|
| Status |
Public on Apr 01, 2017 |
| Title |
MDAMB231-PRRX1-54 |
| Sample type |
SRA |
| |
|
| Source name |
breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
strain: MDAMB231 cells
tissue: breast
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cells using an RNeasy kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw reads in the fastq format were aligned to Human Genome HG19 using the RNA-seq STAR aligner version 2.4.0d (http://www.ncbi.nlm.nih.gov/pubmed/23104886, http://www.ncbi.nlm.nih.gov/pubmed/26334920) as recommended by user manual downloaded along with the software. STAR aligner was chosen for mapping accuracy and speed (http://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2722.html). Mapped reads for each sample were counted for each gene in annotation files in GTF format (gencode.v19.annotation.gtf available for download from GENECODE website (http://www.gencodegenes.org/releases/19.html)) using the FeatureCounts read summarization program (http://www.ncbi.nlm.nih.gov/pubmed/?term=24227677) following the user guide (http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf). Individual count files were merged to generate the raw-counts matrix by an in-house R script, normalized to account for differences in library size and the variance was stabilized by fitting the dispersion to a negative-binomial distribution as implemented in the DESeq R package (http://bioconductor.org/packages/release/bioc/html/DESeq.html)(Anders and Huber, 2010).
Genome_build: HG19
Supplementary_files_format_and_content: txt file contains feature count matrix
|
| |
|
| Submission date |
Mar 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Logan A Walsh |
| E-mail(s) |
[email protected]
|
| Phone |
6468882783
|
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Department |
Human Oncology and Pathogenesis Program
|
| Lab |
Timothy Chan
|
| Street address |
1275 York Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE79586 |
Next generation sequencing facilitates quantitative analysis of changes in mRNA after knock-down of putative master regulators of the breast cancer metastasis transcriptome. |
| GSE79589 |
TRIM25 |
|
| Relations |
| BioSample |
SAMN04578770 |
| SRA |
SRX1660746 |
