Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

79 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ScRNA-seq of human fetal intestinal ileum tissue

ABSTRACT: Here, we performed single cell RNA sequencing (scRNA-seq) of human fetal ileum tissue samples from 3 individual biological specimens ages 11.4, 14.4, and 18.9 weeks post conception. The data set is composed of over 16,000 cells from diverse intestinal lineages.

INSTRUMENT(S): Illumina HiSeq 4000, Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Joshua Wu

PROVIDER: E-MTAB-9906 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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 human fetal lung and intestine tissue

Project description:Here, we performed single cell RNA sequencing (scRNA-seq) of 1 (one) human fetal lung tissue specimen (18.9 week) and 2 (two) human fetal intestine specimens (12.1 and 18.9 week) (total of 3 (three) independent biological specimens). The data set is composed of approximately 5,000 lung cells and 7,500 intestine cells. Lineages captured across both tissues include but are not limited to epithelium, stroma, immune, neurons and endothelium.

2020-12-20 | E-MTAB-9363 | 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

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 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 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 lung explants with R-SPONDIN Inhibition and human fetal lung primary tissue

Project description:Here, we used single cell RNA-sequencing (scRNA-seq) to profile 13-week post-conception distal human fetal lung explants cultured in an air liquid interface system and treated with an LGR5 ectodomain adenovirus that inhibits R-Spondin function or control adenovirus. A third, non-infected, condition was also sequenced. We also performed scRNA-seq on distal human fetal lung tissue from an 8.4-week post-conception biological specimen. Diverse cell lineages were captured in all data sets, and include epithelium, mesenchyme, immune, neurons, and endothelium.

2022-01-01 | E-MTAB-10662 | 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

scRNA-seq of pluripotent stem cell derived human intestinal organoids

Project description: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.

2021-05-21 | E-MTAB-10268 | 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

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