|
Status |
Public on Jan 21, 2022 |
Title |
C03_Q-46-CALGB03-1069427-1 |
Sample type |
SRA |
|
|
Source name |
Breast
|
Organism |
Homo sapiens |
Characteristics |
tissue: Breast carcinoma treatment: None - Pretreatment Neoadjuvant Therapy
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Fresh-frozen RNA was isolated with Qiagen RNeasy 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 |
Sample_PRE_RNA_001 RNA-Seq of Homo sapiens; primary breast; breast carcinoma
|
Data processing |
Basecalls by Casava. 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: CALGB40603.389PreTreat.JUNCTION.salmon_gene_normalized.matrix_FOR_GEO.v2.txt: Tab-delimited, normalized, transcript abundance estimates.
|
|
|
Submission date |
Jul 15, 2020 |
Last update date |
Jan 21, 2022 |
Contact name |
Charles M. Perou |
E-mail(s) |
cperou@med.unc.edu
|
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) |
GSE154524 |
CALGB 40603: Randomized Phase II 2 x 2 Factorial Trial of the Addition of Carboplatin +/- Bevacizumab to Neoadjuvant Weekly Paclitaxel Followed by Dose-Dense AC in Hormone Receptor-Poor/HER2-Negative Resectable Breast Cancer |
|
Relations |
BioSample |
SAMN12549864 |