CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities.
Τίτλος | CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities. |
Publication Type | Journal Article |
Year of Publication | 2015 |
Authors | Sánchez-Castillo, M., Ruau D., Wilkinson A. C., Ng F. S. L., Hannah R., Diamanti E., Lombard P., Wilson N. K., & Göttgens B. |
Journal | Nucleic Acids Res |
Volume | 43 |
Issue | Database issue |
Pagination | D1117-23 |
Date Published | 2015 Jan |
ISSN | 1362-4962 |
Λέξεις κλειδιά | Animals, 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. |
DOI | 10.1093/nar/gku895 |
Alternate Journal | Nucleic Acids Res. |
PubMed ID | 25270877 |
PubMed Central ID | PMC4384009 |
Grant List | 097922/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 |