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Sample GSM984333 Query DataSets for GSM984333
Status Public on Mar 01, 2015
Title 452_T
Sample type SRA
 
Source name Triple-negative breast cancer (Invasive ductal carcinoma)
Organism Homo sapiens
Characteristics age (years): 54
Stage: I
grade: 2
tumor size: 1
recurrence: 0
lymph node metastasis: 0
recurrence-free time (years): 6.6
Extracted molecule total RNA
Extraction protocol Each small RNA library was constructed from total RNA of each sample using the SOLiD Total RNA-Seq Kit (Applied Biosystems, Foster City, CA, USA). Integrity of each small RNA library was examined by using RNA 6000 Nano Chip (Agilent, Santa Clara, CA, USA), Small RNA Chip (Agilent), and Bioanalyzer (Agilent) following the standard protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model AB SOLiD 4 System
 
Data processing All SOLiD small RNA reads generated from ligation sequencing were screened to filter out any reads containing ribosomal RNA, transfer RNA, and adaptor sequences (AB Small RNA Analysis Tool V0.5).
The remaining reads were aligned to human miRNA reference (AB Small RNA Analysis Tool V0.5). The reference databases used for alignment were miRBase (version 17.0) and human genome RefSeq Hg19.
One mismatch was allowed for the first 16 sequences of a SOLiD read and up to 4 maximum mismatches were allowed for a miRNA read count.
Reads that were not uniquely mapped to miRBase reference were disregarded to eliminate ambiguous alignments.
miRNA reads derived from each sample were normalized using the quantile-quantile scaling method. A miRNA mean expression profile obtained from 38 samples was used as the reference for quantile-quantile linear scaling. A scaling factor was determined for each sample dataset to vertically shift all miRNA expression data close to the diagonal line in each log10-scaled quantile-quantile plot.
Genome_build: human genome hg 19
Supplementary_files_format_and_content: tab-delimited text files include miRNA ID, mapped miRNA read counts, RNA strand direction, and genomic coordinates.
 
Submission date Aug 10, 2012
Last update date May 15, 2019
Contact name King-Jen Chang
Organization name National Taiwan University Hospital
Department Department of Surgery
Street address No.1, Changde St., Zhongzheng Dist.
City Taipei
ZIP/Postal code 100
Country Taiwan
 
Platform ID GPL13393
Series (1)
GSE40049 Deregulated microRNAs in triple-negative breast cancer revealed by deep sequencing
Relations
SRA SRX176328
BioSample SAMN01113026

Supplementary file Size Download File type/resource
GSM984333_solid_20101230_KuoWH_SmallRNA_2_F3_452_T.csfasta_extend.counts.35.4.txt.gz 54.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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