Beus_33
Homo sapiens
Protocols: We selected primary ccRCC samples from the Leuven University Hospitals ccRCC tumor bank, which prospectively collects tissue and detailed clinical data from metastatic ccRCC patients after informed consent. Patients were eligible if archived tissue of the primary tumor was available, provided they had not received systemic therapy prior to tissue retrieval. Clear-cell histology was confirmed by an expert uro-pathologist. As a reference, we included paired normal kidney samples from 16 patients as well (healthy tissue block from the nephrectomy specimen removed during ccRCC surgery). H&E-stained sections of the tumor sample were examined by a pathologist to confirm the diagnosis and to estimate tumor content. In the discovery series, tumor content was above 90% in 71 cases and was 70% in 3 cases. Formallin-fixed paraffin-embedded samples were trimmend and dissected in 10µl sections, of which 4-6 whole 10-μm sections were used for RNA extraction. Batch 2014: RNA samples were extracted with the \RecoverAll Total Nucleic Acid Isolation Kit for FFPE\ (Ambion). Sample RNA Integrity Numbers were in the range 1.7 to 2.5 when assayed on an Agilent 2100 Bioanalyzer. Batch 2017: RNA samples were extracted with the \RecoverAll Total Nucleic Acid Isolation Kit for FFPE\ (Ambion). Sample RNA Integrity Numbers were less than 3 when assayed on an Agilent 2100 Bioanalyzer Batch 2014: Sample amounts used ranged between 200 and 500ng of total RNA. They were processed with kit \NEBNext Multiplex Small RNA Library Prep Set for Illumina\ (NEB part # E7300 v2.1) by following manufacturer instructions. Briefly, samples were sequentially ligated to 3' and 5' adapters, with the truncated form of T4 RNA Ligase 2 and the T4 RNA ligase 1, respectively. Reverse transcription with ProtoScript II Reverse Transcriptase yielded cDNA adapter-ligated libraries that were amplified by PCR with LongAmp Taq DNA polymerase mix (12 cycles). Amplified barcoded cDNA from different samples was pooled, and a polyacrylamide gel electrophoresis fraction of 140 to 150 bases -expected to include both miRNA and piRNA libraries- was extracted. Batch 2017: 1000ng of total RNA per sample was processed with kit \NEBNext Multiplex Small RNA Library Prep Set for Illumina\ (NEB E7300) by following manufacturer instructions. Briefly, samples were sequentially ligated to 3' and 5' adapters, with the truncated form of T4 RNA Ligase 2 and the T4 RNA ligase 1, respectively. Reverse transcription with ProtoScript II Reverse Transcriptase yielded cDNA adapter-ligated libraries that were amplified by PCR with LongAmp Taq DNA polymerase mix (15 cycles). Amplified barcoded cDNA from different samples was pooled, and a polyacrylamide gel electrophoresis fraction of 140 to 150 bases -expected to include both miRNA and piRNA libraries- was extracted.
ENA-FIRST-PUBLIC
2020-07-22T17:03:14Z
ENA-LAST-UPDATE
2020-07-22T14:01:03Z
External Id
SAMEA7085313
INSDC center name
KU Leuven
INSDC first public
2020-07-22T17:03:14Z
INSDC last update
2020-07-22T14:01:03Z
INSDC status
public
Submitter Id
E-MTAB-9380:Beus_33
age
61
broker name
ArrayExpress
common name
human
developmental stage
adult
died at data cut-off (1=yes)
1
disease
clear cell renal carcinoma
individual
82
mirnaseq date
01/07/2014
organism part
kidney
overall survival since nephrectomy
6
sample name
E-MTAB-9380:Beus_33
sampling site
neoplasm
scientific_name
Homo sapiens
sex
male
tissue processing
formalin-fixed paraffin embedded
transcriptomic subtypee
ccrcc4