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Sample GSM1842582 Query DataSets for GSM1842582
Status Public on Sep 29, 2015
Title SCC-FAK-/-_rep1
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 10.70966836
ENSMUSG00000000003_at 2.0724457
ENSMUSG00000000028_at 8.400651168
ENSMUSG00000000031_at 3.004955725
ENSMUSG00000000037_at 4.2420651
ENSMUSG00000000049_at 2.583645914
ENSMUSG00000000056_at 7.272454731
ENSMUSG00000000058_at 9.285658707
ENSMUSG00000000078_at 10.66376255
ENSMUSG00000000085_at 4.860569989
ENSMUSG00000000088_at 11.85809268
ENSMUSG00000000093_at 2.982124149
ENSMUSG00000000094_at 4.042947541
ENSMUSG00000000103_at 5.392527353
ENSMUSG00000000120_at 4.614678514
ENSMUSG00000000125_at 2.945427565
ENSMUSG00000000126_at 4.875264712
ENSMUSG00000000127_at 8.612047094
ENSMUSG00000000131_at 8.446977161
ENSMUSG00000000134_at 8.417924013

Total number of rows: 17204

Table truncated, full table size 569 Kbytes.




Supplementary file Size Download File type/resource
GSM1842582_Frame_Musmu_SCC-FAK--1.CEL.gz 3.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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