|
| Status |
Public on Jan 20, 2017 |
| Title |
SUM229neg |
| Sample type |
SRA |
| |
|
| Source name |
EpCAM/CD49f negative SUM229 breast carcinoma subpopulation
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: triple negative breast cancer cell line SUM-229PE
cell subpopulation: SUM229neg
|
| Growth protocol |
F12 supplemented with 5% FBS, 5 µg/ml insulin, 1 µg/ml hydrocortisone, 10 mM HEPES
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from EpCAM+/CD49f+ and EpCAM-/CD49f- FACS populations using Qiagen DNeasy Blood and Tissue Kit and subquently treated with Rnase A.
300 ng genomic DNA was submitted to the UNC High Throughput Sequencing Facility for Illumina Nextera Rapid Capture exome enrichment.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
SUM229variantcalling.xlsx
whole exome sequencing
|
| Data processing |
Alignment to hg19 was performed using BWA-mem.
Variants from the reference were identified using FreeBayes and Strelka was used to call cell line specific mutations in a paired fashion by tretating each cell line individually as the somatic sample.
Variants of high quality (Q>=50) were annotated with SNPeff.
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet containing variant coordinate, gene name, dbSNP ID, minor allele frequency, Q score, and COSMIC overlaps.
|
| |
|
| Submission date |
Sep 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Gary L Johnson |
| E-mail(s) |
glj@med.unc.edu
|
| Organization name |
University of North Carolina School of Medicine
|
| Department |
Pharmacology
|
| Lab |
Gary L. Johnson Lab
|
| Street address |
4009 Genetic Medicine Building, 120 Mason Farm Road
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE87423 |
Enhancer Remodeling During Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacological Targeting of the P-TEFb Complex (Exome-seq) |
| GSE87424 |
Enhancer Remodeling During Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacological Targeting of the P-TEFb Complex |
|
| Relations |
| BioSample |
SAMN05832481 |
| SRA |
SRX2194637 |
