|
| Status |
Public on Jun 01, 2022 |
| Title |
2_1_1 |
| Sample type |
SRA |
| |
|
| Source name |
invasive
|
| Organism |
Homo sapiens |
| Characteristics |
histologic annotation: invasive
pam50 molecular subtype: Basal
paired or unpaired info: BasalTumor_2
|
| 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 |
SAMN20931462 |
| SRA |
SRX11865218 |
