|
| Status |
Public on Jan 08, 2016 |
| Title |
non-cancerous, FFPE, Patient 33, renal biopsy |
| Sample type |
SRA |
| |
|
| Source name |
renal biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
individual: patient 33
tissue: non-cancerous
storage: FFPE
tumor stage: I
fuhrmann degree: 1
nephroctomy type: Partial
gender: male
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted with miRNeasy FFPE kit for samples stored in FFPE, or miRNeasy micro kit (Qiagen) in the case of RNAlater storage.
RNA sequencing libraries were prepared using TruSeq RNA Access library kit (Illumina, Inc., San Diego, CA, USA) according to the manufacturer`s protocol.
RNA-seq exome capture
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
NF33
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single
|
| 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
Raw data are being submitted to EGA.
Genome_build: GRCh38 (hg19)
Supplementary_files_format_and_content: Eikrem_et_al_count_matrix.txt, Eikrem_et_al_logcpm_matrix_filtered.txt
|
| |
|
| Submission date |
Dec 21, 2015 |
| Last update date |
Jan 08, 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) |
| GSE76207 |
Transcriptome Sequencing (RNAseq) enables utilization of Formalin-Fixed, Paraffin-Embedded Biopsies with Clear Cell Renal Cell Carcinoma for Exploration of Disease Biology and Biomarker Development |
|
| Relations |
| BioSample |
SAMN04358202 |
