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Sample GSM896197 Query DataSets for GSM896197
Status Public on Mar 20, 2013
Title Control knockdown, biological rep1
Sample type RNA
 
Source name MCF-7 cell with scamble KD for 72 hours
Organism Homo sapiens
Characteristics cell line: MCF-7
treatment: control KD for 72 hours
Treatment protocol CtBP mRNA targetting oligos and the control oligos are from Dharmacon. Dharmafect1 transfection method was applied to introduce gene knockdown oligoes into the cells following manufacturer's manual.
Growth protocol MCF-7 cells were maintained in regular DMEM supplemented with 10% (v/v) FBS, penicillin-streptomycin (Invitrogen) and insulin.
Extracted molecule total RNA
Extraction protocol Qiagen RNAeasy kit was applied to extract total RNA from MCF-7 cells following manufacturer's manual.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Data processing The data were analyzed with Gene Console using Affymetrix default analysis settings. RMA normalization.
 
Submission date Mar 15, 2012
Last update date Mar 20, 2013
Contact name Lijun Di
E-mail(s) dil@mail.nih.gov
Organization name NCI
Street address 41 center dr
City bethesda
ZIP/Postal code 20892
Country USA
 
Platform ID GPL570
Series (2)
GSE36529 Expression data from CtBP knockdown MCF-7 cells
GSE36598 Global transcriptional role of CtBP in breast cancer cells

Data table header descriptions
ID_REF
VALUE RMA normalized

Data table
ID_REF VALUE
AFFX-BioB-5_at 7.51012
AFFX-BioB-M_at 7.74577
AFFX-BioB-3_at 7.44273
AFFX-BioC-5_at 8.86197
AFFX-BioC-3_at 9.22563
AFFX-BioDn-5_at 10.1301
AFFX-BioDn-3_at 11.1326
AFFX-CreX-5_at 12.3833
AFFX-CreX-3_at 12.8497
AFFX-DapX-5_at 7.04035
AFFX-DapX-M_at 8.40003
AFFX-DapX-3_at 9.28726
AFFX-LysX-5_at 4.49542
AFFX-LysX-M_at 5.25213
AFFX-LysX-3_at 6.30005
AFFX-PheX-5_at 5.3019
AFFX-PheX-M_at 5.64907
AFFX-PheX-3_at 5.92883
AFFX-ThrX-5_at 5.33103
AFFX-ThrX-M_at 5.75433

Total number of rows: 54675

Table truncated, full table size 998 Kbytes.




Supplementary file Size Download File type/resource
GSM896197.CEL.gz 4.3 Mb (ftp)(http) CEL
GSM896197.chp.gz 378.5 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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