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Sample GSM703140 Query DataSets for GSM703140
Status Public on May 26, 2011
Title SiTIF+ rep1
Sample type RNA
 
Source name HMEC-TR, SiRNA anti-TIF1γ, 5 ng/ml TGFβ1 for 24h
Organism Homo sapiens
Characteristics cell type: Human mammary epithelial cells infected with retrovirus carrying hTERT and the oncogenic allele of H-Ras, H-RasV12 described in (Elenbaas B, Spirio L, Koerner F, Fleming MD, Zimonjic DB, Donaher JL, Popescu NC, Hahn WC, and Weinberg RA (2001) Human breast cancer cells generated by oncogenic transformation of primary mammary epithelial cells. Genes Dev 15: 50-65)
Treatment protocol We performed transcriptomic microarrays analysis on control HMEC-TR cells (transfected by scramble si-RNA) and cells inactivated for TIF1γ or Smad4 (SiRNA strategy) and treated or not with TGFβ1 for 24 hours. Inactivation of TIF1γ and Smad4 expression was checked by Western Blot.
Growth protocol Human mammary epithelial cells (HMEC-TR) kindly provided by RA Weinberg have been previously described (Elenbaas B. et al. 2001 and Morel A.P. et al. 2008). These cells were cultured in 1:1 Dulbecco’s Modified Eagle’s Medium DMEM/HAMF12 medium (Invitrogen) complemented with 10% FBS (Cambrex) and 100 U/ml penicillin-streptomycin (Invitrogen), 2 mM L glutamine (Invitrogen), 10 ng/ml human epidermal growth factor (hEGF, PromoCell), 0.5 mg/ml hydrocortisone (Sigma) and 10 mg/ml insulin (Sigma).
Extracted molecule total RNA
Extraction protocol Total RNA from the transfected HMEC-TR cells was isolated by Trizol and miRNeasy Mini extraction kit (Qiagen). RNA quality was assessed by an Agilent Bioanalyzer (model 2100; Agilent Technologies).
Label biotin
Label protocol As per manufacturer (Affymetrix)
 
Hybridization protocol As per manufacturer (Affymetrix)
Scan protocol The Arrays were scanned using the Gene Chip Scanner 3000. Then CEL files were generated using the Affymetrix GeneChip Operating Software (GCOS)
Description rimo4
Data processing CHP files were processed using MAS 5.0 analysis algorithm with Affymetrix GeneChip Operating Software (GCOS)
 
Submission date Apr 07, 2011
Last update date May 26, 2011
Contact name Cedric Hesling
E-mail(s) hesling@lyon.fnclcc.fr
Organization name CRCL
Lab Equipe Ruth Rimokh
Street address 24 rue Laënnec
City Lyon
ZIP/Postal code 69008
Country France
 
Platform ID GPL570
Series (1)
GSE28448 Antagonistic regulation of EMT by TIF1γ and Smad4 in mammary epithelial cells

Data table header descriptions
ID_REF
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 968.027 P 0.000662269
AFFX-BioB-M_at 1138.48 P 4.42873e-05
AFFX-BioB-3_at 867.013 P 8.14279e-05
AFFX-BioC-5_at 2588.51 P 5.16732e-05
AFFX-BioC-3_at 3187.97 P 4.42873e-05
AFFX-BioDn-5_at 5338.78 P 4.42873e-05
AFFX-BioDn-3_at 11805.5 P 0.000126798
AFFX-CreX-5_at 26347.7 P 5.16732e-05
AFFX-CreX-3_at 30259.9 P 4.42873e-05
AFFX-DapX-5_at 4101.81 P 4.42873e-05
AFFX-DapX-M_at 6318.72 P 0.000146581
AFFX-DapX-3_at 6634.84 P 4.42873e-05
AFFX-LysX-5_at 385.223 P 6.02111e-05
AFFX-LysX-M_at 480.198 P 0.00179591
AFFX-LysX-3_at 1177.29 P 5.16732e-05
AFFX-PheX-5_at 785.31 P 5.16732e-05
AFFX-PheX-M_at 712.121 P 6.02111e-05
AFFX-PheX-3_at 577.648 P 4.42873e-05
AFFX-ThrX-5_at 970.17 P 6.02111e-05
AFFX-ThrX-M_at 1421.97 P 4.42873e-05

Total number of rows: 54675

Table truncated, full table size 1627 Kbytes.




Supplementary file Size Download File type/resource
GSM703140.CEL.gz 4.9 Mb (ftp)(http) CEL
GSM703140.CHP.gz 297.6 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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