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An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.

ABSTRACT: We present Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling that works across multiple applications with substantial improvement of signal-to-background ratio and information content. The Omni-ATAC protocol generates chromatin accessibility profiles from archival frozen tissue samples and 50-?m sections, revealing the activities of disease-associated DNA elements in distinct human brain structures. The Omni-ATAC protocol enables the interrogation of personal regulomes in tissue context and translational studies.

SUBMITTER: Corces MR

PROVIDER: S-EPMC5623106 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature

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An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.

Corces M Ryan MR Trevino Alexandro E AE Hamilton Emily G EG Greenside Peyton G PG Sinnott-Armstrong Nicholas A NA Vesuna Sam S Satpathy Ansuman T AT Rubin Adam J AJ Montine Kathleen S KS Wu Beijing B Kathiria Arwa A Cho Seung Woo SW Mumbach Maxwell R MR Carter Ava C AC Kasowski Maya M Orloff Lisa A LA Risca Viviana I VI Kundaje Anshul A Khavari Paul A PA Montine Thomas J TJ Greenleaf William J WJ Chang Howard Y HY

Nature methods 20170828 10

We present Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling that works across multiple applications with substantial improvement of signal-to-background ratio and information content. The Omni-ATAC protocol generates chromatin accessibility profiles from archival frozen tissue samples and 50-μm sections, revealing the activities of disease-associated DNA elements in distinct human brain structures. The Omni-ATAC protocol enables the interrogation of personal regulom ...[more]

PMID: 28846090

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Project description:BACKGROUND:The main bottleneck for genomic studies of tumors is the limited availability of fresh frozen (FF) samples collected from patients, coupled with comprehensive long-term clinical follow-up. This shortage could be alleviated by using existing large archives of routinely obtained and stored Formalin-Fixed Paraffin-Embedded (FFPE) tissues. However, since these samples are partially degraded, their RNA sequencing is technically challenging. RESULTS:In an effort to establish a reliable and practical procedure, we compared three protocols for RNA sequencing using pairs of FF and FFPE samples, both taken from the same breast tumor. In contrast to previous studies, we compared the expression profiles obtained from the two matched sample types, using the same protocol for both. Three protocols were tested on low initial amounts of RNA, as little as 100 ng, to represent the possibly limited availability of clinical samples. For two of the three protocols tested, poly(A) selection (mRNA-seq) and ribosomal-depletion, the total gene expression profiles of matched FF and FFPE pairs were highly correlated. For both protocols, differential gene expression between two FFPE samples was in agreement with their matched FF samples. Notably, although expression levels of FFPE samples by mRNA-seq were mainly represented by the 3'-end of the transcript, they yielded very similar results to those obtained by ribosomal-depletion protocol, which produces uniform coverage across the transcript. Further, focusing on clinically relevant genes, we showed that the high correlation between expression levels persists at higher resolutions. CONCLUSIONS:Using the poly(A) protocol for FFPE exhibited, unexpectedly, similar efficiency to the ribosomal-depletion protocol, with the latter requiring much higher (2-3 fold) sequencing depth to compensate for the relative low fraction of reads mapped to the transcriptome. The results indicate that standard poly(A)-based RNA sequencing of archived FFPE samples is a reliable and cost-effective alternative for measuring mRNA-seq on FF samples. Expression profiling of FFPE samples by mRNA-seq can facilitate much needed extensive retrospective clinical genomic studies.

Dataset Information

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.

Publications

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.

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