Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A high-resolution single-cell multiomic atlas of the human fetal lung - Organoid

ABSTRACT: We obtained human embryonic and fetal lungs from 5-22 pcw for scRNAseq and scATACseq analysis. To focus on epithelial differentiation and region specialization, we deeply sampled 15, 18, 20 and 22 pcw lungs and separated proximal and distal regions while leaving lungs at 5, 6, 9 and 11 pcw intact. These cell samples (except for one at 6pcw) were split and processed for both scRNAseq and scATACseq.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Wei Kheng Teh

PROVIDER: E-MTAB-11267 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

A high-resolution single-cell multiomic atlas of the human fetal lung - Visium

Project description:We obtained human embryonic and fetal lungs from 5-22 pcw for scRNAseq and scATACseq analysis. To focus on epithelial differentiation and region specialization, we deeply sampled 15, 18, 20 and 22 pcw lungs and separated proximal and distal regions while leaving lungs at 5, 6, 9 and 11 pcw intact. These cell samples (except for one at 6pcw) were split and processed for both scRNAseq and scATACseq.

2022-01-27 | E-MTAB-11265 | biostudies-arrayexpress

A high-resolution single-cell multiomic atlas of the human fetal lung - scRNA / GEX / VDJ

2022-01-27 | E-MTAB-11278 | biostudies-arrayexpress

A high-resolution single-cell multiomic atlas of the human fetal lung - ATAC-seq

2022-01-27 | E-MTAB-11266 | 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

Single-cell sequencing of developing human gut reveals transcriptional links to childhood Crohn’s disease

Project description:In this study, we performed single-cell transcriptional profiling of human embryonic and fetal gut samples obtained from 9 human embryos spanning ages 6-10 PCW and three regions (duo-jejunum, ileum and colon). Additionally, we profile mucosal biopsies from the terminal ileum of healthy children aged 4-12 years (n = 8) as well as a group of children newly diagnosed with Crohn’s disease (CD) (n = 7), a common form of IBD. Tissue samples were treated using an enzymatic dissociation protocol and single cell suspensions were then processed using the 3’v2 10x Genomics Chromium workflow. In a subset of samples, the intestinal epithelial cell fraction was enriched by performing magnetic bead sorting for EPCAM. In total, we generate single cell transcriptomes of ~90,000 primary human intestinal cells providing a rich resource and detailed roadmap. Using this data as well as scRNAseq profiles of human fetal gut derived organoids we describe embryonic and fetal epithelium composition, trace their differentiation dynamics and signaling partners, and provide links to regenerating Crohn’s disease epithelium.

2020-12-22 | E-MTAB-8901 | 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

Molecular karyotype analysis of 25 clinical-grade human embryonic stem cell lines

Project description:Clinical-grade human embryonic stem cells (hESCs) from 4 centres in the UK were cultured in self-renewal conditions Genomic DNA was isolated from low passage hESCs and submitted for SNP analysis using Illumina HumanCytoSNP-12 v2.1 BeadChip arrays Evaluation of molecular karyotype of multiple clinical-grade hESC lines.

2015-05-05 | E-GEOD-68508 | biostudies-arrayexpress

MHC class II antigen presentation by intestinal epithelial cells fine-tunes bacteria-reactive CD4 T cell responses

Project description:Intestinal organoids stimulated with conditioned media from inflamed or non-inflamed source.

2023-11-09 | E-MTAB-12414 | biostudies-arrayexpress

RNA-seq of WT, Mbd3-/- and rescue hiPSC during neuroectodermal differentiation and of WT and Mbd3-/- in mEpiSC during neuroectodermal differentiation

Project description:Differentiation of mammalian pluripotent cells involves large-scale changes in transcription and chromatin remodellers are essential to initiate, establish and maintain a new gene regulatory network. In this study, we investigated the structure and function of the nucleosome remodeller and deacetylase (NuRD) complex in human induced pluripotent stem cells (hiPSCs) and in mouse epiblast stem cells (mEpiSCs). We studied gene expression changes at the self-renewal state (0 days) and at 3, 6 and 12 days of neuroectodermal differentiation in WT, Mbd3-/- and rescue hiPSCs and at 2, 4 and 8 days of neuroectodermal differentiation in mEpiSCs. Sequencing libraries were prepared using the NEXTflex Rapid Directional RNA-seq kit (Illumina) or SMARTer® Stranded Total RNA-Seq Kit v2—Pico Input Mammalian (Takara Bio) and sequenced on the Illumina platform at the CRUK Cambridge Institute Genomics Core facility (Cambridge, UK). Illumina sequence files were converted into FASTQ format. The short sequence reads (75 nucleotides) were aligned to the Human reference genome (hg38; http://genome.ucsc.edu/) or to the Mouse reference genome (mm10; http://genome.ucsc.edu/) and assigned to genes using BWA (Li & Durbin, 2009). We used the Subread package (R statistical tool; http://www.r-project.org/) to count aligned reads. Differentially expressed genes were identified using R package edgeR (Chen, Lun, & Smyth, 2016).

2020-03-30 | E-MTAB-8753 | biostudies-arrayexpress

scRNA-seq and snucRNA-seq of human primary trophoblast organoids (PTO) and trophoblast stem cells (TSCs) differentiation into extravillous trophoblast organoids (EVTs)

Project description:This study aims to compare in vivo human trophoblast differentiation into EVTs to different in vitro trophoblast organoids using single-cell and single-nuclei RNA sequencing. The study includes two type of systems: human primary trophoblast organoids (PTO) and trophoblast stem cells (TSCs). Trophoblast stem cell (TSC) lines BTS5 and BTS11 derived by Okae and colleagues were grown as described previously (Okae et al. 2018) and together with EVT media. Primary trophoblast organoids (PTO) were grown and differentiated into EVT as previously described by Turco & Sheridan (Turco et al 2018; Sheridan et al 2020). This study shows that the main regulatory programs mediating EVT invasion in vivo are preserved in in vitro models of EVT differentiation from primary trophoblast organoids and trophoblast stem cells.

2023-02-09 | E-MTAB-12650 | 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