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Sample GSM887229 Query DataSets for GSM887229
Status Public on Mar 20, 2012
Title KNS-42
Sample type RNA
 
Source name HSRRB
Organism Homo sapiens
Characteristics primary site: central_nervous_system
histology: glioma
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 total RNA
Extraction protocol RNA was isolated from frozen cell pellets, containing an average cell count of 4.5 million cells, via Trizol (Invitrogen) extraction following the manufacturers instructions. Samples were quantified using both the Nanodrop 8000 spectrophotometer (ThermoScientific) and via Agilent 2100 Bioanalyzer.
Label Biotin
Label protocol The Affymetrix One-Cycle Target labeling assay was used to synthesize hybridization target using 1 mg of total RNA. Labeled cRNA hybridization target was produced using a 3-day, semi-automated workflow
 
Hybridization protocol Fragmentation of the biotin-labeled cRNA prepared the sample for hybridization on the GeneChip Human U133 2.0 (PN 900467). The washing and staining was performed on the GeneChip Fluidics station using standard Affymetrix protocols outlined in the Expression Analysis Technical Manual, 2001, Affymetrix.
Scan protocol The GeneChip® Scanner 3000 was used for scanning the arrays.
Description Gene expression data from the CCLE
Data processing The data were analyzed with 2.14.0, using the packages affyio_1.22.0 and affy_1.32.0, and RMA as normalization method. rma() was used with default options (normalize=TRUE, background=TRUE) and with the package hgu133plus2hsentrezgcdf_15.0.0 from Brainarray for the CDF file.
 
Submission date Mar 06, 2012
Last update date Sep 01, 2016
Contact name Nicolas Stransky
E-mail(s) stransky@broadinstitute.org
URL http://www.broadinstitute.org/ccle
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 GPL15308
Series (2)
GSE36133 Expression data from the Cancer Cell Line Encyclopedia (CCLE)
GSE36139 SNP and Expression data from the Cancer Cell Line Encyclopedia (CCLE)
Relations
Reanalyzed by GSE86362

Data table header descriptions
ID_REF
VALUE RMA log2 signal intensity

Data table
ID_REF VALUE
1_at 6.526
10_at 4.6905
100_at 6.2491
1000_at 10.316
10000_at 7.1979
100009676_at 5.8508
10001_at 8.3853
10002_at 3.9633
10003_at 3.5423
10004_at 4.539
100048912_at 4.0182
100049716_at 4.1195
10005_at 7.8322
10006_at 8.2718
10007_at 9.8822
10008_at 3.9932
10009_at 9.1873
100093630_at 9.4436
1001_at 6.035
10010_at 9.2399

Total number of rows: 18926

Table truncated, full table size 294 Kbytes.




Supplementary file Size Download File type/resource
GSM887229.CEL.gz 5.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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