Single cell analysis of SHH-patterned hESCs
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina NovaSeq 6000
ORGANISM(S): Homo sapiens
SUBMITTER:
PROVIDER: E-MTAB-15075 | biostudies-arrayexpress |
SECONDARY ACCESSION(S): ERP171898
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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:To investigate the effects of ZIKV infection or ZIKV-NS4B-transduction on the global proteome scale at early stages of hNPC differentiation into neurons, hNPC cells were infected with ZIKV (Asian strain: H/PF/2013; MOI=0.01) or transduced with ZIKV-NS4B or HCV-NS4B and one day later cells were either left under proliferative conditions or neuronal differentiation was induced with ROCK inhibitors treatment and growth factors withdrawals. Five days later samples were harvested and processed for quantitative label-free proteomics.
2018-09-03 | PXD009557 | Pride
Project description:To explore the non-canonical functions of core clock proteins in ESCs, we generated CRISPR/Cas9-edited isogenic human ESC lines carrying targeted truncations of CLOCK, BMAL1, NR1D1, and/or NR1D2. Comprehensive characterization and transcriptomic analyses demonstrated changes in gene expression associated with pluripotency and differentiation, despite the absence of rhythmic activity.
2026-04-13 | E-MTAB-16296 | biostudies-arrayexpress
Project description:Single-cell RNA-seq (parse biosciences) of in vitro differentiated human trophoblast stem cells, infected with RVFV
2025-12-12 | E-MTAB-16352 | biostudies-arrayexpress
Project description:Use of single-cell transcriptomics to measure how well medium spiny projection neurons, derived from human ESC, recapitulate human striatal development in vivo. This in vitro single-cell dataset was derived after exposing hESC lines (H9) to a novel striatal differentiation protocol and performing single-cell RNA-seq after 15 days and 25 days of differentiation.
2023-01-31 | E-MTAB-12080 | biostudies-arrayexpress
Project description:Dysfunctional brain barriers contribute to the pathophysiology of chronic CNS diseases, but few non-viral technologies are established that effectively target these interfaces. In this work, we developed a lipid-siRNA conjugate that modulate gene expression in brain barriers such as the blood-brain-barrier (BBB), which describes the restrictive properties of brain microvascular endothelial cells (BMEC), as well as the blood-CSF-barrier (BCSFB) formed by the choroid plexus. We showed robust delivery and knockdown in brain endothelial cells and the choroid plexus. In this experiment, we used single cell RNA sequencing to determine which CNS cell types exhibit siRNA-mediated gene silencing. To that end, we administered a 20 mg/kg intravenous dose of our lipid siRNA conjugate targeting Ppib or a non-targeting control. Brains were dissociated into single cells and processed for sequencing using PIPseq workflow. We found that gene silencing was specific to the brain barriers; we only detected knockdown in brain endothelial and choroid plexus epithelial cells.
2025-04-02 | E-MTAB-14840 | biostudies-arrayexpress
Project description:We developed a lipid-siRNA conjugate, termed EG18, that potentiates prolonged gene silencing throughout the CNS after injection into CSF. To help inform viable therapeutic targets, we used scRNAseq to determine cell-specific gene silencing. Here, we used an siRNA sequencing targeting Ppib and inject 15 nmol of either Ppib-EG18 or a non-targeting control (NTC)-EG18 into the lateral ventricles of adult mice. After 1 month, brains were dissociated into single cells and bead-sorted into Cd11b+ and Cd11b- populations. The Cd11b+ dataset contains microglia and macrophages, while the Cd11b- sample comprised a sampling of other isolated perivascular and parenchymal populations. scRNAseq revealed gene silencing activity across diverse cell populations in the parenchyma and at brain borders, which may provide new avenues for disease-modifying therapies.
2024-04-30 | E-MTAB-13964 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) have been implicated in regulating multiple processes during brain development in various species. However, the function of miRNAs in human brain development remains largely unexplored. Here, we provide a comprehensive analysis of miRNA expression of regionalized neural progenitor cells derived from human embryonic stem cells and human fetal brain. We found mir-92b-3p and mir-130b-5p to be specifically associated with neural progenitors and several miRNAs that display both age-specific and region-specific expression patterns. Among these miRNAs, we identified miR-10 to be specifically expressed in the human hindbrain and spinal cord, while absent from rostral regions. We found that miR-10 regulates a large number of genes enriched for functions including transcription, actin cytoskeleton and ephrin receptor signaling. When overexpressed, miR-10 influences caudalization of human neural progenitors cells. Together, these data confirms a role for miRNAs in establishing different human neural progenitor populations. This data set also provides a comprehensive resource for future studies investigating the functional role of different miRNAs in human brain development. Human embryonic stem cells (hESCs) were transduced with lentiviral vectors expressing either miR10a-GFP or miR10b-GFP. The expression of the vectors is Tet-regulated and they will only be expressed in the presence of Doxycycline. In order to detect direct targets of the miR10a and miR10b, we differentiated the trasduced hESCs for 14 days, and added doxycycline to only half of the groups - resulting in groups that are overexpressing miR10a or miR10b and some groups that are not overexpressing these miRNAs.
2015-10-26 | E-GEOD-71204 | biostudies-arrayexpress
Project description:To define molecular mechanisms underlying rod and cone differentiation, we generated H9 human embryonic stem cell line carrying a GFP reporter that is controlled by the promoter of cone-rod homeobox (CRX) gene, the first known marker of post-mitotic photoreceptor precursors. CRXp-GFP reporter in H9 line replicates endogenous CRX expression when induced to form self-organizing 3-D retina-like tissue. We define temporal transcriptome dynamics of developing photoreceptors during the establishment of cone and rod cell fate. Our studies provide an essential framework for delineating molecules and cellular pathways that guide human photoreceptor development and should assist in chemical screening and cell-based therapies of retinal degeneration. Undifferentiated CRXp-GFP HP hES cells and 3D-neural retina were collected at days 37, 47, 67 and 90 and dissociated into single cells. Cells were sorted at 4°C and by FACSAria (Becton Dickinson). GFP+ and GFP- cells were separately collected. Total RNA was extracted by RNA purification kit (Norgen Biotek) and analyzed by 2100 Bioanalyzer (Agilent Technologies Genomics). High quality of total RNA (RIN: 7.7-9.2) was subjected to libraries construction using 40-60 ng of total RNA as input. Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases. Fastq files were generated from reads passing chastity filter.
2015-08-03 | E-GEOD-67645 | biostudies-arrayexpress
Project description:The control of cell identity is orchestrated by transcriptional and chromatin regulators in the context of specific chromosome structures. With the recent isolation of human naive embryonic stem cells (ESCs) representative of the ground state of pluripotency, it is possible to deduce this regulatory landscape in one of the earliest stages of human development. Here we generate cohesin ChIA-PET chromatin interaction data in naive and primed human ESCs and use it to reconstruct and compare the 3D regulatory landscapes of these two stages of early human development. The results reveal shared and stage-specific regulatory landscapes of topological domains and their subdomains, which consist of CTCF-CTCF/cohesin loops and enhancer-promoter/cohesin loops. The enhancer-promoter loop data reveal that genes with key roles in pluripotency are nearly always regulated by one or more super-enhancers, and show that these genes tend to occur in insulated neighborhoods. Our results reveal the key features of the 3D regulatory landscape of early human cells that form the foundation for embryonic development. ChIP-seq data from naive and primed human embroynic stem cells.
2015-11-22 | E-GEOD-69646 | biostudies-arrayexpress