|
Status |
Public on Oct 16, 2018 |
Title |
Subject_149: CALGB1047254-A-11 |
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 2000 |
|
|
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 |
GPL11154 |
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 |
SAMN08984400 |
SRA |
SRX4181141 |