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Sample GSM824901 Query DataSets for GSM824901
Status Public on Apr 22, 2014
Title Parental, biological rep4
Sample type RNA
 
Source name Parental
Organism Homo sapiens
Characteristics strain: balb/c
cell line: SW620
sample type: parental
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 Dec 19, 2019
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
Relations
Reanalyzed by GSE142219

Data table header descriptions
ID_REF
VALUE RMA normalized

Data table
ID_REF VALUE
7892501 8.54346356
7892502 5.902022138
7892503 3.812318186
7892504 10.73130499
7892505 4.171521645
7892506 4.783455012
7892507 7.131144034
7892508 4.674459592
7892509 12.95160434
7892510 4.598000893
7892511 3.524942061
7892512 9.31003148
7892513 4.353818776
7892514 11.26769751
7892515 10.74818459
7892516 9.442698394
7892517 6.515948371
7892518 4.27844613
7892519 8.357508454
7892520 10.65309042

Total number of rows: 65535

Table truncated, full table size 1273 Kbytes.




Supplementary file Size Download File type/resource
GSM824901.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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