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Sample GSM873562 Query DataSets for GSM873562
Status Public on Aug 02, 2012
Title SIN3A_siRNA_NS_rep3
Sample type RNA
 
Source name MCF7 cells, SIN3A silenced, NS
Organism Homo sapiens
Characteristics cell line: MCF7 breast cancer
treatment: SIN3A silenced
Biomaterial provider Laura Icardi, Cytokine Receptor Lab, Prof. Jan Tavernier
Treatment protocol Transfected with 50nM SIN3A siRNA. 72h later, cells were cutured 4h without FCS
Growth protocol DMEM+10%FCS
Extracted molecule total RNA
Extraction protocol Cell lysates were homogenized with the QiaShredder Column (Qiagen), and total cellular RNA was extracted with the Rneasy Mini kit (Qiagen) following manufacturer’s instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 nanogram total RNA.
 
Hybridization protocol Following fragmentation, 15 microgram of cRNA were hybridized for 17 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the GeneChip Scanner 3000 7G.
Data processing Data were normalized using RMA as implemented in the Affy package (version 1.28.0) of Bioconductor. Expression values are represented on a log2-scale.
 
Submission date Feb 10, 2012
Last update date Aug 02, 2012
Contact name Rekin's Janky
E-mail(s) Nucleomics.Bioinformatics@vib.be
Organization name VIB
Department Nucleomics Core
Street address Herestraat 49 Box 816
City Leuven
ZIP/Postal code B-3000
Country Belgium
 
Platform ID GPL570
Series (1)
GSE35696 SIN3A-regulated LIF-responsive genes in MCF7 cells

Data table header descriptions
ID_REF
VALUE Data were normalized using RMA as implemented in the Affy package (version 1.28.0) of Bioconductor. Expression values are represented on a log2-scale.
ABS_CALL the MAS 5.0 detection call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
1007_s_at 10.71859896 P 0.000219
1053_at 9.414704919 P 0.000219
117_at 4.999637835 M 0.05447
121_at 7.937209819 P 0.017
1255_g_at 2.964137538 A 0.07383
1294_at 5.693084536 A 0.098054
1316_at 5.026364184 P 0.001892
1320_at 4.382852428 A 0.602006
1405_i_at 3.46673039 A 0.254899
1431_at 4.02438847 P 0.013092
1438_at 5.839613085 A 0.07383
1487_at 8.262279391 P 0.017
1494_f_at 5.899126183 A 0.189687
1552256_a_at 8.28217038 P 0.001673
1552257_a_at 10.02230834 P 0.001673
1552258_at 4.727186243 A 0.464576
1552261_at 4.256760881 A 0.464576
1552263_at 6.675889192 P 0.001673
1552264_a_at 7.52644866 P 0.001673
1552266_at 2.980553265 A 0.123873

Total number of rows: 54675

Table truncated, full table size 1788 Kbytes.




Supplementary file Size Download File type/resource
GSM873562.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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