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| Status |
Public on May 12, 2024 |
| Title |
ATAC-seq of frozen H1 Human Embryonic Stem Cells (hESC) |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We performed Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) to profile genome-wide chromatin accessibility in the human H1 embryonic stem cell (ESC) line. We used this data to train a deep learning model called ChromBPNet which can accurately predict base-resolution accessibility profiles as a function of DNA sequence, while accounting for and correcting biases due the sequence preferences of the Tn5 transposase used in ATAC-seq. We interpreted the models to identify globally predictive transcription factor (TF) motifs, individual predictive motif instances in all accessible regions and Tn5-bias corrected canonical footprints of TFs at these predictive motifs.
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| Overall design |
Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) was used to profile genome-wide chromatin accessibility in the human H1 embryonic stem cell (ESC) line.
We then used this data to develop ChromBPNet, a deep learning model capable of predicting DNA sequence-based base-resolution accessibility profiles, correcting biases from Tn5 transposase in ATAC-seq, and revealing globally predictive transcription factor motifs and their specific instances, along with Tn5-bias-corrected canonical footprints for TFs at these motifs.
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| Contributor(s) |
Kathiria A, Risca V, Greenleaf W, Pampari A, Shcherbina A, Kundaje A |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
May 09, 2024 |
| Last update date |
May 13, 2024 |
| Contact name |
William James Greenleaf |
| E-mail(s) |
wjg@stanford.edu
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| Organization name |
Stanford University
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| Department |
Genetics
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| Lab |
Greenleaf lab
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| Street address |
Beckman Center B-279, Campus Drive West
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (1) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA1109865 |
