Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ScRNA-seq of pluripotent stem cell derived human intestinal organoids

ABSTRACT: Here, we used single cell RNA-sequencing (scRNA-seq) to profile pluripotent stem cell derived human intestinal organoids (HIOs) grown in matrigel or a non-adhesive alginate hydrogel after 28 days of in vitro growth. Additionally, we used scRNA-seq to profile HIOs derived in the presence of Neuregulin 1 (NRG1) and/or EGF after 40 days of in vitro growth.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Joshua Wu

PROVIDER: E-MTAB-10268 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

scRNA-seq of pluripotent stem cell derived human intestinal organoids, adult intestine, and human fetal endoderm derived organs

Project description:Here, we used single cell RNA-sequencing (scRNA-seq) to profile pluripotent stem cell derived human definitive endoderm and intestinal organoids (HIOs) at several timepoints of in vitro growth (7, 14, and 28 days) and after in vivo growth beneath the kidney capsule of a murine host (4 and 8 wks post-transplant). Additionally, we profiled HIOs grown in a non-adhesive alginate hydrogel and also CDX2 knockout HIOs. In order to benchmark the organoid cultures, we used scRNA-seq to profile primary human fetal esophagus (14.3 pcw, 16.7 pcw), stomach (6.7, 14.3, and 16.7 pcw), liver (14.4 pcw), small intestine ( 11.4 and 14.4 pcw) and colon (11.4, 14.4, and 18.9 pcw). Diverse cell lineages were captured across all tissues profiled, including: epithelium, mesenchyme, neurons, endothelium, and immune lineages.

2021-05-21 | E-MTAB-10187 | biostudies-arrayexpress

scRNA-seq of human fetal kidney tissue

Project description:Here, we performed single cell RNA sequencing (scRNA-seq) of human fetal kidney tissue samples from 2 individual biological specimens (13.7 and 15.4 weeks gestation). The data set is composed of approximately 10,000 cells from diverse renal lineages. Lineages captured include nephron progenitors, epithelium, stroma, immune, and endothelium.

2020-12-20 | E-MTAB-9083 | biostudies-arrayexpress

Single-cell RNA-seq (10x Chromium V3) of heterogeneous spheres consisting of melanoma cell line and two types of human primary dermal fibroblasts

Project description:Photo-damage represents an important aspect of cutaneous carcinogenesis. The photo-damaged microenvironment significantly facilitates progression of malignant melanoma. Therefore human primary dermal fibroblasts from photo-damaged adult skin and juvenile sun-protected skin were isolated and expanded as described by Dvorankova et al. (PMID: 29675784). Low passage fibroblasts were mixed in suspension (in ratio 1:1) with G361 malignant melanoma cell line (CVCL_1220). Using the hanging drop technique (PMID: 29786551), the melanoma/fibroblast spheres containing 50,000 cells per sphere were formed during the next 72 hours. The organoids were consequently maintained for another 2 days in non-adhesive culture wells in complete DMEM culture medium. At this time, heterogeneous spheres were harvested for immunohistochemical analysis or for further invasion studies. Single-cell suspensions from heterogeneous spheres were analysed by single-cell RNA sequencing (10x Chromium V3) to reveal the transcriptional heterogeneity of model cell populations under given conditions with emphasis on the features of dermal fibroblasts exposed to the influence of malignant melanoma.

2021-02-27 | E-MTAB-9216 | biostudies-arrayexpress

scRNA-seq of human fetal intestine tissue

Project description:Here, we performed single cell RNA sequencing (scRNA-seq) of human fetal duodenal tissue samples from 8 individual biological specimens across 7-21 weeks of gestation. The data set is composed of over 37,000 cells (between 3,000-9,000 cells per time point) from diverse intestinal lineages. Lineages captured include epithelium, mesenchyme, immune, neurons, and endothelium. These data were used to specifically interrogate the development and emergence of mesenchymal lineages during human development.

