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CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities.

TitleCODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities.
Publication TypeJournal Article
Year of Publication2015
AuthorsSánchez-Castillo, M., Ruau D., Wilkinson A. C., Ng F. S. L., Hannah R., Diamanti E., Lombard P., Wilson N. K., & Göttgens B.
JournalNucleic Acids Res
Volume43
IssueDatabase issue
PaginationD1117-23
Date Published2015 Jan
ISSN1362-4962
KeywordsAnimals, Chromatin Immunoprecipitation, Databases, Genetic, Embryonic Stem Cells, Hematopoiesis, Hematopoietic Stem Cells, High-Throughput Nucleotide Sequencing, Histones, Humans, Internet, Mice, Sequence Analysis, DNA, Sequence Analysis, RNA, Software
Abstract

CODEX (http://codex.stemcells.cam.ac.uk/) is a user-friendly database for the direct access and interrogation of publicly available next-generation sequencing (NGS) data, specifically aimed at experimental biologists. In an era of multi-centre genomic dataset generation, CODEX provides a single database where these samples are collected, uniformly processed and vetted. The main drive of CODEX is to provide the wider scientific community with instant access to high-quality NGS data, which, irrespective of the publishing laboratory, is directly comparable. CODEX allows users to immediately visualize or download processed datasets, or compare user-generated data against the database's cumulative knowledge-base. CODEX contains four types of NGS experiments: transcription factor chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq), histone modification ChIP-Seq, DNase-Seq and RNA-Seq. These are largely encompassed within two specialized repositories, HAEMCODE and ESCODE, which are focused on haematopoiesis and embryonic stem cell samples, respectively. To date, CODEX contains over 1000 samples, including 221 unique TFs and 93 unique cell types. CODEX therefore provides one of the most complete resources of publicly available NGS data for the direct interrogation of transcriptional programmes that regulate cellular identity and fate in the context of mammalian development, homeostasis and disease.

DOI10.1093/nar/gku895
Alternate JournalNucleic Acids Res.
PubMed ID25270877
PubMed Central IDPMC4384009
Grant List097922/Z/11/Z / / Wellcome Trust / United Kingdom
100140/Z/12/Z / / Wellcome Trust / United Kingdom
BB/I00050X/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
G0900951 / / Medical Research Council / United Kingdom
g0900951 / / Medical Research Council / United Kingdom

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