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Series GSE196491 Query DataSets for GSE196491
Status Public on Oct 07, 2022
Title KCNJ6 variants associated with alcohol use disorder (AUD) in human induced neurons
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Noncoding SNP variants in KCNJ6 have been linked with increased risk of alcohol use disorder (AUD) and the endophenotype EEG frontal theta event related oscillation (ERO) power. We prepared iPSC from subjects with contrasting diagnosis of AUD and KCNJ6 variants (AF, affected) or unaffected with reference KCNJ6 (UN). Induced neurons cultures were prepared from each iPSC line and harvested for RNAseq analysis. In these bulk RNAseq analyses, we do not identify meaningful differences by KCNJ6 haplotype, we we can validate expression of the long (18kb) 3'UTR from the KCNJ6 gene, and identify several additional SNPs linked with the original three. Additional studies used single cell RNAseq to isolate differentiated neurons from iN cultures and analysis of these samples found differences in neuron process formation and synaptic function, which were validated with morphometrics, immunocytochemistry, and electrophysiology.
 
Overall design Unbiased RNA sequencing was performed on iPSC-derived human induced neurons (iN) from two groups: AF having a variant KCNJ6 haplotype associated with alcohol use disorder (AUD) and diagnosed with AUD, and UN having reference allele KCNJ6 haplotype and diagnosed with no AUD.
 
Contributor(s) Popova DR, Swerdel MR, Zalamea P, Hart RP
Citation(s) 36207584
NIH grant(s)
Grant ID Grant title Affiliation Name
U10 AA008401 Collaborative Study on the Genetics of Alcoholism (COGA) SUNY DOWNSTATE MEDICAL CENTER BERNICE PORJESZ
Submission date Feb 10, 2022
Last update date Oct 10, 2022
Contact name Ronald P. Hart
E-mail(s) rhart@rutgers.edu
Phone 848-445-1783
Organization name Rutgers University
Department Cell Biology & Neuroscience
Street address 604 Allison Rd Rm B430
City Piscataway
State/province NJ
ZIP/Postal code 08854
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (7)
GSM5885478 AF iN culture 376
GSM5885479 AF iN culture 246
GSM5885480 AF iN culture 351
Relations
BioProject PRJNA805190

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Supplementary file Size Download File type/resource
GSE196491_normalized_counts.tsv.gz 993.1 Kb (ftp)(http) TSV
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Raw data are available in SRA
Processed data are available on Series record

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