RNA-seq in SREBF1-deficient human iPSCs, hiPSC-NSCs and differentiated cells.
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1140208 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Omics analyses and qRT-PCR time-course during the transition from hiPSC to hiPSC-NSC highlighted the up-regulation of SREBF1, a gene involved in cholesterol biosynthesis and lipid homeostasis, suggesting its potential role in NSC commitment/maintenance. To test this hypothesis, we generated SREBF1-deficient hiPSC lines by co-delivering ribonucleoprotein Cas9 with a pool of sgRNA targeting exon 5 of the SREBF1 gene. Upon isolation of three clones harboring the deletion we performed RNA-seq analysis in hiPSC, hiPSC-NSC and differentiated cultures at 7 and 14 days of differentiation, compared to control cells. This analysis will allow to identify the potential role of SREBF1 in affecting hiPSC-to-hiPSC-NSC transition, hiPSC-NSC maintenance and commitment toward differentiated cell populations.
2024-09-23 | GSE273125 | GEO
Project description:Human iPSC-derived neural stem/progenitor cells (hiPSC-NSCs) are a promising source for cell/gene therapy approaches to target neurodegenerative and demyelinating disorders with unmet clinical needs. Despite the great effort in characterizing hiPSC-derived products in both in vitro and in vivo settings, we still lack a comprehensive study addressing hiPSC-NSC identity and safety at genome-wide level, an issue of paramount importance to establish accepted criteria for prospective clinical applications. Here, we evaluated the transcriptional (by poly-A+ RNA-seq) and epigenetic (by H3K27Ac ChIP-seq) signatures in hiPSCs and differentiated hiPSC-NSC progeny, keeping as reference a somatic clinically relevant human fetal NSC (hfNSCs) line. Overall, our comprehensive transcriptomic and epigenomic analysis coupled to a long-term functional in vivo characterization provided insight into the cell identity, safety profile, and therapeutic potential of hiPSC-NSCs, supporting the rationale for the continuous development of hiPSC-NSCs as an alternative source to somatic hfNSCs for treatment of neurodegenerative and demyelinating disorders.
2024-09-23 | GSE239444 | GEO
Project description:Human iPSC-derived neural stem/progenitor cells (hiPSC-NSCs) are a promising source for cell/gene therapy approaches to target neurodegenerative and demyelinating disorders with unmet clinical needs. Despite the great effort in characterizing hiPSC-derived products in both in vitro and in vivo settings, we still lack a comprehensive study addressing hiPSC-NSC identity and safety at genome-wide level, an issue of paramount importance to establish accepted criteria for prospective clinical applications. Here, we evaluated the transcriptional (by poly-A+ RNA-seq) and epigenetic (by H3K27Ac ChIP-seq) signatures in hiPSCs and differentiated hiPSC-NSC progeny, keeping as reference a somatic clinically relevant human fetal NSC (hfNSCs) line. Overall, our comprehensive transcriptomic and epigenomic analysis coupled to a long-term functional in vivo characterization provided insight into the cell identity, safety profile, and therapeutic potential of hiPSC-NSCs, supporting the rationale for the continuous development of hiPSC-NSCs as an alternative source to somatic hfNSCs for treatment of neurodegenerative and demyelinating disorders.
2024-09-23 | GSE239443 | GEO
Project description:Transcriptional profiling of Human ESCs vs Human iPSCs, Human NSCs-ES vs Human NSCs-iPS iPSCs generated by using different method, and are not very good at Neural differentiation comapred with Human ESCs
2016-09-29 | GSE67325 | GEO
Project description:Human iPSCs and NSCs were engineered by AAVS1 and/or C13 safe-harbor TALENs which mediated targeted integration of various reporter genes at single or dual safe-harbor loci. Multiple clones of targeted human iPSCs were used to compare with parental untargeted NCRM5 iPSCs. Polyclonal targeted human NSCs were used to compare with their parental untargeted NCRM1NSCs or H9NSCs. Total RNA obtained from targeted human iPSCs or NSCs compared to untargeted control iPSCs or NSCs.
