Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell RNA-seq of great ape cerebral organoids

ABSTRACT: The human brain has changed dramatically from other primate species, but the genetic and developmental mechanisms behind the differences remains unclear. Here we used single cell RNA sequencing based on 10X technology to explore temporal transcriptomic dynamics and cellular heterogeneity in cerebral organoids derived from human and non-human primates chimpanzee and rhesus macaque stem cells. Using cerebral organoids as a proxy of early brain development, we detect a delayed pace of human brain development relative to the other two primate species. Additional human-specific gene expression patterns resolved to different cell states through progenitors to neurons are also found. Our data provide a transcriptomic cell atlas of primate early brain development, and illustrate features that are unique to humans.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Pan troglodytes

SUBMITTER: Gray Camp

PROVIDER: E-MTAB-7552 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Bulk ATAC-seq of primate cerebral organoids

Project description:Bulk ATAC-seq was performed on human, chimpanzee, bonobo, and macaque stem cell-derived cerebral organoids. ATAC-seq was performed on day 60 (2 months old) and day 120 (4 months old) cerebral organoids.

2019-10-16 | E-MTAB-8228 | biostudies-arrayexpress

The extracellular function of LGALS3BP in neural progenitors during brain development

Project description:This study demonstrates cellular and molecular mechanisms regulating the generation and function of basal radial glia (bRG), a neural stem cell population that was shown to be enriched in the developing human brain and was involved in the formation of cortical expansion. Here, we studied the role of LGALS3BP, a secreted protein whose RNA expression is enriched in bRGs. Based on a combination of three model systems i) in vitro human cerebral organoids, ii) ex vivo embryonic human fetal tissue and iii) in vivo embryonic mouse cortex, and a wide variety of techniques including single-cell RNA-sequencing, proteomics, and immunostaining, we characterized the role of human LGALS3BP mutations.

2021-05-12 | E-MTAB-10485 | biostudies-arrayexpress

Single-cell transcriptome of cerebral organoids with and without methanol fixation

Project description:To study how methanol fixation affects single-cell transcriptomic measurement, two cerebral organoids were dissociated. Cell suspension of each organoid was split into two aliquots. Methanol fixation was applied to one of the two aliquots. Single-cell RNA-seq with 10x Genomics was applied to the two aliquots separately.

2020-08-31 | E-MTAB-9473 | biostudies-arrayexpress

Multiome experiment of the neuroepithelial stage of brain organoid developement

Project description:To investigate the heterogeneity during the neuroepithelial stage of organoid development, we performed a multiome experiment on day 15-18 old brain organoids

2022-10-03 | E-MTAB-12004 | biostudies-arrayexpress

Single cell RNA-seq of great ape cerebral organoids

Project description:The human brain has changed dramatically from other primate species, but the genetic and developmental mechanisms behind the differences remains unclear. Here we used single cell RNA sequencing based on 10X technology to explore temporal transcriptomic dynamics and cellular heterogeneity in cerebral organoids derived from human and non-human primates chimpanzee and rhesus macaque stem cells. Using cerebral organoids as a proxy of early brain development, we detect a delayed pace of human brain development relative to the other two primate species. Additional human-specific gene expression patterns resolved to different cell states through progenitors to neurons are also found. Our data provide a transcriptomic cell atlas of primate early brain development, and illustrate features that are unique to humans.

2019-10-04 | E-MTAB-8234 | biostudies-arrayexpress

Lineage recording in human cerebral organoids (whole organoids)

Project description:Induced pluripotent stem cell (iPSC) derived organoid systems provide models to study human organ development. Single-cell transcriptome sequencing enables highly-resolved descriptions of cell state heterogeneity within these systems and computational methods can reconstruct developmental trajectories. However, new approaches are needed to directly measure lineage relationships in these systems. Here we establish an inducible dual channel lineage recorder, iTracer, that couples reporter barcodes, inducible CRISPR/Cas9 scarring, and single-cell transcriptomics to analyze state and lineage relationships in iPSC-derived systems. This data set include the iTracer data of 12 cerebral organoids.

2021-11-03 | E-MTAB-10974 | biostudies-arrayexpress

Lineage recording in human cerebral organoids (iTracer-perturb)

2021-11-03 | E-MTAB-10971 | biostudies-arrayexpress

Transcriptomic profile of human induced pluripotent stem cells at single cell resolution.

Project description:We assessed the pluripotency of human induced pluripotent stem cells (iPSCs) maintained on an automated platform using StemFlexTM and TeSRTM-E8TM media. Single-cell transcriptome sequencing was performed for 20,962 cells from two cell lines grown in the two media. Analysis of transcriptomic profile revealed similar expression of core pluripotency genes, as well as genes associated with naive and primed states of pluripotency. Single cell analysis of the four samples revealed a shared subpopulation structure with three main subpopulations different in pluripotency states. By implementing a machine learning approach, we estimated that 60-96% of the cells in the ground/naive subpopulations and 98-99% of the cells in the primed subpopulations are similar between all four samples. The single cell RNA sequencing analysis of iPSC lines grown in both media is the first report of the molecular pathways modulated in StemFlex medium and how they compare to those modulated in TeSR-E8 medium.

2019-05-08 | E-MTAB-6524 | biostudies-arrayexpress

scRNA-seq of pluripotent stem cell derived human intestinal organoids grown in an alginate matrix

Project description:Here, we used single-cell RNA-sequencing (scRNA-seq) to profile pluripotent stem cell derived human intestinal organoids (HIOs) grown in an alginate matrix after 3, 7, and 14 days of in vitro growth. Samples were grown in minigut media supplemented with either ENR or EGF.

2022-02-01 | E-MTAB-11338 | biostudies-arrayexpress

Lineage recording in human cerebral organoids (microdissected)

2021-11-03 | E-MTAB-10973 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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