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Sample GSM840625 Query DataSets for GSM840625
Status Public on Apr 03, 2012
Title BW25113 wild-type stationary phase OD 3.0
Sample type RNA
Source name Channel 1
Organism Escherichia coli
Characteristics strain: E. coli BW25113 wild-type
growth phase: stationary phase OD 3.0
time: 0h
sample type: starting culture
medium: LB
cell type: Planktonic cells inoculated at OD 0.05 at 600nm, grown to OD 3.0 at 600nm, exposed to 5 ug/mL ampicillin for 30 min.
temp: 37C
Extracted molecule total RNA
Extraction protocol One-day old single colony was inoculated in 25 mL of LB for 16 h at 37C at 250 rpm. Overnight culture was diluted to be OD 0.05 at 600nm in 25 mL in LB and incubated at 37C at 250 rpm until OD 3.0 at 600nm (harvested at this OD). Ampicillin 5 µg/mL was then added directly to 22 mL of culture and incubated for an additional 30 mins. Cell pellet was collected by centrifuging at 8500 rpm at 4C for 2 min. Supernatant was discarded and the cell pellet was resuspended with 1 mL RNAlater. Then the sample was centrifuged and the supernatant was discarded, the final cell pellet was immediately frozen in dry ice and stored at -80C. After breaking the cells with a bead beater, and the total RNA was isolated with 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 and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).
Hybridization protocol Following affymetrix protocol.
Prepared hybridization cocktail for Single Probe Array (169 mini Format) with total 80 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 labeled cDNA.
After loading of hybridization cocktail in Affymetrix E. coli Genome 2.0 Array, the hybridization was performed at 45°C, 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 stationary phase cells of E. coli BW25113 wild-type exposed to ampicillin 5 ug/mL for 30 mins
Data processing MAS 5.0 Expression Analysis Default Setting
Submission date Nov 29, 2011
Last update date Apr 04, 2012
Contact name Thomas K. Wood
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 (2)
GSE34028 BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type
GSE34177 BW25113 Rif pre-treated persister cells vs. stationary phase BW25113 wild-type

Data table header descriptions
VALUE Signal intensity accepted for the probeset
ABS_CALL Probeset signal: absent or present
DETECTION P-VALUE Probeset signal: p-value (shows the coherency of the results)

Data table
AFFX-BioB-5_at 171.412 P 6.02111e-05
AFFX-BioB-M_at 257.155 P 5.16732e-05
AFFX-BioB-3_at 196.492 P 0.000340305
AFFX-BioC-5_at 69.8075 P 4.42873e-05
AFFX-BioC-3_at 121.858 P 0.000195116
AFFX-BioDn-5_at 87.2952 P 0.000509415
AFFX-BioDn-3_at 145.146 P 0.0044838
AFFX-CreX-5_at 1.87846 A 0.794268
AFFX-CreX-3_at 1.05434 A 0.916408
AFFX-DapX-5_at 893.577 P 4.42873e-05
AFFX-DapX-M_at 810.183 P 4.42873e-05
AFFX-DapX-3_at 637.336 P 4.42873e-05
AFFX-LysX-5_at 61.1662 P 8.14279e-05
AFFX-LysX-M_at 38.2862 P 0.000169227
AFFX-LysX-3_at 43.5679 P 0.00227496
AFFX-PheX-5_at 119.148 P 0.000389384
AFFX-PheX-M_at 93.8658 P 0.000195116
AFFX-PheX-3_at 49.4872 P 0.000508897
AFFX-ThrX-5_at 329.042 P 6.02111e-05
AFFX-ThrX-M_at 180.903 P 6.02111e-05

Total number of rows: 10208

Table truncated, full table size 329 Kbytes.

Supplementary file Size Download File type/resource
GSM840625_stationary_phase_BW25113_WT.CHP.gz 54.3 Kb (ftp)(http) CHP
GSM840625_stationary_phase_BW25113_WT_CEL.CEL.gz 833.2 Kb (ftp)(http) CEL
Processed data included within Sample table
Processed data provided as supplementary file

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