Transcriptomes analysis of marmoset liver progenitor cell line compared with adult marmoset liver
Ontology highlight
ABSTRACT:
ORGANISM(S): Callithrix jacchus
PROVIDER: GSE99168 | GEO | 2018/01/01
SECONDARY ACCESSION(S): PRJNA387460
REPOSITORIES: GEO
Similar Datasets
Project description:Single-nucleus RNA sequencing (snRNA-seq) was used to profile the transcriptome of 7,318 nuclei in marmoset adult testis. This dataset includes two samples from two different individuals. This dataset is part of a larger evolutionary study of adult testis at the single-nucleus level (97,521 single-nuclei in total) across mammals including 10 representatives of the three main mammalian lineages: human, chimpanzee, bonobo, gorilla, gibbon, rhesus macaque, marmoset, mouse (placental mammals); grey short-tailed opossum (marsupials); and platypus (egg-laying monotremes). Corresponding data were generated for a bird (red junglefowl, the progenitor of domestic chicken), to be used as an evolutionary outgroup.
2021-11-08 | E-MTAB-11069 | biostudies-arrayexpress
Project description:RNA sequencing (RNA-seq) was used to annotate chimpanzee, gorilla, gibbon, and marmoset genome and transcript isoforms in adult testis. This dataset is part of a larger evolutionary study of adult testis at the single-nucleus level (97,521 single-nuclei in total) across mammals including 10 representatives of the three main mammalian lineages: human, chimpanzee, bonobo, gorilla, gibbon, rhesus macaque, marmoset, mouse (placental mammals); grey short-tailed opossum (marsupials); and platypus (egg-laying monotremes). Corresponding data were generated for a bird (red junglefowl, the progenitor of domestic chicken), to be used as an evolutionary outgroup.
2021-11-08 | E-MTAB-11074 | biostudies-arrayexpress
Project description:Small RNAs mediate gene silencing by binding Argonaute/Piwi proteins to regulate target RNAs. Here we describe small RNA profiling of the adult testes of Callithrix jacchus, the common marmoset. The most abundant class of small RNAs in the adult testis was piRNAs, while 353 novel miRNAs but few endo-siRNAs were also identified. MARWI, a marmoset homolog of mouse MIWI and a very abundant PIWI in adult testes, associates with piRNAs that show characteristics of mouse pachytene piRNAs. As in other mammals, most marmoset piRNAs are derived from conserved clustered regions in the genome, which are annotated as intergenic regions. However, some of these piRNA cluster regions contain antisense-orientated pseudogenes, suggesting regulation of parental functional protein-coding genes. More piRNAs map to transposable element (TE) subfamilies when they have copies in piRNA clusters. In addition, the strand-bias observed for piRNAs mapped to each TE subfamily correlates with the polarity of copies inserted in clusters. These findings suggest that pachytene piRNA clusters determine the abundance and strand-bias of TE-derived piRNAs, and also regulate protein-coding genes via pseudogene-derived piRNAs. small RNA levels in the adult marmoset testis, and MARWI-IP small RNA levels and RNA levels from the adult marmoset testis with two replicates.
2014-06-01 | E-GEOD-52927 | biostudies-arrayexpress
Project description:The molecular identification of adult hepatic stem/progenitor cells has been hampered by the lack of truly specific markers. To isolate putative adult liver progenitor cells, we used cell surface-marking antibodies, including MIC1-1C3, to isolate subpopulations of liver cells from normal adult mice or those undergoing an oval cell response and tested their capacity to form bilineage colonies in vitro. Robust clonogenic activity was found to be restricted to a subset of biliary duct cells antigenically defined as CD45–/CD11b–/CD31–/MIC1-1C3+/CD133+/CD26–, at a frequency of one of 34 or one of 25 in normal or oval cell injury livers, respectively. Gene expression analyses revealed that Sox9 was expressed exclusively in this subpopulation of normal liver cells and was highly enriched relative to other cell fractions in injured livers. In vivo lineage tracing using Sox9creERT2-R26RYFP mice revealed that the cells that proliferate during progenitor-driven liver regeneration are progeny of Sox9-expressing precursors. A comprehensive array-based comparison of gene expression in progenitor-enriched and progenitor-depleted cells from both normal and DDC (3,5-diethoxycarbonyl-1,4-dihydrocollidine or diethyl1,4-dihydro-2,4,6-trimethyl- 3,5-pyridinedicarboxylate)-treated livers revealed new potential regulators of liver progenitors. Treated and untreated cells were sorted by cell surface markers then compared. M+/133+ untreated: 4 biological and 1 technical replicate - total of 5 M-/133- untreated: 2 biological and 1 technical replicate - total of 3 M+/133+ DDC-treated: 4 biological replicates - total of 4 M-/133- DDC-treated: 4 biological replicates - total of 4
2011-05-07 | E-GEOD-29121 | biostudies-arrayexpress
Project description:The molecular identification of adult hepatic stem/progenitor cells has been hampered by the lack of truly specific markers. To isolate putative adult liver progenitor cells, we used cell surface-marking antibodies, including MIC1-1C3, to isolate subpopulations of liver cells from normal adult mice or those undergoing an oval cell response and tested their capacity to form bilineage colonies in vitro. Robust clonogenic activity was found to be restricted to a subset of biliary duct cells antigenically defined as CD45–/CD11b–/CD31–/MIC1-1C3+/CD133+/CD26–, at a frequency of one of 34 or one of 25 in normal or oval cell injury livers, respectively. Gene expression analyses revealed that Sox9 was expressed exclusively in this subpopulation of normal liver cells and was highly enriched relative to other cell fractions in injured livers. In vivo lineage tracing using Sox9creERT2-R26RYFP mice revealed that the cells that proliferate during progenitor-driven liver regeneration are progeny of Sox9-expressing precursors. A comprehensive array-based comparison of gene expression in progenitor-enriched and progenitor-depleted cells from both normal and DDC (3,5-diethoxycarbonyl-1,4-dihydrocollidine or diethyl1,4-dihydro-2,4,6-trimethyl- 3,5-pyridinedicarboxylate)-treated livers revealed new potential regulators of liver progenitors.
2011-05-07 | GSE29121 | GEO
Project description:Small RNAs mediate gene silencing by binding Argonaute/Piwi proteins to regulate target RNAs. Here we describe small RNA profiling of the adult testes of Callithrix jacchus, the common marmoset. The most abundant class of small RNAs in the adult testis was piRNAs, while 353 novel miRNAs but few endo-siRNAs were also identified. MARWI, a marmoset homolog of mouse MIWI and a very abundant PIWI in adult testes, associates with piRNAs that show characteristics of mouse pachytene piRNAs. As in other mammals, most marmoset piRNAs are derived from conserved clustered regions in the genome, which are annotated as intergenic regions. However, some of these piRNA cluster regions contain antisense-orientated pseudogenes, suggesting regulation of parental functional protein-coding genes. More piRNAs map to transposable element (TE) subfamilies when they have copies in piRNA clusters. In addition, the strand-bias observed for piRNAs mapped to each TE subfamily correlates with the polarity of copies inserted in clusters. These findings suggest that pachytene piRNA clusters determine the abundance and strand-bias of TE-derived piRNAs, and also regulate protein-coding genes via pseudogene-derived piRNAs.
2014-06-01 | GSE52927 | GEO
Project description:Adult-derived human liver stem/progenitor cells (ADHLSC) are obtained after primary culture of the liver parenchymal fraction. The cells are of fibroblastic morphology and exhibit a hepato-mesenchymal phenotype. Hepatic stellate cells (HSC) derived from the liver non-parenchymal fraction present a comparable morphology as ADHLSC. Because both ADHLSC and HSC are described as liver stem/progenitor cells, we strived to extensively compare both cell populations at different levels and to propose tools demonstrating their singularity. The database include full expression (HGU-219) measurements samples from 7 Adult-Derived Human Liver Stem/progenitor (n=7) and human hepatic stellate samples (n=7)
2015-05-11 | E-GEOD-49995 | biostudies-arrayexpress
Project description:Neuborn marmoset fibroblasts were immortalized by piggyBac transposition of hTERT expression cassette. The gene expression of the resulting one polyclonal and two monoclonal immortalized cell lines were then compared with the wild type cells used for their derivation.
2018-10-29 | GSE114965 | GEO
Project description:snRNA-seq of marmoset (Callithrix jacchus) adult testis
| PRJEB48246 | ENA
Project description:Transcriptional profiling of common marmoset embryo stages spanning E5.0 to E7.0 was performed by RNA-seq.
2015-11-05 | E-MTAB-2959 | biostudies-arrayexpress