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Series GSE130711 Query DataSets for GSE130711
Status Public on Sep 09, 2019
Title Simultaneous profiling of 3D genome structure and DNA methylation in single human cells
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Other
Summary Dynamic 3D chromatin conformation is a critical mechanism for gene regulation during development and disease. Despite this, profiling of 3D genome structure from complex tissues with cell-type specific resolution remains challenging. Recent efforts have demonstrated that cell-type specific epigenomic features can be resolved in complex tissues using single-cell assays. However, it remains unclear whether single-cell
Chromatin Conformation Capture (3C) or Hi-C profiles can effectively identify cell types and reconstruct cell-type specific chromatin conformation maps. To address these challenges, we have developed single-nucleus methyl-3C sequencing (sn-m3C-seq) to capture chromatin organization and DNA methylation information and robustly
separate heterogeneous cell types. Applying this method to >4,200 single human brain prefrontal cortex cells, we reconstruct cell-type specific chromatin conformation maps from 14 cortical cell types. These datasets reveal the genome-wide association between cell-type specific chromatin conformation and differential DNA methylation, suggesting
pervasive interactions between epigenetic processes regulating gene expression.
 
Overall design Multi-omic method single-nucleus methyl-3C sequencing (sn-m3C) to profile chromatin conformation and DNA methylation from the same cell.
 
Contributor(s) Luo C, Lee D, Zhou J, Chandran S, Rivkin A, Bartlett A, Nery JR, Fitzpatrick C, O’Connor C, Dixon JR, Ecker JR
Citation(s) 31501549, 35419551
NIH grant(s)
Grant ID Grant title Affiliation Name
R21 HG009274 Multidimensional Epigenomic Single Cell Analyses THE SALK INSTITUTE FOR BIOLOGICAL STUDIES Joseph R Ecker
Submission date May 04, 2019
Last update date Feb 13, 2023
Contact name Joseph R Ecker
E-mail(s) ecker@salk.edu
Phone 8584534100
Organization name HHMI-Salk-Institute
Department Genomic Analysis Laboratory
Lab Ecker lab
Street address 10010 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platforms (2)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (4238)
GSM3748102 181218_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A10_AD001
GSM3748103 181218_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A10_AD004
GSM3748104 181218_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A10_AD006
Relations
BioProject PRJNA541105
SRA SRP195332

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE130711_RAW.tar 759.2 Gb (http)(custom) TAR (of TSV, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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