|
| Status |
Public on Jan 01, 2014 |
| Title |
H1_0136 Pool of 10 breast tumors |
| Sample type |
SRA |
| |
|
| Source name |
breast tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast tumor
|
| 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 SOLiD System 3.0 |
| |
|
| Description |
SOLID_0136_TO_Pool_F3__All.xls
|
| Data processing |
mapping software: BioScope (version 1.3)
genome build: hg18
VarScan version: version 1
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 |
GPL9442 |
| Series (1) |
| GSE43828 |
Investigation of breast cancer-associated mutations in RND1 gene |
|
| Relations |
| SRA |
SRX220325 |
| BioSample |
SAMN01906634 |
