|
| Status |
Public on Apr 27, 2022 |
| Title |
Normal-2 |
| Sample type |
SRA |
| |
|
| Source name |
Paired Normal Tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tumor status: Normal
pam50: Normal
tnbc-high tertiles: Low
er-high tertiles: High
|
| Treatment protocol |
Untreated
|
| Growth protocol |
We obtained 9 flash frozen paired normal and ER+ breast tumor samples, 15 TNBC breast tumor samples, and 7 flash frozen tumor samples from 2 TNBC PDX models (WHIM2 and WHIM30)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA extracted using Qiagen Rneasy Mini Kit
mRNAseq libraries were made from total RNA using the Illumina TruSeq mRNA sample preparation kit and sequenced on an Illumina HiSeq 2500 using a 2x50bp configuration
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
181205_UNC17-D00216_0591_ACD0YEANXX_TCTCTACT-CGCGGTTC_S10_L003
|
| Data processing |
Purity-filtered reads were aligned to the human reference GRCh38/hg38 genome using Spliced Transcripts Aligned to a Reference (STAR) version 2.4.2a1. Transcript (GENCODE v22) abundance estimates were generated by Salmon version 0.6.02 in ‘-quant’ mode, based on the STAR alignments
Raw read counts for all RNAseq samples normalized to fixed upper quartile3
RNAseq normalized gene counts were then log2 transformed (zeros were unchanged) using Cluster 3.0 v1.52
Genes were filtered for those expressed in 70% of samples
Matrix was median centered and column standardized using R studio v1.1.463
Genome_build: hg38
Supplementary_files_format_and_content: txt file. Content: 40n samples logtrans, 70% filtered, median-centered, column standardized
|
| |
|
| Submission date |
May 06, 2021 |
| Last update date |
Apr 27, 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 (1) |
| GSE173991 |
Integrated Metabolic Profiling and Gene Expression Analysis Reveals Therapeutic Modalities in Breast Cancer |
|
| Relations |
| BioSample |
SAMN19041585 |
