PortEco Microarray Pipeline
| Title/Dataset Description | Reference | Platform | GEO Accession | ArrayExpress Accession | Data loaded | Curation completed | Notes | category/subcat | date started |
|---|---|---|---|---|---|---|---|---|---|
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Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions |
E-MEXP-3800 |
JD: skipped it |
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E-MEXP-3799 |
JD: skipped it |
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E-GEOD-43325 |
JD: skipped it |
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E-GEOD-29076 |
JD: skipped it |
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E-GEOD-42702 |
JD: skipped it |
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E-GEOD-34991 |
JD: skipped it |
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E-GEOD-37026 |
JD: skipped it |
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E-MTAB-1347 |
JD: skipped it |
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E-GEOD-21820 |
JD: skipped it |
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E-GEOD-22285 |
JD: skipped |
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E-GEOD-40693 |
JD: skipped it |
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E-GEOD-40648 |
JD: skipped it |
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E-GEOD-21652 |
JD: skipped it |
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E-GEOD-36779 |
jD: skipped it |
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E-GEOD-20380 |
JD: skipped it |
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E-GEOD-39607 |
JD: skipped it |
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E-GEOD-30679 |
JD: skipped it |
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E-GEOD-30692 |
JD: skipped it |
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E-GEOD-30424 |
JD: skipped it |
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E-GEOD-34046 |
JD: skipped it |
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E-GEOD-21857 |
JD: skipped it |
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E-TABM-86 |
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E-GEOD-29803 |
JD: skipped it |
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E-GEOD-40427 |
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E-GEOD-33212 |
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E-GEOD-42205 |
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E-GEOD-40557 |
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E-GEOD-39439 |
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E-GEOD-35049 |
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E-GEOD-35822 |
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E-GEOD-41093 |
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E-GEOD-41940 |
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E-GEOD-41938 |
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E-GEOD-26223 |
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E-MTAB-996 |
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Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields |
http://www.ncbi.nlm.nih.gov/pubmed/22331529 |
Affymetrix E. coli Genome 2.0 Array |
GSE35371 |
E-GEOD-35371 |
in process |
JD |
Transcript profiling/Magnetic field |
02/25/13 | |
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Evolution of gene expression during long term coexistence in a bacterial evolution experiment |
http://www.ncbi.nlm.nih.gov/pubmed/22645336 |
Affymetrix E. coli Genome 2.0 Array |
GSE30639 |
E-GEOD-30639 |
in process |
JD |
evolution/chemostat |
02/26/13 | |
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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. |
http://www.ncbi.nlm.nih.gov/pubmed/20886356 |
Affymetrix GeneChip E.coli Genome 2.0 Array |
E-MEXP-2609 |
in process |
JD |
biofilm/urine |
02/26/13 | ||
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Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase |
no publication |
Affymetrix GeneChip E.coli Genome 2.0 Array |
GSE17526 |
E-GEOD-17526 |
in process |
JD |
ETOH shock/rpoS |
02/26/13 | |
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Expression data from E. coli cells overexpressing GraL for short and long periods of time |
http://www.ncbi.nlm.nih.gov/pubmed/20008510 |
Affymetrix E. coli Genome 2.0 Array |
GSE15406 |
E-GEOD-15406 |
in process |
JD |
Overexpression/???? |
02/26/13 | |
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Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate |
http://www.ncbi.nlm.nih.gov/pubmed/20501031 |
Affymetrix E. coli Genome 2.0 Array |
GSE17519 |
E-GEOD-17519 |
in process |
JD |
benzoate/?????? |
02/26/13 | |
