Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of human intestinal organoids infected with Salmonella enterica at 2.5h and 8h post infection

ABSTRACT: The purpose of this experiment was to identify intestinal epithelial responses to various strains of Salmonella enterica. Human intestinal organoids were infected with three serovars of Salmonella; Typhimurium, Enteritidis and Typhi, as well as type 3 secretion system -1 and -2 mutants in Typhimurium in order to identify host responses that were similar and unique to each serovar, and responses that were dependent on these secretion systems.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Homo sapiens

SUBMITTER: Anna-Lisa Lawrence

PROVIDER: E-MTAB-10451 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of human intestinal organoids co-cultured with human PMNs infected with Salmonella enterica serovar Typhimurium and Enteritidis at 8h post infection

Project description:The purpose of this experiment was to identify the contribution of PMNs in intestinal epithelial responses to Salmonella infection.

2022-12-02 | E-MTAB-11089 | biostudies-arrayexpress

Epithelial maturation of human intestinal organoids from pluripotency entirely in vitro

Project description:In vitro human pluripotent stem cell derived intestinal organoids (HIOs) are immature and lack for diverse differentiated secretory cell types. We would like to test the hypothesis whether addition of a mesenchyme secreting ligand which is depleted in canonical organoid culture media could increase the maturity and secretory cell type diversity in HIOs in vitro. To do this, we adapted the directed differentiation protocol of HIOs by growing HIOs in media with EGF, NOGGIN, R-spondin-1 (ENR) for 30 days, isolated epithelial cells with dispase, recovered them with adult intestinal enteroid media with Wnt-3A (WENR). Then we introduced the mesenchyme secreting ligand NRG1 to the established enteroid culture (WENR+NRG1) and compared them to the enteroids grown in control condition (WENR).

2022-12-31 | E-MTAB-10876 | biostudies-arrayexpress

RNA-seq of transplanted pluripotent stem cells-derived human intestinal organoids upon mechanical lengthening and human jejunum tissues

Project description:Human Intestinal Organoids (HIOs) generated from embryonic and/or induced pluripotent stem cell lines offer an avenue to study both developmental and human specific disease states. Recently, progress has been made in scaling and maturing these inherently immature tissues through transplanting them in vivo. However, these resultant grafts best approximate fetal intestinal tissue thus limiting their utility. To induce growth and maturation of HIOs we used a nitinol spring device to mechanically induce enterogenesis of HIO in vivo. HIOs are cultured prior to implantation within the mesentery of immunodeficient mice. They are allowed to grow, vascularize, and mature before a second procedure is performed wherein a compressed nitinol spring is implanted within the lumen of the transplanted HIO (tHIO). Next Generation RNA sequencing was performed across transplanted samples as well as on human surgical samples to highlight the transcriptional similarities and differences between groups. Transcriptionally, the tHIO+S samples were more similar to human tissues than the tHIO. With these initial experiments, we concluded that the application of an intraluminal uniaxial force is a practical method to induce maturation of tHIOs in vivo without concomitant architectural disruptions. While our current system does lack certain complexities, we have demonstrated enterogenesis by means of mechanical manipulation.

