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| Status |
Public on May 05, 2020 |
| Title |
Allele-specific open chromatin in human neurons elucidates functional noncoding disease variants |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
ASoC variants are prevalent and cell type-specific ASoC variants were over-represented in intergenic regions and active enhancers. The collection includes ATAC-Seq and RNA-Seq data that were taken from human iPS cells and their derived neuronal cells (neural progenitor cells, cortical glutamatergic neurons, GABAergic neurons, and dopaminergic neurons).
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| Overall design |
In order to detect the changes in chromatin accessibility as well as associated changes at the transcriptional level during neuronal differentiation, we applied human induced pluripotent stem cells (hiPSCs) and hiPSC-derived neurons as a neurodevelopmental model. Generally, 8 iPSC lines from RUCDR were induced to differentiate into neural progenitor cells (NPC), 15-day cortical glutamatergic neurons (CN, Glut d15), GABAergic neurons, and dopaminergic neurons. Their open chromatin landscape, as well as transcriptional activities, were measured using ATAC-Seq and bulk RNA-Seq, respectively. An additional 12 lines were used to generate NPC cells and Glut-d15 neurons for ATAC-Seq, with the aim in gaining extended statistic power for ASoC analysis.
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| Contributor(s) |
Duan J, Zhang S |
| Citation(s) |
32732423, 34308291 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 MH106575 |
Systematic Functional Interpretation of Regulatory Variants in Schizophrenia |
NorthShore University HealthSystem |
Jubao Duan |
|
| Submission date |
Mar 28, 2019 |
| Last update date |
Jul 28, 2021 |
| Contact name |
Jubao Duan |
| E-mail(s) |
jduan69@gmail.com
|
| Phone |
(224) 364-7564
|
| Organization name |
NorthShore University HealthSystem
|
| Department |
Center for Psychiatric Genetics
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| Lab |
Unit of Functional Genomics in Psychiatry
|
| Street address |
1001 University Place
|
| City |
Evanston |
| State/province |
IL |
| ZIP/Postal code |
60201 |
| Country |
USA |
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| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (118)
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| Relations |
| BioProject |
PRJNA529717 |
| SRA |
SRP189815 |
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