Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ena-DATASET-WTCHG-06-03-2019-11:21:24:784-222 - samples

ABSTRACT: This dataset contains 27 mapped bam files. The samples were generated with 3 different protocols for deriving pancreatic progenitors from hPSC. Three parallel differentiations were performed, all done in a hPSC NKX6.1-GFP reporter line. For each protocol there are three cellular populations: total (presort), GFP+ and GFP- . In summary: 3 differentiations x 3 protocols x 3 cellular populations. We prepared ATAC-seq libraries for the 27 samples, and sequenced them on Illumina HiSeq4000.

PROVIDER: EGAD00001004824 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

ena-DATASET-WTCHG-06-03-2019-11:18:49:142-220 - samples

Project description:This dataset contains 26 mapped bam files. The samples were generated with 3 different protocols for deriving pancreatic progenitors from hPSC. Three parallel differentiations were performed, all done in a hPSC NKX6.1-GFP reporter line. For each protocol there are three cellular populations: total (presort), GFP+ and GFP- . In summary: 3 differentiations x 3 protocols x 3 cellular populations. We prepared Smart-Seq2 RNA-seq libraries for the 27 samples, 1 sample failed library preparation and is not therefore included in this dataset.

| EGAD00001004823 | EGA

ena-DATASET-WTCHG-18-01-2018-10:47:14:003-216 - samples

Project description:We generated human induced pluripotent stem cell (iPSC) lines with a GFP reporter inserted in the endogenous NKX6.1 locus. Characterisation of the reporter lines demonstrated faithful GFP labelling of NKX6.1 expression during pancreas and motor neuron differentiation. We performed three independent in vitro differentiations towards the pancreatic endocrine lineage. We FACS-purified GFP positive and negative cells from stage 7 cultures, and generated Smart-Seq2 RNA-sequencing libraries for the pre-sorted cells, as well as the two GFP-sorted cell populations. Gene expression profiling by RNA-sequencing reveals that the NKX6.1-positive population closely resembles mature human beta cells and the functional evaluation of purified populations shows that the glucose-responsive beta-like cells are enriched within the NKX6.1-positive population. These reporter lines provide a valuable resource to the scientific community for the derivation of functional relevant pancreas and neuronal cell subtypes.

| EGAD00001003911 | EGA

Mapping human pluripotent stem cell differentiation pathways via high throughput single-cell RNA-sequencing

Project description:Human pluripotent stem cells (hPSCs) provide both powerful models for studying cellular differentiations, and unlimited sources of cells for regenerative medicine. However, a comprehensive single cell level differentiation roadmap for hPSCs has not been achieved yet. Here, we used high throughput single-cell RNA-sequencing (scRNA-seq) method, based on optimized microfluidic circuits, to profile early differentiation lineages in the human embryoid body (EB) system. We presented a cellular landscape for hPSC early differentiations covering different cellular lineages, including neural cell, muscle cell, endothelial cell, stromal cell, liver cell, and epithelial cell. Through pseudotemporal analysis, we constructed the differentiation trajectories of these progenitor cells and revealed the gene expression dynamics in the process of differentiation. We reset Primed H9 into Naïve-like H9 and studied cell state transition process via scRNA-seq. We found that mesendoderm genes are enriched in Naïve-like H9. Functionally, Naïve-like H9 showed better potency for differentiation into the hematopoietic lineages. We constructed the differentiation landscape of hPSC early differentiation by scRNA-seq analysis. We offer new insights into molecular pathways of early embryonic lineages that can be harnessed for optimization of differentiation protocols. (Pipeline for C1 data demultiplex : https://github.com/bioeauty/sccpipe)

2018-03-06 | GSE107552 | GEO

Digital gene expression of directed differenciation protocols

Project description:Lung and hindgut directed differentiations with multiple protocols and time points

2020-01-13 | GSE128922 | GEO

RNA-seq profiling of NKX6.1 reporter iPSC lines for isolation and analysis of functionally relevant neuronal and pancreas populations

| EGAS00001002802 | EGA

IL-27 production by splenic immune cells throughout persistent LCMV infection

Project description:The pleiotropic cytokine IL-27 is essential for the clearance of the persistent LCMV strain Clone 13, however the cellular sources of IL-27 during viral infection are incompletely mapped and their relative importance unknown. Here we utilised single-cell RNA-sequencing of splenocytes from IL27-p28-GFP mice infected with Clone 13 to quantify the temporal patterns of IL-27 p28 production. IL-27-p28-GFP+ and IL-27-p28-GFP- splenocytes were sorted at 4 timepoints during Clone 13 infection and analysed by 3' single-cell transcriptome sequencing. Dendritic cells were major producers of early IL-27 with macrophages and monocytes being the predominant IL-27 producers during acute and persistent phases of infection. Interestingly, we also identified activated B cells and plasma cells as a prominent subset of IL-27-producing splenocytes and through B-cell-specific deletion of IL-27-p28 demonstrated that B-cell derived IL-27 is essential for sustained function of CD4 T cells and eventual clearance of Clone 13.

