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| Status |
Public on Jul 07, 2021 |
| Title |
Single-Cell Chromatin Accessibility Landscape of Human Umbilical Cord Blood in Trisomy 18 Syndrome |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Trisomy 18 syndrome (Edwards Syndrome, ES) is a type of aneuploidy caused by the presence of an extra chromosome 18, and just the second most common autosomal trisomy syndrome after trisomy 21 (known as Down syndrome). Aneuploidy is the leading cause of early pregnancy loss, mental retardation, and multiple congenital anomalies. We used the commercial system Chromium platform (10x Genomics) to performed scATAC-seq to measure chromatin accessibility in 11,611 single umbilical cord blood cells, derived from 2 samples, respectively one Trisomy 18 Syndrome and one healthy donor. We obtain 13 distinct major clusters of cells, identified as 6 human umbilical cord blood mononuclear cell types marker-free and characterized the driving regulatory factors and differentially accessible loci that define each cluster. We set out to generate a single-cell atlas of chromatin accessibility among health and the 18 trisomy syndrome human umbilical cord blood. Finally, the cell-type-specific gene regulatory networks analysis at a single-cell resolution of this differential accessibility-related loci genes was carried out and disease-related transcription factors (TFs) and corresponding genes are predicted. These screened disease-related transcription factors (TFs) and corresponding genes provide a basis for further research and understanding of trisomy 18 syndrome. Finally, a cell-type-specific gene regulatory network analysis of these differentially accessible related locus genes was performed at single-cell resolution and predicted disease-related transcription factors (TFs) and corresponding genes. In detail, CCBN2 and MCM3 may be essential for the development of trisomy 18 and disease differential genes are enriched in the human T-cell leukemia virus 1 infection pathway.
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| Overall design |
Single-cell chromatin accessibility (scATAC) profiles of Human Umbilical Cord Blood in Trisomy 18 Syndrome
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| Contributor(s) |
Qiu X, Dai Y |
| Citation(s) |
34193281 |
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| Submission date |
Sep 17, 2020 |
| Last update date |
Jul 08, 2021 |
| Contact name |
qiu fxiaofen |
| E-mail(s) |
qxf0512@gmail.com
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| Phone |
17770750424
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| Organization name |
Guangxi Normal University
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| Street address |
Guangxi Normal University, Guilin, Guangxi
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| City |
guilin |
| State/province |
sz |
| ZIP/Postal code |
541000 |
| Country |
China |
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| Platforms (1) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA664208 |
| SRA |
SRP283130 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE158178_RAW.tar |
26.3 Mb |
(http)(custom) |
TAR (of BED, MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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