14/13

3/17/13 - DAS

sdrf file at AE didn't have a column for Sample Name

JD
E-GEOD-31140.sdrf.txt
E-GEOD-31140.idf.txt
needs c3-c4

antimicrobial agent/transcription profile

02/26/13

+

+

+

complete (redone 05/08/13)

public

Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock

pmid
paper

Affymetrix E. coli Genome 2.0 Array

GSE17465

E-GEOD-17465

loaded 07/16/13

JD
E-GEOD-17465.sdrf.txt
E-GEOD-17465.sidf.txt
needs c1-c4

Salt tolerance/Radiation resistance

02/26/13

public

Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.

PMID:22008207

Affymetrix GeneChip E.coli Genome 2.0 Array

E-MTAB-623

loaded 07/09/13

JD

E-MTAB-623.idf.txt
E-MTAB-623.sdrf.txt

needs c3-c4

cold-shock/water activity

02/27/13

public

Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.

PMID:17145952

Affymetrix GeneChip E.coli Genome 2.0 Array

E-MEXP-926

loaded 6/27/13

JD

E-MEXP-926.idf.txt
E-MEXP-926.sdrf.txt

needs c2-4

urine/biofilm

02/27/13

public

Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.

PMID:20444967

Affymetrix GeneChip E.coli Genome 2.0 Array

E-MEXP-2298

loaded 6/27/13

JD

E-MEXP-2298.idf.txt
E-MEXP-2298.sdrf.txt

needs c1-c4

urine/biofilm

02/27/13

public

Impact of cranberry on Escherichia coli cellular surface characteristics.

PMID:18957286

Affymetrix E. coli Genome 2.0 Array

GSE12554

E-GEOD-12554

loaded 07/03/13

JD

E-GEOD-12554.idf.txt
E-GEOD-12554.sdrf.txt

needs c3-c4

antibacterial agent/cranberry juice

02/27/13

public

Evolvability and hierarchy in rewired bacterial gene networks.

PMID:18421347

Affymetrix GeneChip E.coli Genome 2.0 Array

E-MEXP-732

loaded 6/28/13

JD


E-MEXP-732.idf.txt
E-MEXP-732.sdrf.txt
needs c1-c4

regulatory networks/evolvability

02/28/13

public

Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites

23472115 plosone

Affymetrix GeneChip E.coli Genome 2.0 Array

GSE34275

E-GEOD-34275

loaded 6/25/13

JD

E-GEOD-34275.idf.txt
E-GEOD-34275.sdrf.txt
needs c1-c4

Growth medium/glycerol

02/28/13

public

Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli

PMID:22018139

Affymetrix E. coli Genome 2.0 Array

GSE29440

E-GEOD-29440

loaded 06/24/13

JD

E-GEOD-29440.idf.txt
E-GEOD-29440.sdrf.txt

needs c1-c4

biotechnology/recombinant proteins

02/28/13

public

Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data

PMID:22018139

www.amb-express.com

PMID:22134216

pubs.rsc.org

Affymetrix E. coli Genome 2.0 Array

GSE28412

E-GEOD-28412

loaded 06/07/13

JD

E-GEOD-28412.idf.txt
E-GEOD-28412.sdrf.txt

needs c1-c4

stress/recombinant proteins

02/28/13

public

Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture

PMID:22018139

Affymetrix E. coli Genome 2.0 Array

GSE29439

E-GEOD-29439

loaded 06/24/13

JD

E-GEOD-29439.idf.txt
E-GEOD-29439.sdrf.txt

needs c1-c4

recombinant proteins/transcript profiling

02/28/13

public

Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli

no publication

Affymetrix E. coli Genome 2.0 Array

GSE29486

E-GEOD-29486

loaded 07/16/13

JD E-GEOD-29486.idf.txt
E-GEOD-29486.idf.txt

needs c1-c4

biotechnology/recombinant proteins

02/28/13

public

Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.

