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Protocols

CODEX specifications

Information


Unique identifier OMICS_05871
Name CODEX
Restrictions to use None
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Publication for CODEX

CODEX citations

 (7)
library_books

Dynamics of promoter bivalency and RNAP II pausing in mouse stem and differentiated cells

2018
BMC Dev Biol
PMCID: 5819258
PMID: 29458328
DOI: 10.1186/s12861-018-0163-7

[…] To investigate whether clusters were enriched for binding of specific transcription and epigenetic controllers, we calculated binding enrichment using the CODEX [] ChIP sequencing data compendium (see Methods). All clusters were significantly enriched (hypergeometric test - P value < 0.001) for at least one factor (Fig. ). Highly-active clusters 19, 21 […]

library_books

An extended model for culture dependent heterogenous gene expression and proliferation dynamics in mouse embryonic stem cells

2017
NPJ Syst Biol Appl
PMCID: 5543144
PMID: 28794899
DOI: 10.1038/s41540-017-0020-5

[…] otal) were then filtered to include only those that interact with the core pluripotency factors (i.e., Oct4, Sox2 and Nanog). This was done using an updated compendium for mESC transcription factors, CODEX,, based on chromatin immunoprecipitation (ChIP) for transcription factors and histone modifications coupled to deep sequencing (ChIP-Seq), DNase-Seq and RNA-Seq data sets (Supplementary Fig. ); […]

library_books

Genome wide association study of red blood cell traits in Hispanics/Latinos: The Hispanic Community Health Study/Study of Latinos

2017
PLoS Genet
PMCID: 5428979
PMID: 28453575
DOI: 10.1371/journal.pgen.1006760

[…] ells[, , ]. The ENCODE and BLUEPRINT datasets were accessed through the ENCODE analysis Hub and Blueprint Hub respectively via the UCSC genome browser[, ]. Datasets from Xu, et al, were accessed from codex (http://codex.stemcells.cam.ac.uk, last accessed Dec 2016)[, ]. To hypothesize likely mode of action via which the causal variants influence the trait, we report eQTL targets and or motifs disru […]

library_books

Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype specific epigenome signatures and transcription regulatory networks

2016
Nat Commun
PMCID: 5494194
PMID: 27346425
DOI: 10.1038/ncomms11938

[…] was performed on the significantly variable regions of each group using LOLA with its core databases: transcription factor binding sites from ENCODE, tissue clustered DNase hypersensitive sites, the CODEX database, UCSC Genome Browser annotation tracks, the Cistrome database and data from the BLUEPRINT project. Motif enrichment analysis was performed with the AME tool from the MEME suite using 25 […]

call_split

Epigenetic program and transcription factor circuitry of dendritic cell development

2015
Nucleic Acids Res
PMCID: 4787753
PMID: 26476451
DOI: 10.1093/nar/gkv1056
call_split See protocol

[…] m GSE21953, GSE31233, GSE21621 and GSE36104. The ChIP-seq data of Irf4, Irf8 and Stat3 in cDC and Irf8 and Tcf4 in pDC are from GSE36104, GSE53311, GSE27161, GSE62702, GSE43876 and GSE66899 (see also CODEX database ()).Short reads of the ChIP-seq experiments were aligned to the mouse reference genome (NCBI37/mm9) using Bowtie. The aligned ChIP-seq data sets of transcription factor PU.1 and the enh […]

library_books

Genome scale definition of the transcriptional programme associated with compromised PU.1 activity in acute myeloid leukaemia

2015
Leukemia
PMCID: 4705427
PMID: 26126967
DOI: 10.1038/leu.2015.172

[…] ifs (q-value⩽0.01) with ⩾5% peak coverage were reported. Geneset enrichment analyses were performed using Enrichr. ChIP-Seq peaks were compared with those of primary macrophages (GSM537983) using the Codex webtool. PU.1 target genes were used for unsupervised analysis of published expression arrays (GSE34723 (ref. ) and GSE6891 (ref. )) in R with the pvclust package. Heatmaps were generated using […]


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CODEX institution(s)
Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK; Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK

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