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Sample GSM1842581 Query DataSets for GSM1842581
Status Public on Sep 29, 2015
Title SCC-FAK-wt_rep3
Sample type RNA
Source name SCC FAK-wt 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-wt 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
VALUE log2 RMA signal

Data table
ENSMUSG00000000001_at 10.77481035
ENSMUSG00000000003_at 2.033117268
ENSMUSG00000000028_at 8.657617842
ENSMUSG00000000031_at 3.583374933
ENSMUSG00000000037_at 3.884544997
ENSMUSG00000000049_at 3.320557921
ENSMUSG00000000056_at 7.495023723
ENSMUSG00000000058_at 9.158735548
ENSMUSG00000000078_at 10.33699576
ENSMUSG00000000085_at 5.175340569
ENSMUSG00000000088_at 11.98230053
ENSMUSG00000000093_at 3.029393156
ENSMUSG00000000094_at 4.168681222
ENSMUSG00000000103_at 5.449099781
ENSMUSG00000000120_at 4.612063011
ENSMUSG00000000125_at 3.001175737
ENSMUSG00000000126_at 4.714997393
ENSMUSG00000000127_at 8.667229085
ENSMUSG00000000131_at 8.855699625
ENSMUSG00000000134_at 8.292010737

Total number of rows: 17204

Table truncated, full table size 569 Kbytes.

Supplementary file Size Download File type/resource
GSM1842581_Frame_Musmu_SCC-FAK-wt3.CEL.gz 3.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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