NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM887670 Query DataSets for GSM887670
Status Public on Mar 20, 2012
Title SW-1710
Sample type RNA
 
Source name DSMZ
Organism Homo sapiens
Characteristics primary site: urinary_tract
histology: carcinoma
histology subtype1: transitional_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 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 5.1413
10_at 4.436
100_at 8.1924
1000_at 10.204
10000_at 8.3706
100009676_at 5.5886
10001_at 8.1821
10002_at 3.7577
10003_at 3.6062
10004_at 4.3331
100048912_at 4.0743
100049716_at 4.9548
10005_at 8.2471
10006_at 9.62
10007_at 10.104
10008_at 3.9342
10009_at 8.6625
100093630_at 10.125
1001_at 5.6486
10010_at 9.3336

Total number of rows: 18926

Table truncated, full table size 294 Kbytes.




Supplementary file Size Download File type/resource
GSM887670.CEL.gz 4.7 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap