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Series GSE130096 Query DataSets for GSE130096
Status Public on May 01, 2019
Title ATAC-Me captures spatiotemporal dynamics of DNA methylation across the chromatin accessible genome
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary DNA methylation of enhancers is dynamic, cell-type specific, and vital for cell fate progression. However, current models inadequately define its role within the highly ordered steps of gene regulation. An analysis of independent datasets show an unanticipated overlap between DNA methylation and chromatin accessibility at enhancers of steady state stem cells, suggesting that two opposing features might exist concurrently. To temporally define the relationship between these two events, we developed ATAC-Me, which probes accessibility and methylation from a single library preparation. We identified waves of accessibility, both transient and persistent, occurring rapidly across thousands of myeloid enhancers as monocyte cells transition to a macrophage state. Persistent methylation states were observed at a majority of these sites while transcriptional responses of nearby genes tracked closely with accessibility. ATAC-Me uncovers a significant disconnect between chromatin accessibility, DNA methylation status, and gene activity. This unexpected observation highlights the value of ATAC-Me in constructing precise molecular timelines for understanding the role of DNA methylation in gene regulation.
Overall design RNA-seq and ATAC-Me-seq libraries were generated for 5 time points of PMA stimulated THP-1 monocytes (0, 0.5, 1, 2, 24hrs), in biological replicate. Standard ATAC-seq libraries were generated at two time points (0, 24hr) in biological replicate. WGBS libraries were generated at two time points (0, 24 hr).
Contributor(s) Barnett KR, Hodges EC
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Submission date Apr 19, 2019
Last update date May 03, 2019
Contact name Emily Hodges
Organization name Vanderbilt University
Department Biochemistry
Lab Hodges
Street address 2212 Garland Ave.
City Nashville
State/province TN
ZIP/Postal code 37232
Country USA
Platforms (4)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL20795 HiSeq X Ten (Homo sapiens)
Samples (26)
GSM3731833 ATACMe_THP1_0hrPMA_rep1
GSM3731834 ATACMe_THP1_2hrPMA_rep1
GSM3731835 ATACMe_THP1_24hrPMA_rep1
BioProject PRJNA533829
SRA SRP193115

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Supplementary file Size Download File type/resource
GSE130096_RAW.tar 1.6 Gb (http)(custom) TAR (of BROADPEAK, TXT)
GSE130096_THP1_PMAtimecourse_RNAseq_DESeq2_NormalizedCountsTable.txt.gz 1.9 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file

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