Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Genome-wide maps of H3K36me3 in metastatic renal cell carcinoma and isogenic renal cell carcinoma cell lines

ABSTRACT: We report the application of H3K36me3 ChIP sequencing in SETD2 genotyped samples Examination of H3K36me3 in SETD2 wild-type, mutant renal cell carcinoma and SETD2 isogenic cell lines

ORGANISM(S): Homo sapiens

SUBMITTER: Jeff Nie

PROVIDER: E-GEOD-66884 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

High-resolution profiling of histone h3 lysine 36 trimethylation in metastatic renal cell carcinoma.

Ho T H TH Park I Y IY Zhao H H Tong P P Champion M D MD Yan H H Monzon F A FA Hoang A A Tamboli P P Parker A S AS Joseph R W RW Qiao W W Dykema K K Tannir N M NM Castle E P EP Nunez-Nateras R R Teh B T BT Wang J J Walker C L CL Hung M-C MC Jonasch E E

Oncogene 20150615 12

Mutations in SETD2, a histone H3 lysine trimethyltransferase, have been identified in clear cell renal cell carcinoma (ccRCC); however it is unclear if loss of SETD2 function alters the genomic distribution of histone 3 lysine 36 trimethylation (H3K36me3) in ccRCC. Furthermore, published epigenomic profiles are not specific to H3K36me3 or metastatic tumors. To determine if progressive SETD2 and H3K36me3 dysregulation occurs in metastatic tumors, H3K36me3, SETD2 copy number (CN) or SETD2 mRNA abu ...[more]

PMID: 26073078

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Project description:To address the need to study frozen clinical specimens using next-generation RNA, DNA, chromatin immunoprecipitation (ChIP) sequencing and protein analyses, we developed a biobank work flow to prospectively collect biospecimens from patients with renal cell carcinoma (RCC). We describe our standard operating procedures and work flow to annotate pathologic results and clinical outcomes. We report quality control outcomes, nucleic acid yields of our RCC submissions (N=16) to The Cancer Genome Atlas (TCGA) project, as well as newer discovery platforms by describing mass spectrometry analysis of albumin oxidation in plasma and 6 ChIP sequencing libraries generated from nephrectomy specimens after histone H3 lysine 36 trimethylation (H3K36me3) immunoprecipitation. From June 1, 2010, through January 1, 2013, we enrolled 328 patients with RCC. Our mean (SD) TCGA RNA integrity numbers (RINs) were 8.1 (0.8) for papillary RCC, with a 12.5% overall rate of sample disqualification for RIN <7. Banked plasma had significantly less albumin oxidation (by mass spectrometry analysis) than plasma kept at 25°C (P<.001). For ChIP sequencing, the FastQC score for average read quality was at least 30 for 91-95% of paired-end reads. In parallel, we analyzed frozen tissue by RNA sequencing and after genome alignments, only 0.2-0.4% of total reads failed the default quality check steps of Bowtie2, which was comparable to the disqualification ratio (0.1%) of the 786-O RCC cell line, prepared under optimal RNA isolation conditions. The overall correlation coefficients for gene expression between the Mayo Clinic vs. TCGA tissues ranged from 0.75 to 0.82. These data support the generation of high-quality nucleic acids for genomic analyses from banked RCC. Importantly, the protocol does not interfere with routine clinical care. Collections over defined time points during disease treatment further enhance collaborative efforts to integrate genomic information with outcomes. Examination of H3K36me3 in ccRCC

Dataset Information

Genome-wide maps of H3K36me3 in metastatic renal cell carcinoma and isogenic renal cell carcinoma cell lines

Publications

High-resolution profiling of histone h3 lysine 36 trimethylation in metastatic renal cell carcinoma.

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