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Series GSE193499 Query DataSets for GSE193499
Status Public on Dec 11, 2023
Title Individual Variability in Human Cell Type Transcriptomes and Epigenomes [YM3B]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Diversity and individual variability are essential to human cognitive function. Identifying the conserved and variable (epi)genomic signatures of the brain’s cellular components is critical for understanding the neurobiological basis of individual variation in brain function.  We applied single nucleus methylome and transcriptome sequence (snmCT-seq) to neurons from the frontal cortex of 11 adult human donors spanning a range of ages from 23 to 74, including males and females (Broadmann Area BA46). We clustered cells into brain cell types based on methylation features. We then examined the transcriptome and epigenome features in each cell type between and within individual donors. Taking advantage of the multimodal measurements in single cells, we also identified the relation between RNA expression and methylation level.These data with multiomics measurement from donors with sex and age diversity aims to approach the dimension of inter-individual variability.
Overall design We apply snmCT-seq to identify the transcriptomic and epigenomic features of neurons from individual adult human frontal cortex, including 3 aged male donors (age range 70-71), 3 aged female donors (71-74 years old), 3 young male donors  (25 years old) and 2 young female donors  (23-30 years old). For each donor, 2 chunks of brain tissue were collected and processed separately, to assess within-donor variability. Data in this series was from chunk B of a 25 years old male.
Contributor(s) Chien J, Bartlett A, Liu H, Castanon R, Nery JR, Wang B, Johnson N, Osteen J, Behrens MM, Mukamel EA, Ecker JR
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Submission date Jan 11, 2022
Last update date Dec 11, 2023
Contact name Joseph R Ecker
Phone 8584534100
Organization name HHMI-Salk-Institute
Department Genomic Analysis Laboratory
Lab Ecker lab
Street address 10010 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (3045)
GSM5808547 5679_YM3B_1-1-B11-A13
GSM5808548 5679_YM3B_1-1-B11-A14
GSM5808549 5679_YM3B_1-1-B11-A1
BioProject PRJNA796532
SRA SRP354670

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Supplementary file Size Download File type/resource
GSE193499_RAW.tar 267.2 Gb (http)(custom) TAR (of TSV)
GSE193499_YM3B_TotalRNAData.csv.gz 31.6 Mb (ftp)(http) CSV
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Raw data are available in SRA
Processed data provided as supplementary file

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