EXPERIMENT_TITLE: GSM3263088: day00.HERV1.KO.HiC.Rep2; 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: day00.HERV1.KO.HiC.Rep2
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 HERV1-KO"}]
Pool_Member_@attributes_sample_title: day00.HERV1.KO.HiC.Rep2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: day00.HERV1.KO.HiC.Rep2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR7506665", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7506665/SRR7506665", "size": "27009551822", "date": "2018-07-12 15:11:43", "md5": "4ec68392cff90ef2ee21ef2a8d4117e0", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR7506665.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR007/506/SRR7506665.sralite.1", "size": "14933117030", "date": "2021-06-16 05:17:16", "md5": "3aeb1f152a4dbc4af8f94017865ac073", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "RH_351_R2.fastq.bz2", "size": "15825301582", "date": "2020-02-22 17:47:55", "md5": "ae4b06dcc9dff1aa3438840d87a1184e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "RH_351_R1.fastq.bz2", "size": "13428849392", "date": "2020-02-22 13:46:01", "md5": "361dd195f720e32d2697b0d4bd501c71", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]