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Series GSE249399 Query DataSets for GSE249399
Status Public on Dec 12, 2023
Title Individual Variability in Human Cell Type Transcriptomes and Epigenomes [YM2A]
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Other
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. This sample is from chunk A of a 25 years old male.
 
Contributor(s) Chien J, Liu H, Wang B, Luo C, Bartlett A, Castanon R, Johnson ND, Nery JR, Osteen J, Li J, Altshul J, Kenworthy M, Valadon C, Liem M, Claffey N, O'Connor C, Seeker LA, Ecker JR, Behrens MM, Mukamel EA
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Submission date Dec 05, 2023
Last update date Dec 13, 2023
Contact name Joseph R Ecker
E-mail(s) ecker@salk.edu
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 (3051)
GSM7943627 5730_YM2A_1-1-B11-A13
GSM7943628 5730_YM2A_1-1-B11-A14
GSM7943629 5730_YM2A_1-1-B11-A2
Relations
BioProject PRJNA1049139

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE249399_RAW.tar 217.3 Gb (http)(custom) TAR (of TSV)
GSE249399_YM2A_TotalRNAData.csv.gz 29.5 Mb (ftp)(http) CSV
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