Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

78 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-nucleus RNA-seq of prefrontal cortex in adult human, chimp and macaque

ABSTRACT: The human brain has changed dramatically since humans diverged from our closest living relatives, chimpanzees and the other great apes. However, the genetic and developmental programs underlying this divergence are not fully understood. Here, we generate single-nucleus RNA-seq data of human, chimpanzee and macaque adult prefrontal cortex. Spatial information is obtained by isolating nuclei from sequential sections sliced from basal to apical positions. By comparing transcriptome of different cell types in the three species, we map human-specific expression in adult prefrontal cortex. By comparing to single cell RNA-seq data of cerebral organoids of the same species, we find developmental differences that persist into adulthood, as well as cell state-specific changes that occur exclusively in the adult brain.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): mixed sample

SUBMITTER: Barbara Treutlein

PROVIDER: E-MTAB-8230 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single-cell RNA+ATAC sequencing of human CRL-1459 colonic fibroblasts

Project description:The 10x multiome (RNA+ATAC) kit was applied to CRL-1459 cells in culture at passage 10 and 15

2024-07-13 | E-MTAB-14220 | biostudies-arrayexpress

Single cell profiling of a Caki-1:HeLa cell mixture by scATAC-seq and scGET-seq

Project description:A mixture of Caki-1 and HeLa cells in known proportions (80:20) is profiled using 10x Chromium scATAC-seq or scGET-seq protocols.

2021-08-17 | E-MTAB-9650 | biostudies-arrayexpress

scGET-seq profile of NIH-3T3 cells with Kdm5c knockdown

Project description:scGET-seq profiling of NIH3T3 cells in which Kdm5c was silenced with antisense shRNA or with a control scramble shRNA.

2021-08-17 | E-MTAB-9651 | biostudies-arrayexpress

RNA-seq of prefrontal cortex in adult human, chimp and macaque

Project description:The human brain has changed dramatically since humans diverged from our closest living relatives, chimpanzees and the other great apes. However, the genetic and developmental programs underlying this divergence are not fully understood. Here, we generate single-nucleus RNA-seq data of human, chimpanzee and macaque adult prefrontal cortex. Spatial information is obtained by isolating nuclei from sequential sections sliced from basal to apical positions. Bulk RNA-seq is performed for the same sections to determine positional information of the sections, by comparing the section transcriptome with published transcriptome data of cortical layers in human, chimpanzee and macaque.

2019-10-04 | E-MTAB-8231 | biostudies-arrayexpress

A primate nigrostriatal atlas of neuronal vulnerability and resilience in a model of Parkinson’s disease

Project description:The degenerative process in Parkinson’s disease (PD) causes a progressive loss of dopaminergic neurons (DaNs) in the nigrostriatal system. Resolving the differences in neuronal susceptibility warrants an amenable PD model that, in comparison to post-mortem human specimens, controls for environmental and genetic differences in PD pathogenesis. At present study, we generated a primate model of PD by carotid artery injection of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine MPTP and sampled substantia nigra and putamen of macaque for single cell sequencing analysis.

2023-11-19 | E-MTAB-13437 | biostudies-arrayexpress

Single-nucleus RNA-seq of the human musculotendinous unit, the myotendinous junction

Project description:Identification of cell types in the interphase between muscle and tendon by single-nuclei RNA-seq of three human semitendinous muscle-tendon biopsies. With special focus on the myotendinous junction specific myonuclei, transcripts were identified and confirmed to myotendinous junction with immunofluorescence.

2023-03-02 | E-MTAB-12529 | biostudies-arrayexpress

Single nuclei chromatin profiles of midbrain from genetically distinct mouse strains reveal cell identity transcription factors and cell type-specific gene regulatory variation

Project description:Here we report 20 658 single nuclei chromatin accessibility profiles of ventral midbrain cell types from two genetically diverse and commonly used mouse strains, C57BL6/J and A/J. In total we identify over 260 000 unique accessible sites. The distinct chromatin profiles are consistent with gene expression levels from single cell RNA-seq data and can distinguish ten midbrain cell types. Transcription factor (TF) binding motifs enriched at accessible regions controlling cell identity genes highlight the key TFs of each major cell type. The gene regulatory differences between the mouse strains manifest more on transcriptome than chromatin level.

2022-01-14 | E-MTAB-9225 | biostudies-arrayexpress

Single-cell multiome analysis of human tonsil B cells

Project description:B cells from tonsils of human donors were extracted for combined RNAseq+ATACseq from the same cell. One sample was prepared separately ("old") and is of lower quality, but still included. It primarily holds ATACseq information.

2023-04-13 | E-MTAB-12632 | biostudies-arrayexpress

Analysis of epithelial and mesenchymal populations in tumor-derived cell lines by scGET-seq

Project description:This experiment includes single cell epigenome data (by scGET-seq) for the epithelial and mesenchymal populations isolated from a pancreatic tumor induced in GEM mouse.

2024-06-01 | E-MTAB-13052 | biostudies-arrayexpress

scATAC-seq of mouse liver tissue derived from young and old mice II

Project description:We investigate if the differences in phenotype and transcriptome over age might be explained by an underlying change on the epigenetic level. We performed single-cell ATAC sequencing using the 10x Chromium platform. We profiled 2259 nuclei prepared from 3 young liver tissues and 2490 nuclei from 3 old liver tissues.

2023-11-09 | E-MTAB-12560 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data