Organized By Mark Tracks

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Cotney Heart hub organized by mark tracks

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All
	ChromHMM	Chromatin State tracks from Heart Data
	DNase	DNase tracks from Heart Data
	H2A.Z	H2A.Z tracks from Heart Data
	H3K27ac	H3K27ac tracks from Heart Data
	H3K27me3	H3K27me3 tracks from Heart Data
	H3K36me3	H3K36me3 tracks from Heart Data
	H3K4me1	H3K4me1 tracks from Heart Data
	H3K4me2	H3K4me2 tracks from Heart Data
	H3K4me3	H3K4me3 tracks from Heart Data
	H3K79me2	H3K79me2 tracks from Heart Data
	H3K9ac	H3K9ac tracks from Heart Data
	H3K9me3	H3K9me3 tracks from Heart Data
	H4K20me1	H4K20me1 tracks from Heart Data

Assembly: Human Dec. 2013 (GRCh38/hg38)

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

DNase - DNase
H2A.Z - H2A.Z
H3K27ac - H3K27ac
H3K27me3 - H3K27me3
H3K36me3 - H3K36me3
H3K4me1 - H3K4me1
H3K4me2 - H3K4me2
H3K4me3 - H3K4me3
H3K79me2 - H3K79me2
H3K9ac - H3K9ac
H3K9me3 - H3K9me3
H4K20me1 - H4K20me1

Primary Core Marks segmentation

State 1 - Red - TssA (Active_TSS)
State 2 - OrangeRed - TssAFlnk (Flanking_Active_TSS)
State 3 - LimeGreen - TxFlnk (Transcr_at_gene_5_and_3primer)
State 4 - Green - Tx (Strong_transcription)
State 5 - DarkGreen - TxWk (Weak_transcription)
State 6 - GreenYellow - EnhG (Genic_enhancers)
State 7 - Yellow - Enh (Enhancers)
State 8 - MediumAquamarine - ZNF/Rpts (ZNF_genes&repeats)
State 9 - PaleTurquoise - Het (Heterochromatin)
State 10 - IndianRed - TssBiv (Bivalent/Poised_TSS)
State 11 - DarkSalmon - BivFlnk (Flanking_Bivalent_TSS/Enh)
State 12 - DarkKhaki - EnhBiv (Bivalent_Enhancer)
State 13 - Silver - ReprPC (Repressed_PolyComb)
State 14 - Gainsboro - ReprPCWk (Weak_Repressed_PolyComb)
State 15 - White - Quies (Quiescent/Low)

Auxiliary Core Marks + K27ac segmentation

State 1 - Red - TssA (Active_TSS)
State 2 - Orange_Red - TssFlnk (Flanking_TSS)
State 3 - Orange_Red - TssFlnkU (Flanking_TSS_Upstream)
State 4 - Orange_Red - TssFlnkD (Flanking_TSS_Downstream)
State 5 - Green - Tx (Strong_transcription)
State 6 - DarkGreen - TxWk (Weak_transcription)
State 7 - GreenYellow - EnhG1 (Genic_enhancer1)
State 8 - GreenYellow - EnhG2 (Genic_enhancer2)
State 9 - Orange - EnhA1 (Active_Enhancer1)
State 10 - Orange - EnhA2 (Active_Enhancer2)
State 11 - Yellow - EnhWk (Weak_Enhancer)
State 12 - Medium_Aquamarine - ZNF/Rpts (ZNF_genes&repeats)
State 13 - PaleTurquoise - Het (Heterochromatin)
State 14 - IndianRed - TssBiv (Bivalent/Poised_TSS)
State 15 - DarkKhaki - EnhBiv (Bivalent_Enhancer)
State 16 - Silver - ReprPC (Repressed_PolyComb)
State 17 - Gainsboro - ReprPCWk (Weak_Repressed_PolyComb)
State 18 - White - Quies (Quiescent/Low)

Imputed Marks Segmentation

State 1 - Red - TssA (Active TSS)
State 2 - Orange Red - PromU (Promoter Upstream TSS)
State 3 - Orange Red - PromD1 (Promoter Downstream TSS with DNase)
State 4 - Orange Red - PromD2 (Promoter Downstream TSS)
State 5 - Green - Tx5' (Transcription 5')
State 6 - Green - Tx (Transcription)
State 7 - Green - Tx3' (Transcription 3')
State 8 - Light Green - TxWk (Weak transcription)
State 9 - GreenYellow - TxReg (Transcription Regulatory)
State 10 - GreenYellow - TxEnh5' (Transcription 5' Enhancer)
State 11 - GreenYellow - TxEnh3' (Transcription 3' Enhancer)
State 12 - GreenYellow - TxEnhW (Transcription Weak Enhancer)
State 13 - Orange - EnhA1 (Active Enhancer 1)
State 14 - Orange - EnhA2 (Active Enhancer 2)
State 15 - Orange - EnhAF (Active Enhancer Flank)
State 16 - Yellow - EnhW1 (Weak Enhancer 1)
State 17 - Yellow - EnhW2 (Weak Enhancer 2)
State 18 - Yellow - EnhAc (Enhancer Acetylation Only)
State 19 - Light Yellow - DNase (DNase only)
State 20 - Medium Aquamarine - ZNF/Rpts (ZNF genes & repeats)
State 21 - PaleTurquoise - Het (Heterochromatin)
State 22 - Light Purple - PromP (Poised Promoter)
State 23 - Purple - PromBiv (Bivalent Promoter)
State 24 - Silver - ReprPC (Repressed PolyComb)
State 25 - White - Quies (Quiescent/Low)

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.