2022-01-10 | GSE186898 | GEO

Functional Connection with Cardiac Tissues Confers Maturation Phenotypes in hPSC-Derived PHOX2B::GFP Expressing Sympathetic Neurons

Project description:Neurons derived from human pluripotent stem cells (hPSCs) are a remarkable tool for modeling human neural development and diseases. However, it remains largely unknown whether the hPSC-derived neurons can be functionally coupled with their target tissues in vitro, which is essential for understanding inter-cellular physiology and further translational studies. Here, we demonstrate that hPSC-derived sympathetic neurons can be obtained from hPSCs and that the resulting neurons form physical and functional connections with cardiac muscle cells. By use of multiple hPSC reporter lines, we recapitulated human autonomic neuron development in vitro, and successfully isolated PHOX2B::eGFP+ neurons exhibiting sympathetic marker expression, electrophysiological properties, and norepinephrine secretion. With pharmacological and optogenetic manipulations, the PHOX2B::eGFP+ neurons controlled the beating rates of cardiomyocytes, and their physical interaction led to neuronal maturation. Our study lays a foundation for the specification of human sympathetic neurons and for the hPSC-based neuronal control of end organs in a dish. Using the four genetic reporter systems (OCT4::eGFP, SOX10::eGFP, ASCL1::eGFP, and PHOX2B::eGFP reporter hESC lines), we were able to purify discrete cell populations at four differentiation stages, recapitulating the sympathoadrenal differentiation process in vitro with purified and defined populations in four specific differentiation stages. We performed transcriptome analysis of OCT4::eGFP+ cells (3 biological replicates, representing undifferentiated hESCs), SOX10::eGFP+ cells (3 biological replicates, multi-potent neural crest), ASCL1::eGFP+ cells (3 biological replicates, putative sympathoadrenal progenitors), and PHOX2B::eGFP+ cells (2 biological replicates, putative sympathetic neuronal precursors).

2016-07-01 | E-GEOD-80689 | biostudies-arrayexpress

Antisense miRNA-221/222 (si221/222) and control inhibitor (GFP) treated fulvestrant-resistant breast cancer cells

Project description:Full title: Expression data from antisense miRNA-221/222 (si221/222) and control inhibitor (GFP) treated fulvestrant-resistant breast cancer cells The expression of miR-221/222 were found to be upregulated in fulvestrant resistant breast cancer cells MCF7-FR compared to its drug-sensitive counterpart MCF7. To investigate the role of miR-221/222 in acquired resistance to fulvestrant, we lowered the level of miR-221/222 in MCF7-FR cells using miRNA inhibitors (antagomirs), and compared gene expression profiles before and after treatment. Fulvestrant-resistant breast cancer cells MCF7-FR (originated from drug-sentitive breast cancer model cell line MCF7) were transient-transfected by antigomirs targeting miR221 or miR222 (i.e. si221, si222). All three cell lines, MCF7-FR, siR221, siRNA222 were subjected to gene expression profiling.

2011-01-29 | E-GEOD-19777 | biostudies-arrayexpress

ERBB3 and NGFR mark distinct skeletal muscle progenitor cells in human development enabling enrichment and maturation of hPSC muscle

Project description:Abstract: Human pluripotent stem cells (hPSCs) can be directed to differentiate into skeletal muscle progenitor cells (SMPCs). However, the myogenic potential of hPSC-SMPCs compared to human fetal or adult satellite cells (Scs) remains unclear. This study demonstrates hPSC-SMPCs derived by commonly used protocols are functionally less mature than freshly-isolated human fetal or adult Scs. We utilized RNA-SEQ of human fetal Scs to identify differentially expressed genes including NGFR, ERBB3, which enriched for MYOD+ or PAX7+ cells. Furthermore, inhibition of TGFβ (TGFβi) improved hPSC-muscle maturation in three independent lines as measured by TEM and expression of myosins. Engraftment of CRISPR/Cas9-corrected Duchenne Muscular Dystrophy (DMD) hiPSC-SMPC subpopulations treated with TGFβi in vivo, increased dystrophin-positive fibers to levels of engrafted cultured fetal Scs in mdx mouse models of DMD. This work provides the first characterization of the developmental status of hPSC-SMPCs and identifies candidates to enable robust myogenic activity in vitro and in vivo.

2016-09-27 | GSE87365 | GEO

Gene expression profiling (RNA-seq) of SGBS human preadipocytes (days 0, 2, 8 and 16 of differentiation to adipocytes) and iPSC-derived hypothalamic neurons (days 12, 16 and 27 of differentiation)

Project description:Human SGBS preadipocytes were differentiated into adipocytes, and human iPSCs were differentiated into hypothalamic neurons. Cells were collected for RNA-seq at several differentiation stages. The differentiations were performed in one biological replicate, with three technical replicates (different wells of the differentiation that were also processed individually during library preparation). SGBS Day0: Represents the preadipocyte state. SGBS Day2: Represents immature adipocytes. SGBS Day8: Represents early mature adipocytes. SGBS Day16: Represents mature adipocytes. Hypothalamic Day 12: Represents early hypothalamic neurons. Hypothalamic Day 16: Represents mid hypothalamic neurons. Hypothalamic Day 27: Represents mature hypothalamic neurons.

2021-05-22 | E-MTAB-10461 | 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