CROP-seq of 2 month old brain organoids
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina NovaSeq 6000
ORGANISM(S): Homo sapiens
SUBMITTER: Sophie Jansen
PROVIDER: E-MTAB-11999 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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:In order to provide multi-omic resolution to human retinal organoid developmental dynamics, we performed scRNA-seq and scATAC-seq from the same cell suspension across a time course (6-46 weeks) of human retinal organoid development. This data set covers all the retinal organoid scRNA-seq data generated from IMR90 and409B2-iCas9 cell lines.
2023-03-12 | E-MTAB-12715 | 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 iTracer data of two microdissected regions of one cerebral organoid.
2021-11-03 | E-MTAB-10973 | biostudies-arrayexpress
Project description:In order to provide multi-omic resolution to human retinal organoid developmental dynamics, we performed scRNA-seq and scATAC-seq from the same cell suspension across a time course (6-46 weeks) of human retinal organoid development. This data set covers all the retinal organoid scATAC-seq data generated from IMR90 and 409B2-iCas9 cell lines.
2023-03-12 | E-MTAB-12714 | biostudies-arrayexpress
Project description:Kabuki Syndrome (KS) is a multisystemic rare disorder, characterized by growth delay, distinctive facial features, intellectual disability, and rarely autism spectrum disorder. This condition is mostly caused by de novo mutations of KMT2D, encoding a catalytic subunit of the COMPASS complex involved in enhancer regulation. KMT2D catalyzes the deposition of histone-3-lysine-4 mono-methyl (H3K4Me1) that marks active and poised enhancers. To assess the impact of KMT2D mutations in the chromatin landscape of KS tissues, we have generated patient-derived induced pluripotent stem cells (iPSC), which we further differentiated into neural crest stem cells (NCSC), mesenchymal stem cells (MSC) and cortical neurons (iN). In addition, we further collected blood samples from 5 additional KS patients. To complete our disease modeling cohort we generated an isogenic KMT2D mutant line from human embryonic stem cells, which we differentiated into neural precursor and mature neurons. Micro-electrode-array (MEA)-based neural network analysis of KS iNs revealed an altered pattern of spontaneous network-bursts in a Kabuki-specific pattern. RNA-seq profiling was performed to relate this aberrant MEA pattern to transcriptional dysregulations, revealing that dysregulated genes were enriched for neuronal functions, such as ion channels, synapse activity, and electrophysiological activity. Here we show that KMT2D haploinsufficiency tends to heavily affect the transcriptome of cortical neurons and differentiated tissues while sparing multipotent states, suggesting that KMT2D has a most prevalent role in terminally differentiated cell and activate transcriptional circuitry unique to each cell type. Moreover, thorough profiling of H3K4Me1 unveiled the almost complete uncoupling between this chromatin mark and the regulatory effects of KMT2D on transcription, which is instead reflected by a defect of H3K27Ac. By integrating RNA-seq with ChIP-seq data we defined TEAD and REST as the master effectors of KMT2D haploinsufficiency. Also, we identified a subset of genes whose regulation is controlled by the balance between KMT2D and EZH2 dosage. Finally, we identified the bona fide direct targets of KMT2D in healthy and KS mature cortical neurons and TEAD2 as the main proxy of KMT2D dysregulation in KS. Overall, our study provides the transcriptional and epigenomic characterization of patient-derived tissues as well as iPSCs and differentiated disease-relevant cell types, as well as the identification of KMT2D direct target in cortical neurons, together with the identification of a neuronal phenotype of the spontaneous electrical activity.
2022-12-25 | E-MTAB-10244 | biostudies-arrayexpress
Project description:Comparison of gene expression signatures in undifferentiated hESCs against differentiated embryoid bodies to identify key signatures defining self-renewal of hESCs. Using H1 and H9 hESC lines, we performed gene expression microarray analysis (Affymetrix Human Genome U133 Plus 2.0 Array) and analyzed the interaction patterns of 54,614 genes using WGCNA in R programming
2014-01-18 | E-GEOD-54186 | biostudies-arrayexpress
Project description:Bulk RNA-seq of H9 human embryonic stem cells undergoing conversion from primed to naive pluripotency using the chemical/epigenetic resetting method in tt2iL+Go-based media conditions. The dataset includes three wild-type clones (WT1-3) and two KLF17-null clones (KO1-2) generated through CRISPR-Cas9-mediated gene editing. Samples were collected at day 0 (primed cells in mTeSR1 (StemCell Technologies)), then throughout resetting at day 2 (cells in cRM-1), day 8 (cells in cRM-2+XAV939, immediately prior to the first passage), naive passage 5 (p5), 7 (p7) and 10 (p10) (cells in tt2iL+Go).
2021-09-30 | E-MTAB-10914 | 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:Microarray analysis of isolated hES cells from day 3 of cardiac differentiation was used to identify differences between MIXL1eGFP+ and MIXL1eGFP- transcriptomes. We identified 6,757 differentially regulated genes, of which 2,520 were upregulated â¥2-fold in the eGFP+ (MIXL1+) mesoderm population A stencil differentiation protocol was used to isolate mesodermal cells based on GFP expression from the MIXL1 locus. Microarray analysis of isolated cells from day 3 of differentiation was used to identify differences between MIXL1eGFP+ and MIXL1eGFP- transcriptomes.
2015-11-05 | E-GEOD-74664 | biostudies-arrayexpress