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| Status |
Public on Jan 27, 2018 |
| Title |
Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
|
| Summary |
Analysis of chromatin accessibility can reveal transcriptional regulatory sequences, but heterogeneity of primary tissues poses a significant challenge in mapping the precise chromatin landscape in specific cell types. Here we report single-nucleus ATAC-seq, a combinatorial barcoding-assisted single-cell assay for transposase-accessible chromatin that is optimized for use on flash-frozen primary tissue samples. We apply this technique on the mouse forebrain through eight developmental stages. Through analysis of more than 15,000 nuclei, we identify 20 distinct cell populations corresponding to major neuronal and non-neuronal cell types. We further define cell-type-specific transcriptional regulatory sequences, infer potential master transcriptional regulators and delineate developmental changes in forebrain cellular composition. Our results provide insight into the molecular and cellular dynamics that underlie forebrain development in the mouse and establish technical and analytical frameworks that are broadly applicable to other heterogeneous tissues.
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| Overall design |
We performed combinatorial single-nucleus ATAC-seq for 7 stages of embryonic forebrain development from E11.5 to P0 and adult forebrain. Data analysis pipeline used in this study: https://github.com/r3fang/snATAC
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| Citation(s) |
29434377, 29497140 |
| Submission date |
Jun 14, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Rongxin Fang |
| E-mail(s) |
r3fang@ucsd.edu
|
| Organization name |
Ludwig Institute for Cancer Research
|
| Lab |
Ren Lab
|
| Street address |
9500 Gilman Dr #3080
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platforms (3) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
| GPL22245 |
Illumina HiSeq 2500 (Homo sapiens; Mus musculus) |
|
| Samples (11)
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| Relations |
| BioProject |
PRJNA390526 |
| SRA |
SRP133390 |
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