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| Status |
Public on Nov 21, 2016 |
| Title |
non-cancerous, FFPE, Patient 59, renal biopsy |
| Sample type |
SRA |
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| Source name |
renal biopsy
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| Organism |
Homo sapiens |
| Characteristics |
tissue: kidney
individual: patient 59
disease state: non-cancerous
storage: FFPE
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
59NF
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| 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
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| Submission date |
Jun 01, 2016 |
| Last update date |
Nov 21, 2016 |
| Contact name |
Philipp Strauss |
| E-mail(s) |
Philipp.Strauss@uib.no
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| Organization name |
University of Bergen
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| Street address |
Haukeland Universitetssykehus Laboratoriebygget, 7. etg. Heis øst
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| City |
Bergen |
| ZIP/Postal code |
5020 |
| Country |
Norway |
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| 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 |
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| Relations |
| BioSample |
SAMN05194882 |
| Supplementary data files not provided |
| Raw data not provided for this record |
| Processed data are available on Series record |
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