{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T13:41:44Z","timestamp":1760708504255},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Chromatin immunoprecipitation and DNase I hypersensitivity assays with high-throughput sequencing have greatly accelerated the understanding of transcriptional and epigenetic regulation, although data reuse for the community of experimental biologists has been challenging. We created a data portal CistromeFinder that can help query, evaluate and visualize publicly available Chromatin immunoprecipitation and DNase I hypersensitivity assays with high-throughput sequencing data in human and mouse. The database currently contains 6378 samples over 4391 datasets, 313 factors and 102 cell lines or cell populations. Each dataset has gone through a consistent analysis and quality control pipeline; therefore, users could evaluate the overall quality of each dataset before examining binding sites near their genes of interest. CistromeFinder is integrated with UCSC genome browser for visualization, Primer3Plus for ChIP-qPCR primer design and CistromeMap for submitting newly available datasets. It also allows users to leave comments to facilitate data evaluation and update.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/cistrome.org\/finder.<\/jats:p>\n               <jats:p>Contact: \u00a0xsliu@jimmy.harvard.edu or henry_long@dfci.harvard.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt135","type":"journal-article","created":{"date-parts":[[2013,3,19]],"date-time":"2013-03-19T00:40:12Z","timestamp":1363653612000},"page":"1352-1354","source":"Crossref","is-referenced-by-count":16,"title":["CistromeFinder for ChIP-seq and DNase-seq data reuse"],"prefix":"10.1093","volume":"29","author":[{"given":"Hanfei","family":"Sun","sequence":"first","affiliation":[{"name":"1 Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 20092, China, 2Center for Functional Cancer Epigenetics, Dana-Faber Cancer Institute, Boston, MA 02215, USA, 3Department of Biostatistics and Computational Biology, Dana-Faber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA, 4Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute and 5Department of Medicine, Brigham and Women\u2019s Hospital and Harvard Medical School, Boston, MA 02215, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bo","family":"Qin","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 20092, China, 2Center for Functional Cancer Epigenetics, Dana-Faber Cancer Institute, Boston, MA 02215, USA, 3Department of Biostatistics and Computational Biology, Dana-Faber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA, 4Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute and 5Department of Medicine, Brigham and Women\u2019s Hospital and Harvard Medical School, Boston, MA 02215, 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Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA, 4Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute and 5Department of Medicine, Brigham and Women\u2019s Hospital and Harvard Medical School, Boston, MA 02215, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qixuan","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 20092, China, 2Center for Functional Cancer Epigenetics, Dana-Faber Cancer Institute, Boston, MA 02215, USA, 3Department of Biostatistics and Computational Biology, Dana-Faber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA, 4Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute and 5Department of Medicine, Brigham and Women\u2019s Hospital and Harvard Medical School, Boston, MA 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