An optimized platform to generate human cerebral organoids
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ABSTRACT:
PROVIDER: PRJNA573699 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We established a protocol to generate morphologically uniform human cerebral organoids with similar cell type composition at various time points of maturation as determined by single cell sequencing.
2020-04-11 | GSE137877 | GEO
Project description:We utilized patient-derived induced pluripotent stem cells (iPSCs) to generate 3D cerebral organoids to model neuropathology of Scz during this critical period. We discovered that Scz organoids exhibited ventricular neuropathology resulting in altered progenitor survival and disrupted neurogenesis. cz organoids principally differed not in their proteomic diversity, but specifically in their total quantity of disease and neurodevelopmental factors at the molecular level. Provides unique insights into the proteome landscape of schizophrenia in patient-derived cerebral organoids
2021-11-17 | PXD027812 | Pride
Project description:Brain organoids reproducibly generate the cellular diversity of the human cerebral cortex
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Project description:Bulk ATAC-seq was performed on human, chimpanzee, bonobo, and macaque stem cell-derived cerebral organoids. ATAC-seq was performed on day 60 (2 months old) and day 120 (4 months old) cerebral organoids.
2019-10-16 | E-MTAB-8228 | biostudies-arrayexpress
Project description:Pluripotent stem cells (PSC) can differentiate inot any cell type of an organism. Their remarkable capability of self-organization enables the formation of three-dimensional structures that resembles miniature organs, including cerebral organoids. These organoids can recreate early steps of the human cerebral cortex development, and show great potential for modeling human diseases, particularly for those with a developmental component. This data evidences stem cell-derived cerebral organoids as a key model to study brain development and neurodevelopmental, neurodegenerative and neuropsychiatric diseases.
2019-11-15 | PXD011605 | Pride
Project description:Cerebral organoids â three-dimensional cultures of human cerebral tissue derived from pluripotent stem cells â have emerged as models of human cortical development. However, the extent to which in vitro organoid systems recapitulate neural progenitor cell proliferation and neuronal differentiation programs observed in vivo remains unclear. Here we use single-cell RNA sequencing (scRNA-seq) to dissect and compare cell composition and progenitor-to-neuron lineage relationships in human cerebral organoids and fetal neocortex. Covariation network analysis using the fetal neocortex data reveals known and novel interactions among genes central to neural progenitor proliferation and neuronal differentiation. In the organoid, we detect diverse progenitors and differentiated cell types of neuronal and mesenchymal lineages, and identify cells that derived from regions resembling the fetal neocortex. We find that these organoid cortical cells use gene expression programs remarkably similar to those of the fetal tissue in order to organize into cerebral cortex-like regions. Our comparison of in vivo and in vitro cortical single cell transcriptomes illuminates the genetic features underlying human cortical development that can be studied in organoid cultures. 734 single-cell transcriptomes from human fetal neocortex or human cerebral organoids from multiple time points were analyzed in this study. All single cell samples were processed on the microfluidic Fluidigm C1 platform and contain 92 external RNA spike-ins. Fetal neocortex data were generated at 12 weeks post conception (chip 1: 81 cells; chip 2: 83 cells) and 13 weeks post conception (62 cells). Cerebral organoid data were generated from dissociated whole organoids derived from induced pluripotent stem cell line 409B2 (iPSC 409B2) at 33 days (40 cells), 35 days (68 cells), 37 days (71 cells), 41 days (74 cells), and 65 days (80 cells) after the start of embryoid body culture. Cerebral organoid data were also generated from microdissected cortical-like regions from H9 embryonic stem cell derived organoids at 53 days (region 1, 48 cells; region 2, 48 cells) or from iPSC 409B2 organoids at 58 days (region 3, 43 cells; region 4, 36 cells).
2015-12-07 | E-GEOD-75140 | biostudies-arrayexpress
Project description:Single cell ATAC-seq (scATAC-seq) was performed on bonobo induced pluripotent stem cells (iPSC) derived cerebral organoids. scATAC-seq was performed on day 60 (2 months old cerebral organoid) and day 120 (4 months old cerebral organoid).
2019-10-16 | E-MTAB-8083 | biostudies-arrayexpress
Project description:Single cell ATAC-seq (scATAC-seq) was performed on macaque embryonic stem cell-derived cerebral organoids. scATAC-seq was performed on day 60 (2 months old cerebral organoid).
2019-10-16 | E-MTAB-8087 | biostudies-arrayexpress
Project description:Human induced pluripotent stem cell (iPSC)-derived lung organoids, engineered to carry targeted genes, offer a robust platform for investigating mechanistic insights in lung research. Although lentiviral vectors (LVVs) are highly effective for stable expression due to their integrative properties, achieving efficient transduction in human iPSC-derived lung organoids poses a significant technical challenge, likely due to the complex structure of these organoids. In this study, we optimized a method to enhance LVV transduction efficiency by physically disrupting the organoids to increase surface area, followed by spinoculation to apply shear force during cell dissociation. This approach, combined with the use of an optimized culture medium, significantly improved transduction efficiency. The success of this method was validated at both the gene and protein levels using single-cell RNA sequencing (scRNA-seq) and various cellular and molecular assays. Our optimized transduction protocol may provide a valuable tool for investigating specific cellular and molecular mechanisms in development and disease models using human iPSCs-derived lung organoids.
2025-01-02 | GSE284689 | GEO
Project description:Single cell ATAC-seq (scATAC-seq) was performed at various stages of differentiation of human pluripotent stem cells to 4 month old cerebral organoids. scATAC-seq was performed on the following days of differentiation: day 0 (pluripotent stem cell), day 4 (embryoid body), day 10 (neuroectoderm), day 15 (neuroepithelium), day 30 (1 month old cerebral organoid), day 60 (2 months old cerebral organoid), and day 120 (4 months old cerebral organoid).
2019-10-16 | E-MTAB-8089 | biostudies-arrayexpress