Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Rapid Genome-Scale Mapping of Chromatin Accessibility in Tissue

ABSTRACT: Here we introduce a novel technique that specifically identifies Tissue Accessible Chromatin (TACh). The TACh method uses pulverized frozen tissue as starting material and employs one of the two robust endonucleases, Benzonase or Cyansase, which are fully active under a range of stringent conditions such as high levels of detergent and DTT. As a proof of principle we applied TACh to frozen mouse liver tissue. Combined with massive parallel sequencing TACh identifies accessible regions that are associated with euchromatic features and accessibility at transcriptional start sites correlates positively with levels of gene transcription. Idetification of accessible chromatin in forzen adult mouse liver tissue

ORGANISM(S): Mus musculus

SUBMITTER: Songjoon Baek

PROVIDER: E-GEOD-39982 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Rapid genome-scale mapping of chromatin accessibility in tissue.

Grøntved Lars L Bandle Russell R John Sam S Baek Songjoon S Chung Hye-Jung HJ Liu Ying Y Aguilera Greti G Oberholtzer Carl C Hager Gordon L GL Levens David D

Epigenetics & chromatin 20120626 1

<h4>Background</h4>The challenge in extracting genome-wide chromatin features from limiting clinical samples poses a significant hurdle in identification of regulatory marks that impact the physiological or pathological state. Current methods that identify nuclease accessible chromatin are reliant on large amounts of purified nuclei as starting material. This complicates analysis of trace clinical tissue samples that are often stored frozen. We have developed an alternative nuclease based proced ...[more]

PMID: 22734930

Similar Datasets

Project description:Background: The majority of multi-omics studies make use of adjacent fresh-frozen tissue pieces for different analyses. This approach however is not considering the intrinsic tissue heterogeneity and can lead to a biological mismatch of different omics layers. To overcome this limitation, we here propose an alternative approach where tissue is cryogenically pulverized and lyophilized, obtaining a homogenous tissue powder that can be used for subsequent omics studies. The purpose of this study was to investigate how omics analysis differ or coincide when comparing adjacent tissue slices to homogenized powder using three major mammalian organs from a wildtype mouse model. Methods: Healthy fresh-frozen and pulverized-lyophilized mouse tissue from brain, kidney, and liver was subjected to DNA methylation and genome sequencing (genomics), RNA sequencing (transcriptomics), protein (proteomics), and metabolite (metabolomics) analysis. Obtained analytical results were investigated by statistical and quality control measures, including dendrograms, correlation analysis, principal component analysis, RNA integrity, feature coverage, and energy charge estimation. Results: DNA methylation was not affected differently by the two different tissue processing methods. The RNA integrity obtained was comparable between fresh-frozen tissue slicing and pulverization-lyophilization. The coverage of gene transcripts, proteins, and metabolites was preserved similarly by both methodological approaches. Overall the pulverization-lyophilization approach resulted in a reduced heterogeneity between biological replicates. Conclusions: Cryogenically pulverized and lyophilized tissue preserves the most important cellular molecular features, such as RNA integrity, DNA methylation status, gene transcript, protein, and metabolite coverage. Therefore, it is a suitable alternative method for improved multi-omics analysis, providing reduced sample heterogeneity, beneficial for batch reproducibility, as well as easier transportation and storage conditions due to complete water removal.

Dataset Information

Rapid Genome-Scale Mapping of Chromatin Accessibility in Tissue

Publications

Rapid genome-scale mapping of chromatin accessibility in tissue.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets