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Sample GSM320083 Query DataSets for GSM320083
Status Public on Oct 01, 2008
Title RKO_NEGsiRNA_6hDMSO_REP1
Sample type RNA
 
Source name RKO cells transfected with NEG Stealth siRNA treated 6 h with vehicle 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 Negative Control siRNA (Invitrogen Catalog# 12935-300) and subsequently treated for 6 hours with 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 7.70266
7892502 4.96335
7892503 4.40452
7892504 8.41526
7892505 3.92282
7892506 3.96083
7892507 6.98111
7892508 3.9107
7892509 11.9668
7892510 3.19533
7892511 5.05795
7892512 6.93269
7892513 4.26788
7892514 11.4415
7892515 9.90424
7892516 10.6311
7892517 5.15187
7892518 3.27025
7892519 5.72191
7892520 9.71425

Total number of rows: 33297

Table truncated, full table size 516 Kbytes.




Supplementary file Size Download File type/resource
GSM320083.CEL.gz 3.8 Mb (ftp)(http) CEL
GSM320083.chp.gz 255.5 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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