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Sample GSM1842583 Query DataSets for GSM1842583
Status Public on Sep 29, 2015
Title SCC-FAK-/-_rep2
Sample type RNA
 
Source name SCC FAK-/- cells
Organism Mus musculus
Characteristics background strain: FVB
genotype: K14CreER FAKflox/flox
cell type: Squamous cell carcinoma
Treatment protocol Cells were washed three times with ice-cold phosphate-buffered saline.
Growth protocol Cells were cultured in Glasgow minimum essential medium (MEM) (Sigma) supplemented with 2 mM L-glutamine, MEM vitamins, 1 mM sodium pyruvate (all Sigma), MEM amino acids, and 10% fetal bovine serum (both Life Technologies). Cell lines re-expressing FAK-wt were maintained under selection using 0.25 mg/ml hygromycin.
Extracted molecule total RNA
Extraction protocol Total RNA extraction and on-column DNase I digestion were performed using an RNeasy kit (Qiagen) according to manufacturer's instructions.
Label biotin
Label protocol cDNA synthesis and amplification was performed using the Ovation Pico WTA System V2 (NuGEN Technologies) with an input of 50 ng total RNA according to manufacturer’s instructions. PolyA controls (Affymetrix, part no. 900433) were included at the same concentration as the sample. 5 µg of the cDNA was then fragmented and biotin labelled using an Encore Biotin Module kit (NuGEN) according to manufacturer’s instructions.
 
Hybridization protocol Fragmented and labelled cDNA was hybridised to GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix) for 16 h at 45 ºC with rotation at 60 rpm. Arrays were washed and stained using the Affymetrix GeneChip Fluidics Station 450 using protocol EukGE-WS2v4_450.
Scan protocol Arrays were scanned using the Affymetrix GeneChip Scanner 3000 system with autoloader and AGCC software.
Description Gene expression data from SCC FAK-/- cells
Data processing Gene expression data were analyzed using packages within Bioconductor implemented in the R statistical programming language. The gene expression data were summarised from CEL files using Ensembl gene identifiers (BRAINARRAY v17.0.0), ENSG and normalized using the Robust Multi-array Average (RMA) algorithm within the ‘affy’ package.
 
Submission date Aug 03, 2015
Last update date Sep 29, 2015
Contact name Adam Byron
Organization name University of Edinburgh
Department Edinburgh Cancer Research UK Centre
Street address Western General Hospital, Crewe Road South
City Edinburgh
ZIP/Postal code EH4 2XR
Country United Kingdom
 
Platform ID GPL20766
Series (1)
GSE71662 Gene expression data from mouse squamous cell carcinoma cells

Data table header descriptions
ID_REF
VALUE log2 RMA signal

Data table
ID_REF VALUE
ENSMUSG00000000001_at 10.74503237
ENSMUSG00000000003_at 2.241702314
ENSMUSG00000000028_at 8.368038335
ENSMUSG00000000031_at 3.384805831
ENSMUSG00000000037_at 3.904374128
ENSMUSG00000000049_at 3.111888962
ENSMUSG00000000056_at 7.540266672
ENSMUSG00000000058_at 9.148284018
ENSMUSG00000000078_at 10.61541524
ENSMUSG00000000085_at 4.750710019
ENSMUSG00000000088_at 11.82215171
ENSMUSG00000000093_at 3.137928609
ENSMUSG00000000094_at 4.18715235
ENSMUSG00000000103_at 5.756411647
ENSMUSG00000000120_at 4.913043023
ENSMUSG00000000125_at 3.03982394
ENSMUSG00000000126_at 4.915330468
ENSMUSG00000000127_at 8.750182725
ENSMUSG00000000131_at 8.542296185
ENSMUSG00000000134_at 8.273912859

Total number of rows: 17204

Table truncated, full table size 569 Kbytes.




Supplementary file Size Download File type/resource
GSM1842583_Frame_Musmu_SCC-FAK--2.CEL.gz 3.5 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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