PMID:23090957
IAI

Affymetrix E. coli Genome 2.0 Array

GSE28399

E-GEOD-28399

loaded on 5/16/13

4/3/13 - DAS

JD: missing one cel file

E-GEOD-28399.idf.txt

E-GEOD-28399.sdrf.txt

missing one cel file

UPEC/high osmolarity

02/28/13

+

+ OsmolarityUPEC

+

complete 5/17/13

public

Metabolic and transcriptional response to cofactor perturbations in Escherichia coli

PMID:20299454
PMC2878514

Affymetrix E. coli Genome 2.0 Array

GSE20374

E-GEOD-20374

loaded 06/07/13

C1-C4 Completed AMS

JD

GEOD-20374.idf.txt
E-GEOD-20374.sdrf.txt

needs c1-c4

cofactor/transcriptional profiling

02/28/13

public

Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies

PMID:19806199

Affymetrix E. coli Genome 2.0 Array

GSE14796

E-GEOD-14796

loaded 06/24/13

07/08/2013 - DAS

07/09/2013 - sent to JD

JD

E-GEOD-14796.idf.txt
E-GEOD-14796.sdrf.txt

Colony/control or L-form

03/01/13

+

+

+

complete 07/10/13

public

Identification of genes induced on nitrate, role of OxyR

PMID:22539721
Science

Affymetrix E. coli Genome 2.0 Array

GSE24524

E-GEOD-24524

loaded 07/03/13

JD

E-GEOD-24524.idf.txt
E-GEOD-24524.sdrf.txt

need c3-4

anaerobic growth/S-Nitrosylation

03/01/13

public

Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM

PMID:22144490

PMC3264324

Affymetrix E. coli Genome 2.0 Array

GSE33895

E-GEOD-33895

loaded 6/25/13

JD

E-GEOD-33895.idf.txt
E-GEOD-33895.sdrf.txt

needs c2-c4

virulence/His kinase

03/01/13

public

Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa

PMID:22101045

Affymetrix E. coli Genome 2.0 Array

GSE26931

E-GEOD-26931

data are loaded in database 03/19/13 re-loaded 04/15/13

used annot from batch loading

JD

E-GEOD-26931.idf.txt
E-GEOD-26931.sdrf.txt

needs c1-c4

only loading 4 slides, the ones that are assayed on coli platform

mixed culture/transcript profiling

03/01/13

+ (with GSE26932)

+ (with GSE26932)

+ (with GSE26932)

complete (redone 5/10/13)

public

A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.

PMID:21169565
PMC3047162

Affymetrix E. coli Genome 2.0 Array

GSE21551

E-GEOD-21551

loaded 03/19/13 re-loaded 04/13/13

03-11-13 - DAS (waiting to hear about strains but OK to load)

JD

GEOD-21551.idf.txt
E-GEOD-21551.sdrf.txt


needs c1-4: DAS added on 03/11/13

strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used

beta-methylthiolation/regulation of gene expression

03/01/13

+

+

+

complete (redone 5/8/13)

public

Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol

PMID:22936779
PMID:22936779

Affymetrix E. coli Genome 2.0 Array

GSE34631

E-GEOD-34631

loaded 03/19/13 re-loaded 04/14/13

03/12/13 - DAS

JD

GEOD-34631.idf.txt
E-GEOD-34631.sdrf.txt

needs c3-4: done

Carbon sources/Enzyme evolution

03/01/13

+

+

+

complete (redone 5/7/13)

public

Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans

PMID:22792156
PMC3390347

Affymetrix E. coli Genome 2.0 Array

GSE30441

E-GEOD-30441

loaded 5/16/13

c1-4 done, AMS

05/15/13 DAS sent idf, sdrf to JD

JD

GEOD-30441.idf.txt

GEOD-30441.sdrf.txt

Stress resistance/EtOH

03/01/13

+

+ Ethanol-irrE

+

complete 5/17/13

public

First insights into the unexplored two-component system YehU/YehT in Escherichia coli.

PMID:22685278
PMC3416263

Affymetrix GeneChip E.coli Genome 2.0 Array

E-MTAB-984

loaded 6/27/13

JD

E-MTAB-984.idf.txt
E-MTAB-984.sdrf.txt

needs c1-4

Two-component systems/?????

