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Nucleic Acids Res. 2017 Jan 4;45(D1):D658-D662. doi: 10.1093/nar/gkw983. Epub 2016 Oct 26.

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse.

Mei S1,2, Qin Q1,2, Wu Q1,2, Sun H2, Zheng R2, Zang C3,4, Zhu M2, Wu J5, Shi X2, Taing L3, Liu T6, Brown M4,7, Meyer CA8,4, Liu XS9,2,3,4.

Author information

1
Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University, Shanghai 200433, China.
2
Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
3
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA.
4
Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
5
MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing 100084, China.
6
Department of Biochemistry, University at Buffalo, Buffalo, NY 14214, USA.
7
Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA.
8
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA cliff@jimmy.harvard.edu.
9
Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University, Shanghai 200433, China xsliu@jimmy.harvard.edu.

Abstract

Chromatin immunoprecipitation, DNase I hypersensitivity and transposase-accessibility assays combined with high-throughput sequencing enable the genome-wide study of chromatin dynamics, transcription factor binding and gene regulation. Although rapidly accumulating publicly available ChIP-seq, DNase-seq and ATAC-seq data are a valuable resource for the systematic investigation of gene regulation processes, a lack of standardized curation, quality control and analysis procedures have hindered extensive reuse of these data. To overcome this challenge, we built the Cistrome database, a collection of ChIP-seq and chromatin accessibility data (DNase-seq and ATAC-seq) published before January 1, 2016, including 13 366 human and 9953 mouse samples. All the data have been carefully curated and processed with a streamlined analysis pipeline and evaluated with comprehensive quality control metrics. We have also created a user-friendly web server for data query, exploration and visualization. The resulting Cistrome DB (Cistrome Data Browser), available online at http://cistrome.org/db, is expected to become a valuable resource for transcriptional and epigenetic regulation studies.

PMID:
27789702
PMCID:
PMC5210658
DOI:
10.1093/nar/gkw983
[Indexed for MEDLINE]
Free PMC Article

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