PortEco Microarray Pipeline: Difference between revisions

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biotechnology/recombinant proteins
biotechnology/recombinant proteins
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02/28/13
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Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.
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http://www.ncbi.nlm.nih.gov/pubmed/23090957<br/>
http://iai.asm.org/content/81/1/80.long
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Affymetrix E. coli Genome 2.0 Array
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GSE28399
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E-GEOD-28399
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in process
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|
JD
http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt<br/>
http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt
needs c3-c4
missing one cel file
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UPEC/high osmolarity
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02/28/13  
02/28/13  

Revision as of 01:15, 1 March 2013

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

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

E-MEXP-3800 

JD: skipped it

E-MEXP-3799 

JD: skipped it

E-GEOD-43325

E-GEOD-29076 

JD: skipped it

E-GEOD-42702

E-GEOD-34991

E-GEOD-37026

E-MTAB-1347

E-GEOD-21820

E-GEOD-22285

E-GEOD-40693

E-GEOD-40648

E-GEOD-21652 

JD: skipped it

E-GEOD-36779

E-GEOD-20380

E-GEOD-39607 

JD: skipped it

E-GEOD-30679

E-GEOD-30692

E-GEOD-30424

E-GEOD-34046

E-GEOD-21857

E-TABM-86

E-GEOD-29803

E-GEOD-40427

E-GEOD-33212

E-GEOD-42205

E-GEOD-40557

E-GEOD-39439

E-GEOD-35049

E-GEOD-35822

E-GEOD-41093

E-GEOD-41940

E-GEOD-41938

E-GEOD-26223

E-MTAB-996

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

http://www.ncbi.nlm.nih.gov/pubmed/22331529
http://onlinelibrary.wiley.com/doi/10.1002/bem.21709/full

Affymetrix E. coli Genome 2.0 Array

GSE35371

E-GEOD-35371

in process

JD
http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt
needs c3-c4

Transcript profiling/Magnetic field

02/25/13

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

http://www.ncbi.nlm.nih.gov/pubmed/22645336
http://www.pnas.org/content/109/24/9487.long

Affymetrix E. coli Genome 2.0 Array

GSE30639

E-GEOD-30639

in process

JD
http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt
http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt
needs c3-c4

evolution/chemostat

02/26/13

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
http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html

Affymetrix GeneChip E.coli Genome 2.0 Array

E-MEXP-2609

in process

JD
http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt
http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt

biofilm/urine

02/26/13

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
http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt
http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt

ETOH shock/rpoS

02/26/13

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

http://www.ncbi.nlm.nih.gov/pubmed/20008510
http://nar.oxfordjournals.org/content/38/5/1636.long

Affymetrix E. coli Genome 2.0 Array

GSE15406
(GSE15404, GSE15405)

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

in process

JD
http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt
http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt
needs c1-c4

Overexpression/????

02/26/13

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

http://www.ncbi.nlm.nih.gov/pubmed/20501031
http://www.ingentaconnect.com/content/iafp/jfp/2010/00000073/00000005/art00002?token=0052126e147e442f2067217a763b442e237b4524406a687627502b333e3568263c2b40304a62d62140

Affymetrix E. coli Genome 2.0 Array

GSE17519

E-GEOD-17519

in process

JD
http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt
http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt
c1-c4

benzoate/??????

02/26/13

E.coli response to Antimicrobial Arylamides

http://www.ncbi.nlm.nih.gov/pubmed/21844313
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3195038/#B7

Affymetrix E. coli Genome 2.0 Array

GSE31140

E-GEOD-31140

in process

JD
http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt
http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt
needs c3-c4

antimicrobial agent/transcription profile

02/26/13

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

http://globethesis.com/?t=1100360275976128

Affymetrix E. coli Genome 2.0 Array

GSE17465

E-GEOD-17465

in process

JD
http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt
http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt
needs c1-c4

Salt tolerance/Radiation resistance

02/26/13

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
http://www.mcponline.org/content/11/1/M111.009019.long

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
http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt 

needs c3-c4

cold treatment/water activity

02/27/13

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
http://iai.asm.org/content/75/2/966.long

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
http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt 

needs c2-4

urine/biofilm

02/27/13

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

http://www.ncbi.nlm.nih.gov/pubmed/20444967
http://jcm.asm.org/content/48/7/2449.full

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
http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt

needs c1-c4

urine/biofilm

02/27/13

Impact of cranberry on Escherichia coli cellular surface characteristics.

http://www.ncbi.nlm.nih.gov/pubmed/18957286
http://www.sciencedirect.com/science/article/pii/S0006291X08020913

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
http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt 

needs c3-c4

antibacterial agent/cranberry juice

02/27/13

Evolvability and hierarchy in rewired bacterial gene networks.

http://www.ncbi.nlm.nih.gov/pubmed/18421347
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666274
http://www.nature.com/nature/journal/v452/n7189/full/nature06847.html

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
http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt
needs c1-c4

regulatory networks/evolvability

02/28/13

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
http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt

needs c1-c4

Growth medium/glycerol

02/28/13

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

http://www.ncbi.nlm.nih.gov/pubmed/22018139
http://www.amb-express.com/content/1/1/33

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
http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt 

needs c1-c4

biotechnology/recombinant proteins

02/28/13

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
http://www.amb-express.com/content/1/1/33
http://www.ncbi.nlm.nih.gov/pubmed/22134216
http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g

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
http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt 

needs c1-c4

biotechnology/recombinant proteins

02/28/13

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
http://www.amb-express.com/content/1/1/33

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
http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt 

needs c1-c4

biotechnology/recombinant proteins

02/28/13

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
http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt 

needs c1-c4

biotechnology/recombinant proteins

02/28/13

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

http://www.ncbi.nlm.nih.gov/pubmed/23090957
http://iai.asm.org/content/81/1/80.long

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
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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