03/01/13

public

Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli

PMID:22684885 biotech_bioeng

Affymetrix E. coli Genome 2.0 Array

GSE35100

E-GEOD-35100

loaded 03/25/13 re-loaded 04/13/13

03/20/13 - DAS

JD

E-GEOD-35100.idf.txt
E-GEOD-35100.sdrf.txt

Chemical effects/Mutant vs Wild-type

03/01/13

+

+

+

complete (redone 5/7/13)

public

Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine

PMID:22101045

PMC3255741

Affymetrix E. coli Genome 2.0 Array

GSE)

E-GEOD-26932

data loaded 03/19/13 re-loaded 04/15/13

used annotation from batch loading

JD

E-GEOD-26932.idf.txt
E-GEOD-26932.sdrf.txt

needs c3-4

use only data on E. coli platform

mixed culture/N-acetyl glucosamine

actual in database: co-culture/minimal medium

03/04/13

+ (with GSE26931)

+ (with GSE26931)

+ (with GSE26931)

complete (redone 5/10/13)

public

Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock

PMID:23247721
pubs.rsc.org

Affymetrix E. coli Genome 2.0 Array

GSE30838

E-GEOD-30838

completed, 03/18/13 re-loaded 04/15/13

03/14/13 - DAS

DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.

JD

E-GEOD-30838.idf.txt
E-GEOD-30838.sdrf.txt

needs c1-4: done

pUC-A1501 described in PMID:19799945

glyphosate shock/transcriptional profiling

03/04/13

+

+

+

complete (redone 5/8/13)

public

Relative expression profiling of ycdC knockout strain secreting HlyA protein

PMID:22505047
full text

Affymetrix E. coli Genome 2.0 Array

GSE29266

E-GEOD-29266

loaded 07/10/13

JD

E-GEOD-29266.idf.txt
E-GEOD-29266.sdrf.txt

needs c1-c4

biotechnology/protein secretion

03/04/13

public

Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis

PMID:22210763
PMC3294818

Affymetrix E. coli Genome 2.0 Array

GSE23417

E-GEOD-23417

loaded 07/15/13

JD

E-GEOD-23417.idf.txt
E-GEOD-23417.sdrf.txt

needs c1-c4

persistence/Zinc metabolism

03/04/13

public

Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)

corresponding author confirmed that data were published in PMID:22196016

Affymetrix E. coli Genome 2.0 Array

GSE11303

E-GEOD-11303

loaded 03/18/13

03/13/2013 - DAS

JD

E-GEOD-11303.idf.txt
E-GEOD-11303.sdrf.txt

needs c3-4: done

stress/zinc or Chemical effects/zinc

03/04/13

+

+

+

complete (redone 5/9/13)

public

Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol

PMID:22389366
PMC3346451

Affymetrix E. coli Genome 2.0 Array

GSE35797

E-GEOD-35797

loaded 07/15/13

AMS c1-4 done

JD

E-GEOD-35797.idf.txt
E-GEOD-35797.sdrf.txt

needs c3-4

Biofilms/drug treatment

03/04/13

public

Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.

PMID:21398637
PMC3141248

Affymetrix E. coli Genome 2.0 Array

GSE22207

E-GEOD-22207

loaded 07/03/13

JD E-GEOD-22207.idf.txt
E-GEOD-22207.sdrf.txt

needs c3-4

promoter/sigma factor

03/04/13

public

Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC

PMID:21255366
PMC3158428

Affymetrix E. coli Genome 2.0 Array

GSE21604

E-GEOD-21604

loaded 06/24/13

JD E-GEOD-21604.idf.txt
E-GEOD-21604.sdfr.txt

needs c2-4

biofilm/mutagenesis

03/04/13

public

The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.

PMID:20855516
PMC2981326

Affymetrix E. coli Genome 2.0 Array

GSE21893

E-GEOD-21893

loaded 07/11/13

JD E-GEOD-21893.idf.txt
E-GEOD-21893.sdrf.txt

needs c3-4

APEC/type VI secretion system

03/05/13

public

BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type

PMID:22221537
full text

Affymetrix E. coli Genome 2.0 Array

GSE34028

E-GEOD-34028

loaded 03/19/13 re-loaded 04/14/13

03/12/2013 - DAS

JD E-GEOD-34028.idf.txt
E-GEOD-34028.sdrf.txt

needs c3-4: DAS added 3/12/2013

Persister cells/Mutant vs Wild-type

03/05/13

+

+

+

complete (redone 5/7/13)