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E.coli response to Antimicrobial Arylamides |
http://www.ncbi.nlm.nih.gov/pubmed/21844313 |
Affymetrix E. coli Genome 2.0 Array |
GSE31140 |
E-GEOD-31140 |
in process |
JD |
antimicrobial agent/transcription profile |
02/26/13 | |
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Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock |
Affymetrix E. coli Genome 2.0 Array |
GSE17465 |
E-GEOD-17465 |
in process |
JD |
Salt tolerance/Radiation resistance |
02/26/13 | ||
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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. |
http://www.ncbi.nlm.nih.gov/pubmed/22008207 |
Affymetrix GeneChip E.coli Genome 2.0 Array |
E-MTAB-623 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt needs c3-c4 |
cold treatment/water activity |
02/27/13 | ||
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Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine. |
http://www.ncbi.nlm.nih.gov/pubmed/?term=17145952 |
Affymetrix GeneChip E.coli Genome 2.0 Array |
E-MEXP-926 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt needs c2-4 |
urine/biofilm |
02/27/13 | ||
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Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine. |
http://www.ncbi.nlm.nih.gov/pubmed/20444967 |
Affymetrix GeneChip E.coli Genome 2.0 Array |
E-MEXP-2298 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt needs c1-c4 |
urine/biofilm |
02/27/13 | ||
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Impact of cranberry on Escherichia coli cellular surface characteristics. |
http://www.ncbi.nlm.nih.gov/pubmed/18957286 |
Affymetrix E. coli Genome 2.0 Array |
GSE12554 |
E-GEOD-12554 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt needs c3-c4 |
antibacterial agent/cranberry juice |
02/27/13 | |
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Evolvability and hierarchy in rewired bacterial gene networks. |
http://www.ncbi.nlm.nih.gov/pubmed/18421347 |
Affymetrix GeneChip E.coli Genome 2.0 Array |
E-MEXP-732 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt |
regulatory networks/evolvability |
02/28/13 | ||
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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 |
no publication |
Affymetrix GeneChip E.coli Genome 2.0 Array |
GSE34275 |
E-GEOD-34275 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt needs c1-c4 |
Growth medium/glycerol |
02/28/13 | |
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Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli |
http://www.ncbi.nlm.nih.gov/pubmed/22018139 |
Affymetrix E. coli Genome 2.0 Array |
GSE29440 |
E-GEOD-29440 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt needs c1-c4 |
biotechnology/recombinant proteins |
02/28/13 | |
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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 |
http://www.ncbi.nlm.nih.gov/pubmed/22018139 |
Affymetrix E. coli Genome 2.0 Array |
GSE28412 |
E-GEOD-28412 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt needs c1-c4 |
biotechnology/recombinant proteins |
02/28/13 | |
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Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture |
http://www.ncbi.nlm.nih.gov/pubmed/22018139 |
Affymetrix E. coli Genome 2.0 Array |
GSE29439 |
E-GEOD-29439 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt needs c1-c4 |
biotechnology/recombinant proteins |
02/28/13 | |
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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 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt needs c1-c4 |
biotechnology/recombinant proteins |
02/28/13 | |
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Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea. |
http://www.ncbi.nlm.nih.gov/pubmed/23090957 |
Affymetrix E. coli Genome 2.0 Array |
GSE28399 |
E-GEOD-28399 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt needs c3-c4 missing one cel file |
UPEC/high osmolarity |
02/28/13 | |
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Metabolic and transcriptional response to cofactor perturbations in Escherichia coli |
http://www.ncbi.nlm.nih.gov/pubmed/20299454 |
Affymetrix E. coli Genome 2.0 Array |
GSE20374 |
E-GEOD-20374 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt needs c1-c4 |
cofactor/transcriptional profiling |
02/28/13 | |
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Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies |
http://www.ncbi.nlm.nih.gov/pubmed/?term=19806199 |
Affymetrix E. coli Genome 2.0 Array |
GSE14796 |
E-GEOD-14796 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt needs c3-4 |
L-form/transcription profiling |
03/01/13 | |
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Identification of genes induced on nitrate, role of OxyR |
