NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM703146 Query DataSets for GSM703146
Status Public on May 26, 2011
Title SiTIF+ rep2
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 rimo10
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 741.879 P 0.000389797
AFFX-BioB-M_at 987.807 P 4.42873e-05
AFFX-BioB-3_at 723.559 P 7.00668e-05
AFFX-BioC-5_at 1964.77 P 5.16732e-05
AFFX-BioC-3_at 2638.39 P 4.42873e-05
AFFX-BioDn-5_at 4620.29 P 4.42873e-05
AFFX-BioDn-3_at 8854.86 P 8.14279e-05
AFFX-CreX-5_at 20350 P 5.16732e-05
AFFX-CreX-3_at 23997.3 P 4.42873e-05
AFFX-DapX-5_at 2299.09 P 4.42873e-05
AFFX-DapX-M_at 3460.6 P 0.000195116
AFFX-DapX-3_at 3583.72 P 5.16732e-05
AFFX-LysX-5_at 202.5 P 4.42873e-05
AFFX-LysX-M_at 243.985 P 0.0020226
AFFX-LysX-3_at 522.273 P 6.02111e-05
AFFX-PheX-5_at 479.123 P 6.02111e-05
AFFX-PheX-M_at 443.98 P 5.16732e-05
AFFX-PheX-3_at 330.681 P 4.42873e-05
AFFX-ThrX-5_at 579.752 P 7.00668e-05
AFFX-ThrX-M_at 725.332 P 4.42873e-05

Total number of rows: 54675

Table truncated, full table size 1637 Kbytes.




Supplementary file Size Download File type/resource
GSM703146.CEL.gz 4.9 Mb (ftp)(http) CEL
GSM703146.CHP.gz 297.2 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap