SERIES = GSE106688
Series_title = Dynamic reorganization of nuclear architecture during human cardiogenesis [RNA-seq]
Series_geo_accession = GSE106688
Series_status = Public on Jan 04 2018
Series_submission_date = Nov 08 2017
Series_last_update_date = Aug 20 2018
Series_summary = While chromosomal architecture varies among cell types, little is known about how this organization is established or its role in development. We integrated Hi-C, RNA-seq and ATAC-seq during cardiac differentiation from human pluripotent stem cells to generate a comprehensive profile of chromosomal architecture. We identified active and repressive domains that are dynamic during cardiogenesis and recapitulate in vivo cardiomyocytes. During differentiation, heterochromatic regions condense in cis. In contrast, many cardiac-specific genes, such as TTN (titin), transition to an active compartment coincident with upregulation. Moreover, we identify a network of genes, including TTN, that share the heart-specific splicing factor, RBM20, and become associated in trans during differentiation, suggesting the existence of a 3D nuclear splicing factory. Our results demonstrate both the dynamic nature in nuclear architecture and provide insights into how developmental genes are coordinately regulated.
Series_overall_design = Hi-C, RNA-seq and ATAC-seq analysis of four stages of human pluripotent stem cell differentiation to cardiomyocytes, including stem cell, mesoderm, cardiac progenitor, and cardiomyocyte, with two biological replicates of each condition. Hi-C and RNA-seq analysis of two biological replicates fetal heart samples.
Series_type = Expression profiling by high throughput sequencing
Series_contributor = Paul,A,Fields
Series_contributor = Charles,E,Murry
Series_sample_id = GSM2845458
Series_sample_id = GSM2845459
Series_sample_id = GSM2845460
Series_sample_id = GSM2845461
Series_sample_id = GSM2845462
Series_sample_id = GSM2845463
Series_sample_id = GSM2845464
Series_sample_id = GSM2845465
Series_sample_id = GSM2845466
Series_sample_id = GSM2845467
Series_contact_name = Charles,,Murry
Series_contact_email = murry@uw.edu
Series_contact_department = Institute for Stem Cell and Regenerative Medicine
Series_contact_institute = University of Washington
Series_contact_address = 850 Republican St
Series_contact_city = Seattle
Series_contact_state = WA
Series_contact_zip/postal_code = 98109
Series_contact_country = USA
Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106688/suppl/GSE106688_cuffdiff_gene_exp.diff.gz
Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106688/suppl/GSE106688_genes.count_table.txt.gz
Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106688/suppl/GSE106688_genes.fpkm_table.txt.gz
Series_citation = DOI: https://doi.org/10.1101/222877
Series_platform_id = GPL18573
Series_platform_organism = Homo sapiens
Series_platform_taxid = 9606
Series_sample_organism = Homo sapiens
Series_sample_taxid = 9606
Series_relation = SubSeries of: GSE106690
Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA417683
Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP124631
