R3TH3J last accessed: 2022-11-04

codex_ngs
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:49.057732

Other names: Codex, A comprehensive and functional compendium of Next Generation Sequencing experiments., codex_ngs

ChIP-Seq, RNA-Seq and DNase-Seq data for haematopoietic and embryonic stem cells

Webpage:

http://codex.stemcells.cam.ac.uk/

Licence:

Name: Public Domain
URL: http://codex.stemcells.cam.ac.uk/doc_pipeline.php

Publications:

Publications
More detailed information about this field from each metasource.

CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities
PMID: 25270877
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:49.057732

http://dx.doi.org/10.1093/nar/gku895
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities PubMed citations: 72.

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

Structure, function, and evolution of plant ADP-glucose pyrophosphorylase. PMID:35006475
A bipartite element with allele-specific functions safeguards DNA methylation imprints at the Dlk1-Dio3 locus. PMID:34710357
Comprehensive multi-omics integration identifies differentially active enhancers during human brain development with clinical relevance. PMID:34663447
Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR. PMID:34530905
Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation. PMID:34493871
Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. PMID:34155196
A comprehensive survey of regulatory network inference methods using single cell RNA sequencing data. PMID:34020546
Sex-specific DNA methylation differences in Alzheimer's disease pathology. PMID:33902726
A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells. PMID:33712417
Insights into the genomic repertoire of Aquimarina litoralis CCMR20, a symbiont of coral Mussismilia braziliensis. PMID:33675372
Human DNA methylation signatures differentiate persistent from resolving MRSA bacteremia. PMID:33649198
Identification and Characterisation of Putative Enhancer Elements in Mouse Embryonic Stem Cells. PMID:33623376
Metabolic control of DNA methylation in naive pluripotent cells. PMID:33526924
Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells. PMID:33253153
Interactions between lineage-associated transcription factors govern haematopoietic progenitor states. PMID:33103827
Reference-free deconvolution, visualization and interpretation of complex DNA methylation data using DecompPipeline, MeDeCom and FactorViz. PMID:32978601
Chromatin accessibility mapping of the striatum identifies tyrosine kinase FYN as a therapeutic target for heroin use disorder. PMID:32929078
COCOA: coordinate covariation analysis of epigenetic heterogeneity. PMID:32894181
Circadian rhythm influences induction of trained immunity by BCG vaccination. PMID:32692732
The transcriptional regulator ZNF398 mediates pluripotency and epithelial character downstream of TGF-beta in human PSCs. PMID:32398665
An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis. PMID:32132109
Informatics Approaches for Harmonized Intelligent Integration of Stem Cell Research. PMID:32099411
Chromatin mapping and single-cell immune profiling define the temporal dynamics of ibrutinib response in CLL. PMID:31996669
ChIPSummitDB: a ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them. PMID:31942977
A comprehensive resource for retrieving, visualizing, and integrating functional genomics data. PMID:31818883
Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells. PMID:31769130
Systematic characterization of BAF mutations provides insights into intracomplex synthetic lethalities in human cancers. PMID:31427792
Integrative Approaches to Cancer Immunotherapy. PMID:31311655
KLF4 protein stability regulated by interaction with pluripotency transcription factors overrides transcriptional control. PMID:31221664
Risk variants disrupting enhancers of TH1 and TREG cells in type 1 diabetes. PMID:30910956
LSD1 inhibition by tranylcypromine derivatives interferes with GFI1-mediated repression of PU.1 target genes and induces differentiation in AML. PMID:30679800
A common molecular logic determines embryonic stem cell self-renewal and reprogramming. PMID:30482756
Insights into mammalian transcription control by systematic analysis of ChIP sequencing data. PMID:30453943
Causal Transcription Regulatory Network Inference Using Enhancer Activity as a Causal Anchor. PMID:30445760
Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. PMID:30033119
LincU Preserves Naïve Pluripotency by Restricting ERK Activity in Embryonic Stem Cells. PMID:30017820
LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis. PMID:29878235
Exit from Naive Pluripotency Induces a Transient X Chromosome Inactivation-like State in Males. PMID:29804891
KLF4 Nuclear Export Requires ERK Activation and Initiates Exit from Naive Pluripotency. PMID:29526737
Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition. PMID:29514091
Dynamics of promoter bivalency and RNAP II pausing in mouse stem and differentiated cells. PMID:29458328
STAT5BN642H is a driver mutation for T cell neoplasia. PMID:29200404
StemMapper: a curated gene expression database for stem cell lineage analysis. PMID:29045725
An extended model for culture-dependent heterogenous gene expression and proliferation dynamics in mouse embryonic stem cells. PMID:28794899
Genome-wide association study of red blood cell traits in Hispanics/Latinos: The Hispanic Community Health Study/Study of Latinos. PMID:28453575
DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma. PMID:28134926
Biological Databases for Hematology Research. PMID:27965103
Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes. PMID:27895109
A graphical model approach visualizes regulatory relationships between genome-wide transcription factor binding profiles. PMID:27780826
Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data. PMID:27551778
Specification of tissue-resident macrophages during organogenesis. PMID:27492475
Sall4 controls differentiation of pluripotent cells independently of the Nucleosome Remodelling and Deacetylation (NuRD) complex. PMID:27471257
Resolving early mesoderm diversification through single-cell expression profiling. PMID:27383781
Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data. PMID:27378302
Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype-specific epigenome signatures and transcription regulatory networks. PMID:27346425
Systematic identification of gene family regulators in mouse and human embryonic stem cells. PMID:27084933
Finding partners to play the music of regulation. PMID:27034416
Stat3 promotes mitochondrial transcription and oxidative respiration during maintenance and induction of naive pluripotency. PMID:26903601
An experimentally validated network of nine haematopoietic transcription factors reveals mechanisms of cell state stability. PMID:26901438
Convergence of cMyc and β-catenin on Tcf7l1 enables endoderm specification. PMID:26675138
SBR-Blood: systems biology repository for hematopoietic cells. PMID:26590403
CpG island erosion, polycomb occupancy and sequence motif enrichment at bivalent promoters in mammalian embryonic stem cells. PMID:26582124
LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor. PMID:26508757
BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis. PMID:26507857
Epigenetic program and transcription factor circuitry of dendritic cell development. PMID:26476451
The LMO2 -25 Region Harbours GATA2-Dependent Myeloid Enhancer and RUNX-Dependent T-Lymphoid Repressor Activity. PMID:26161748
Genome-scale definition of the transcriptional programme associated with compromised PU.1 activity in acute myeloid leukaemia. PMID:26126967
Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility. PMID:25984238
Web resources for stem cell research. PMID:25701763
Decoding the regulatory network of early blood development from single-cell gene expression measurements. PMID:25664528
A Sox2 distal enhancer cluster regulates embryonic stem cell differentiation potential. PMID:25512558
Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells. PMID:25428352
http://dx.doi.org/10.1093/nar/gku895

