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Sample GSM2281842 Query DataSets for GSM2281842
Status Public on Nov 18, 2017
Title Z2014-10616
Sample type SRA
 
Source name serum
Organism Homo sapiens
Characteristics gender: female
age: 66
disease state (dignity): renal cell carcinoma
t-stage: 1
n-stage: 0
m-stage: 0
grade: 1
uicc: 1
Extracted molecule total RNA
Extraction protocol RNA was isolated using the miRNeasy serum/plasma Kit (Qiagen) following the manufacturer instructions. The RNA concentration was determined using the Nanodrop UV-Vis Spectrophotometer (Thermo Fisher Scientific).
NEBNext small RNA library prep kit (New England Biolabs) was used according to the manufacturers instructions, followed by Illumina single-end sequencing with read length of 75bp on the NextSeq 500 Sequencing System (Illumina). There were 20 M indexed reads per sample on average.
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NextSeq 500
 
Description Processed data files: annex 2_miRNA result tables.xlsx, annex 3_miRNA counts.xlsx, annex 3_piRNA counts.xlsx, annex 4_miRNA expression.xlsx, annex 4_piRNA expression.xlsx, annex 5_isomiR counts.xlsx, annex 5_piRNA result tables.xlsx, annex 6_counts other small RNAs.txt
Data processing Sequencing reads are processed using Cobra, Biogazelle’s proprietary small RNA sequencing pipeline for read QC, adapter trimming, read mapping and read annotation.
Mapped reads are annotated based on the latest miRBase release. Read QC, read annotation and read length distribution are provided for each sample.
Raw and normalized expression data is reported for each mature miRNA in miRBase. In addition, expression levels for individual isomiRs is provided.
Genome_build: miRBase Release 21 (June 2014)
Supplementary_files_format_and_content: abundance measurements
 
Submission date Aug 16, 2016
Last update date May 15, 2019
Contact name Jörg Ellinger
E-mail(s) joerg.ellinger@ukb.uni-bonn.de
Organization name Universitätsklinikum Bonn
Department Urologie
Street address Sigmund-Freud-Straße 25
City Bonnn
State/province NRW
ZIP/Postal code 53127
Country Germany
 
Platform ID GPL18573
Series (1)
GSE85699 Serum miR-122-5p and miR-206 expression: Non-invasive prognostic biomarkers for renal cell carcinoma
Relations
BioSample SAMN05579930
SRA SRX2026427

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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