2020-12-12 | E-MTAB-9489 | 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

Single cell RNA sequencing of fetal mouse intestine at key stages of development (E13.5, E14.5, E15.5, E16 and E17.5)

Project description:Here, we present the fetal mouse intestine data from the project \\"Comparison of human and mouse mesenchyme identifies common and unique aspects of intestinal patterning\\". Whole intestines were harvested from fetuses from timed pregnant matings for wildtype C57BL/6 mice (Jax strain #000664). Fetal stages were confirmed according to the Theiler staging chart (https://www.emouseatlas.org/emap/ema/staging_criteria/staging_criteria.html). Whole intestines (from the common bile duct through the cecum) were collected at key stages of development (E13.5, E14.5, E15.5, E16 and E17.5). Male and female intestines from each stage were pooled and dissociated to single cells for single cell RNA sequencing as previously described (Miller et al. 2020 Dev Cell). Specifically, E13.5 was 6 intestines, E14.5 was 5 intestines, E15.5 was 4 intestines, E16 was 3 intestines and E17.5 was 3 intestines.

2024-04-01 | E-MTAB-13201 | biostudies-arrayexpress

scRNA-seq of human fetal lung primary tissues and cell cultures derived from fetal bud tip progenitors under dual SMAD treatment

Project description:Underdeveloped lungs are a primary cause of morbidity and mortality in premature infants, but our ability to help these patients by speeding up lung development are hindered by a lack of understanding of human lung developmental biology. Here, we performed single cell RNA sequencing of the human fetal lung from samples spanning from 11.5 weeks gestation to 21 weeks gestation from the distal lung, middle airways, and the tracheal epithelium. The primary goal of this experiment was to define fetal cell states to serve as a gold standard for pluripotent stem cell-derived lung cells and tissues, and to identify potential signaling pathways that drive differentiation of lung progenitor cells to mature cell types. Additionally, we generated bud tip progenitor organoids from 12 week human fetal lung bud tip progenitors. We show that treatment of bud tip progenitor organoids with a short pulse of dual SMAD activation (BMP4+TGFb1) led to the upregulation of lung basal cell markers, a cell type that serves as a critical stem cell for the adult airway, and that further treatment with dual SMAD inhibition leads to the generation of airway-like organoids containing differentiated cell types of the adult airway, including basal stem cells.

2020-04-17 | E-MTAB-8221 | biostudies-arrayexpress

Single-cell RNA-seq of fibroblasts influenced by exosomes derived from melanoma cell line G361

Project description:In this in-vitro study, we demonstrated the different effects of exosomes produced by G361 melanoma cells on the functional properties of normal dermal fibroblasts and fibroblasts prepared from skin metastasis of cutaneous malignant melanoma. Both normal and cancer-associated fibroblasts were cultivated in either DMEM with 10% EDS (exosome-depleted serum) (control) or DMEM with 10% EDS + 10 microg/ml G361 exosomes (EXO). The cells were harvested after 24 hours of cultivation.

2021-12-31 | E-MTAB-10290 | biostudies-arrayexpress

scRNA-seq of hPSC-derived human intestinal organoids with endogenous vascular endothelial cells

Project description:The development of human pluripotent stem cell (hPSC)- derived small intestinal organoids (HIOs) has led to an improved understanding of human intestinal development and physiology. HIOs generated using directed differentiation lack some cellular populations found in the native organ, including vasculature. We performed single cell RNA sequencing (scRNA-seq) on approximately 13,000 cells at various timepoints (0, 3, 7, and 14 days) across HIO in vitro development and observed a transient population of endothelial-like cells (ECs) present within HIOs early during differentiation. Our data demonstrate that EC-like cells fail to be robustly maintained in long term culture. Here, we have developed a new directed differentiation approach to enhance co-differentiation and maintenance of ECs within HIOs, leading to the development of vascularized HIOs (vHIOs). scRNAseq was used to compare vHIOs to control HIOs after 59d months in culture.

2020-12-20 | E-MTAB-9228 | biostudies-arrayexpress

scRNA-seq of human fetal intestinal jejunum tissue

Project description:Here, we performed single-cell RNA sequencing (scRNA-seq) of a human fetal jejunum tissue sample from 1 individual biological specimen age 40 weeks post conception. The data set is composed of cells from diverse intestinal lineages.

2022-02-01 | E-MTAB-11335 | 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