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Sample GSM1153997 Query DataSets for GSM1153997
Status Public on Dec 31, 2014
Title Immortalized human bone marrow-derived mesenchymal stromal cell line iMSC#3, Affymetrix SNP 6
Sample type genomic
Source name iMSC#3
Organism Homo sapiens
Characteristics cell line: iMSC#3
sample origin: Human bone marrow-derived mesenchymal stromal cell
gender: Male
Growth protocol iMSC#3 was cultured in minimum essential medium (MEM) Alpha medium (cat. no. 22561) supplemented with 10% FBS (PAA Laboratories), GlutaMAX, penicillin (100U/mL), and streptomycin (100 mg/mL) (all from Life Technologies) at 37C and 5% CO2. Non-adherent cells were removed after approximately 24 h by replacement of the medium. Subsequently, the adherent cells were allowed to expand until 70% confluence (5–6 days) before they were harvested and further expanded.
Extracted molecule genomic DNA
Extraction protocol DNA was isolated using the Wizard Genomic DNA Purification Kit (Promega, Madison, USA).
Label Biotin
Label protocol Standard Affymetrix label protocol
Hybridization protocol Standard Affymetrix hyb protocol
Scan protocol Standard Affymetrix scan protocol
Data processing Quality control was performed using the Genotyping Console v3.0.1 software (Affymetrix), applying the contrast quality control (CQC) algorithm with a minimal call rate of > 86 %. DNA copy number analysis was performed using the Nexus software (BioDiscovery, California, USA), with the SNPRank segmentation algorithm using default settings (threshold of 0.6 for high copy gain, 0.2 for gain, -0.2 for loss and -1.0 for homozygous loss).
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
Copy number probes and segments, as well as SNP calls and segments obtained from NEXUS copy number. Used Hg19
Submission date Jun 05, 2013
Last update date Dec 31, 2014
Contact name Leonardo A. Meza-Zepeda
Phone +47-99035706
Organization name Oslo University Hospital
Department Department of Tumor Biology
Lab Meza-Zepeda
Street address Ullernchausseen 70
City Oslo
ZIP/Postal code 0310
Country Norway
Platform ID GPL6801
Series (2)
GSE47646 Generation and Characterization of an immortalized human mesenchymal stromal cell line model [Affymetrix]
GSE47651 Generation and Characterization of an immortalized human mesenchymal stromal cell line model

Data table header descriptions

Data table
SNP_A-2131660 NC 0.542076 AB 517.152588 5261.489258
SNP_A-1967418 NC 0.183898 BB 301.618622 1028.479492
SNP_A-1969580 NC 0.436496 AB 1734.628296 9196.764648
SNP_A-4263484 NC 0.233385 BB 3679.612061 2289.968018
SNP_A-1978185 NC 0.208987 BB 827.184998 335.922821
SNP_A-4264431 NC 0.643501 BB 1651.133179 356.634796
SNP_A-1980898 NC 0.169035 AB 711.974609 693.204407
SNP_A-1983139 NC 0.450413 AB 8108.090820 1071.197876
SNP_A-4265735 NC 0.555910 AB 4832.362793 620.065247
SNP_A-1995832 NC 0.766452 AB 4618.123535 508.738373
SNP_A-1995893 NC 0.586873 AB 5444.660645 1238.188232
SNP_A-1997689 NC 0.812868 AB 593.528015 4429.126953
SNP_A-1997709 NC 0.490077 AB 4168.932617 297.087891
SNP_A-1997896 NC 0.898335 BB 1582.524780 550.809570
SNP_A-1997922 NC 0.196112 BB 625.890442 322.977844
SNP_A-2000230 NC 0.690476 AB 3405.178467 1246.602417
SNP_A-2000332 NC 0.549631 AB 5620.712402 853.074951
SNP_A-2000337 NC 0.741576 BB 2021.359741 370.227020
SNP_A-2000342 NC 0.644721 AB 4209.062012 768.932556
SNP_A-4268173 NC 0.196012 BB 1304.854858 941.748047

Total number of rows: 909622

Table truncated, full table size 46126 Kbytes.

Supplementary file Size Download File type/resource
GSM1153997_iMSC3.CEL.gz 28.1 Mb (ftp)(http) CEL
GSM1153997_iMSC3.birdseed-v2.chp.gz 12.2 Mb (ftp)(http) CHP
GSM1153997_iMSC_3_CN_probes.txt.gz 29.0 Mb (ftp)(http) TXT
GSM1153997_iMSC_3_CN_segments.txt.gz 27.1 Kb (ftp)(http) TXT
GSM1153997_iMSC_3_snps.txt.gz 11.2 Mb (ftp)(http) TXT
GSM1153997_iMSC_3_snpsegments.txt.gz 24.6 Kb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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