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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

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

PROVIDER: PRJEB39029 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR4289972_1.fastq.gz	Fastqsanger.gz
	ERR4289972_2.fastq.gz	Fastqsanger.gz
	ERR4289973_1.fastq.gz	Fastqsanger.gz
	ERR4289973_2.fastq.gz	Fastqsanger.gz
	ERR4289974_1.fastq.gz	Fastqsanger.gz

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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

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

Global gene expression profile and splicing events of iPS-derived motorneurons from SMA patient, unaffected father and TGC-treated cells

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Global gene expression profiles of iPSC from SMA patient, unaffected father and iPS 19.9 compared to transcriptomic data obtained by corresponding fibroblasts

2013-01-04 | GSE27206 | GEO

Global gene expression profile and splicing events of iPS-derived motorneurons from SMA patient, unaffected father and TGC-treated cells

Project description:Spinal Muscular Atrophy (SMA) is an autosomal recessive motor neuron disease and is the second most common genetic disorder leading to death in childhood. Motoneurons derived from induced pluripotent stem cells (iPSC) obtained by reprogramming SMA patient and his healthy father fibroblasts, and genetically corrected SMA-iPSC obtained converting SMN2 into SMN1 with target gene correction (TGC), were used to study gene expression and splicing events linked to pathogenetic mechanisms. Microarray technology was used to assess the global gene expression profile as well as splicing events of iPS-derived motorneurons from SMA patient, unaffected father and TGC-treated cells. The microarray data derived from three different groups: SMA patient, healty father and treated SMA patient's cells. Each population consists of three RNA profiling cell samples.

2013-01-04 | E-GEOD-27205 | biostudies-arrayexpress

Global gene expression profiles of iPSC from SMA patient, unaffected father and iPS 19.9 compared to transcriptomic data obtained by corresponding fibroblasts

Project description:Spinal Muscular Atrophy (SMA) is an autosomal recessive motor neuron disease and is the second most common genetic disorder leading to death in childhood. Motoneurons derived from induced pluripotent stem cells (iPS cells) obtained by reprogramming SMA patient and his healthy father fibroblasts, and genetically corrected SMA-iPSC obtained converting SMN2 into SMN1 with target gene correction (TGC), were used to study gene expression and splicing events linked to pathogenetic mechanisms. Microarray technology was used to assess global gene expression profiles of iPSC from SMA patient, unaffected father and iPS 19.9 (Prof. J. Thomson's lab) compared to transcriptomic data obtained by corresponding fibroblasts. The microarray data derived from three different individuals: SMA patient, healthy father and control iPS cells (19.9). We analyzed iPSC from SMA patient (n=2), iPS- from healthy father (n=1) and iPS-19.9 from Prof. Thomson's lab (n=3). The expression profile was compared to SMA patient's fibroblasts (n=2) and healthy father's fibroblasts (n=1)

2013-01-04 | E-GEOD-27206 | biostudies-arrayexpress

GRO-seq in mouse Epiblast-primed, Primitive endoderm-primed, and differentiated endoderm cells

Project description:The identification of changes in transcriptional regulation during priming and differentiation of embryonic stem (ES) cells towards the endoderm lineage. Specific populations of ES cells, either primed or committed to endoderm, were isolated and subjected to global nuclear run on sequencing (GRO-Seq). The hHex-Venus (HV) reporter ES cell line, HVJu5.1 (Canham et al., 2010) was used to isolate HV- and HV+ ES cells. Primed ES cells were identified based on the expression of the HV marker in addition to the cell surface marker of undifferentiated ES cells, SSEA-1, (the lower and upper 25% of SSEA-1+, HV expressing cells). When challenged to differentiate, HV- ES cells are primed towards an epiblast fate, while HV+ ES cells are primed towards primitive endoderm. However, these populations are considered primed, rather than committed, as they will readily interconvert when re-introduced into standard ES cell culture conditions. ES cells were grown in self-renewing conditions (GMEM, LIF, 10% FCS, plated on gelatin coated dishes). Endoderm was obtained by differentiating ES cells in medium without the cytokine LIF for 5 days. The HV+, SSEA-1- differentiated fraction was then sorted and represents an early stage in endoderm differentiation.

2022-01-03 | GSE58503 | GEO

Transcription profling of human embryonic stem cells differentiated into endoderm progenitors in chemically-defined media.

Project description:Human embryonic stem cells differentiated into endoderm progenitors in chemically-defined media.

2010-04-02 | E-MEXP-2373 | biostudies-arrayexpress

Dynamic proteomic profiling of extra-embryonic endoderm differentiation in mouse embryonic stem cells

Project description:During mammalian pre-implantation development, the cells of the blastocyst’s inner cell mass differentiate into the epiblast and primitive endoderm lineages, which give rise to the fetus and extra-embryonic tissues, respectively. Extra-embryonic endoderm differentiation can be modeled in vitro by induced expression of GATA transcription factors in mouse embryonic stem cells. Here we use this GATA-inducible system to quantitatively monitor the dynamics of global proteomic changes during the early stages of this differentiation event and also investigate the fully differentiated phenotype, as represented by embryo-derived extra-embryonic endoderm (XEN) cells. Using mass spectrometry-based quantitative proteomic profiling with multivariate data analysis tools, we reproducibly quantified 2,336 proteins across three biological replicates and have identified clusters of proteins characterized by distinct, dynamic temporal abundance profiles. We first used this approach to highlight novel marker candidates of the pluripotent state and extra-embryonic endoderm differentiation. Through functional annotation enrichment analysis, we have shown that the downregulation of chromatin-modifying enzymes, the re-organization of membrane trafficking machinery and the breakdown of cell-cell adhesion are successive steps of the extra-embryonic differentiation process. Thus, applying a range of sophisticated clustering approaches to a time-resolved proteomic dataset has allowed the elucidation of complex biological processes which characterize stem cell differentiation and could establish a general paradigm for the investigation of these processes.

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