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| Status |
Public on Mar 03, 2017 |
| Title |
Whole genome developmental time course of Tn5 transposon accessible chromatin patterns in sea urchin embryos |
| Organism |
Strongylocentrotus purpuratus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We have adapted ATAC-seq to sea urchin embryos. As a proof of concept, we documented strong ATAC-seq signals over the locations of a number of previously authenticated, developmentally active, cell type specific cis-regulatory modules. We then used the method to generate a systematic developmental series for embryos from three independent batches, obtained every six hours from blastula stage until completion of embryogenesis at 72h. The independent batches provide internal reproducibility controls.
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| Overall design |
In order to identify sites of active transcription through correlation of Tn5 accessible open chromatin with other genome feature, we collected embryos from three independent matings at 18 hour post fertilization (hpf), 24hpf, 30hpf, 50hpf, 60hpf and 70hpf. The nuclei were isolated and then processed by standard methods for Tn5 transposon binding. The subsequent labelled fragments were read on the Illumina latform and mapped to the genome.
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| Contributor(s) |
Vielmas E, Kudtarkar P, Antoshechkin I, Cameron RA |
| Citation missing |
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| |
| Submission date |
Mar 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert Andrew Cameron |
| E-mail(s) |
parulk@caltech.edu
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| Organization name |
California Institute of Technology
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| Department |
Biology and Biological Engineering
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| Lab |
Center for Computational Regulator Genomics
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| Street address |
Caltech 1200 EAST CALIFORNIA BOULEVARD
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| City |
PASADENA |
| State/province |
CA |
| ZIP/Postal code |
91125 |
| Country |
USA |
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| Platforms (1) |
| GPL20965 |
Illumina HiSeq 2500 (Strongylocentrotus purpuratus) |
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| Samples (21)
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| Relations |
| BioProject |
PRJNA377768 |
| SRA |
SRP101305 |
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