2018-03-30 | E-MTAB-6017 | biostudies-arrayexpress

Transcriptional characterization of Human Lung Organoids (HLOs) using RNAseq

Project description:Human lung organoids (HLOs) were derived from human embryonic stem cell line H9 NIH registry #0062. Sequencing of HLOs was performed by the UM DNA Sequencing Core, using Illumina Hi-Seq platform and single-end 50 bp reads. The UM Bioinformatics Core downloaded the reads files from the Sequencing Core storage, and concatenated those into a single .fastq file for each sample. 3 HLOs were cultured for 65 days and 3 HLOs were cultured in vitro for 110 days. HLO Culture Protocol 4-day Activin A (R&D systems) differentiation protocol was used to derive definitive endoderm from human pluripotent stem cells (hPSCs). Cells were treated with Activin A (100ngml-1) for three consecutive days in RPMI 1640 media (Life Technologies) with increasing concentrations of 0%, 0.2% and 2% HyClone defined fetal bovine serum (dFBS, Thermo Scientific). The fourth day was a repeat of day 3 media (2% HyClone FBS). After differentiation into definitive endoderm, cells were incubated in foregut media (advanced DMEM/F12 plus N-2 and B27 supplement, 10mM Hepes, 1x L-Glutamine (200mM), 1x Penicillin-streptomycin (5,000 U/mL, all from Life Technologies)) with 200ng/mL Noggin (NOG, R&D Systems) and 10uM SB431542 (SB, Stemgent) for 4 days, SB, 500ng/mL FGF4 (R&D Systems), and 2 uM CHIR99021 (Chiron, Stemgent), and 1uM SAG (Enzo Life Sciences) for 4-6 days. After 4 days with treatment of growth factors, three-dimensional floating spheroids were present in the culture. Three-dimensional spheroids were transferred into Matrigel to support 3D growth. Spheroids were embedded in a droplet of Matrigel (BD Bioscience #356237) in one well of a 24 well plate, and incubated at room temperature for 10 minutes. After the Matrigel solidified, foregut media with 1% Fetal bovine serum (FBS, CAT#: 16000-044, Life Technologies) and 500ng/mL FGF10 (R&D Systems) were overlaid and replaced every 4 days. Organoids were transferred into new Matrigel droplets every 10 to 15 days.

2015-03-09 | E-MTAB-3339 | 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

Gene expression patterns in developing intestinal organoids exposed to prolonged FGF4- and Wnt-signaling

Project description:Based on the ability of FGF and/or WNT signaling to control posterior fate and intestinal lineage commitment, several groups have reported that treating mouse or human Pluripotent Stem Cell (PSC) derived definitive endoderm (DE) with small molecules or ligands that activate WNT signaling, or a combination of WNT and FGF signaling can induce an intestinal fate in human DE. In this current study, we leverage hESC derived human intestinal organoids (HIOs) to test the hypothesis that the duration of exposure to high levels of FGF and WNT signaling controls regional intestinal identity, with shorter durations generating intestine similar to the proximal duodenum, and longer durations distalizing HIOs to become similar to jejunum/ileum. Our results demonstrate that exposing human definitive endoderm (DE) cultures to short or long incubations of media that activate WNT and FGF siganling results in gene and protein expression profiles that are consistent with tissue that has been patterned into proximal (duodenum) or distal (ileum) small intestine, respectively.

2016-07-04 | E-MTAB-4168 | biostudies-arrayexpress

Epithelium-only cultured stem cells isolated from human pluripotent stem cell derived intestinal organoids grown in matrigel and alginate

Project description:Human intestinal organoids were grown in a typical 3D matrigel culture environment, or in an alginate gel, then a subset from each condition were xenotransplanted to vascularized and mature in vivo. Epithelium was isolated and epithelial only organoids (enteroids) were then grown from each condition prior to sequencing bulk RNA-sequencing.

2019-06-27 | E-MTAB-7000 | biostudies-arrayexpress

scRNA-seq of pluripotent stem cell-derived human intestinal organoids grown in Epiregulin

Project description:Here, we used single-cell RNA-sequencing (scRNA-seq) to profile pluripotent stem cell-derived human intestinal organoids (HIOs) grown in media comprised of minigut media + varying concentrations of Epiregulin (EREG) 1 ng/ml, 10 ng/ml, 100 ng/ml after 28 days of in vitro growth.

2023-10-31 | E-MTAB-13463 | biostudies-arrayexpress

RNA-seq of transplanted Human Intestinal Organoids differentiated with and without PVDF-TrFE Substrate

Project description:Experiment was aimed at testing the compatibility of a piezoelectric material with the differentiation and proper patterning of human intestinal organoids.

2023-12-30 | E-MTAB-13578 | 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