public

Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin

PMID:22221537
full text

Affymetrix E. coli Genome 2.0 Array

GSE31054

E-GEOD-31054

loaded 07/09/13

JD E-GEOD-31054.idf.txt
E-GEOD-31054.sdrf.txt

needs c3-4

Persister cells/Stress resistance

03/05/13

public

Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm

PMID:22047137
full text

Affymetrix E. coli Genome 2.0 Array

GSE28193

E-GEOD-28193

loaded 6/28/13

JD E-GEOD-28193.idf.txt
E-GEOD-28193.sdrf.txt

needs c3-4

biofilm/honey

03/05/13

public

The E. coli deletion mutant of the nusB gene

PMID:21873492

Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]

E-MEXP-3335

loaded 5/15/13

4/4/13 - DAS

JD

E-MEXP-3335.idf.txt

E-MEXP-3335.idf.txt

needs c3-4

tRNA modificaton/transcript profiling

03/05/13

+

+

+

complete 5/16/13

public

E. coli ygjD gene temperature sensitive mutant incubated at 37 oC

PMID:21873492
JB

Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]

E-MEXP-3334

loaded 6/28/13

JD E-MEXP-3334.idf.txt
E-MEXP-3334.sdrf.txt

needs c1-4

tRNA modification/transcript profiling

03/05/13

public

The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.

PMID:21873492
JB

Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]

E-MEXP-3333

loaded 6/28/13

JD E-MEXP-3333.idf.txt
E-MEXP-3333.sdrf.txt

needs c2-4

tRNA modification/transcript profiling

03/05/13

public

Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages

PMID:21221972
PMC3158427

Affymetrix E. coli Genome 2.0 Array

GSE19953

E-GEOD-19953

loaded 06/06/13

C1-C4 Complete AMS

JD E-GEOD-19953.idf.txt
E-GEOD-19953.sdrf.txt

needs c3-4

EHEC/biofilm

03/05/13

public

An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.

PMID:20005205

Affymetrix E. coli Genome 2.0 Array

GSE18972

E-GEOD-18972

loaded 03/19/13 re-loaded 04/13/13

03/11/13 - DAS

JD

E-GEOD-18972.idf.txt
E-GEOD-18972.sdrf.txt

needs c1-4

no cel files in ae

biofuel/glycerol

03/05/13

+

+

+

complete (redone 5/8/13)

public

QseA regulation of virulence factors in EHEC

PMID:20444105
PMC2936457

Affymetrix E. coli Genome 2.0 Array

GSE18118

E-GEOD-18118

loaded 07/10/13

JD

E-GEOD-18118.idf.txt
E-GEOD-18118.idf.txt

needs c2-4

EHEC/virulence

03/05/13

public

Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development

PMID:19060153
PMC2632003

Affymetrix E. coli Genome 2.0 Array

GSE12701

E-GEOD-12701

was already loaded as part of publication: "Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae." together with E-GEOD-11932

c1-4 done, AMS

05/15/13 DAS sent idf, sdrf to JD

JD E-GEOD-12701.idf.txt
E-GEOD-12701.idf.txt

needs c2-4

modified matrix file Absent->A, ...

biofilm/toxin-antitoxin system

03/05/13

+

+

+

complete

public

Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)

unpublished

Affymetrix E. coli Genome 2.0 Array

GSE44273

E-GEOD-44273

loaded 6/25/13

JD

E-GEOD-44273.idf.txt
E-GEOD-44273.sdrf.txt

needs c1-4

persistence/transcript profiling

03/06/13

public

Overexpression of BglJ and LeuO in Escherichia coli K12

PMID:22295907
full text

Affymetrix E. coli Genome 2.0 Array

GSE34023

loaded 07/08/13

JD: dataset not in ae, idf/sdrf made from scratch E-GEOD-34023.idf.txt
E-GEOD-34023.sdrf.txt

needs c1-4

Virulence/Regulation of gene expression

03/06/13

public

Expression data from laboratory evolution of Escherichia coli on lactate or glycerol

PMID:16204189
PMC1240078

Ecoli_ASv2

GSE33147

E-GEOD-33147

loaded 05/14/13

C1-4 done, AMS

sent idf, sdrf to JD on 5/13/13

JD E-GEOD-33147.idf.txt
E-GEOD-33147.sdrf.txt

needs c3-4

evolution/carbon source

03/07/13

+

+

+

complete

public

Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.

