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Sample GSM2183833 Query DataSets for GSM2183833
Status Public on Nov 21, 2016
Title non-cancerous, FFPE, Patient 57, renal biopsy
Sample type SRA
 
Source name renal biopsy
Organism Homo sapiens
Characteristics tissue: kidney
individual: patient 57
disease state: non-cancerous
storage: FFPE
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted with miRNeasy FFPE kit (Qiagen, Germany).
Sequencing libraries were generated using TruSeq RNA Access library kit (Illumina, Inc., San Diego, CA, USA) according to the manufacturer`s protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description 57NF
Data processing Basecalls performed using CASAVA version 1.8.2
Assembly of reads and alignment of the contigs to the Human genome assembly GRCh38 was guided by Tophat and Bowtie
logcpm (counts per million) were calculated using EdgeR (R bioconductor)
features with logcpm>=15 in at least 8 samples were considered further
Genome_build: GRCh38 (hg19)
Supplementary_files_format_and_content: Eikrem_counts.txt, Eikrem_logcpm_filtered.txt
Genome_build: GRCh38 (hg19)
Supplementary_files_format_and_content: Eikrem_counts.txt was generated by assembling the raw count data into a single matrix using Cufflinks
Supplementary_files_format_and_content: Eikrem_logcpm_filtered.txt was generated by keeping the count data features with logcpm>=15 in at least 8 samples
 
Submission date Jun 01, 2016
Last update date Nov 21, 2016
Contact name Philipp Strauss
E-mail(s) Philipp.Strauss@uib.no
Organization name University of Bergen
Street address Haukeland Universitetssykehus Laboratoriebygget, 7. etg. Heis øst
City Bergen
ZIP/Postal code 5020
Country Norway
 
Platform ID GPL16791
Series (1)
GSE82122 Confirmation dataset of Transcriptome Sequencing (RNAseq) data utilizing Formalin-Fixed, Paraffin-Embedded Biopsies with Clear Cell Renal Cell Carcinoma for Exploration of Disease Biology and Biomarker Development
Relations
BioSample SAMN05194880

Supplementary data files not provided
Raw data not provided for this record
Processed data are available on Series record

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