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Series GSE187332 Query DataSets for GSE187332
Status Public on Sep 13, 2022
Title Decay of heterochromatin domains at selective gene loci in aging mouse brain cells
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Other
Summary Aging is characterized by a progressive decline of organismal function and increase in vulnerability to diseases. Loss of heterochromatin during aging has been observed in a variety of organisms, however, understanding its role in aging-related phenotypes has been limited by the lack of information about the specific cell types and gene loci affected by this type of epigenetic changes. To address this bottleneck, we probed dynamic changes in chromatin landscape at single cell resolution in the forebrain, hippocampus, heart, skeletal muscle and bone marrows from 3-month, 10-month and 18-month-old mice, and characterized age-associated changes in chromatin accessibility at over 300,000 candidate regulatory elements across 34 major cell types. We report that excitatory neurons displayed profound changes in a specific set of heterochromatin domains during aging, evidenced by an increase in chromatin accessibility, a decrease in the heterochromatin marker H3K9me3, and de-repression of non-coding RNA species. These results suggest that heterochromatin maintenance are impaired in aging excitatory neurons, and this may be associated with increased repetitive element activity and neurodegenerative diseases.
 
Overall design We collected the dorsal hippocampus, frontal cortex, heart, leg muscles and bone marrow from male C57BL/6JN mice in three age groups, namely 3-month, 10-month, and 18-month, and performed single-nucleus ATAC-seq to profile open chormatin changes during aging. We also performed single-nucleus RNA-seq and paired-tag for H3K9me3 on dorsal hippocampus and frontal cortex.
 
Contributor(s) Zhang Y, Amaral ML, Ren B
Citation(s) 36207411
Submission date Nov 03, 2021
Last update date Oct 22, 2024
Contact name Bing Ren
E-mail(s) biren@ucsd.edu
Organization name University of California, San Diego
Street address 9500 Gilman Drive
City La Jolla
ZIP/Postal code 92093
Country USA
 
Platforms (4)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
GPL21626 NextSeq 550 (Mus musculus)
Samples (59)
GSM5667881 ATAC.DH.rep1
GSM5667882 ATAC.DH.rep2
GSM5667883 ATAC.FC.rep1
Relations
BioProject PRJNA777446
SRA SRP344344

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
GSE187332_BM.bigwigs.tar.gz 2.0 Gb (ftp)(http) TAR
GSE187332_DH.bigwigs.tar.gz 1.1 Gb (ftp)(http) TAR
GSE187332_DH_final_seurat_object.RDS.gz 435.3 Mb (ftp)(http) RDS
GSE187332_FC.bigwigs.tar.gz 1.5 Gb (ftp)(http) TAR
GSE187332_FC_final_seurat_object.RDS.gz 699.6 Mb (ftp)(http) RDS
GSE187332_HT.bigwigs.tar.gz 846.0 Mb (ftp)(http) TAR
GSE187332_LM.bigwigs.tar.gz 920.3 Mb (ftp)(http) TAR
GSE187332_barcodes_hiSeq2500.txt.gz 5.4 Kb (ftp)(http) TXT
GSE187332_barcodes_nextSeq_comp.txt.gz 5.4 Kb (ftp)(http) TXT
GSE187332_barcodes_nextSeq_comp_768_p7.txt.gz 6.9 Kb (ftp)(http) TXT
GSE187332_demultiplex.sample_info.txt.gz 323 b (ftp)(http) TXT
GSE187332_paired_tag_h3k9me3_bigwig.tar.gz 46.9 Mb (ftp)(http) TAR
GSE187332_paired_tag_rna_2020_09_21_remove_lowqual.RDS.gz 3.4 Gb (ftp)(http) RDS
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Processed data are available on Series record

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