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Series GSE128367 Query DataSets for GSE128367
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
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.
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.
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
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
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (20)
GSM3672553 1-2607-C
GSM3672554 10-2607-i1
GSM3672555 11-2607-i1
BioProject PRJNA527281
SRA SRP188549

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Supplementary file Size Download File type/resource
GSE128367_expression.log2cpm.tsv.gz 2.7 Mb (ftp)(http) TSV
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