Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell sequencing of human intestinal organoid cells.

ABSTRACT: Unbiased and FACS was performed on human intestinal organoid cells and coupled to single cell sorting by the SortSeq protocol (Muraro et al., 2016).

ORGANISM(S): Homo sapiens

PROVIDER: GSE181560 | GEO | 2021/08/17

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Single cell and bulk RNA sequencing of Enteroendocrine cells from human hormone reporter organoids

Project description:Enteroendocrine cell subpopulations were sorted by positivity for endogenous knock-in reporters in different hormones. Unbiased and biased FAC sorting was performed and coupled to single cell sorting by the SortSeq protocol (Muraro et al., 2016) and bulk sequencing.

2020-05-13 | GSE146799 | GEO

Single-cell sequencing of human lacrimal gland tissue and organoids

Project description:Human lacrimal gland tissue and organoids, cultured in expansion or differentiation, were FAC sorted into plates to follow the SORTseq protocol (Muraro et al., 2016).

2021-03-16 | GSE164403 | GEO

Single-cell RNA-sequencing of human intestinal organoid cells

Project description:We focused on a rare cell population of human intestine, the BEST4+ cells. Using human intestinal organoid as a model, the BEST4+ cells could be differentiated, FACS-enriched and analyzed by scRNA-seq, together with the BEST4- cell lineages such as the enterocytes, goble cells and EECs.

2023-09-13 | GSE242765 | GEO

Human intestinal organoid cell transcriptomic profiling

Project description:Human intestinal organoid cell transcriptomic profiling

| PRJNA623537 | ENA

Development and Validation of a Simplified Method to Generate Human Microglia from Pluripotent Stem Cells

Project description:Comparison of published protocol (Abud et al. Neuron 2016) to simplified method of microglial differentiation which does not require hypoxia or FACS. We show each method produced highly similar microglia.

2018-12-05 | GSE117829 | GEO

Mosaic perturbation of transcription factors in human retinal organoid development

Project description:To begin to understand how TFs regulate retinal cell type identity in human tissues, we established a pooled loss of function (LOF) experiment based on the CROP-seq protocol in developed retinal organoids. We targeted five TFs (OTX2, NRL, CRX, VSX2, and PAX6) that are important for retinal development and expressed dynamically over the organoid developmental time course.

2023-02-24 | E-MTAB-12622 | biostudies-arrayexpress

Human intestinal organoid cell transcriptomic profiling

Project description:We purified two populations of human ileal enteroendocrine cells (Venus+ and Venus-) from mature differentiated hGLU-Venus organoids by FACS and identified transcripts enriched in endocrine cell lineages.

2020-06-30 | GSE148224 | GEO

Gruffi removes stressed cells from brain organoid datasets

Project description:Organoids enable disease modeling in complex and structured human tissue, in vitro. Like most 3D cultures, they lack sufficient oxygen supply, leading to cellular stress. These negative effects are particularly prominent in complex models, like brain organoids, where they can prevent proper lineage commitment. Here, we analyze brain organoid and fetal single cell RNA sequencing (scRNAseq) data from published and new datasets totaling about 190,000 cells. We describe a unique stress signature found in all organoid samples, but not in fetal samples. We demonstrate that cell stress is limited to a defined organoid cell population, and present Gruffi, an algorithm that uses granular functional filtering to identify and remove stressed cells from any organoid scRNAseq dataset in an unbiased manner and validate our findings on six further datasets from different organoid protocols and early brains. Our data show that adverse effects of cell stress can be corrected by bioinformatic analysis, improving developmental trajectories and resemblance to fetal data.

2022-06-06 | GSE205554 | GEO

Single-cell sequencing of muose thymic epithelial cell organoids

Project description:Mouse thymic epithelial cell organoids, cultured in (1) expansion medium, (2) differentiation medium, or (3) differentiation medium with Rank ligand and retinoic acid (DM+RR), were FACS sorted into plates to follow the SORT-seq protocol (Muraro et al., 2016).

2024-04-05 | GSE236925 | GEO

Cell type purification by single-cell transcriptome-trained sorting

Project description:Traditional cell type enrichment using fluorescence activated cell sorting (FACS) relies on methods that specifically label the cell type of interest. Here we propose GateID, a computational method that combines single-cell transcriptomics, for unbiased cell type identification, with FACS index sorting, to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without resorting to specific antibodies or transgenes.

2019-10-07 | GSE112438 | GEO

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