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microarray data and other gene expression databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

chip-seq
metasource: re3data.org
version: re3data.org: Codex; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3TH3J last accessed: 2022-11-04

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:49.057732

dnase-seq
metasource: re3data.org
version: re3data.org: Codex; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3TH3J last accessed: 2022-11-04

rna-seq
metasource: re3data.org
version: re3data.org: Codex; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3TH3J last accessed: 2022-11-04

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:49.057732

bioinformatics
metasource: re3data.org
version: re3data.org: Codex; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3TH3J last accessed: 2022-11-04

embryonic systems
metasource: re3data.org
version: re3data.org: Codex; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3TH3J last accessed: 2022-11-04

haematopoiesis
metasource: re3data.org
version: re3data.org: Codex; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3TH3J last accessed: 2022-11-04

next generation sequencing ngs
metasource: re3data.org
version: re3data.org: Codex; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3TH3J last accessed: 2022-11-04

stem cell
metasource: re3data.org
version: re3data.org: Codex; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3TH3J last accessed: 2022-11-04

sequencing
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:49.057732

regenerative medicine
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:49.057732

microarray data and other gene expression chip-seq dnase-seq rna sequence bioinformatics embryonic systems haematopoiesis next generation sequencing ngs stem cell sequencing regenerative medicine

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RNAi codex

LifeMap Discovery

Minimum Information for Reporting Next Generation Sequencing Genotyping

Stem Cell Commons

CistromeDB

UK Stem Cell Bank

LINCS Extended Metadata Standard: Embryonic Stem Cells

ESCDb

ChIP-Seq Transcription Factor Data

National Stem Cell Resource Bank

NGSmethDB

Human Pluripotent Stem Cell Registry

NGS ontology

Ontology of RNA Sequencing

BloodExpress

STEMFORMATICS

Integrated Collection Stem Cell Bank

GeneTrap

Stem Cell Discovery Engine

LINCS Extended Metadata Standard: Induced Pluripotent Stem Cells