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| Status |
Public on Jan 15, 2024 |
| Title |
Construction of zebrafish chromatin accessibility landscape at a single-cell level using CH-ATAC-seq |
| Organism |
Danio rerio |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) at single-cell level can provide different perspectives of regulatory patterns based on cell type-specific accessible regions. While human genomic elements have been well studied, understanding how nuclear acid sequence regulates the expression of target genes in a genome-wide level in other organisms remains a major challenge. Batch effects, expensive machines are still constraints nowadays to build a cross-species landscape for further analysis, a platform with high throughput and low cost will be extremely required.Here, we constructed a cross-species accessible chromatin landscape by combinatorial-hybridization-based single-cell ATAC-seq, a single-cell ATAC-seq platform with high throughput and signal-noise ratio using fresh nuclei as input.
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| Overall design |
Whole bodies of wild-type strain AB zebrafishes at 4 months were dissociated into single-nucleus suspensions, followed by single-cell DNA library construction, high-throughput sequencing, and bioinformatics analysis.
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| Contributor(s) |
Guo G, Zhang G, Fu Y, Yang L, Ye F, Zhang P, Zhang S, Han X, Wang J |
| Citation(s) |
38330939 |
| Submission date |
May 09, 2023 |
| Last update date |
Apr 15, 2024 |
| Contact name |
Guoji Guo |
| Organization name |
Center for Stem Cell and Regenerative Medicine
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| Department |
Zhejiang University School of Medicine
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| Street address |
Yuhangtang street 866
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| City |
Hanzhou |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platforms (1) |
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| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE232162 |
Construction of a cross-species chromatin accessibility landscape at a single-cell level using CH-ATAC-seq |
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| Relations |
| BioProject |
PRJNA970700 |
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