Tools and Resources

Assay for transposase-accessible chromatin using sequencing (ATAC-seq), based on direct in vitro transposition of sequencing adaptors into native chromatin, is a rapid (<24 hr) and sensitive(<50,000 cells) method for integrative epigenomic analysis.

Learn more about the ATAC-seq protocol:
ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide

Join the forum for FAQ answers and feedback from the community of developers.

Domain-specific chromatin isolation by RNA purification (dChIRP) is a technique for dissecting the functional domains of a target RNA in situ. dChIRP can identify domain-level intramolecular and intermolecular RNA-RNA, RNA-protein, and RNA-DNA interactions, and maps the RNA’s genomic binding sites with high precision.

Learn more about dCHIRP:
In situ dissection of RNA functional subunits by domain-specific chromatin isolation by RNA purification (dChIRP)

Long-read sequencing one can often (i) cover the entire molecule, (ii) determine the allele it originated from, and (iii) record its entire exon-intron structure within a single read, thus producing a full-length, allele-specific view of an individual’s transcriptome.

Learn more about long single molecule sequencing

We have characterized the open chromatin and transcriptional landscapes in 13 cell types from healthy human blood and 3 cell types from human acute myeloid leukemia. GEO accession GSE75384 contains the ATAC-sequencing and RNA-sequencing data associated with this manuscript.

Additionally, we provide these data as a UCSC track hub and Washington University Epigenome browser session for visualization purposes. For UCSC Genome Browser, go to http://genome.ucsc.edu/cgi-bin/hgHubConnect, click on the "My Hubs" tab, and paste "https://s3-us-west-1.amazonaws.com/chang-public-data/2016_NatGen_ATAC-AML/hub.txt" into the URL box. Then click "Add Hub" and navigate to your region of interest. For Washington University Epigenome Browser, please click here

Please use the button link below to access the HiChIP Protocol resource document.

Please use the button link below to access the Omni-ATAC Protocol resource document.

The paper can be accessed via the link below:

http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4396.html

Please use the link listed below to access the Software:

Link to softwares scABC, PECA, Coupled NMF, and arcSV