http://www.ncbi.nlm.nih.gov/pubmed/22539721 |
Affymetrix E. coli Genome 2.0 Array |
GSE24524 |
E-GEOD-24524 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt need c3-4 |
anaerobic growth/S-Nitrosylation |
03/01/13 | |
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Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM |
http://www.ncbi.nlm.nih.gov/pubmed/22144490 |
Affymetrix E. coli Genome 2.0 Array |
GSE33895 |
E-GEOD-33895 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt needs c2-c4 |
virulence/His kinase |
03/01/13 | |
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Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa |
http://www.ncbi.nlm.nih.gov/pubmed/22101045 |
Affymetrix E. coli Genome 2.0 Array |
GSE26931 |
E-GEOD-26931 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt needs c1-c4 only loading 4 slides, the ones that are assayed on coli platform |
mixed culture/transcription profiling |
03/01/13 | |
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A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12. |
http://www.ncbi.nlm.nih.gov/pubmed/21169565 |
Affymetrix E. coli Genome 2.0 Array |
GSE21551 |
E-GEOD-21551 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt needs c1-4: DAS added on 03/11/13 strains used are unclear (mg1655/w3110?): DAS wrote corresponding author about mutant alleles used 03/11/13 |
beta-methylthiolation/regulation |
03/01/13 | |
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Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol |
http://www.ncbi.nlm.nih.gov/pubmed/22936779 |
Affymetrix E. coli Genome 2.0 Array |
GSE34631 |
E-GEOD-34631 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt needs c3-4 |
carbon source/????? |
03/01/13 | |
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Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans |
http://www.ncbi.nlm.nih.gov/pubmed/?term=22792156 |
Affymetrix E. coli Genome 2.0 Array |
GSE30441 |
E-GEOD-30441 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt needs c1-4 |
Stress resistance/EtOH |
03/01/13 | |
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First insights into the unexplored two-component system YehU/YehT in Escherichia coli. |
http://www.ncbi.nlm.nih.gov/pubmed/22685278 |
Affymetrix GeneChip E.coli Genome 2.0 Array |
E-MTAB-984 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt needs c1-4 |
Two-component systems/????? |
03/01/13 | ||
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Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli |
http://www.ncbi.nlm.nih.gov/pubmed/22684885 |
Affymetrix E. coli Genome 2.0 Array |
GSE35100 |
E-GEOD-35100 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt needs c1-c4 |
stress/?????? |
03/01/13 | |
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Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine |
http://www.ncbi.nlm.nih.gov/pubmed/22101045 |
Affymetrix E. coli Genome 2.0 Array |
GSE26932 |
E-GEOD-26932 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt needs c3-4 use only data on E. coli platform |
mixed culture/N-acetyl glucosamine |
03/04/13 | |
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Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock |
http://www.ncbi.nlm.nih.gov/pubmed/23247721 |
Affymetrix E. coli Genome 2.0 Array |
GSE30838 |
E-GEOD-30838 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt needs c1-4 |
glyphosate shock/transcriptional profiling |
03/04/13 | |
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Relative expression profiling of ycdC knockout strain secreting HlyA protein |
http://www.ncbi.nlm.nih.gov/pubmed/22505047 |
Affymetrix E. coli Genome 2.0 Array |
GSE29266 |
E-GEOD-29266 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt needs c1-c4 |
biotechnology/protein expression |
03/04/13 | |
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Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis |
http://www.ncbi.nlm.nih.gov/pubmed/22210763 |
Affymetrix E. coli Genome 2.0 Array |
GSE23417 |
E-GEOD-23417 |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt needs c1-c4 |
persistence/Zinc metabolism |
03/04/13 | ||
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Transcriptional responses of Escherichia coli k12 TPEN |
unpublished |
Affymetrix E. coli Genome 2.0 Array |
GSE11303 |
E-GEOD-11303 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt needs c3-4 |
stress/zinc |
03/04/13 | |
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Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol |
http://www.ncbi.nlm.nih.gov/pubmed/22389366 |
Affymetrix E. coli Genome 2.0 Array |
GSE35797 |
E-GEOD-35797 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt needs c3-4 |
Biofilms/drug effects |
03/04/13 | |
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Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase. |
http://www.ncbi.nlm.nih.gov/pubmed/21398637 |
Affymetrix E. coli Genome 2.0 Array |
GSE22207 |
E-GEOD-22207 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt needs c3-4 |
promoter/sigma factor |
03/04/13 | |
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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 |
http://www.ncbi.nlm.nih.gov/pubmed/21255366 |
Affymetrix E. coli Genome 2.0 Array |
GSE21604 |
E-GEOD-21604 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt<r/> http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt needs c2-4 no raw data files in ae |
biofilm/mutagenesis |
03/04/13 | |
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The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain. |
http://www.ncbi.nlm.nih.gov/pubmed/20855516 |
Affymetrix E. coli Genome 2.0 Array |
GSE21893 |
E-GEOD-21893 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt needs c3-4 |
APEC/type Vi secretion system |
03/05/13 | |
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BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type |
http://www.ncbi.nlm.nih.gov/pubmed/22221537 |
Affymetrix E. coli Genome 2.0 Array |
GSE34028 |
E-GEOD-34028 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt needs c3-4 |
persistence/?????? |
03/05/13 | |
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Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin |
http://www.ncbi.nlm.nih.gov/pubmed/22221537 |
Affymetrix E. coli Genome 2.0 Array |
GSE31054 |
E-GEOD-31054 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt needs c3-4 |
presistence/??????? |
03/05/13 | |
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Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm |
http://www.ncbi.nlm.nih.gov/pubmed/22047137 |
Affymetrix E. coli Genome 2.0 Array |
GSE28193 |
E-GEOD-28193 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt needs c3-4 |
biofilm/honey |
03/05/13 | |
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The E. coli deletion mutant of the nusB gene |
www.ncbi.nlm.nih.gov/pubmed/21873492 |
Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2] |
E-MEXP-3335 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt needs c3-4 |
tRNA modificaton/transcript profiling |
03/05/13 | ||
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E. coli ygjD gene temperature sensitive mutant incubated at 37 oC |
www.ncbi.nlm.nih.gov/pubmed/21873492 |
Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2] |
E-MEXP-3334 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt needs c1-4 |
tRNA modification/transcript profiling |
03/05/13 | ||
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The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C. |
www.ncbi.nlm.nih.gov/pubmed/21873492 |
Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2] |
E-MEXP-3333 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt needs c2-4 |
tRNA modification/transcript profiling |
03/05/13 | ||
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Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages |
http://www.ncbi.nlm.nih.gov/pubmed/21221972 |
Affymetrix E. coli Genome 2.0 Array |
GSE19953 |
E-GEOD-19953 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt needs c3-4 |
EHEC/biofilm |
03/05/13 | |
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An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol. |
http://www.ncbi.nlm.nih.gov/pubmed/20005205 |
Affymetrix E. coli Genome 2.0 Array |
GSE18972 |
E-GEOD-18972 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt needs c1-4 no cel files in ae |
biofuel/glycerol |
03/05/13 | |
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QseA regulation of virulence factors in EHEC |
http://www.ncbi.nlm.nih.gov/pubmed/20444105 |
Affymetrix E. coli Genome 2.0 Array |
GSE18118 |
E-GEOD-18118 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt needs c2-4 |
EHEC/virulence |
03/05/13 | |
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Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development |
http://www.ncbi.nlm.nih.gov/pubmed/19060153 |
Affymetrix E. coli Genome 2.0 Array |
GSE12701 |
E-GEOD-12701 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt needs c2-4 modified matrix file Absent->A, ... |
biofilm/toxin-antitoxin system |
03/05/13 | |
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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 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt needs c1-4 |
persistence/transcript profiling |
03/06/13 | |
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Overexpression of BglJ and LeuO in Escherichia coli K12 |
http://www.ncbi.nlm.nih.gov/pubmed/22295907 |
