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Sample GSM1071811 Query DataSets for GSM1071811
Status Public on Jan 01, 2014
Title C2_0270 Pool of 8 normal tissues
Sample type SRA
 
Source name normal mammary tissue
Organism Homo sapiens
Characteristics tissue: normal mammary tissue
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted using Formapure kit (Beckman Coulter Genomics).
Amplicons spanning RND1 exons were pooled for 10 samples after amplification by PCR. 1ug of pooled amplicons was concatenated, sheared for 5 minutes (covaris), end repaired, and ligated with barcoded SOLiD sequencing adaptors. 8 cycles of PCR were performed and 2ng of the final 10 libraries were then pooled for one full size emulsion PCR using the EZbead system. The enriched beads were sequenced in an octet of a SOLiD sequencing system for 50bp run with the Exact Call Chemistry module (ECC). An average of 6.2 million reads were generated per pool, the mapping rates ranged from 86.9% and 89.1%.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model AB 5500 Genetic Analyzer
 
Description SOLID_0270__ALL__CHARITY.xls
Data processing mapping software: LifeScope (version 1)
genome build: hg19
VarScan version: version 2.2

CSFASTA files were mapped to human genome
Samtools mpileup was used to generate pileups from the mapped BAM files.
VarScan was used to call mutations
Events were annotated using a custom script and database built from RefSeq.
Supplementary_files_format_and_content: tab-delimited files containing events and annotations
 
Submission date Jan 28, 2013
Last update date May 15, 2019
Contact name Bic MSKCC
Organization name Memorial SLoan-Kettering Cancer Center
Street address 1275 York Ave.
City New York
State/province NY
ZIP/Postal code 10021
Country USA
 
Platform ID GPL16558
Series (1)
GSE43828 Investigation of breast cancer-associated mutations in RND1 gene
Relations
SRA SRX220331
BioSample SAMN01906640

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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