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Sample GSM824904 Query DataSets for GSM824904
Status Public on Apr 22, 2014
Title Liver Met, biological rep3
Sample type RNA
 
Source name Liver metastasis derivative
Organism Homo sapiens
Characteristics strain: balb/c
cell line: SW620
sample type: liver 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 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 9.136441727
7892502 5.559064171
7892503 4.449428094
7892504 11.08426122
7892505 4.593292129
7892506 4.230517274
7892507 6.493691069
7892508 3.602120004
7892509 13.04916361
7892510 5.349103215
7892511 3.634550118
7892512 9.540782127
7892513 4.049257439
7892514 10.86769233
7892515 11.18483082
7892516 9.037465565
7892517 6.519118381
7892518 4.214173534
7892519 8.208778433
7892520 10.36146138

Total number of rows: 65535

Table truncated, full table size 1272 Kbytes.




Supplementary file Size Download File type/resource
GSM824904.CEL.gz 4.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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