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| Status |
Public on Nov 13, 2020 |
| Title |
EOFAD-causing mutations in psen1 orchestrate dedifferentiation through remodeling of the chromatin landscape in hiPSC-derived neurons [ATAC-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
In this work, we used an integrative, multi-omics approach and systems-level analysis to generate a mechanistic disease model for EOFAD in an hiPSC-derived neuron model system.
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| Overall design |
hiPSC-derived neurons were generated from patient-specific Non-Demented Control, PSEN1M146L, PSEN1H163R, PSEN1A246E, and PSEN1A431E fibroblasts and subjected to RNA-Seq, ATAC-Seq, and histone methylation ChiP-Seq. For ATAC-Seq, transposition experiments were performed as previously reported on 50,000 NDC (n = 5), PSEN1M146L (n = 2), PSEN1H163R (n = 3), PSEN1A246E (n = 2), and PSEN1A431E (n = 3) hiPSC-derived neuron cells using the Illumina Nextera DNA Sample Preperation kit and Qiagen MinElute PCR Purification kit. ATAC-Seq libraries were generated from transposed DNA using the Kapa Biosystems Real-Time Library Amplification kit and further purified using the Qiagen MinElute PCR Purification kit; sequencing was performed an Illumina HiSeq4000 platform generating Paired-End, 50bp reads with an average of 25 million reads per sample.
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| Contributor(s) |
Caldwell AB, Liu Q, Schroth GP, Galasko DR, Yuan SH, Wagner SL, Subramaniam S |
| Citation(s) |
33188013 |
| |
| Submission date |
Dec 17, 2018 |
| Last update date |
Dec 04, 2020 |
| Contact name |
Shankar Subramaniam |
| Organization name |
University of California, San Diego
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| Department |
Department of Bioengineering
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| Street address |
9500 Gilman Drive
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093-0412 |
| Country |
USA |
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| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (15)
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| This SubSeries is part of SuperSeries: |
| GSE123998 |
EOFAD-causing mutations in psen1 orchestrate dedifferentiation through remodeling of the chromatin landscape in hiPSC-derived neurons |
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| Relations |
| BioProject |
PRJNA510453 |
| SRA |
SRP173733 |
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