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Sample GSM824906 Query DataSets for GSM824906
Status Public on Apr 22, 2014
Title Lung Met, biological rep2
Sample type RNA
 
Source name Lung metastasis derivative
Organism Homo sapiens
Characteristics strain: balb/c
cell line: SW620
sample type: lung metastasis
Growth protocol cells were maintained in 5% CO2 at 37oC in DMEM medium (Gibco) supplemented with 5% fetal bovine serum (FBS) (Biological Industries), Glutamine 0.29 mg/ml (Biological Industries), Penicillin 100 U/ml (Biological Industries) and Streptomycin 0.1 mg/ml (Biological Industries)
Extracted molecule total RNA
Extraction protocol RNA was extracted from cells using RNeasy mini kit (Qiagen)
Label biotin
Label protocol Labeling of the samples to HG1.0ST gene expression chip (Affymetrix) were performed by Functional Genomics Core Facility of IRB, Barcelona using standard methodology
 
Hybridization protocol Hybridization of the samples to HG1.0ST gene expression chip (Affymetrix) were performed by Functional Genomics Core Facility of IRB, Barcelona using standard methodology
Scan protocol Gene chips were scanned using GeneChip Scanner 3000 from affymetrix
Data processing Data analysis was performed using R (Bioconductor). Quantile normalization and RMA summarization were used to obtain probeset level expression estimates as implemented in the “oligo” package of Bioconductor. In order to prevent non-specific or miss-targeted probesets to bias the gene level expression estimates, for each gene we selected the 50% of the probesets with highest inter-quartile range across all samples and obtained a gene level expression estimate via median polish, in a fashion analogous to RMA
 
Submission date Oct 31, 2011
Last update date Apr 23, 2014
Contact name Xabier Garcia-Albeniz
E-mail(s) xgarciad@hsph.harvard.edu
Organization name IRB Barcelona
Lab Metlab
Street address Baldiri Reixac 10
City Barcelona
ZIP/Postal code 08028
Country Spain
 
Platform ID GPL10739
Series (1)
GSE33350 Comparison of metastatic derivatives of colon cancer cell line selected in vivo

Data table header descriptions
ID_REF
VALUE RMA normalized

Data table
ID_REF VALUE
7892501 7.514531714
7892502 5.865563251
7892503 4.305618384
7892504 10.66823038
7892505 4.24587554
7892506 4.327774109
7892507 6.626205963
7892508 4.132995448
7892509 12.86652004
7892510 5.100503579
7892511 3.913676547
7892512 9.196440935
7892513 4.141278047
7892514 10.32071243
7892515 10.76536279
7892516 8.45602595
7892517 6.563798792
7892518 3.485521505
7892519 8.37678464
7892520 10.64402349

Total number of rows: 65535

Table truncated, full table size 1272 Kbytes.




Supplementary file Size Download File type/resource
GSM824906.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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