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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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MRNA-based generation of marmoset PGCLCs capable of differentiation into gonocyte-like cells

ABSTRACT: We developed a mRNA transfection-based method for the efficient generation of primordial germ cell like cells (PGCLCs) in marmoset. Single cell RNA-seq analyses (10X) confirmed that the induced marmoset PGCLCs show transcriptome profile similar to in vivo PGCs. For comparison we sequenced iPSCs, E74 ovaries, E82 ovaries, NB ovaries, E87 testes, and day 22 testes.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Callithrix jacchus

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PROVIDER: E-MTAB-12123 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): ERP140468

REPOSITORIES: biostudies-arrayexpress

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Induced pluripotent stem cells from CINCA syndrome patients as a model for dissecting somatic mosaicism and drug discovery

Project description:Chronic infantile neurological cutaneous and articular (CINCA) syndrome is an IL-1-driven autoinflammatory disorder caused mainly by NLRP3 mutations. The pathogenesis of CINCA syndrome patients who carry NLRP3 mutations as somatic mosaicism has not been precisely described because of the difficulty in separating individual cells based on the presence or absence of the mutation. Here, we report the generation of NLRP3-mutant and non-mutant induced pluripotent stem cell (iPSC) lines from two CINCA syndrome patients with somatic mosaicism, and describe their differentiation into macrophages (iPS-MPs). We found that mutant cells are predominantly responsible for the pathogenesis in these mosaic patients because only mutant iPS-MPs showed the disease relevant phenotype of abnormal IL-1M-NM-2 secretion. We also confirmed that the existing anti-inflammatory compounds inhibited the abnormal IL-1M-NM-2 secretion, indicating that mutant iPS-MPs are applicable for drug screening for CINCA syndrome and other NLRP3-related inflammatory conditions. Our results illustrate that patient-derived iPSCs are useful for dissecting somatic mosaicism, and that NLRP3-mutant iPSCs can provide a valuable platform for drug discovery for multiple NLRP3-related disorders. To characterize iPS and differentiated cells, RNA expression profiles were evaluated by microarray analysis.We analyzed iPC cells and macrophage from healthy volunteers and CINCA syndrome patients. Human ES cella and fibroblasts were used as control.

2012-06-10 | E-GEOD-38626 | biostudies-arrayexpress

Transcriptional dysregulation associated with chromatin accessibility of iPSC and hepatocytes derived from a Cornelia de Lange syndrome patient (scRNA-Seq)

Project description:Cornelia de Lange syndrome (CdLS) is a rare genetic disease associated with cohesinopathy. A novel iPSC line was generated from the CdLS patient carrying a heterozygous missense point-mutation of the NIPBL gene. iPSC lines prepared from the healthy parents and the mutation-corrected isogenic cell lines are used as the respective controls. Upon differentiation into hepatocytes, the patient-derived iPSC demonstrate the capacity to express hepatocyte-specific marker transcripts and the respective proteins, however, the efficiency of differentiation is significantly inferior to those of the respective controls, demonstrated by single-cell RNA sequencing and immune-fluorescent analyses. Global change of transcriptome in the patient-derived iPSC relative to the control cells is associated with altered chromatin accessibility, assessed by RNAseq combined with ATACseq analysis. Differentially down-regulated genes in the patient-derived iPSC, in particular, are those coding for proteins related to neural differentiation and transcription factors, while up-regulated genes contain some of antisense RNA coding genes, pseudo genes and long non-coding RNAs. Some of the differentially regulated genes are consistent with the altered chromatin accessibility and this observation is consistent during hepatocyte differentiation. Thus, the mutation in the NIPBL gene of the CdLS patient could be responsible for defects of differentiation primarily due to alteration of chromatin accessibility.

2023-06-15 | E-MTAB-12636 | biostudies-arrayexpress

Single-cell RNA-sequencing of cells from spinal cord central canal region of young adult and aged mice

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2022-12-13 | E-MTAB-11561 | biostudies-arrayexpress

Translational co-culture model reveals epithelial-mesenchymal mechanisms of lung fibrosis and identifies NF-κB as potential therapeutic target

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2022-10-03 | E-MTAB-11847 | biostudies-arrayexpress

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2024-04-18 | E-MTAB-13721 | biostudies-arrayexpress

Integrated longitudinal immunophenotyping, transcriptional and repertoire analyses depict principles of protective immune responses and memory formation in COVID-19 patients

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2021-07-30 | E-MTAB-9652 | biostudies-arrayexpress

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2022-02-11 | E-MTAB-11289 | biostudies-arrayexpress

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2023-11-23 | E-MTAB-13494 | biostudies-arrayexpress

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2024-01-30 | E-MTAB-11207 | biostudies-arrayexpress

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