Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA299895 | ENA |
REPOSITORIES: ENA
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Project description:<p>During development of the human brain, multiple cell types with diverse regional identities are generated. Here we report a system to generate early human brain forebrain and mid/hindbrain cell types from human embryonic stem cells (hESCs), and infer and experimentally confirm a lineage tree for the generation of these types based on single-cell RNA-Seq analysis. We engineered <i>SOX2<sup>Cit/+</sup></i> and <i>DCX<sup>Cit/Y</sup></i> hESC lines to target progenitors and neurons throughout neural differentiation for single-cell transcriptomic profiling, then identified discrete cell types consisting of both rostral (cortical) and caudal (mid/hindbrain) identities. Direct comparison of the cell types were made to primary tissues using gene expression atlases and fetal human brain single-cell gene expression data, and this established that the cell types resembled early human brain cell types, including preplate cells. From the single-cell transcriptomic data a Bayesian algorithm generated a unified lineage tree, and predicted novel regulatory transcription factors. The lineage tree highlighted a prominent bifurcation between cortical and mid/hindbrain cell types, confirmed by clonal analysis experiments. We demonstrated that cell types from either branch could preferentially be generated by manipulation of the canonical Wnt/beta-catenin pathway. In summary, we present an experimentally validated lineage tree that encompasses multiple brain regions, and our work sheds light on the molecular regulation of region-specific neural lineages during human brain development.</p>
| phs001205 | dbGaP
Project description:Expression data from human embryonic stem cells(hESCs)
| PRJNA168456 | ENA
Project description:To compare transcriptomic profiles between UCSF4 hESCs and their neural derivatives, neural precursor cells (NPCs), we performed microarray analysis using the Affymetrix Human Gene 2.0 ST array platform.
2016-03-01 | GSE74378 | GEO
Project description:To compare transcriptomic profiles between UCSF4 hESCs and their neural derivatives, neural precursor cells (NPCs), we performed microarray analysis using the Affymetrix Human Gene 2.0 ST array platform. Six biological samples, three biological replicates for each developmental cell stage (in vitro)
2016-03-01 | E-GEOD-74378 | biostudies-arrayexpress
Project description:Assessing relevant molecular differences between human-induced pluripotent stem cells (hiPSCs) and human embryonic stem cells (hESCs) is important, given that such differences may impact their potential therapeutic use. Controversy surrounds recent gene expression studies comparing hiPSCs and hESCs. Here, we present an in-depth quantitative mass spectrometry-based analysis of hESCs, two different hiPSCs and their precursor fibroblast cell lines. Our comparisons confirmed the high similarity of hESCs and hiPSCS at the proteome level as 97.8% of the proteins were found unchanged. Nevertheless, a small group of 58 proteins, mainly related to metabolism, antigen processing and cell adhesion, was found significantly differentially expressed between hiPSCs and hESCs. A comparison of the regulated proteins with previously published transcriptomic studies showed a low overlap, highlighting the emerging notion that differences between both pluripotent cell lines rather reflect experimental conditions than a recurrent molecular signature. See the Data Processing section of the published paper concerning the bioinformatics pipeline used. PMCID: PMC3261715 PMID: 22108792 Mol Syst Biol. 2011 Nov 22;7:550. doi: 10.1038/msb.2011.84. The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells. Munoz J, Low TY, Kok YJ, Chin A, Frese CK, Ding V, Choo A, Heck AJ. Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.
2013-02-01 | PXD000134 | Pride
Project description:While the transcriptional network of human embryonic stem cells (hESCs) has been extensively studied, relatively little is known about how post-transcriptional modulations determine hESC function. RNA-binding proteins play central roles in RNA regulation, including translation and turnover. Here we show that the RNA-binding protein CSDE1 is highly expressed in hESCs to maintain their undifferentiated state and prevent default neural fate. Notably, loss of CSDE1 accelerates neural differentiation and potentiates neurogenesis. Conversely, ectopic expression of CSDE1 impairs neural differentiation. We find that CSDE1 post-transcriptionally modulates core components of multiple regulatory nodes of hESC identity, neuroectoderm commitment and neurogenesis. Among these key pro-neural/neuronal factors, CSDE1 binds fatty acid binding protein 7 (FABP7) and vimentin (VIM) mRNAs as well as transcripts involved in neuron projection development regulating their stability and translation. Thus, our results uncover CSDE1 as a central post-transcriptional regulator of hESC identity and neurogenesis. This proteomics dataset contains the data from co-immunopreciptation experiments using CSDE1 antibody in hESCs
2018-05-16 | PXD007271 | Pride
Project description:Whole proteome profiling and quantification was performed on an isogenic Huntington disease (IsoHD) human embryonic stem cell (hESC) allelic panel. The IsoHD hESCs harbour 30, 45, 65 and 81 CAG repeats in the first exon of HTT. Whole proteome quantification was also performed on neural progenitor cells derived from the IsoHD hESC panel.
2019-02-14 | PXD006585 | JPOST Repository
Project description:Expression data from shRFP, shATF1 in human embryonic stem cells (hESCs)
| PRJNA352056 | ENA
Project description:Recurrent genomic instability of chromosome 1q in neural derivatives of human embryonic stem cells
| PRJNA148481 | ENA
Project description:Pluripotent human embryonic stem cells were compared with essentially pure multipotent neural stem cell derivatives.
2016-07-13 | GSE39876 | GEO