|
| Status |
Public on Mar 01, 2012 |
| Title |
DMEM-HI + E.coli HS PCM 1%, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
E24377A grown in DMEM-HI glucose + PCM from E.coli HS (1% v/v)
|
| Organism |
Escherichia coli O139:H28 str. E24377A |
| Characteristics |
treatment: grown in DMEM-HI glucose + PCM from E.coli HS (1% v/v)
|
| Growth protocol |
Single colonies were grown overnight at 37C and 225 rpm in 5 ml LB. The next day, cultures were diluted 1:100 in 25 ml LB, grown at 37C at 225 rpm
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures were either extracted using the RiboPure RNA kit from ambion, or a acid phenol/lithium chloride method
|
| Label |
biotin
|
| Label protocol |
Digested cDNA was end-labeled with Biotin-11-ddATP (Perkin Elmer, P/N NEL548001EA) using Terminal Deoxynucleotidyl Transferase, and verified by gel shift assay, according to Affymetrix standard protocols
|
| |
|
| Hybridization protocol |
A hybridization mixture was prepared that contained labeled cDNA, 7.8% DMSO and OligoB2 mixture (Affymetrix, P/N 900301) according to the manufacturers protocols. GeneChips were prepared by pre-hybridization for 10 minutes at 45ºC with the kit pre-hybridization solution; samples were denatured at 95ºC for 1 minute, equilibrated to 45ºC, centrifuged, and transferred to prepared arrays. Hybridization was continued in a rotating incubator for 16h at 60 rpm and 45ºC. Post-hybridization, the hybridization cocktail was recovered and the arrays washed and stained using the standard Affymetrix ProkGE-WS2v3_450 fluidics protocol and GeneChip Hybridization, Wash and Stain Kit reagents (Affymetrix, P/N 900720).
|
| Scan protocol |
Chips were scanned with the Affymetrix GCOS software
|
| Description |
Expression in PCM from human commensal, lower concentration
|
| Data processing |
Array data was processed with the Simpleaffy bioconductor package in R
|
| |
|
| Submission date |
Aug 31, 2011 |
| Last update date |
Mar 01, 2012 |
| Contact name |
Jason Sahl |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Maryland
|
| Department |
School of Medicine
|
| Lab |
Institute for Genome Sciences
|
| Street address |
801 West Baltimore St.
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21201 |
| Country |
USA |
| |
|
| Platform ID |
GPL13175 |
| Series (2) |
| GSE31804 |
Expression data of enterotoxigenic (ETEC) isolate E24377A |
| GSE31806 |
E. coli strain E24377A |
|
