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| Status |
Public on Oct 30, 2020 |
| Title |
Transcriptomic analysis of ATP6V1A knock-down and amyloid beta-treated neurons |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
ATP6V1A plays a unique role in synapse function in neurons and we found decreased neuronal activity in ATP6V1A-deficient neurons. To characterize the molecular pathways regulated by ATP6V1A under both normal and stressed conditions, we generated hiPSC-derived NGN2-neurons with reduced ATP6V1A expression by CRISPRi knock-down (KD) and performed RNA-seq analysis on the wild-type and KD neurons which were subject to amyloid-beta or vehicle treatment. A number of gene ontology (GO)/pathways were identified in KD neurons without amyloid-beta treatment (proton transporting V-ATPase complex, phagosome acidification and trivalent inorganic cation transport were down-regulated, and mitochondrial protein complex up-regulated), while KD in amyloid-beta treated cells specifically resulted in down-regulation of cell adhesion, synapse assembly and structure/activity and up-regulation of UPR and ER stress response.
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| Overall design |
RNA from four groups of hiPSC-derived NGN2-neurons (designated WT-V and WT-Aβ for vehicle-treated and amylod beta (Ab)-treated ATP6V1A wild-type (WT) neurons, respectively, and KD-V and KD-Aβ for vehicle-treated and Aβ-treated ATP6V1A KD neurons, respectively) were collected and loaded to RNA-sequencing analysis. There are five independent neuronal differentiation experiments in each group.
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| Contributor(s) |
Li A, Wang M, Yu A, Lyu L, Brennand KJ, Zhang B |
| Citation(s) |
33238137, 34151300 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| U01 AG046170 |
Integrative Network Biology Approaches to Identify, Characterize and Validate Molecular Subtypes in Alzheimer's Disease |
MOUNT SINAI SCHOOL OF MEDICINE |
Bin Zhang |
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| |
| Submission date |
Mar 15, 2019 |
| Last update date |
Jul 01, 2021 |
| Contact name |
Bin Zhang |
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Genetics and Genomic Sciences
|
| Street address |
1470 Madison Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (20)
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| Relations |
| BioProject |
PRJNA527281 |
| SRA |
SRP188549 |
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