Cd5a7c31-323a-463d-ba9f-37db5feb6d99 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001009288 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Human iPSC derived dopaminergic neurons were characterized using unbiased single cell transcriptomics. Then study the genetic effect of the A-syn A53T mutation along with oxidative and ER stress induced by rotenone and tunicamycin respectively.
2020-05-29 | E-MTAB-9154 | biostudies-arrayexpress
Project description:To examine the protein spatial and temporal changes upon carfilzomib-mediated proteasome inhibition in cardiac cells, we produced human iPSC-derived cardiomyocytes using a standard small molecule based protocol. Cardiomyocyte identity was confirmed by morphology, observation of contraction, and the presence of GFP tagged MLC-2a in the reporter line. We then applied the SPLAT protocol to untreated and carfilzomib-exposed iPSC-cardiomyocytes.
2023-04-28 | PXD041386 | JPOST Repository
Project description:To examine the protein spatial and temporal changes upon carfilzomib-mediated proteasome inhibition in cardiac cells, we produced human iPSC-derived cardiomyocytes using a standard small molecule based protocol. Cardiomyocyte identity was confirmed by morphology, observation of contraction, and the presence of GFP tagged MLC-2a in the reporter line. We then applied the SPLAT protocol to untreated and carfilzomib-exposed iPSC-cardiomyocytes.
2023-11-03 | PXD046649 | JPOST Repository
Project description:To identify epigenetic programs underlying differentiation of mouse retina, we performed ATAC-Seq on bulk native retina (NaR) and iPSC-derived 3D retinal aggregates (3D-RA) at three matched stages of development: embryonic day (E)13 vs differentiation day (DD)13, postnatal day (P)0 vs DD21, and P5 vs DD25. We produced a total of 24 ATAC-seq libraries with two technical replicates (using either 1 ul or 2 ul of TDE1 enzyme) of two biological replicates, and two genomic DNA libraries to use for background controls.
2021-06-30 | E-MTAB-9440 | biostudies-arrayexpress
Project description:Induced pluripotent stem cell (iPSC) derived organoid systems provide models to study human organ development. Single-cell transcriptome sequencing enables highly-resolved descriptions of cell state heterogeneity within these systems and computational methods can reconstruct developmental trajectories. However, new approaches are needed to directly measure lineage relationships in these systems. Here we establish an inducible dual channel lineage recorder, iTracer, that couples reporter barcodes, inducible CRISPR/Cas9 scarring, and single-cell transcriptomics to analyze state and lineage relationships in iPSC-derived systems. This data set include the iTracer data of 12 cerebral organoids.
2021-11-03 | E-MTAB-10974 | biostudies-arrayexpress
Project description:Induced pluripotent stem cell (iPSC) derived organoid systems provide models to study human organ development. Single-cell transcriptome sequencing enables highly-resolved descriptions of cell state heterogeneity within these systems and computational methods can reconstruct developmental trajectories. However, new approaches are needed to directly measure lineage relationships in these systems. Here we establish an inducible dual channel lineage recorder, iTracer, that couples reporter barcodes, inducible CRISPR/Cas9 scarring, and single-cell transcriptomics to analyze state and lineage relationships in iPSC-derived systems. This data set include the spatial iTracer data of three slices of one cerebral organoid measured by 10x Visium.
2021-11-03 | E-MTAB-10972 | biostudies-arrayexpress
Project description:Induced pluripotent stem cell (iPSC) derived organoid systems provide models to study human organ development. Single-cell transcriptome sequencing enables highly-resolved descriptions of cell state heterogeneity within these systems and computational methods can reconstruct developmental trajectories. However, new approaches are needed to directly measure lineage relationships in these systems. Here we establish an inducible dual channel lineage recorder, iTracer, that couples reporter barcodes, inducible CRISPR/Cas9 scarring, and single-cell transcriptomics to analyze state and lineage relationships in iPSC-derived systems. This data set include the iTracer data of two microdissected regions of one cerebral organoid.
2021-11-03 | E-MTAB-10973 | biostudies-arrayexpress
Project description:Induced pluripotent stem cell (iPSC) derived organoid systems provide models to study human organ development. Single-cell transcriptome sequencing enables highly-resolved descriptions of cell state heterogeneity within these systems and computational methods can reconstruct developmental trajectories. However, new approaches are needed to directly measure lineage relationships in these systems. Here we establish an inducible dual channel lineage recorder, iTracer, that couples reporter barcodes, inducible CRISPR/Cas9 scarring, and single-cell transcriptomics to analyze state and lineage relationships in iPSC-derived systems. This data set include the iTracer-perturb data of one cerebral organoid with simultaneous TSC2 perturbation and lineage recording.
2021-11-03 | E-MTAB-10971 | biostudies-arrayexpress
Project description:To compare chromatin accessibility across three primate species, between wild-type (WT) and genetically modified induced pluripotent stem cell (iPSC) lines, and between the iPSC state and neural precursor cells (NPCs) derived from these iPSCs, we generated ATAC-seq data from nine primate samples. The samples included two gorilla WT iPSC samples and one gorilla KRAB-dCas9 iPSC sample (all from the same individual), one orangutan WT iPSC sample, one orangutan KRAB-dCas9 iPSC sample and two orangutan NPC samples (from two different individuals), and one cynomolgus macaque WT iPSC sample and one cynomolgus macaque KRAB-dCas9 iPSC sample (from the same individual). The gorilla and orangutan iPSCs were derived from urinary stem cells (Geuder et al. 2021), while the cynomolgus macaque iPSCs were derived from skin-fibroblasts. The KRAB-dCas9 iPS cell lines were created by stably integrating dox-inducible KRAB-dCas9-HA-P2A-mCherry construct at the AAVS1 locus (Edenhofer et al. 2024). NPCs were obtained by the directed differentiation of iPSCs via dual-SMAD inhibition (Chambers et al. 2009; Ohnuki et al. 2014). ATAC-seq libraries were generated using the Omni-ATAC protocol (Corces et al. 2017) with minor modifications.
2025-10-30 | E-MTAB-15654 | biostudies-arrayexpress
Project description:Induced pluripotent stem cell (iPSC)-derived dopamine neurons provide an opportunity to model Parkinson’s disease (PD) but neuronal cultures are confounded by cellular heterogeneity. By applying high-resolution single cell transcriptomic analyses to Parkinson’s iPSC-derived dopamine neurons carrying the GBA-N370S risk variant, we exploited intra-culture cellular heterogeneity to identify a progressive axis of gene expression variation leading to endoplasmic reticulum stress. Analysis of genes differentially-expressed (DE) along this axis identified the transcriptional repressor histone deacetylase 4 (HDAC4) as an upstream regulator of disease progression. HDAC4 was mislocalized to the nucleus in PD iPSC-derived dopamine neurons and repressed genes early in the disease axis, leading to late deficits in protein homeostasis. Treatment of iPSC-derived dopamine neurons with compounds known to modulate HDAC4 activity upregulated genes early in the DE axis, and corrected Parkinson’s-related cellular phenotypes. Our study demonstrates how single cell transcriptomics can exploit cellular heterogeneity to reveal disease mechanisms and identify therapeutic targets.
2018-10-17 | E-MTAB-7303 | biostudies-arrayexpress