2014-09-01 | E-GEOD-55975 | biostudies-arrayexpress
Project description:Purpose: There exists a rich bio-resource of numerous lymphoblastoid cell line (LCL) repositories generated from a wide array of patients, many of them with extensive genotypic and phenotypic data already generated. We have developed a highly efficient LCL to induced pluripotent stem cells (iPSC) reprogramming method and performed whole genome mRNA and miRNA analysis to understand mechanistic changes that take place at the transcriptome and cellular functional level during reprogramming of LCLs into iPSCs and further differentiation. Methods: Applying our optimized protocol which utilizes episomal plasmids encoding pluripotency transcription factors and mouse p53DD - p53 carboxy-terminal dominant-negative fragment and commercially available reprogramming media, we reprogrammed six LCLs into iPSCs and then differentiated them into neural stem cells (NSC). The LCLs, their reprogrammed iPSCs and differentiated NSC (n=18) were sequenced for mRNA and smallRNA on an illumina HiSeq 2500. Differential gene expression analysis was performed between LCL-iPSC and iPSC-NSC pairs in combination with functional annotations and Ingenuity® Pathway Analysis (IPA). Results: Our LCL reprogrammed iPSCs express the majority of genes and miRNAs known to contribute to stemness in human ESCs. The functional enrichment analysis of the up-regulated genes and activation of human pluripotency pathways in the reprogrammed iPSCs showed that the generated iPSCs have a transcriptional and functional profile very similar to that of human ESCs. The reprogrammed iPSCs also showed the potential to differentiate into cells of all three germ layers. Significantly, the transcriptomic effect of EBV encoded oncoproteins which were very pronounced in LCLs, were significantly inhibited in reprogrammed iPSCs. The transcriptomic and functional enrichment analysis of the NSC differentiated from the reprogrammed iPSCs showed that they share a functional profile of self-renewing NSCs. Conclusions: We have been able to develop a MEF feeder free protocol for efficient and reproducible reprogramming of LCLs into iPSC. In addition our comprehensive analysis of genome wide miRNA and mRNA of LCLs, their reprogrammed iPSC and differentiated NSCs provides important documentation of differentially expressed genes and miRNAs and their functional consequences during LCL to iPSC reprogramming and NSC differentiations that were previously unknown.
2017-02-11 | GSE74289 | GEO
Project description:Human iPSCs were differentiated towards an induced-SMC (iSMC) phenotype in a 10-day protocol. Proteomics was performed throughout the entire differentiation time course to provide a robust, well-defined starting and ending cell population. Proteomics data verified iPSC differentiation to iSMCs. Proteomics comparison with primary human SMCs showed a high correlation with iSMCs. After iSMC differentiation, we initiated calcification in the iSMCs by culturing the cells in osteogenic media for 17 days.
2022-10-14 | PXD032353 | Pride
Project description:Neural stem cells can migrate towards tumors of both neural and non-neural origins, which is crucial for the success in treating disseminated tumors. Although the understanding of the molecular mechanisms underlying NSC tumor tropism is limited, it has been noted that several cytokines, growth factors and receptors direct the migration in vitro. A proper understanding of the basic molecular mechanisms of NSC migration towards tumors, especially identification of key cellular regulators of the migration, will have important implications in improving the effectiveness of engineering and employing NSCs as tumor therapy agents. We compared gene expression profiles between migratory and non-migratory hiPSC-NSCs towards cancer cells using cDNA microarray profiling. We collected human iPSCs derived NSCs migrating and not migrating towards mouse 4T1 breast cancer cells in an in vitro migration system for total RNA extraction and hybridization to Affymetrix microarrays
2013-02-28 | E-GEOD-40750 | biostudies-arrayexpress
Project description:Neural stem cells can migrate towards tumors of both neural and non-neural origins, which is crucial for the success in treating disseminated tumors. Although the understanding of the molecular mechanisms underlying NSC tumor tropism is limited, it has been noted that several cytokines, growth factors and receptors direct the migration in vitro. A proper understanding of the basic molecular mechanisms of NSC migration towards tumors, especially identification of key cellular regulators of the migration, will have important implications in improving the effectiveness of engineering and employing NSCs as tumor therapy agents. We compared gene expression profiles between migratory and non-migratory hiPSC-NSCs towards cancer cells using cDNA microarray profiling. We collected human iPSCs derived NSCs migrating and not migrating towards human U87 glioma cells in an in vitro migration system for total RNA extraction and hybridization to Affymetrix microarrays
2013-02-28 | E-GEOD-40749 | biostudies-arrayexpress
Project description:PolyA RNA-seq from differentiated iPSCs
| PRJNA854943 | ENA