PMID:17112383
PMC1664580

Ecoli_ASv2

GSE5239

E-GEOD-5239

loaded 05/27/13

loaded 05/26/13

JD dataset has no cel files and only intensity values! E-GEOD-5239.idf.txt
E-GEOD-5239.sdrf.txt

plasmid/metabolism

03/07/13

+

+

- (no cel files)

complete (5/31/13)

public

Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains

PMID:17768236
full text

Ecoli_ASv2

GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)

E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)

loaded 06/07/13

C1-4 done, AMS

JD E-GEOD-7398.idf.txt
E-GEOD-7398.sdrf.txt

needs c1-4

growth phase/fis

03/07/13

public

Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media

unpublished

Ecoli_ASv2

E-TABM-103

in process

JD: can't figure out how the experiment was done.

E-TABM-103.idf.txt
E-TABM-103.sdrf.txt

03/07/13

public

Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli

PMID:15705577
JB

Ecoli_ASv2

GSE2037

E-GEOD-2037

loaded 6/28/13

JD

E-GEOD-2037.idf.txt
E-GEOD-2037.sdrf.txt

needs c3-4

no cel files available

carbon source/transcript profiling

03/07/13

public

Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.

PMID:17576668
PMC1935009

Ecoli_ASv2

GSE5818

E-GEOD-5818

loaded on 5/17/13

03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)

JD: no cel files available

E-GEOD-5818.idf.txt
E-GEOD-5818.sdrf.txt

needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)

flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD

flagellum/regulation

03/08/13

+

+

no - no cel files available

complete 5/17/13

public

Enterobactin is required for biofilm development in reduced-genome Escherichia coli

PMID:21980953
full text

Ecoli_ASv2

E-MEXP-1408

loaded 05/30/13

05/22/13 - DAS

JD

E-MEXP-1408.idf.txt
E-MEXP-1408.sdrf.txt

needs c1-4

biofilm/transcription profiling

DAS suggests biofilm/Reduced genome

03/08/13

+

+

+

complete 05/30/13

public

Indole cell signaling occurs primarily at low temperatures in Escherichia coli

PMID:18528414

Ecoli_ASv2 and E_coli_2

GSE9923

E-GEOD-9923

loaded 07/03/13

JD

E-GEOD-9923.idf.txt
E-GEOD-9923.sdrf.txt

needs c2-4

biofilm/indole

03/08/13

public

Effect of RyhB Small RNA on Global Iron Use in Escherichia coli

PMID:16199566
PMC1251601

Ecoli_ASv2

GSE3105

E-GEOD-3105

loaded 5/16/13

04/16/13 - DAS

DAS sent idf, sdrf to JD 05/14/13

JD: no cel files available

E-GEOD-3105.idf.txt E-GEOD-3105.sdrf.txt

iron/non-coding RNA

03/08/13

+

+

no: no cel files

complete 5/17/13

public

sigma32 over-expression in E. coli

PMID:15757896
JBC

Ecoli_ASv2

GSE2140

E-GEOD-2140

loaded 05/31/13

05/26/13 - DAS

JD E-GEOD-2140.idf.txt
E-GEOD-2140.sdrf.txt

needs c2-4

no cel files available

sigma factor/transcription profiling

03/08/13

+

+

- (no cel files)

complete (5/31/13)

public

Temporal gene-expression in Escherichia coli K-12 biofilms

PMID:17222132
full text

Ecoli_ASv2

GSE3905

E-GEOD-3905

loaded 07/11/13

JD no cel file available

E-GEOD-3905.idf.txt
E-GEOD-3905.sdrf.txt

needs c3-4

biofilm/transcription profiling

03/08/13

public

Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation

PMID:20809290

Full Text

Ecoli_ASv2

E-MEXP-1001

loaded 05/30/13

05/27/13 - DAS

JD

E-MEXP-1001.idf.txt
E-MEXP-1001.sdrf.txt

needs c3-4

biofilm/F- phenocopy

03/11/13

+

+

+

complete (06/05/13)

