# Core B - Epigenomics Core

> **NIH NIH P01** · UNIVERSITY OF CALIFORNIA, SAN DIEGO · 2021 · $163,305

## Abstract

PROJECT SUMMARY – Core B: Epigenomics
The epigenetic modifications found in chromatin (DNA methylation and post-translational modifications of
histones) are involved in gene regulation during development and differentiation. Core B will generate
epigenomics data from massive parallel, multi-omic sequencing from human and mouse and xenopus
developing neural tube. The Core will identify gene regulatory elements and epigenomic variants having the
potential to cause or influence phenotypes. The Program PI and Director of Core B have worked together
extensively in the past with great success producing significant mouse neural tube epigenomic data. Dr. Ecker
has worked broadly in the area of genomics and epigenomics and in the development methodologies employing
multi-modal ‘multi-omics’ techniques for generation multiple types of NGS datasets from single cells. The data
generated from Core B, as well as imported from Project I, II and III, will be delivered to Core C for extraction of
results which will be delivered to each of the Projects for further validation. These goals will be accomplished by
developing the key pipelines of Core B that involve data production, and analysis: 1] Bulk whole genome
bisulfite sequencing (WGBS) Pipeline. The Ecker lab published the first human methylome and thus has
significant expertise in the workflow for data production. Our data workflow was established, and standard
operating procedures developed and adopted, by the ENCODE project and will take advantage of the same
features of our WGBS workflow that has made it successful for that effort. 2] Single cell methylome
sequencing (snmC-seq) pipeline. The methods for production and analysis of single cell methylome data
snmC-seq2 and more recently snmC-seq3, were established and standard operating procedures develop for the
NIH BRAIN initiative. 3] Multi-omics analysis combining two different NGS datasets measured from single
cells. These include snMethyl-3C-seq, snPaired-seq and snMethyl-HiC. The Epigenomics Core and the
Bioinformatics Core will work together to perform analysis of all epigenomic data produced by Core B, will work
with existing pipelines or create new pipelines as need demands, and will share data the Projects I, II and III. We
anticipate that 25,000 single cell methylomes/yr will be generated, along with detailed analyses. Data processing
quantification of genome wide unmethylated and methylated cytosine base calls are generated using an
algorithm that we previously developed called Methylpy. Clustering of snmC-seq2 data for cell type classification
will utilize both mCG and mCH patterns to effectively classify both neuronal and non-neuronal cell types in the
developing neural tube. These analyses will result in a prioritized list of candidate marker features (genes and
predicted regulatory elements) that will be provided to the project PIs for further examination and validation.

## Key facts

- **NIH application ID:** 10154463
- **Project number:** 1P01HD104436-01
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN DIEGO
- **Principal Investigator:** Joseph R Ecker
- **Activity code:** P01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $163,305
- **Award type:** 1
- **Project period:** 2020-12-01 → 2025-11-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10154463

## Citation

> US National Institutes of Health, RePORTER application 10154463, Core B - Epigenomics Core (1P01HD104436-01). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10154463. Licensed CC0.

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