EXPERIMENT_TITLE: GSM3734960: HERV2-ins-clone2.HiC.Rep1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Briefly, 2 million cells were cross-linked with 1% formaldehyde for 10min at RT and reaction was quenched using 125 mM of Glycine for 5 min at RT. Nuclei were isolated and directly applied for digestion using 4 cutter restriction enzyme MboI (NEB) at 37 °C o/n. All libraries were constructed using standard illumina TruSeq LT library prep.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: The three-dimensional chromatin architecture plays a critical role in the establishment of cell-type-specific gene regulatory networks in eukaryotic cells.  How pluripotent stem cells (PSC) alter their chromatin architecture to direct cell fate specification remains to be elucidated.  Here, using a human PSC cardiomyocyte differentiation model, we analyze the dynamic reorganization of chromatin structure and gene regulatory networks during key transitional stages of cardiomyocyte development.  We show that many human PSC-specific topologically associating domains (TADs) are driven by active transcription of the primate-specific retroviruses HERVH.  These HERVH are silenced at the earliest stages of differentiation , accompanied by loss of TAD borders and subsequent merging of cognate TADs during differentiation, which leads to repression of gene expression within these domains .  In line with these findings, deletion of select HERVHs results in elimination of corresponding TAD boundaries in human PSCs. We further discovered developmental stage-specific chromatin loop interactions that predict target genes of cardiac-related trait/disease non-coding genetic variants.  Overall, our results not only highlight a novel role for endogenous retroviruses in shaping species-specific PSC chromatin architecture during evolution but also provide a genomic blueprint for understanding the impact of non-coding variants in congenital and adult heart disease/traits. Overall design: hESCs are differentiated into cardiomyocyte. We used a transgenic H9 hESC line expressing a H2B-GFP fusion protein under control of the ventricular cardiomyocyte specific MYL2 promoter. We collected samples at six critical time points during differentiation: human embryonic stem cells (hESC) (Day 0), hESC mesodermal cells (Day 2), hESC-cardiac mesodermal cells (Day 5), hESC-cardiac progenitor cell (Day 7), hESC-primitive cardiomyocytes (Day 15) and hESC-ventricular cardiomyocytes (Day 80). We performed HiC, ATAC-seq, RNA-seq, and ChIP-seq for H3K27ac, H3K27me3, H3K4me1, H3K4me3, H3K9me3 and CTCF for every time point, each with two biological replicates. We also made CRISPR edited deletion at two HERV-H loci and performed RNA-seq and Hi-C, each with two replicates.
SAMPLE_TITLE: HERV2-ins-clone2.HiC.Rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Embryonic stem cell"}, {"TAG": "tissue", "VALUE": "Embryonic stem cell"}, {"TAG": "differentiation time", "VALUE": "day00"}, {"TAG": "genotype", "VALUE": "H9 MLC2v:H2B HERV2-ins-clone2"}]
Pool_Member_@attributes_sample_title: HERV2-ins-clone2.HiC.Rep1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HERV2-ins-clone2.HiC.Rep1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR8950087.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR008/950/SRR8950087.sralite.1", "size": "14585163113", "date": "2020-06-20 02:50:50", "md5": "539c67a5f43c2bc96a9fa3856f0e6d23", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR8950087", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8950087/SRR8950087", "size": "28411628353", "date": "2019-04-24 17:14:57", "md5": "787e2f2046b4aa5bd85ddbc94fab59d5", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "RH492_R2.fastq.bz2", "size": "16862554234", "date": "2020-01-24 21:47:49", "md5": "5d67239543994e522bd78ea63a7113fd", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "RH492_R1.fastq.bz2", "size": "13670166029", "date": "2020-01-25 04:33:16", "md5": "c6dd4fceef9174228372f0b39a1cff13", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]