public

Indole is an inter-species biofilm signal mediated by SdiA

PMID:17511876
PMC1899176

Ecoli_ASv2

GSE4562

E-GEOD-4562

loaded 07/03/13

JD

E-GEOD-4562.idf.txt
E-GEOD-4562.sdrf.txt

needs c3-4

biofilm/indole

03/11/13

public

Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture

PMID:17557827
PMC1952038

Ecoli_ASv2

GSE9203

E-GEOD-9203

loaded 06/97/13

Created C1-C4 AMS

JD: no cel files available E-GEOD-9203.idf.txt
E-GEOD-9203.sdrf.txt

needs c3-4

Quorum sensing/biofilm

03/11/13

public

YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling

PMID:16597943
PMC1448992

Ecoli_ASv2

GSE3937

E-GEOD-3937

loaded 5/26/13

05/21/13 - DAS

JD: no cel files available E-GEOD-3937.idf.txt
E-GEOD-3937.sdrf.txt

needs c3-4

Quorum sensing/biofilm

03/11/13

+

+

- (no cel files)

complete (05/30/13)

public

Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)

PMID:18309357

The ISME Journal

Ecoli_ASv2

GSE8706

E-GEOD-8706

loaded

C1-4 done, AMS

05/14/13: DAS sent idf/sdrf files to JD

JD

E-GEOD-8706.idf.txt
E-GEOD-8706.sdrf.txt

needs c3-4

Quorum sensing/biofilm

03/11/13

+

+

+

complete (6/05/13)

public

luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling

PMID:16321939

Ecoli_ASv2

GSE9587

E-GEOD-9587

loaded 06/06/13)

C1-C4 Complete AMS

JD: one cel file is corrupted - GSM242209 - had to use chp files given

E-GEOD-9587.idf.txt
E-GEOD-9587.sdrf.txt

needs c3-4

paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.

Quorum sensing/(Mutant/wild-type)

03/12/13

public

Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli

PMID:18790864
JB

Ecoli_ASv2

E-MEXP-1145

loaded 5/15/13

04/03/13 - DAS

JD: E-MEXP-953 is part of same pub - already in porteco E-MEXP-1145.idf.txt
E-MEXP-1145.sdrf.txt

Biofilm/F plasmid

03/12/13

+

+

+

complete 5/15/13

public

YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport

PMID:16385049

Ecoli_ASv2

GSE3514

E-GEOD-3514

loaded 07/15/13

AMS c1-4 done

JD: no cel files available

E-GEOD-3514.idf.txt
E-GEOD-3514.sdrf.txt

needs c3-4

Quorum sensing/biofilm

03/12/13

public

YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity

PMID:17293424
PMC1855844

Ecoli_ASv2

GSE5904

E-GEOD-5904

loaded 07/15/13

AMS c1-4 done

JD: no cel files available E-GEOD-5904.idf.txt
E-GEOD-5904.sdrf.txt

needs c3-4

Biofilm/transcription profiling

03/12/13

public

Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803

PMID:17521447

Ecoli_ASv2

GSE5905

E-GEOD-5905

loaded 07/08/13

JD: no cel files available E-GEOD-5905.idf.txt
E-GEOD-5905.sdrf.txt

needs c3-4

biofuel/biotechnology

03/12/13

public

A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS

PMID:22941047
nchembio

Affymetrix E. coli Genome 2.0 Array

GSE36779

E-GEOD-36779

loaded 03/26/13 re-loaded 04/12/13

4/4/13 - DAS

JD

E-GEOD-36779.idf.txt

E-GEOD-36779.sdrf.txt

ready to load? - yes (4/4/13 DAS)

Toxin-antitoxin system/transcription profiling

03/22/13

+

+

+

complete (redone - 5/7/13)

public

Evolutionary genome engineering using a restriction–modification system

PMID:21785135

PMC3203608

Ecoli_ASv2

GSE21869

the experimental data are loaded:

