|
| Status |
Public on Oct 16, 2018 |
| Title |
Subject_137: CALGB1046543-D-38 |
| Sample type |
SRA |
| |
|
| Source name |
Breast
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast cancer
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Fresh-frozen RNA was isolated with Qiagen RNAeasy kit. Illumina TruSeq RNA Sample Preparation Kit (RS-122-2001 or RS-122-2002)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Fresh-frozen RNA was isolated with Qiagen RNAeasy kit. Illumina TruSeq RNA Sample Preparation Kit (RS-122-2001 or RS-122-2002)
|
| Data processing |
Basecalls by Casava
Alignment by MapSplice2
Genome to transcriptome coordiantes by UBU (https://github.com/mozack/ubu/wiki)
Gene expression estimates by RSEM using Sept 2011 UCSC knownGene transcript definitions
More information on the pipeline can be found here: https://webshare.bioinf.unc.edu/public/mRNAseq_TCGA/
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited matrix of gene level count estimates
Purity-filtered reads were aligned to the human reference GRCh38/hg38 genome using Spliced Transcripts Aligned to a Reference (STAR) version 2.4.2a
Transcript (GENCODE v22) abundance estimates were generated by Salmon version 0.6.030 in ‘-quant’ mode, based on the STAR alignments
Fixed upper quartile normalization
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited, normalized, transcript abundance estimates
|
| |
|
| Submission date |
Jun 27, 2018 |
| Last update date |
Mar 27, 2020 |
| Contact name |
Charles M. Perou |
| E-mail(s) |
[email protected]
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center
|
| Street address |
12-044 Lineberger Comprehensive Cancer Center CB# 7295
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7264 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE116335 |
CALGB 40601: Randomized Phase III Trial of Paclitaxel Combined With Trastuzumab, Lapatinib, or Both As Neoadjuvant Treatment of HER2-Positive Primary Breast Cancer |
|
| Relations |
| BioSample |
SAMN08984630 |
| SRA |
SRX4181129 |
