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Sample GSM436890 Query DataSets for GSM436890
Status Public on Jul 20, 2010
Title BW25113 log, biological rep2
Sample type RNA
 
Source name Escherichia coli BW25113
Organism Escherichia coli
Characteristics genotype: wild type
genetic background: BW25113
Treatment protocol E.coli cells grown in M9 media with at 37º C until stationary phase (2.0), after that the cells were harvested to extract RNA.
Growth protocol E.coli cells grown with aeration in M9 media at 37º C until stationary phase (2.0) and were treated with 15%(v/v) ethanol shock for 15 min , after that the cells were harvested to extract RNA. M9 medium recipe is as follow: NH4Cl 0.5g Na2HPO4 3.0g KH2PO4 1.5g 2% (w/v)Dextrose per 1 liter.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the commercial product TRIzol Reagent (Invitrogen, Carlsbad, CA).Disrupt about 107cells with a homogenizer with 1ml TRIzol Reafent on ice. Store the homogenate for 5 minutes at room temperature to permit the complete dissociation of nucleoprotein complexes. Next, supplement the homogenate with 0.2 ml chloroform per 1 ml of TRI Reagent, cover the samples tightly and shake vigorously for 15 seconds. Store the resulting mixture at room temperature for 2-15 minutes and centrifuge at 12,000 g for 15 minutes at 4 C. Following centrifugation, the mixture separates into a lower red phenol-chloroform phase, interphase and the colorless upper aqueous phase. Transfer the aqueous phase to a fresh tube. Precipitate RNA from the aqueous phase by mixing with isopropanol. Use 0.5 ml of isopropanol per 1 ml of TRI Reagent used for the initial homogenization. Store samples at room temperature for 5-10 minutes and centrifuge at 12,000 g for 8 minutes at 4 - 25 C. Remove the supernatant and wash the RNA pellet ( by vortexing) with 75% ethanol and subsequent centrifugation at 7,500 g for 5 minutes at 4 - 25 C. Add at least 1 ml of 75% ethanol per 1 ml TRI Reagent used for the initial homogenization. Remove the ethanol wash and briefly air-dry the RNA pellet for 3 - 5 min. Dissolve RNA in DEPC-treated water by passing solution a few times through a pipette tip. Using an on-column DNase digestion with RNase-free DNase I (Qiagen) to purify the total RNA.
Label biotin
Label protocol Affymetrix Technical Manual, Prokaryotic Sample and Array Processing
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol The data were collected by using Affymetrix GeneChip Scanner 3000.
Description n/a
Data processing Affymetrix GeneChip Operating Software (GCOS) Version 1.4
 
Submission date Aug 05, 2009
Last update date Aug 12, 2009
Contact name Ming Chen
E-mail(s) chenmingbio@hotmail.com
Organization name Biotechnology Research Institute, Chinese academy of Agricultural Sciences
Street address Zhongguancun Nandajie 12th,Haidian Zone
City Beijing
ZIP/Postal code 100081
Country China
 
Platform ID GPL3154
Series (1)
GSE17526 Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase

Data table header descriptions
ID_REF
VALUE MAS 5 signal

Data table
ID_REF VALUE
AFFX-BioB-5_at 83.2
AFFX-BioB-M_at 129.6
AFFX-BioB-3_at 103.4
AFFX-BioC-5_at 58.8
AFFX-BioC-3_at 60.3
AFFX-BioDn-5_at 67.2
AFFX-BioDn-3_at 111
AFFX-CreX-5_at 1.1
AFFX-CreX-3_at 1.3
AFFX-DapX-5_at 4486.3
AFFX-DapX-M_at 4831.3
AFFX-DapX-3_at 3291.4
AFFX-LysX-5_at 708.3
AFFX-LysX-M_at 403.9
AFFX-LysX-3_at 412.9
AFFX-PheX-5_at 1360.4
AFFX-PheX-M_at 981.5
AFFX-PheX-3_at 595.2
AFFX-ThrX-5_at 1898.5
AFFX-ThrX-M_at 1853.4

Total number of rows: 10208

Table truncated, full table size 176 Kbytes.




Supplementary file Size Download File type/resource
GSM436890.CEL.gz 970.5 Kb (ftp)(http) CEL
Processed data included within Sample table

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