Affymetrix E. coli Genome 2.0 Array |
GSE34023 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt needs c1-4 dataset not in ae, idf/sdrf made from scratch |
????/?????? |
03/06/13 | ||
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Expression data from laboratory evolution of Escherichia coli on lactate or glycerol |
http://www.ncbi.nlm.nih.gov/pubmed/16204189 |
Ecoli_ASv2 |
GSE33147 |
E-GEOD-33147 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt needs c3-4 |
evolution/carbon source |
03/07/13 | |
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Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism. |
http://www.ncbi.nlm.nih.gov/pubmed/17112383 |
Ecoli_ASv2 |
GSE5239 |
E-GEOD-5239 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt needs c1-4 dataset has no cel files |
plasmid/metabolism |
03/07/13 | |
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Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains |
http://www.ncbi.nlm.nih.gov/pubmed/17768236 |
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) |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt needs c1-4 |
????/transcription profiling |
03/07/13 | |
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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 |
JD: can't figure out how the experiment was done. http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt |
03/07/13 | ||||
|
Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli |
http://www.ncbi.nlm.nih.gov/pubmed/15705577 |
Ecoli_ASv2 |
GSE2037 |
E-GEOD-2037 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt no cel files available |
carbon source/transcript profiling |
03/07/13 | |
|
Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli. |
http://www.ncbi.nlm.nih.gov/pubmed/17576668 |
Ecoli_ASv2 |
GSE5818 |
E-GEOD-5818 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.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) no cel files available 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 |
flagellum/regulation |
03/08/13 | |
|
Enterobactin is required for biofilm development in reduced-genome Escherichia coli |
http://www.ncbi.nlm.nih.gov/pubmed/21980953 |
Ecoli_ASv2 |
E-MEXP-1408 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt needs c1-4 |
biofilm/transcription profiling |
03/08/13 | ||
|
Indole cell signaling occurs primarily at low temperatures in Escherichia coli |
http://www.ncbi.nlm.nih.gov/pubmed/18528414 |
Ecoli_ASv2 and E_coli_2 |
GSE9923 |
E-GEOD-9923 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt needs c2-4 |
biofilm/indole |
03/08/13 | |
|
Effect of RyhB Small RNA on Global Iron Use in Escherichia coli |
http://www.ncbi.nlm.nih.gov/pubmed/16199566 |
Ecoli_ASv2 |
GSE3105 |
E-GEOD-3105 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt needs c2-4 no cel files available |
iron/non-coding RNA |
03/08/13 | |
|
sigma32 over-expression in E. coli |
http://www.ncbi.nlm.nih.gov/pubmed/15757896 |
Ecoli_ASv2 |
GSE2140 |
E-GEOD-2140 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt needs c2-4 no cel files available |
sigma factor/transcription profiling |
03/08/13 | |
|
Temporal gene-expression in Escherichia coli K-12 biofilms |
http://www.ncbi.nlm.nih.gov/pubmed/17222132 |
Ecoli_ASv2 |
GSE3905 |
E-GEOD-3905 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt needs c3-4 ne cel file available |
biofilm/transcription profiling |
03/08/13 | |
|
Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation |
http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt |
Ecoli_ASv2 |
E-MEXP-1001 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt needs c3-4 |
biofilm/F- phenocopy |
03/11/13 | ||
|
Indole is an inter-species biofilm signal mediated by SdiA |
http://www.ncbi.nlm.nih.gov/pubmed/17511876 |
Ecoli_ASv2 |
GSE4562 |
E-GEOD-4562 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt needs c3-4 |
biofilm/indole |
03/11/13 | |
|
Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture |
http://www.ncbi.nlm.nih.gov/pubmed/17557827 |
Ecoli_ASv2 |
GSE9203 |
E-GEOD-9203 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt needs c3-4 no cel files available |
Quorum sensing/biofilm |
03/11/13 | |
|
Ecoli_ASv2 |
E-GEOD-3937 |
JD |
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Ecoli_ASv2 |
E-GEOD-8706 |
JD |
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Ecoli_ASv2 |
E-GEOD-9587 |
JD |
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Ecoli_ASv2 |
E-MEXP-1145 |
JD |
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Ecoli_ASv2 |
E-GEOD-3514 |
JD |
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Ecoli_ASv2 |
E-GEOD-5904 |
JD |
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Ecoli_ASv2 |
E-GEOD-5905 |
JD |
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