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Sample GSM4407546 Query DataSets for GSM4407546
Status Public on Feb 23, 2021
Title cell transfected siFra-2-rep1
Sample type RNA
 
Source name MDA-MB-231
Organism Homo sapiens
Characteristics batch: T1- transcriptome 1
cell line: MDA-MB-231
treatment: siFra2
replicate: A
Growth protocol MDA-MB-231 cells were cultured in in Dulbecco’s modified Eagle’s medium containing 10% fetal calf serum and penicillin/streptomycin (100µg/ml each)
Extracted molecule total RNA
Extraction protocol RNAs were extracted using the Qiagen miRNeasy kit according to the supplier's specifications and controlled for purity and integrity using the Agilent Bioanalyser with RNA600 nano LabChipkits (Agilent technologies). On-column DNAse I digestions were performed as described in the user’s guide. RNA with neither signs of contamination nor of degradation (RIN>9) were further processed to generate aplified and biotinylated sense-strand cDNA
Label Biotin
Label protocol biotinylated sense-strand cDNA were produced using the GeneChip WT PLUS Reagent kit from Affymetrix according to the manufacturer’s specifications
 
Hybridization protocol cDNA targets were used to probe Affymetrix GeneChip Human Gene 2.0 ST arrays, which were then washed, stained and scanned according to Affymetrix instructions (user manual P/N 702731 Rev. 3)
Scan protocol GeneChips were scanned using GeneChip Scanner 3000
Data processing 21 CEL (7 conditions, n=3 each) files generated after array scanning were imported into the Partek Genomics Suite 6.6 (Partek) for preprocessing (default Partek options)
 
Submission date Mar 11, 2020
Last update date Feb 23, 2021
Contact name Isabelle Jariel-Encontre
E-mail(s) [email protected]
Phone 00 33 (0)4 11 28 31 53
Organization name IRCM-U1194- INSERM
Street address 208 Avenue des Apothicaires
City Montpellier
State/province Montpellier Cedex5
ZIP/Postal code 34298
Country France
 
Platform ID GPL16686
Series (2)
GSE146823 Identification of Fra-1 and/or Fra-2 regulated genes in MDA-MB231 cells
GSE146825 Transcriptional regulation by Fra-1 in triple negative breast cancers

Data table header descriptions
ID_REF
VALUE default Partek signal intensity

Data table
ID_REF VALUE
16650001 5.61933
16650003 3.83439
16650005 3.2632
16650007 4.44652
16650009 3.78913
16650011 3.7575
16650013 5.45137
16650015 6.66721
16650017 5.33837
16650019 3.9263
16650021 3.6032
16650023 3.99485
16650025 4.15662
16650027 4.43194
16650029 5.68566
16650031 3.50081
16650033 4.8011
16650035 4.94087
16650037 5.04798
16650041 3.96595

Total number of rows: 53617

Table truncated, full table size 884 Kbytes.




Supplementary file Size Download File type/resource
GSM4407546_T1.siFra2.A.CEL.gz 8.1 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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