description: 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.
attributes.tag: ENA first public
attributes.value: 2021-07-08
attributes.tag: ENA last update
attributes.value: 2021-07-08
attributes.tag: External Id
attributes.value: SAMEA9273904
attributes.tag: INSDC center alias
attributes.value: General medical oncology, University Hospitals Leuven
attributes.tag: INSDC center name
attributes.value: General medical oncology, University Hospitals Leuven
attributes.tag: INSDC first public
attributes.value: 2021-07-08T00:12:03Z
attributes.tag: INSDC last update
attributes.value: 2021-07-08T00:12:03Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-10586:Beus_77
attributes.tag: age
attributes.value: 67
attributes.tag: age at diagnosis
attributes.value: 67
attributes.tag: alive at endpoint
attributes.value: yes
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: clinical information
attributes.value: IMDC risk score intermediate
attributes.tag: clinical treatment
attributes.value: sunitinib
attributes.tag: common name
attributes.value: human
attributes.tag: developmental stage
attributes.value: adult
attributes.tag: disease
attributes.value: clear cell renal carcinoma
attributes.tag: disease progression at data cutoff
attributes.value: yes
attributes.tag: individual
attributes.value: 102
attributes.tag: mirnaseq date
attributes.value: 2014
attributes.tag: organism part
attributes.value: kidney
attributes.tag: progression free survival
attributes.value: 9
attributes.tag: sample name
attributes.value: E-MTAB-10586:Beus_77
attributes.tag: sampling site
attributes.value: neoplasm
attributes.tag: sex
attributes.value: male
attributes.tag: specimen with known storage state
attributes.value: FFPE specimen
attributes.tag: survival time
attributes.value: 9
attributes.tag: tumor shrinkage (according to recist v1.1)
attributes.value: 0.63