UCSD Human Reference Epigenome Mapping Project
The human embryonic stem cells (hESCs) are a unique model system for investigating the mechanisms of human development due to their ability to replicate indefinitely while retaining the capacity to differentiate into a host of functionally distinct cell types. In addition, these cells could be potentially used as therapeutic agents in regenerative medicine. Differentiation of hESCs involves selective activation or silencing of genes, a process controlled in part by the epigenetic state of the ce...
Provenance — who produced it, who reused it
Linked to 56 papers in the literature. Roles are inferred factual signals (who deposited the data vs who reused it), with counts — never a judgement about any author.
- Detection of differentially methylated regions from whole-genome... 2015 · 360 cites
- Integrative analysis of haplotype-resolved epigenomes across hum... 2015 · 236 cites
- Genomic modelling of the ESR1 Y537S mutation for evaluating func... 2016 · 178 cites
- lncRNA DIGIT and BRD3 protein form phase-separated condensates t... 2020 · 173 cites
- Single nucleus multi-omics identifies human cortical cell regula... 2022 · 162 cites
- Synergistic action of master transcription factors controls epit... 2016 · 126 cites
- Whole-genome bisulfite sequencing with improved accuracy and cos... 2018 · 126 cites
- Discovering high-resolution patterns of differential DNA methyla... 2013 · 123 cites
- A comprehensive comparison of tools for differential ChIP-seq an... 2016 · 123 cites
- Epigenomic landscape of human colorectal cancer unveils an aberr... 2021 · 116 cites
- The transcriptional regulator network of human inflammatory macr... 2016 · 113 cites
- MacroH2A1.1 and PARP-1 cooperate to regulate transcription by pr... 2014 · 111 cites
- Epigenomic footprints across 111 reference epigenomes reveal tis... 2015 · 100 cites
- Large DNA Methylation Nadirs Anchor Chromatin Loops Maintaining... 2020 · 95 cites
- tDRmapper: challenges and solutions to mapping, naming, and quan... 2015 · 86 cites
- Links between DNA methylation and nucleosome occupancy in the hu... 2017 · 84 cites
- The hyper-activation of transcriptional enhancers in breast canc... 2019 · 80 cites
- Alternative splicing links histone modifications to stem cell fa... 2018 · 73 cites
- Many chronological aging clocks can be found throughout the epig... 2021 · 71 cites
35 further papers cite this accession but reuse could not be confirmed.
Deep data QC
insufficient data to scoreStandardized, field-standard QC computed by touching the data — every metric states how it was obtained
The insufficient grade is a transparent weighted average. Each metric below scored from 0–100% against the published ChIP-seq thresholds, weighted by its importance; nothing is hidden or subjective.
measured = computed from the data · extrapolated/reported = derived or from the repository · dq-1.0
Scientific quality
Based on hands-on reproduction of the papers that use this dataset. A reproducible paper that stands on this data is positive evidence; a flagged one is a prompt to look closer — never a verdict on the dataset itself without the evidence.