Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA279008 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1922720.fastq.gz | Fastqsanger.gz | |||
| SRR1922730.fastq.gz | Fastqsanger.gz | |||
| SRR1922721.fastq.gz | Fastqsanger.gz | |||
| SRR1922731.fastq.gz | Fastqsanger.gz | |||
| SRR1922722.fastq.gz | Fastqsanger.gz |
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Project description:RNA-seq Analysis of Control DPSC and DPSC Derived Neurons
| PRJNA279007 | ENA
Project description:A major problem in studying neurogenetic syndromes is obtaining live neurons from people with these disorders. We have taken a novel approach to studying gene expression in neurons from Angelman or Dup15q syndrome subjects using dental pulp stem cells (DPSC). Shed teeth were collected to generate DPSC lines from 3 AS deletion, 3 15q Duplication and three neurotypical subjects. mRNAseq was performed on DPSC and DPSC derived neurons. We identified 20 genes in AS, 120 genes in 15q duplication and 3 genes in both groups (DPT, MED12L and AKRIC1) that were significantly different from control DPSC-neurons. Copy number correlated to gene expression for most genes across the 15q11.2-q13.1 critical region. Two thirds of the genes differentially regulated in 15q duplication were down-regulated compared to controls including the transcription factors FOXO1 and HAND2, while in AS the genes did not show a clear trend except in the 15q region. Pathway analysis revealed increased cytokine activity related genes including four genes that increased in 15q duplication samples: CCL7, CCL2, MMP2 and MMP3; while steroid hormone biosynthesis genes were slightly enriched in both 15q duplication and AS neurons. Overall there were more dramatic changes in gene expression in the 15q) duplication than AS deletion cell lines, perhaps because the mechanism of AS may be through protein targeting by UBE3A. Nonetheless, the finding of a significant increase in both HERC2 and UBE3A in 15q duplication neurons and significant decrease in these two genes in AS deletion neurons may impact the AS phenotype, at least in deletion cases.
2017-03-17 | GSE67122 | GEO
Project description:A major challenge to the study and treatment of neurogenetic syndromes is the difficulty in gaining access to live neurons from individuals with these disorders. Although other sources of stem cells are currently available for differentiation into neurons, these can involve invasive procedures and be difficult or expensive to generate limiting their use on a broad scale, especially for rare syndromes which may not be well represented in the local population. Dental pulp stem cells (DPSC) are neural crest derived multipotent stem cells that reside deep the pulp of shed (baby) teeth and have the potential for broad use in the study of neurogenetic disease. In order to investigate the characteristics of DPSC which make them a valuable resource for the study of neurogenetic syndromes we performed a set of viability, senescence and immortalization studies on control DPSC and DPSC derived neurons. We investigated the basic transport conditions and determined the maximum passage number for primary DPSCs. We then immortalized control DPSC using human telomerase reverse trancriptase (hTERT) and evaluated both neuronal differentiation potential and gene expression changes using RNAseq. Here we show that immortalized DPSC share morphological and electrophysiological properties with non-immortalized DPSC. We also show that differentiation of DPSC into neurons changes gene expression for 1305 transcripts, while immortalized neurons differ significantly in gene expression for 183 transcripts of which 94 also changed during differentiation. Taken together, these studies indicate that immortalized dental pulp derived neruons may be a new and powerful resource for the study of rare neurological disorders where patient samples are rare or difficult to obtain. RNA-seq Analysis of 3 neurotypical control DPSC, 3 DPSC derived neurons and 3 each immortalized versions of DPSC and DPSC neurons (~3 weeks post maturation)
2016-08-08 | E-GEOD-67124 | biostudies-arrayexpress
Project description:RNA extracted at 240min. Samples are rRNA depleted. Expression measurement of Homo sapiens genes.
2019-07-31 | GSE114179 | GEO
Project description:A major challenge to the study and treatment of neurogenetic syndromes is the difficulty in gaining access to live neurons from individuals with these disorders. Although other sources of stem cells are currently available for differentiation into neurons, these can involve invasive procedures and be difficult or expensive to generate limiting their use on a broad scale, especially for rare syndromes which may not be well represented in the local population. Dental pulp stem cells (DPSC) are neural crest derived multipotent stem cells that reside deep the pulp of shed (baby) teeth and have the potential for broad use in the study of neurogenetic disease. In order to investigate the characteristics of DPSC which make them a valuable resource for the study of neurogenetic syndromes we performed a set of viability, senescence and immortalization studies on control DPSC and DPSC derived neurons. We investigated the basic transport conditions and determined the maximum passage number for primary DPSCs. We then immortalized control DPSC using human telomerase reverse trancriptase (hTERT) and evaluated both neuronal differentiation potential and gene expression changes using RNAseq. Here we show that immortalized DPSC share morphological and electrophysiological properties with non-immortalized DPSC. We also show that differentiation of DPSC into neurons changes gene expression for 1305 transcripts, while immortalized neurons differ significantly in gene expression for 183 transcripts of which 94 also changed during differentiation. Taken together, these studies indicate that immortalized dental pulp derived neruons may be a new and powerful resource for the study of rare neurological disorders where patient samples are rare or difficult to obtain.
