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Status |
Public on Nov 03, 2011 |
Title |
HCC38_STY |
Sample type |
genomic |
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|
Source name |
Breast cell line HCC38
|
Organism |
Homo sapiens |
Characteristics |
cell line: HCC38
|
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).
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|
|
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 HCC38
|
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.
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|
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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 |
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