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Transcriptome analysis of pancreatic progenitors differentiated from H9 human embryonic stem cells and induced pluripotent stem cells derived from a Mitchell-Riley Syndrome patient

ABSTRACT: Transcriptome analysis of pancreatic progenitors differentiated from H9 human embryonic stem cells and induced pluripotent stem cells derived from a Mitchell-Riley Syndrome patient

PROVIDER: PRJEB25729 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2445940.fastq.gz	Fastqsanger.gz
	ERR2445950.fastq.gz	Fastqsanger.gz
	ERR2445960.fastq.gz	Fastqsanger.gz
	ERR2445941.fastq.gz	Fastqsanger.gz
	ERR2445951.fastq.gz	Fastqsanger.gz

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Transcriptome analysis of pancreatic progenitors differentiated from H9 human embryonic stem cells and induced pluripotent stem cells derived from a Mitchell-Riley Syndrome patient

Project description:Skin biopsies were obtained from a patient with Mitchell-Riley syndrome caused by a homozygous frame-shift mutation (c.1129C>T) in the RFX6 gene that leads to a premature stop codon (p.Arg377X). The patient suffered severe pancreatic agenesis, in common with other Mitchell-Riley syndrome patients. Fibroblasts from the biopsy were reprogrammed to generate a human induced pluripotent stem cell (hiPSC) line (MRS2-6). To assess the effects of the mutant RFX6 allele on pancreas formation and identify direct targets of the transcription factor RFX6, MRS2-6 and H9 control human embryonic stem cells (hESC) were differentiated into pancreatic progenitors. Samples were harvested for RNA isolation and whole transcriptome analysis at days 4 (definitive endoderm), 7 and 8 (gut tube), and 12 (pancreatic progenitors).

2020-03-30 | E-MTAB-6626 | biostudies-arrayexpress

4sUDRB-seq of human PA1 cells, undifferentiated H9 cells and H9 differentiated FB neurons

Project description:We have optimized the metabolic tagging of newly transcribed RNAs by 4-thiouridine (4sU) to identify newly-transcribed (nascent) circRNAs from human PA1 cells, undifferentiated H9 cells and H9 differentiated FB neurons.

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Transcriptome analysis of pancreatic endoderm differentiated from induced pluripotent stem cells derived from a patient with Mitchell-Riley Syndrome and her unaffected father

Project description:Skin biopsies were obtained from a patient with Mitchell-Riley syndrome and her unaffected father. The patient suffered neonatal diabetes, anaemia, intrauterine growth restriction, pancreatic hypoplasia and duodenal atresia, in common with other Mitchell-Riley syndrome patients. The disease was found to be caused by a homozygous frame-shift mutation (c.1129C>T) in the RFX6 gene that leads to a premature stop codon (p.Arg377Ter), of which her father is a carrier. Fibroblasts from the biopsies were reprogrammed to generate human induced pluripotent stem cell (hiPSC) lines: two from the patient (MRS2-6 & MRS2-10) and two from the father (F14 & F18). To assess the effects of the mutant RFX6 allele on pancreas formation, these iPSC were differentiated into PDX1+ pancreatic endoderm and samples harvested for RNA isolation and whole transcriptome analysis. The number of biological replicates (independent differentiation experiments) carried out for each cell line are as follows: F14 (2), F18 (2), MRS2-6 (1), MRS2-10 (2). Two technical replicates were sequenced for each independent experiment.

2020-10-23 | E-MTAB-9243 | biostudies-arrayexpress

RNA-seq of UGP2 mutant human embryonic stem cells and in vitro differentiated neural stem cells

Project description:We report transcriptome analysis of human embryonic stem cells and in vitro differentiated neural stem cells, comparing wild type H9, UGP2 homozygous knock-out and UGP2 mutant cells harboring a homozygous A>G nucleotide change affecting the start codon of UGP2 isoform 2 that was introduced by CRISPR-Cas9 engineering

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Analysis of the protein cargo of extracellular vesicles isolated from cultured line H9 human stem cells

Project description:Extracellular vesicles (EV) are secreted by nearly every mammalian cell type and contain a wealth of bioactive cargo capable of modulating target cell physiology and function though a variety of paracrine signaling mechanisms (Leavitt et al., 2019). Human embryonic stem cell (hESC)-derived extracellular vesicles (hESC-derived EV), were extracted from the hESC line H9 (WA09 Wicell Research Institute, Inc., Madison, WI). We analyzed the bioactive protein cargo to identify components that help to resolve radiation-induced injury to the lung in mice when injected in vivo.

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Project description:Human ES (H9) cells were directed towards a neuromesodermal progenitor-like cell state and these cells were then subsequently differentiated towards a neural cell fate. Human ES cells (H9) were differentiated into neuromesodermal progenitor-like cells by culturing in Neurobasal/1x N2/1x B27 medium (N2/B27) supplemented with 20 ng/ml bFgf and 3 μM CHIR99021 for 3 days and exposure to dual SMAD inhibition (dSMADi) (Noggin 50 ng/ml and the TGFb receptor type 1 inhibitor SB431542 10 μM) during day 3 (D3). Transcriptome analysis was then carried out following a selection procedure to enrich for NMP-like cells (sD3/NMP-like). This involved use of a hES (H9) cell line engineered with CRISPR-Cas9 to express GFP under the control of the endogenous Nkx1.2 promoter. At the end of day 3 cells were selected for high GFP expression, as high Nkx1.2 transcription is characteristic of NMP cell populations in mouse and chick embryos. These cells were then lysed and RNA extracted for RNASeq. Humans ES cells (H9) differentiated into NMP-like cells as above (without selection) were also allowed to develop further on day 4 (in the presence of dSMADi and Retinoic acid (RA) 100nM, in N2/B27) and then in RA alone until end of day 8 (D8). These cells were then lysed and RNA extracted for RNASeq.

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Bulk RNAsequencing of H9 Primed and Naïve Pluripotent Stem Cells with and without EZH2 inhibition.

Project description:Bulk RNAseq of 3 replicates of primed H9 +/- EZH2i (E8Flex) and 3 replicates of naive H9 +/- EZH2i (PXGL) to assess the effect of EZH2i in human pluripotent stem cells

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Gene expression analysis of H9 hESC derived cardiomyocytes (CM) and neuron stem cells (NSC)

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Fosl1 transdifferentiate embryonic stem cells to differentiated trophoblast stem cells

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