|
| Status |
Public on Aug 20, 2014 |
| Title |
9830-020310B-FF_RIBO0 |
| Sample type |
SRA |
| |
|
| Source name |
breast tumor
|
| Organism |
Homo sapiens |
| Characteristics |
age: 40
er (1=positive; 0=negative): 1
pr (1=positive; 0=negative): 1
node status (1=positive=1 or more nodes; 0=negative): 0
grade: 2
tumor size (1= <=2cm; 2= >2cm to <=5cm; 3= >5cm; 4=any size with direct extension to chest wall or skin): 3
rfs event (0=no relapse; 1=relapsed at any site or died of disease): 0
rfs months: 24
overall survival event (0=alive; 1=dod or doc): 0
overall suvival months: 24
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fresh-frozen: Autopsy breast tissue sample was flash frozen on dry ice. RNA was retrieved using Qiagen RNeasy mini kit.
Ribo-zero: rRNA was removed using epicentre's Ribo-Zero rRNA Removal kit cat# RZH110424. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used for the construction of sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8. Quality score is phred33 scale.
Sequenced reads were to hg19 whole genome using MapSplice v12_07 with the default configuration.
The number of fragments derived from genes was estimated using RSEM v1.1.13 with the default setting and the reference transcriptome of UCSC hg19 GAF2.1 KnownGenes on standard chromosomes. Estimated counts were then transformed by upper quartile normalization.
Gene abundance was normalized by the upper quartile across all genes within each lane.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file of normalized gene counts for each sample.
Raw data is to be made available through dbGaP (controlled access) due to patient privacy concerns:
http://www.ncbi.nlm.nih.gov/gap/?term=phs000676
|
| |
|
| Submission date |
Oct 28, 2013 |
| Last update date |
May 15, 2019 |
| 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) |
| GSE51783 |
Comparison of Poly(A) capture versus Ribosomal RNA depletion methods for RNA-seq |
|
| Relations |
| BioSample |
SAMN02420004 |
| SRA |
SRX474651 |
