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Sample GSM320165 Query DataSets for GSM320165
Status Public on Oct 01, 2008
Title RKO_HSF1siRNA_6hDMSO_REP1
Sample type RNA
 
Source name RKO cells transfected with HSF1 Stealth siRNA treated 6 h with DMSO 0.5%
Organism Homo sapiens
Characteristics RKO colon carcinoma cells (ATCC #CRL-2577), cultured in DMEM (Invitrogen Catalog#10569) containing 10% FBS (Atlas Biologicals)
Extracted molecule total RNA
Extraction protocol Cells from 10 cm plates were scraped and pelleted by centrifugation, followed by resuspension in 1 ml Trizol, incubation for 5 in at room temp, and addition of 200 ul CHCl3 with vigorous shaking by hand. After centrifugation 10 min 14,000 rpm, aqueous phase combined with equal volume of 70% EtOH, and subsequent cleanup on Qiagen RNeasy kit (Catalog# 74104)
Label Biotin
Label protocol First Strand and Second Strand synthesis, followed by 2 rounds of SPIA amplification to generate cDNA was performed using WT-Ovation™ FFPE System V2 (Nugen Catalog#3400-60, Lot#801142-A). Fragmentaion and Biotinylation were completed using FL-Ovation™ cDNA Biotin Module V2 (Nugen Catalog# 4200, lot#709151-F)
 
Hybridization protocol Hybridization performed according to standard Affymetrix protocols
Scan protocol Scanned on Affymetrix GeneChip Scanner 3000 7G
Description Cells transfected with Stealth HSF1 siRNA (5'CGGAUUCAGGGAAGCAGCUGGUGCA) and subsequently treated for 6 hours with vehicle 0.5% DMSO in DMEM Media containing 10% FBS
Data processing Data processed using Affymetrix Expression Console software using default RMA parameters, log2 scale
 
Submission date Sep 12, 2008
Last update date Sep 12, 2008
Contact name Aaron Thomas Jacobs
Organization name Vanderbilt University
Department Biochemistry
Lab Lawrence J. Marnett
Street address 23rd Ave. @ Pierce Ave.
City Nashville
State/province TN
ZIP/Postal code 37232
Country USA
 
Platform ID GPL6244
Series (1)
GSE12762 Effect of 4-Hydroxynonenal on gene expression. Comparison of HSF1-siRNA silenced vs control cells

Data table header descriptions
ID_REF
VALUE Default Affymetrix Expression Console parameters (Gene-RMA), log2 scale

Data table
ID_REF VALUE
7892501 8.06739
7892502 4.17742
7892503 4.76483
7892504 8.44327
7892505 2.69443
7892506 3.54441
7892507 6.62713
7892508 4.58826
7892509 11.6471
7892510 3.32757
7892511 4.02058
7892512 7.35698
7892513 4.37108
7892514 11.5544
7892515 9.90419
7892516 10.6556
7892517 4.33903
7892518 2.88017
7892519 5.86956
7892520 9.29265

Total number of rows: 33297

Table truncated, full table size 516 Kbytes.




Supplementary file Size Download File type/resource
GSM320165.CEL.gz 4.1 Mb (ftp)(http) CEL
GSM320165.chp.gz 255.7 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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