PortEco Publication

C1-4 done, AMS

faked idf/sdrf

Evolution/Parental strain Evolution/Evolved strain Evolution/Mutant

Nov 2012

+

+

+

complete (redone 5/10/13)

public

Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli

PMID:19909729

bbrc

Affymetrix E. coli Genome 2.0 Array

GSE18852

E-GEOD-18852

reload

yes

JD

E-GEOD-18852.idf
E-GEOD-18852.sdrf

persister cells/toxin-antitoxin systems

04/01/13

+

+

+

complete (5/14/13)

public

The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli

PMID:21292161

mol_cell

Affymetrix E. coli Genome 2.0 Array

GSE24875

E-GEOD-24875

reload

yes

JD

E-GEOD-24875.idf
E-GEOD-24875.sdrf

catabolite repression/non-coding RNA

04/01/13

wasn't missing - did not need to reload

public

A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP

PMID:16377617

jbc

PMID:17921306

jbact

A-GEOD-1246.adf.txt A-GEOD-3051.adf.txt

GSE3591

E-GEOD-3591

reload

yes

JD E-GEOD-3591.idf
E-GEOD-3591.sdrf 

2-channel

aerobic anaerobic transition/(nitrite/nitrate)

04/01/13

+

+

+

complete (redone 5/9/13)

public

The PurR regulon in Escherichia coli K-12 MG1655

PMID:21572102

nar

Affymetrix E. coli Genome 2.0 Array

GSE26588

E-GEOD-26588

reload

yes

JD

E-GEOD-26588.idf
E-GEOD-26588.sdrf

purine metabolism/transcript profiling OR Chemical effects/wild-type vs mutant

04/01/13

+

+

+

complete (redone 5/8/13)

public

Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal

PMID:21059164

env_micro

Affymetrix E. coli Genome 2.0 Array

GSE22057

E-GEOD-22057

reload

yes

JD E-GEOD-22057.idf
E-GEOD-22057.sdrf

biofilm dispersal/transcript profiling

04/01/13

+

+

+

complete (redone 5/8/13)

public

Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]

PMID:21984790

jbact

Affymetrix E. coli Genome 2.0 Array

GSE30893

E-GEOD-30893

reload

yes

JD E-GEOD-30893.idf
E-GEOD-30893.sdrf

type III secretion system/transcript profiling

04/01/13

+

+

+

complete (redone 05/08/13)

public

Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]

PMID:21930760

infect_immun

Affymetrix E. coli Genome 2.0 Array

GSE28144

E-GEOD-28144

reload

yes

JD E-GEOD-28144.idf
E-GEOD-28144.sdrf

biofilms/antioxidants

04/01/13

+

+

+

complete (redone 5/7/13)

public

Dynamic omics approach identifies nutrition-mediated microbial interactions.

PMID:21058740

j_prot_res

Affymetrix E. coli Genome 2.0 Array

GSE18474

E-GEOD-18474

reload

yes

JD

E-GEOD-18474.idf
E-GEOD-18474.sdrf

load only coli data

co-culture/transcript profiling

04/01/13

+

+

+

complete (redone 5/8/13)

public

Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD

PMID:20105222

env_micro

Affymetrix E. coli Genome 2.0 Array Affymetrix E. coli Antisense Genome Array

GSE14203

E-GEOD-14203

reload - expression data only

yes

JD

E-GEOD-14203.idf
E-GEOD-14203.sdrf

two platforms - sdrf only contains data for genome 2.0 array

toxin antitoxin systems/transcript profiling

04/01/13

+

+

+

complete (redone 5/9/13)

public

Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli

PMID:21695201

plosone

Affymetrix GeneChip E.coli Antisense Genome Array

E-MEXP-3191

reload

yes

JD E-MEXP-3191.idf
E-MEXP-3191.sdrf

Heat shock/critical high temperature

04/01/13

+

+

+

complete (redone 5/8/13)

public

Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.

