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Series GSE3514 Query DataSets for GSE3514
Status Public on Nov 01, 2005
Title Differential gene expression of ydgG mutant
Platform organism Escherichia coli K-12
Sample organism Escherichia coli
Experiment type Expression profiling by array
Summary The E. coli Genechip antisense genome array was used to study the differential gene expression profile of E. coli K12 ydgG mutant compared to its isogenic wild type in a mature biofilm.
Keywords: E. coli K12 antisense chip
 
Overall design Overnight cultures were diluted 100X into 1 L shake flasks containing 250 mL of LB + 0.2 % and 10 g of glass wool. The cells were shaken at 250 rpm and 37 C for 24 hours (final OD600=5 for the suspended cells), to form a biofilm on the glass wool, and RNA was isolated from the biofilm and Affymetrix protocol was used for preparing fragmented and labelled cDNA that was hybrizide to the chips.
 
Contributor(s) Herzberg M, Kaye IK, Peti W, Wood TK
Citation(s) 16385049
Submission date Oct 26, 2005
Last update date Mar 16, 2012
Contact name Thomas K Wood
E-mail(s) twood@engr.uconn.edu
Organization name University of Connecticut
Department Chemical Engineering
Street address 191 Auditorium Rd
City Storrs
State/province CT
ZIP/Postal code 06269
Country USA
 
Platforms (1)
GPL199 [Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array
Samples (2)
GSM81020 E. coli K12 delta ydgG
GSM81021 E. coli K12 BW25113 wildtype
Relations
BioProject PRJNA93559

ydgG mutant gene expression vs E. coli K12 wild type in biofilm cultures header descriptions
ID_REF
VALUE
fold change
Change p-value

Data table
ID_REF VALUE fold change Change p-value
acrE_b3265_at 4.6 24.25146506 0.000032
bioF_b0776_at 4.4 21.11212657 0.000065
yjiP_b4338_at 4.3 19.69831061 0.000003
b2971_at 4.2 18.37917368 0.000022
b0967_at 4.1 17.1483754 0.000611
ybcJ_b0528_at 4.1 17.1483754 0.000012
yfjR_b2634_at 4 16 0.004413
focB_b2492_at 3.8 13.92880901 0.000002
pflD_b3951_at 3.8 13.92880901 0.00001
b2374_at 3.6 12.12573253 0.000002
citG_b0613_at 3.6 12.12573253 0.000269
ybfG_b0690_at 3.6 12.12573253 0.000001
yihN_b3874_at 3.6 12.12573253 0.000332
ttdA_b3061_at 3.5 11.3137085 0.000009
yafX_b0248_at 3.5 11.3137085 0.000002
yceO_b1058_at 3.5 11.3137085 0.000001
yihR_b3879_at 3.5 11.3137085 0.000003
yjhQ_b4307_at 3.5 11.3137085 0.000005
nth_b1633_at 3.4 10.55606329 0.000087
yihP_b3877_at 3.4 10.55606329 0.000001

Total number of rows: 1661

Table truncated, full table size 58 Kbytes.




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