NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE152020 Query DataSets for GSE152020
Status Public on Dec 15, 2020
Title Joint profiling of histone modifications and transcriptome in single cells from mouse brain
Organisms Homo sapiens; Mus musculus
Experiment type Other
Genome binding/occupancy profiling by high throughput sequencing
Summary Genome-wide profiling of histone modifications can reveal not only the location and activity state of regulatory elements, but also the regulatory mechanisms involved in cell-type-specific gene expression during development and disease pathology. Conventional assays to profile histone modifications in bulk tissue lack resolution due to the cellular heterogeneity. Here, we describe an ultra-high throughput method for single-cell joint profiling of histone modifications and transcriptome that could produce cell-type-resolved maps of chromatin state and transcriptome in complex tissues. We used this method to profile five histone modifications jointly with transcriptome in the adult mouse frontal cortex and hippocampus. Integrative analysis of the resulting maps identified distinct groups of genes subject to divergent epigenetic regulatory mechanisms. Our results demonstrate a general approach for comprehensive analysis of chromatin state and gene regulation in complex tissues and provide insights into the gene regulatory processes in major neuron cell types in the mouse.
 
Overall design Combined analysis of RNA and histone modifcations in single-cells.
 
Contributor(s) Zhu C, Ren B
Citation(s) 33589836
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 AG066018 Epigenome-based Cell Census and Regulatory Element Discovery in the Aging Mouse Brain THE SALK INSTITUTE FOR BIOLOGICAL STUDIES Bing Ren
K99 HG011483 Studying the mammalian regulatory circuits by developing single-cell multi-omics technologies Ludwig Institute for Cancer Research Ltd Chenxu Zhu
K99 CA252020 Dissecting the cis-regulatory roles of transposable elements in human cancers Ludwig Institute for Cancer Research Ltd Yanxiao Zhang
R01 MH112763 The role of DNA methylation dynamics and patterning in postmitotic neuronal-maturation THE SALK INSTITUTE FOR BIOLOGICAL STUDIES M MARGARITA BEHRENS
Submission date Jun 08, 2020
Last update date Feb 17, 2021
Contact name Zhu Chenxu
E-mail(s) cxzhu@pku.edu.cn, czhu@nygenome.org
Organization name New York Genome Center
Street address 101 Avenue of the Americas
City New York
State/province New York
ZIP/Postal code 10044
Country USA
 
Platforms (2)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (102)
GSM4598799 Bulk_HeLa_H3K4me1_rep1
GSM4598800 Bulk_HeLa_H3K4me1_rep2
GSM4598801 Bulk_HeLa_H3K27ac_rep1
Relations
BioProject PRJNA638110
SRA SRP266461

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
GSE152020_ChromHMM_output.tar.gz 33.1 Mb (ftp)(http) TAR
GSE152020_Paired-Tag_H3K27ac_DNA_filtered_matrix.tar.gz 46.5 Mb (ftp)(http) TAR
GSE152020_Paired-Tag_H3K27me3_DNA_filtered_matrix.tar.gz 17.2 Mb (ftp)(http) TAR
GSE152020_Paired-Tag_H3K4me1_DNA_filtered_matrix.tar.gz 102.6 Mb (ftp)(http) TAR
GSE152020_Paired-Tag_H3K4me3_DNA_filtered_matrix.tar.gz 23.1 Mb (ftp)(http) TAR
GSE152020_Paired-Tag_H3K9me3_DNA_filtered_matrix.tar.gz 73.0 Mb (ftp)(http) TAR
GSE152020_Paired-Tag_RNA_filtered_matrix.tar.gz 183.2 Mb (ftp)(http) TAR
GSE152020_Paired-Tag_bigwigs.tar.gz 2.0 Gb (ftp)(http) TAR
GSE152020_Paired-seq_DNA_filtered_matrix.tar.gz 123.8 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap