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Sample GSM1614043 Query DataSets for GSM1614043
Status Public on Aug 03, 2015
Title MDA-MB-231 cells siControl, biological replica C
Sample type RNA
Source name control cells
Organism Homo sapiens
Characteristics cell line: MDA-MB-231
cell type: breast cancer
transfection construct: Control siRNA
Treatment protocol Cells were transfected on day 2 with siRNA oligonucleotides (final concentration 33nM) by using RNAi MAX (Life Technologies), following a direct transfection protocol as indicated by manifacturer's instructions. On day 3, medium was renewed. On day 4, cells were washed with 1XHBSS and harvested for RNA extraction.
Growth protocol Cells were seeded at low confluence on day 1 in standard growth medium (DMEM/F12 with 2mM Glutamine, 17.5mM D-glucose, without antibiotics, 10% Fetal Bovine Serum).
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA, followed by DNAseI digestion to reduce genomic DNA contaminations, was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared using the 3'IVT Kit ( Affymetrix, Santa Clara, USA, CA) according to manufacturer's intructions.
Hybridization protocol Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GeneChip Command Console Software (AGCC)
Description Gene expression data from control MDA-MB-231 cells
Data processing RMA of .CEL files using affy Bioconductor library and Brainarray HGU133Plus2_Hs_ENTREZG_v17 custom cdf. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization
Submission date Feb 19, 2015
Last update date Aug 03, 2015
Contact name Silvio Bicciato
Phone +39-049-827-6108
Organization name University of Padova
Department Molecular Medicine
Street address via U. Bassi 59/b
City Padova
ZIP/Postal code 35131
Country Italy
Platform ID GPL17811
Series (2)
GSE66082 Widespread association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth [gene expression]
GSE66083 Widespread association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth
Reanalysis of GSM1431024

Data table header descriptions
VALUE RMA-calculated signal intensity (log2)

Data table
1_at 6.407844341
10_at 5.426227606
100_at 5.938960545
1000_at 5.063147701
10000_at 7.136497742
100009676_at 6.234892172
10001_at 9.45765798
10002_at 4.985316926
10003_at 5.548134828
10004_at 5.231358616
100048912_at 3.827037852
100049716_at 5.130933746
10005_at 8.643401689
10006_at 9.582367705
10007_at 9.753446255
10008_at 4.286747854
10009_at 8.848521593
100093630_at 10.21420255
100093698_at 3.50264799
1001_at 5.396955476

Total number of rows: 18960

Table truncated, full table size 388 Kbytes.

Supplementary file Size Download File type/resource
GSM1614043_MDA231_23_HG-U133_Plus_2_.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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