PMID:19240136

pmc

A-MEXP-1444

E-MEXP-1872

reload

yes

blue-light response/two-component system

+

+

+

complete (reloaded 5/14/13)

public

Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine

PMID:22753377

iai

Affymetrix GeneChip E.coli Genome 2.0 Array

E-MEXP-584

reload

yes

JD

E-MEXP-584.idf
E-MEXP-584.sdrf

Asymptomatic Bacteriuria/transcription profiling

04/01/13

+

=

+

complete (redone 5/9/13)

public

Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC

PMID:19240136

pmc

A-MEXP-1444

E-MEXP-1877

reload

yes

blue-light response/two-component system

+

+

+

complete (reloaded 5/14/13)

public

Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110

PMID:18302792

Affymetrix E. coli Antisense Genome Array

GSE4778

E-GEOD-4778

reloaded 6/25/13

redoing this data set because there was a problem with the original loading

Stress/pH (external)

06/21/2013

+

+

+

complete 06/25/13

public

changes of global gene expression in E. coli during an oxygen shift

pmid:15129285 nature

Affymetrix E. coli Antisense Genome Array

GSE1121 GSE1106 GSE1107

E-GEOD-1121

reloaded 6/28/13

yes

reloaded due to error during original loading

(aerobic/anaerobic)/(mutant/wild-type)

+

+

+

6/28/13

public

Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation

PMID:17504765

Affymetrix E. coli Antisense Genome Array

GSE6425

E-GEOD-6425

reloaded 7/02/13

yes

redoing this data set because there was a problem with the original loading

Strain comparison/(Anaerobic growth/Aerobic Growth)

+

+

+

complete 07/02/13

public

Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series

PMID:17504765

Affymetrix E. coli Antisense Genome Array

GSE6426

E-GEOD-6426

reloaded 7/02/13

yes

redoing this data set because there was a problem with the original loading

Strain comparison/cecum

+

+

+

complete 07/02/13

public

GSE26591

E-GEOD-26591

loaded (partially, as E-GEOD-26588)

JD: this is a superset of expression data (E-GEOD-26588) and chip-chip data. The expression data is loaded

public

Transcription profiling by array of Escherichia coli (strain MG1655) to study cellular responses to the oxidizing effects of bleach

PMID:23536188

jbc

Affymetrix GeneChip E.coli Genome 2.0 Array

E-MEXP-3639

loaded 07/16/13

JD: E-MEXP-3639.idf.txt

E-MEXP-3639.sdrf.txt

needs c1 - c4

bleach/transcription profiling

07/16/13

public

Transcription profiling by array of wild-type E. coli W3110 and hns, stpA, hha, ydgT mutants

pmid
paper

Affymetrix GeneChip E.coli Genome 2.0 Array

E-MEXP-3811

loaded 07/16/13

JD

needs c1-4

nucleoid/transcript profiling

07/16/13

public

Transcription profiling of E.coli reveals indole cell signaling occurs primarily at low temperatures in Escherichia coli

pmid
paper

Affymetrix GeneChip E.coli Antisense Genome Array
Affymetrix GeneChip E.coli Genome 2.0 Array

GSE9923

E-GEOD-9923

loaded (partially)

JD: 4 slides from antisense platform are not loaded

public

Enterohemorrhagic Escherichia coli (EHEC) 86-24 double deletions of kdpE and cra grown in DMEM

PMID:23524613

Affymetrix GeneChip E.coli Genome 2.0 Array

GSE43659

E-GEOD-43659

loaded 07/16/13

07/23/13 - DAS updated idf,sdrf

JD: needs c1-c4

virulence/transcript profiling

07/16/13

+

+

+

07/23/13

public

Expression data from Avian Pathogenic Escherichia coli

not published

Affymetrix GeneChip E.coli Genome 2.0 Array

GSE48015

E-GEOD-48015

loaded 07/17/13

APEC/transcript profiling

07/17/13

public

Expression data of Enterohemorrhagic E. coli O157:H7 (EHEC) strain 86-24 when cultured with Bacteroides thetaiotaomicron VPI-5482

not published

Affymetrix GeneChip E.coli Genome 2.0 Array

GSE47418

E-GEOD-47418

loaded 07/17/13

EHEC/co-culture

07/17/13

public

Expression profiling of wt and ydcR mutant strains

not published

E. coli Genome 2.0 Array

GSE48776

not yet in AE

in process

JD: wait for mage_tab files
This is part of a superset: GSE48832, which also includes hts dataset GSE48829.


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Title/Dataset Description Reference Platform GEO Accession ArrayExpress Accession Data loaded Curation completed Notes category/subcat date started geneprofile wdk zscore finished

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