|
| Status |
Public on Oct 31, 2010 |
| Title |
BW25113 frdC 5h 37C in glycerol medium |
| Sample type |
RNA |
| |
|
| Source name |
frdC
|
| Organism |
Escherichia coli |
| Characteristics |
strain: BW25113 frdC
conditions: anaerobic
medium: glycerol
growth time: 5h
growth temperature: 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After anaerobic incubation for 5 h at 37°C with shaking (250 rpm), cells were collected and broken with a bead beater, and the total RNA was isolated with the Qiagen RNeasy mini Kit (Cat# 74104).
|
| Label |
Biotin
|
| Label protocol |
Following Affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using the Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).
|
| |
|
| Hybridization protocol |
Following Affymetrix protocol.
Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybridization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA.
After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours.
After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).
|
| Scan protocol |
Following Affymetrix protocol.
After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).
|
| Description |
RNA extracted from cells of BW25113 frdC after 5h anaerobic growth in glycerol medium at 37oC.
|
| Data processing |
MAS 5.0 Expression Analysis Default Setting
|
| |
|
| Submission date |
Nov 11, 2009 |
| Last update date |
Oct 31, 2010 |
| Contact name |
Thomas K. Wood |
| E-mail(s) |
twood@engr.psu.edu
|
| Phone |
814-863-4811
|
| Organization name |
Pennsylvania State University
|
| Department |
Chemical Engineering & Biochemistry and Molecular Biology
|
| Lab |
Dr. Wood's Lab
|
| Street address |
Room 161 Fenske Laboratory, University Park
|
| City |
State College |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL3154 |
| Series (1) |
| GSE18972 |
E. coli BW25113 frdC vs. E. coli BW25113 HW2 |
|
