NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM827303 Query DataSets for GSM827303
Status Public on Nov 03, 2011
Title T84_STY
Sample type genomic
 
Source name Intestine cell line T84
Organism Homo sapiens
Characteristics cell line: T84
Treatment protocol None.
Growth protocol Cell lines were grown according to standard conditions.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted with the Qiagen Blood Amp kit (P/N 51161).
Label biotin
Label protocol Labeling was performed as described in the 500k assay manual (P/N 701930 Rev. 2).
 
Hybridization protocol Hybridization was performed as described in the 500k assay manual (P/N 701930 Rev. 2).
Scan protocol The Arrays were scanned using the Gene Chip Scanner 3000 with autoloader and 7G upgrade and images were acquired using GenChip operating software version 1.4.
Description Hybridized to 250K_Sty
T84
Data processing CEL files and TXT files (generated by Affymetrix GTYPE using the Dynamic Model Mapping algorithm) were processed by dCHIP version 2008 using Model-based expression. The following parameters were used: Background subtraction--Mismatch probe (PM/MM difference); Normalization--Invariant set probe selection method and Running median smoothing method (baseline array NA06990); Raw copy number determination--Signal / (mean signal of normal samples at this SNP) * 2; log2 ratio--log2(Signal / mean signal of normal samples at this SNP); Inferred copy number method-- Median smoothing with window size of 3.

The SNP calls are available in the supplementary .txt file that is linked to this record. The data table containing the Signal values (analgous to the expression value in expression array analysis) for each SNP probe produced by dCHIP is available in the supplementary .txt file that is linked to the Series GSE20306 record.
 
Submission date Nov 03, 2011
Last update date Nov 03, 2011
Contact name Stephen Michael Rothenberg
Organization name Massachusetts General Hospital
Department Cancer Center
Street address 13th Street, Bldg. 149, 7th Floor
City Charlestown
State/province MA
ZIP/Postal code 02129
Country USA
 
Platform ID GPL3720
Series (1)
GSE20306 A genome-wide screen for microdeletions reveals disruption of polarity complex genes in diverse human cancers

Supplementary file Size Download File type/resource
GSM827303.CEL.gz 26.6 Mb (ftp)(http) CEL
GSM827303.txt.gz 960.7 Kb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data provided as supplementary file
Processed data is available on Series record

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