2016-08-08 | GSE67124 | GEO
Project description:To explore the functions of MXRA5 for DPSC proliferation and migration, we established DPSC in which MXRA5 has been knocked down by 2 independent siRNAs.We then performed gene expression profiling analysis using data obtained from RNA-seq of DPSC-si-control, DPSC-siMXRA5-1, and DPSC-siMXRA5-2.
2023-04-21 | GSE228136 | GEO
Project description:Kynureninase is a member of a large family of catalytically diverse but structurally homologous pyridoxal 5'-phosphate (PLP) dependent enzymes known as the aspartate aminotransferase superfamily or alpha-family. The Homo sapiens and other eukaryotic constitutive kynureninases preferentially catalyze the hydrolytic cleavage of 3-hydroxy-l-kynurenine to produce 3-hydroxyanthranilate and l-alanine, while l-kynurenine is the substrate of many prokaryotic inducible kynureninases. The human enzyme was cloned with an N-terminal hexahistidine tag, expressed, and purified from a bacterial expression system using Ni metal ion affinity chromatography. Kinetic characterization of the recombinant enzyme reveals classic Michaelis-Menten behavior, with a Km of 28.3 +/- 1.9 microM and a specific activity of 1.75 micromol min-1 mg-1 for 3-hydroxy-dl-kynurenine. Crystals of recombinant kynureninase that diffracted to 2.0 A were obtained, and the atomic structure of the PLP-bound holoenzyme was determined by molecular replacement using the Pseudomonas fluorescens kynureninase structure (PDB entry 1qz9) as the phasing model. A structural superposition with the P. fluorescens kynureninase revealed that these two structures resemble the "open" and "closed" conformations of aspartate aminotransferase. The comparison illustrates the dynamic nature of these proteins' small domains and reveals a role for Arg-434 similar to its role in other AAT alpha-family members. Docking of 3-hydroxy-l-kynurenine into the human kynureninase active site suggests that Asn-333 and His-102 are involved in substrate binding and molecular discrimination between inducible and constitutive kynureninase substrates.
| S-EPMC2531291 | biostudies-literature
Project description:As the evolution of miRNA genes has been found to be one of the important factors in formation of the modern type of man, we performed a comparative analysis of the evolution of miRNA genes in two archaic hominines, Homo sapiens neanderthalensis and Homo sapiens denisova, and elucidated the expression of their target mRNAs in bain.A comparative analysis of the genomes of primates, including species in the genus Homo, identified a group of miRNA genes having fixed substitutions with important implications for the evolution of Homo sapiens neanderthalensis and Homo sapiens denisova. The mRNAs targeted by miRNAs with mutations specific for Homo sapiens denisova exhibited enhanced expression during postnatal brain development in modern humans. By contrast, the expression of mRNAs targeted by miRNAs bearing variations specific for Homo sapiens neanderthalensis was shown to be enhanced in prenatal brain development.Our results highlight the importance of changes in miRNA gene sequences in the course of Homo sapiens denisova and Homo sapiens neanderthalensis evolution. The genetic alterations of miRNAs regulating the spatiotemporal expression of multiple genes in the prenatal and postnatal brain may contribute to the progressive evolution of brain function, which is consistent with the observations of fine technical and typological properties of tools and decorative items reported from archaeological Denisovan sites. The data also suggest that differential spatial-temporal regulation of gene products promoted by the subspecies-specific mutations in the miRNA genes might have occurred in the brains of Homo sapiens denisova and Homo sapiens neanderthalensis, potentially contributing to the cultural differences between these two archaic hominines.
| S-EPMC4686780 | biostudies-literature
Project description:PurposeWe investigated the evidence of recent positive selection in the human phototransduction system at single nucleotide polymorphism (SNP) and gene level.MethodsSNP genotyping data from the International HapMap Project for European, Eastern Asian, and African populations was used to discover differences in haplotype length and allele frequency between these populations. Numeric selection metrics were computed for each SNP and aggregated into gene-level metrics to measure evidence of recent positive selection. The level of recent positive selection in phototransduction genes was evaluated and compared to a set of genes shown previously to be under recent selection, and a set of highly conserved genes as positive and negative controls, respectively.ResultsSix of 20 phototransduction genes evaluated had gene-level selection metrics above the 90th percentile: RGS9, GNB1, RHO, PDE6G, GNAT1, and SLC24A1. The selection signal across these genes was found to be of similar magnitude to the positive control genes and much greater than the negative control genes.ConclusionsThere is evidence for selective pressure in the genes involved in retinal phototransduction, and traces of this selective pressure can be demonstrated using SNP-level and gene-level metrics of allelic variation. We hypothesize that the selective pressure on these genes was related to their role in low light vision and retinal adaptation to ambient light changes. Uncovering the underlying genetics of evolutionary adaptations in phototransduction not only allows greater understanding of vision and visual diseases, but also the development of patient-specific diagnostic and intervention strategies.
| S-EPMC3743458 | biostudies-literature