|
| Status |
Public on Jan 21, 2022 |
| Title |
CALGB03-1042459-K-43 |
| 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_005
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 |
SAMN12549723 |
