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Sample GSM888402 Query DataSets for GSM888402
Status Public on Mar 20, 2012
Title MKN7
Sample type genomic
Source name RIKEN
Organism Homo sapiens
Characteristics primary site: stomach
histology: carcinoma
histology subtype1: tubular_adenocarcinoma
Treatment protocol None
Growth protocol Cells lines were cultured following growth recommendations from the cell line source vendors. Cells were incubated at 37 ºC at 5% CO2 until 70% confluency was reached. Pellets were harvested 48 hours post media change, flash frozen, and stored at -80 ºC until nucleic acid extraction.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from frozen cell pellets, containing an average cell count of 4.5 million cells, using the Qiagen Gentra Puregene method following the manufacturers recommendations. Samples were quantified using picogreen on a ThermoScientific Varioskan Flash instrument.
Label Biotin
Label protocol PCR amplification fragments (200 and 1100 bp) are labeled using terminal deoxynucleotidyl transferase following the Affymetrix GenomeWideSNP_6 protocol
Hybridization protocol After denaturation, 200ul of sample are injected into a Genome-Wide Human SNP 6.0 array. Arrays are loaded in the GeneChip® Hybridization Oven 640 @ 50 °C temp, rotating arrays @ 60 rpm. Samples are hybridized for 16 to 18 hours.
Scan protocol Genome-Wide Human SNP Array 6.0 are stained using the GeneChip® Fluidics Station 450 and scanned using the GeneChip® Scanner 3000
Description SNP array data from the CCLE
Data processing The raw CEL files were normalized to copy number estimates using a GenePattern pipeline, as described in Cancer Genome Atlas Research Network et al, Nature, 2008, and hg18 Affymetrix probe annotations. Normalized copy number estimates (log2 ratios) were segmented using the Circular Binary Segmentation (CBS) algorithm, followed by median centering of the segment values to a value of zero in each sample.
Submission date Mar 06, 2012
Last update date Aug 17, 2016
Contact name Nicolas Stransky
Organization name Broad Institute
Department Cancer Program
Lab Levi Garraway
Street address 7 Cambridge center
City Cambridge
State/province MA
ZIP/Postal code 02118
Country USA
Platform ID GPL15315
Series (2)
GSE36138 SNP array data from the Cancer Cell Line Encyclopedia (CCLE)
GSE36139 SNP and Expression data from the Cancer Cell Line Encyclopedia (CCLE)
Reanalyzed by GSE85466

Data table header descriptions
VALUE For each gene, log2(CN/2) is reported. In case a gene encompasses more than one segment, the value reported is the one that has the highest absolute value.

Data table
WASH7P 0.2436
OR4F5 0.2436
LOC100132062 0.2436
OR4F16 0.2436
OR4F3 0.2436
OR4F29 0.2436
MIR1977 0.2436
LOC100288069 0.2436
NCRNA00115 0.2436
LOC643837 0.2436
FAM41C 0.2436
FLJ39609 0.2436
SAMD11 0.2436
NOC2L 0.2436
KLHL17 0.2436
PLEKHN1 0.2436
C1orf170 0.2436
HES4 0.2436
ISG15 0.2436
AGRN 0.2436

Total number of rows: 22519

Table truncated, full table size 312 Kbytes.

Supplementary file Size Download File type/resource
GSM888402.CEL.gz 33.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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