|
Status |
Public on Jun 01, 2022 |
Title |
4_1_1 |
Sample type |
SRA |
|
|
Source name |
DCIS
|
Organism |
Homo sapiens |
Characteristics |
histologic annotation: DCIS pam50 molecular subtype: Basal paired or unpaired info: BasalTumor_3
|
Extracted molecule |
total RNA |
Extraction protocol |
For bulk RNAseq; FFPE block sections were used and RNA was isolated using the RNeasy FFPE Kit (Cat. No. / ID: 73504, Qiagen) according to manufacturer protocol. Libraries were made using the Illumina Total RNA (Ribo Zero Gold) kit following the TruSeq Stranded Total RNA Sample Preparation Guide 15031048 E For bulk mRNA-Seq Paired end (2 50bp) sequencing was performed on the Illumina HiSeq 2000/2500 sequencer
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
FFPE block sections
|
Data processing |
Bulk mRNA-Seq libraries were aligned to the hg38 genome using STAR. The alignment profile was determined by Picard Tools v1.64 (http://broadinstitute.github.io/picard/). Transcript abundance estimates for each sample were performed using Salmon Genome_build: hg38 Supplementary_files_format_and_content: Normlaized and log-transformed data
|
|
|
Submission date |
Aug 18, 2021 |
Last update date |
Jun 01, 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 |
GPL16791 |
Series (2) |
GSE182387 |
Molecular signatures of in-situ to invasive progression for basal-like breast cancers: An integrated mouse model and human tumor study [human] |
GSE182389 |
Molecular signatures of in-situ to invasive progression for basal-like breast cancers: An integrated mouse model and human tumor study |
|
Relations |
BioSample |
SAMN20931465 |
SRA |
SRX11865221 |