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| Status |
Public on Jan 11, 2018 |
| Title |
Regulatory elements governing neurogenesis and proliferation in developing human neocortex |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Non-coding regions compose most of the human genome, yet their functionality is poorly defined. In the developing human neocortex, non-coding regulatory elements tightly regulate expression to direct neural progenitor proliferation and neurogenesis. Here, we define thousands of non-coding elements involved in human neurogenesis by contrasting chromatin accessibility via ATAC-seq from the germinal zone and cortical plate.
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| Overall design |
Tissues were obtained from three independent donors (15-17 post conception weeks) and three to four technical replicates from each tissue were processed for ATAC-seq. Coronal sections were taken from dissociated tissue that visually appeared cortical. Under a dissection microscope, the coronal sections were cut with a razor blade along the less dense intermediate zone to divide the tissue into two segments from each donor (1) GZ: the neural progenitor rich region encompassing the ventricular zone, subventricular zone, and intermediate zone and (2) CP: the neuron rich region encompassing the subplate, cortical plate, and marginal zone. ATAC-seq processing followed the original protocol (Buenrostro et al., Nat Methods, 2013).
Please note that RNA-Seq raw data will be made available through dbGaP (controlled access; phs001438) due to patient privacy concerns.
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| Contributor(s) |
Geschwind DH, de la Torre-Ubieta L, Stein JL |
| Citation(s) |
29307494 |
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| Submission date |
Feb 17, 2017 |
| Last update date |
Mar 27, 2019 |
| Contact name |
Jason L Stein |
| E-mail(s) |
jason_stein@med.unc.edu
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| Organization name |
UNC Chapel Hill
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| Department |
Genetics
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| Lab |
Stein lab
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| Street address |
Neuroscience Research Building 8109C, 115 Mason Farm Rd
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| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7250 |
| Country |
USA |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (19)
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| Relations |
| BioProject |
PRJNA375750 |
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