|
| Status |
Public on May 07, 2021 |
| Title |
Decoding dynamic epigenetic landscapes in human oocytes using single-cell multi-omics sequencing |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
|
| Summary |
Developing female human germ cells undergo genome-wide epigenetic reprogramming, but de novo DNA methylation dynamics and their interplay with chromatin states and transcriptional activation in developing oocytes is poorly understood. Here, we developed a single-cell multi-omics sequencing method, scChaRM-seq, that enables simultaneous profiling of the DNA methylome, transcriptome, and chromatin accessibility in single human oocytes and ovarian somatic cells. We observed a global increase in DNA methylation during human oocyte growth that correlates with chromatin accessibility, whereas increases of DNA methylation at specific features were associated with active transcription. Integrated analyses of multi-omics data from humans and mice revealed species-specific gene expression, and promoter accessi- bility contributes to gene body methylation programs. Alu elements retained low DNA methylation levels and high accessibility in early growing oocytes and were located near developmental genes in humans and mice. Together, these findings show how scChaRM-seq can provide insight into DNA methylation pattern estab- lishment.
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| |
|
| Overall design |
953 single human oocytes and somatic cells were performed by scChaRM-seq. Only 899 single cells that passed through the quality control were uploaded.
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| |
|
| Contributor(s) |
Gu C, Yan R, Guo F |
| Citation(s) |
33957080 |
| |
| Submission date |
Jul 20, 2020 |
| Last update date |
Oct 28, 2021 |
| Contact name |
Fan Guo |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Zoology, Chinese Academy of Sciences
|
| Department |
The State Key Laboratory of Stem Cell and Reproductive Biology
|
| Lab |
Group of Reproductive Epigenetics
|
| Street address |
1 Beichen West Road, Chaoyang District
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
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| Platforms (1) |
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| Samples (941)
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| Relations |
| BioProject |
PRJNA647391 |
| SRA |
SRP272635 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE154762_FGO.gch.merge.bw |
830.6 Mb |
(ftp)(http) |
BW |
| GSE154762_FGO.wcg.merge.bw |
168.7 Mb |
(ftp)(http) |
BW |
| GSE154762_GO.gch.merge.bw |
1.1 Gb |
(ftp)(http) |
BW |
| GSE154762_GO.wcg.merge.bw |
194.8 Mb |
(ftp)(http) |
BW |
| GSE154762_Granulosa.gch.merge.bw |
899.6 Mb |
(ftp)(http) |
BW |
| GSE154762_Granulosa.wcg.merge.bw |
117.0 Mb |
(ftp)(http) |
BW |
| GSE154762_Immune.gch.merge.bw |
752.8 Mb |
(ftp)(http) |
BW |
| GSE154762_Immune.wcg.merge.bw |
121.9 Mb |
(ftp)(http) |
BW |
| GSE154762_MI.gch.merge.bw |
937.8 Mb |
(ftp)(http) |
BW |
| GSE154762_MI.wcg.merge.bw |
182.2 Mb |
(ftp)(http) |
BW |
| GSE154762_MII.gch.merge.bw |
804.9 Mb |
(ftp)(http) |
BW |
| GSE154762_MII.wcg.merge.bw |
115.7 Mb |
(ftp)(http) |
BW |
| GSE154762_RAW.tar |
33.3 Gb |
(http)(custom) |
TAR (of BW) |
| GSE154762_StromaC1.gch.merge.bw |
996.4 Mb |
(ftp)(http) |
BW |
| GSE154762_StromaC1.wcg.merge.bw |
174.2 Mb |
(ftp)(http) |
BW |
| GSE154762_StromaC2.gch.merge.bw |
979.1 Mb |
(ftp)(http) |
BW |
| GSE154762_StromaC2.wcg.merge.bw |
170.2 Mb |
(ftp)(http) |
BW |
| GSE154762_barcodes_and_cell_information.xlsx |
23.5 Kb |
(ftp)(http) |
XLSX |
| GSE154762_hO_scChaRM_count_matix.txt.gz |
7.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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