Jennifer VanOudenhove at UCONN HEALTH built this track, and the Cotney Lab is responsible for its contents.

Methods Description

Human embryonic heart tissue was collected, staged and provided by the Joint MRC/Wellcome Trust Human Developmental Biology Resource. Each embryon is identified by stage_ID. Tissues were flash frozen upon collection and stored at -80C. Fixed cells pellets were processed for ChIP as previously described (Cotney and Noonan, 2015).

ChIP-Seq Data Analysis

ChIP-seq libraries were sequenced using the NextSeq500/550 (Illumina). Fastq files were demultiplexed by barcode yielding Fastq files for each tissue replicate. Quality control was performed on ChIP-seq reads using FastQC (version [v.] 0.11.5) and MultiQC (v.1.1). Trimming for adapters, quality and length was performed using Trimmomatic (v.0.36) for single end data. ChIP-seq reads were aligned to the human genome (hg19) using Bowtie2 (v. 2.2.5) (Langmead and Salzberg, 2012). Fragment sizes of each library were estimated using PhantomPeakQualTools (v.1.14). We then generated p value-based signal tracks relative to appropriate input controls based on estimated library fragment size using MACS2 (2.1.1.20160309) Bedgraph files for all p-value signals from primary ChIP-Seq data were converted to 25 bp resolution and processed for model training and generation of imputed signals for all samples using ChromImpute (v1.0.3) as previously described (Ernst and Kellis, 2015). Resulting imputed signal tracks were converted to bigWig format for display in UCSC genome browser and converted for use with ChromHMM (v1.12) (Ernst and Kellis, 2012) , using ChromImpute’s ExportToChromHMM. Overall protocol was similar to what was used in (Wilderman, 2018).

Display conventions

Each track can be turned on/off individually. All tracks displays read density data in form of wiggle plots. For Histone/DNase, there also enrichment signal tracks using MACS based on pvalue or fold Change. There are also imputed signal for segmentations tracks.

Histone/DNase Signal/Peak Color Legend

Primary Core Marks segmentation

Auxiliary Core Marks + K27ac segmentation

Imputed Marks Segmentation

References

Cotney, J.L., and Noonan, J.P. (2015). Chromatin immunoprecipitation with fixed animal tissues and preparation for high-throughput sequencing. Cold Spring Harb Protoc 2015, 191–199.

Ernst, J., and Kellis, M. (2012). ChromHMM: automating chromatin-state discovery and characterization. Nat Methods 9, 215–216.

Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nature methods. 2012;9(4):357-359. doi:10.1038/nmeth.1923.

Wilderman, A., VanOudenhove, J., Kron, J., Noonan, J.P., and Cotney, J. (2018). High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development. Cell Rep. 23, 1581–1597.

Contacts

Please email Jennifer VanOudenhove or Justin Cotney for questions.