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Sample GSM888113 Query DataSets for GSM888113
Status Public on Mar 20, 2012
Title HCC-15
Sample type genomic
Source name DSMZ
Organism Homo sapiens
Characteristics primary site: lung
histology: carcinoma
histology subtype1: squamous_cell_carcinoma
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 Dec 21, 2012
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)

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 -0.5729
OR4F5 -0.5729
LOC100132062 0.1087
OR4F16 0.1087
OR4F3 0.1087
OR4F29 0.1087
MIR1977 0.1087
LOC100288069 0.1087
NCRNA00115 0.1087
LOC643837 0.1087
FAM41C 0.1087
FLJ39609 0.1087
SAMD11 0.1087
NOC2L 0.1087
KLHL17 0.1087
PLEKHN1 0.1087
C1orf170 0.1087
HES4 0.1087
ISG15 0.1087
AGRN 0.1087

Total number of rows: 22519

Table truncated, full table size 309 Kbytes.

Supplementary file Size Download File type/resource
GSM888113.CEL.gz 31.7 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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