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Series GSE138852 Query DataSets for GSE138852
Status Public on Oct 16, 2019
Title A single-cell atlas of the human cortex reveals drivers of transcriptional changes in Alzheimer’s disease in specific cell subpopulations
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary There is currently little information about how individual cell types contribute to Alzheimer’s disease (AD). Here, we applied single-nucleus RNA-seq (snRNA-seq) on the entorhinal cortex from control and AD brains of twelve individuals, yielding a total of 13,214 high quality nuclei. We detail cell-type-specific gene expression patterns, unveiling how transcriptional changes in specific cell subpopulations contribute to AD. We report that the AD risk gene, APOE, is specifically repressed in AD oligodendrocyte progenitor cells and astrocyte subpopulations, and upregulated in an AD-specific microglial subopulation. Integrating transcription factor regulatory modules with AD risk loci revealed drivers of cell-type-specific fate transitions towards AD. For example, transcription factor EB, a master regulator of lysosomal function, regulates multiple disease genes in a specific AD astrocyte sub-population. These results provide insights into the coordinated control of AD risk genes and their cell-type specific contribution to disease susceptibility and are available at
Overall design Single Nuclei RNA sequencing of 8 10x libraries with each library containing 2 individuals (n =16)
Contributor(s) Chew G, Grubman A, Ouyang JF, Rackham O, Polo J, Petretto E
Citation(s) 31768052
Submission date Oct 15, 2019
Last update date Dec 05, 2019
Contact name Gabriel Chew
Organization name Duke-NUS Medical School
Street address 8 College Road
City Singapore
ZIP/Postal code 169857
Country Singapore
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (8)
GSM4120422 Human Entorhinal Cortex of aged AD individuals AD7-AD8
GSM4120423 Human Entorhinal Cortex of aged AD individuals AD5-AD6
GSM4120424 Human Entorhinal Cortex of aged AD individuals AD3-AD4
BioProject PRJNA577618
SRA SRP225693

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Supplementary file Size Download File type/resource
GSE138852_counts.csv.gz 11.9 Mb (ftp)(http) CSV
GSE138852_covariates.csv.gz 84.8 Kb (ftp)(http) CSV
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