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Sample GSM3228362 Query DataSets for GSM3228362
Status Public on Oct 16, 2018
Title Subject_149: CALGB1047254-A-11
Sample type SRA
 
Source name Breast
Organism Homo sapiens
Characteristics tissue: breast cancer
Extracted molecule polyA RNA
Extraction protocol Fresh-frozen RNA was isolated with Qiagen RNAeasy kit. Illumina TruSeq RNA Sample Preparation Kit (RS-122-2001 or RS-122-2002)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Fresh-frozen RNA was isolated with Qiagen RNAeasy kit. Illumina TruSeq RNA Sample Preparation Kit (RS-122-2001 or RS-122-2002)
Data processing Basecalls by Casava
Alignment by MapSplice2
Genome to transcriptome coordiantes by UBU (https://github.com/mozack/ubu/wiki)
Gene expression estimates by RSEM using Sept 2011 UCSC knownGene transcript definitions
More information on the pipeline can be found here: https://webshare.bioinf.unc.edu/public/mRNAseq_TCGA/
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited matrix of gene level count estimates
Purity-filtered reads were aligned to the human reference GRCh38/hg38 genome using Spliced Transcripts Aligned to a Reference (STAR) version 2.4.2a
Transcript (GENCODE v22) abundance estimates were generated by Salmon version 0.6.030 in ‘-quant’ mode, based on the STAR alignments
Fixed upper quartile normalization
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited, normalized, transcript abundance estimates
 
Submission date Jun 27, 2018
Last update date Mar 27, 2020
Contact name Charles M. Perou
E-mail(s) [email protected]
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)
GSE116335 CALGB 40601: Randomized Phase III Trial of Paclitaxel Combined With Trastuzumab, Lapatinib, or Both As Neoadjuvant Treatment of HER2-Positive Primary Breast Cancer
Relations
BioSample SAMN08984400
SRA SRX4181141

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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