|
Status |
Public on Aug 31, 2020 |
Title |
phs001866_AP_175 |
Sample type |
SRA |
|
|
Source name |
breast
|
Organism |
Homo sapiens |
Characteristics |
tumor_type: primary tumor
|
Extracted molecule |
total RNA |
Extraction protocol |
Tumor tissue was disrupted using roto-stator homogenization. RNA was isolated using the RNeasy Mini Kit (QIAGEN) according to manufacturer protocol. RNA was quantified using a NanoDrop® Spectrophotometer, and the quality of RNA was then analyzed via 2100 Bioanalyzer Instrumentwhich using the RNA 6000 Nano assay (Agilent) for determination of an RNA Integrity Number (RIN). Briefly, 1 μg of total RNA was converted to RNAseq libraries using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) and sequenced on an Illumina HiSeq 2500 using a 2x50bp configuration with an average of 136 million read pairs per sample.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
RNA-Seq of human breast primary tumor
|
Data processing |
Quality-control-passed reads were aligned to the human reference CGRh38/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, an expectation-maximization algorithm using the UCSC gene definitions. Genome_build: CGRh38/hg38 genome Supplementary_files_format_and_content: Raw read counts for all RNAseq samples were normalized to a fixed upper quartile (166_AP206_UQN.final.tsv). RNAseq normalized gene counts from primary and metastatic tumors were log2 transformed, the zeros were added again after log transformation and the genes were filtered for those expressed in 70% of samples using the cluster 3.0 software and the samples were median centered. (166_AP206_UQN_w0_log2_70p_mdctr.final.tsv)
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|
|
Submission date |
Mar 20, 2020 |
Last update date |
Aug 31, 2020 |
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) |
GSE147322 |
FGFR4 is a regulator of tumor subtype differentiation in luminal breast cancer and metastatic disease II |
|
Relations |
BioSample |
SAMN13494186 |
SRA |
SRX7513875 |