title: Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse.
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.
authors: Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University, Shanghai 200433, China.|Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
authors: Shenglin
authors: S
authors: Mei
authors: Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University, Shanghai 200433, China.|Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
authors: Qian
authors: Q
authors: Qin
authors: Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University, Shanghai 200433, China.|Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
authors: Qiu
authors: Q
authors: Wu
authors: Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
authors: Hanfei
authors: H
authors: Sun
authors: Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
authors: Rongbin
authors: R
authors: Zheng
authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA.|Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
authors: Chongzhi
authors: C
authors: Zang
authors: Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
authors: Muyuan
authors: M
authors: Zhu
authors: MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing 100084, China.
authors: Jiaxin
authors: J
authors: Wu
authors: Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
authors: Xiaohui
authors: X
authors: Shi
authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA.
authors: Len
authors: L
authors: Taing
authors: Department of Biochemistry, University at Buffalo, Buffalo, NY 14214, USA.
authors: Tao
authors: T
authors: Liu
authors: Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA.|Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA.
authors: Myles
authors: M
authors: Brown
authors: 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.|Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
authors: Clifford A
authors: CA
authors: Meyer
authors: Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University, Shanghai 200433, China xsliu@jimmy.harvard.edu.|Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.|Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA.|Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
authors: X Shirley
authors: XS
authors: Liu
mesh_terms: D000818:Animals; D042002:Chromatin Assembly and Disassembly; D047369:Chromatin Immunoprecipitation; D030541:Databases, Genetic; D044127:Epigenesis, Genetic; D057890:Epigenomics / Q000379:methods; D005786:Gene Expression Regulation; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D051379:Mice; D064878:Web Browser