{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Segmentation\" and tissue_curation = \"Gonad\"", "rows": [[43832, "SRR6163072", "SRX3274594", "SRS2585897", "SRP119825", "PRJNA414036", "The vertebrate protein Dead end maintains primordial germ cell fate by inhibiting somatic differentiation", "GSE104855", "Transcriptome Analysis", "Maintaining cell fate relies on robust mechanisms that prevent the differentiation of specified cells into other cell types. This is especially critical during embryogenesis  when extensive cell proliferation  patterning and migration events take place. Here we show that vertebrate primordial germ cells PGCs are protected from reprogramming into other cell types by the RNA binding protein Dead end Dnd. PGCs knocked down for Dnd lose their characteristic morphology and adopt that of various somatic cell types. Concomitantly  they gain a gene expression profile reflecting differentiation into cells of different germ layers  in a process that we could direct by expression of specific cell fate determinants. Importantly  we visualized these events within live zebrafish embryos  which provide temporal information regarding cell reprogramming. Our results shed light on the mechanisms controlling germ cell fate maintenance and are relevant for the formation of teratoma  a tumor class composed of cells from more than one germ layer. Overall design: Transcriptome profiling of 13hpf sorted germ cells of zebrafish embryos injected with either control or dead end Morpholino", null, "pubmed:29257950", null, "13hpf PGC   dead end MO  2", "GSM2808858", null, "tissue:germ cells|agent:dead end MO|strain:AB|cell type:germ cell|developmental stage:13 hpf", "13hpf PGC   dead end MO  2", "post trimming of remaining adapter sequences and primers with Cutadapt v1.10 Martin  2011  reads were aligned against GRCz10 using STAR v2.5.2b Dobin et al.  2013. Gene level differential expression between the Dnd knockdown sample and the control was assessed using Cufflinks v2.2.1 Trapnell et al.  2012. Results not passing Cuffdiff\u2019s default test criteria were filtered out and a cutoff for the FDR adjusted p value of 0.05 Student's t test\u00a0was chosen. Data were subsequently divided into separate lists containing either up  or downregulated transcripts. For gene ontology GO analysis  a cutoff of 10 FPKM/transcript was applied in the list of upregulated transcripts in this case at least 10 FPKM/transcript in Dnd knockdown condition and downregulated transcripts in this case at least 10 FPKM/transcript in control condition. GO analysis was performed using the PANTHER Overrepresentation test Mi et al.  2013 and the \u201cGO biological process complete\u201d annotation dataset based on the Gene ontology database released 2017 02 28. Subsequently  terms with a minimum of 5 fold enrichment were visualized using REVIGO Supek et al.  2011 Reduce and visualize GO  0.9 similarity large and SimRel as a semantic similarity measure. 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Overall design: Transcriptome profiling of 13hpf sorted germ cells of zebrafish embryos injected with either control or dead end Morpholino", null, "pubmed:29257950", null, "13hpf PGC   control MO  2", "GSM2808857", null, "tissue:germ cells|agent:control MO|strain:AB|cell type:germ cell|developmental stage:13 hpf", "13hpf PGC   control MO  2", "post trimming of remaining adapter sequences and primers with Cutadapt v1.10 Martin  2011  reads were aligned against GRCz10 using STAR v2.5.2b Dobin et al.  2013. Gene level differential expression between the Dnd knockdown sample and the control was assessed using Cufflinks v2.2.1 Trapnell et al.  2012. Results not passing Cuffdiff\u2019s default test criteria were filtered out and a cutoff for the FDR adjusted p value of 0.05 Student's t test\u00a0was chosen. Data were subsequently divided into separate lists containing either up  or downregulated transcripts. For gene ontology GO analysis  a cutoff of 10 FPKM/transcript was applied in the list of upregulated transcripts in this case at least 10 FPKM/transcript in Dnd knockdown condition and downregulated transcripts in this case at least 10 FPKM/transcript in control condition. GO analysis was performed using the PANTHER Overrepresentation test Mi et al.  2013 and the \u201cGO biological process complete\u201d annotation dataset based on the Gene ontology database released 2017 02 28. Subsequently  terms with a minimum of 5 fold enrichment were visualized using REVIGO Supek et al.  2011 Reduce and visualize GO  0.9 similarity large and SimRel as a semantic similarity measure. 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This is especially critical during embryogenesis  when extensive cell proliferation  patterning and migration events take place. Here we show that vertebrate primordial germ cells PGCs are protected from reprogramming into other cell types by the RNA binding protein Dead end Dnd. PGCs knocked down for Dnd lose their characteristic morphology and adopt that of various somatic cell types. Concomitantly  they gain a gene expression profile reflecting differentiation into cells of different germ layers  in a process that we could direct by expression of specific cell fate determinants. Importantly  we visualized these events within live zebrafish embryos  which provide temporal information regarding cell reprogramming. Our results shed light on the mechanisms controlling germ cell fate maintenance and are relevant for the formation of teratoma  a tumor class composed of cells from more than one germ layer. Overall design: Transcriptome profiling of 13hpf sorted germ cells of zebrafish embryos injected with either control or dead end Morpholino", null, "pubmed:29257950", null, "13hpf PGC   dead end MO  1", "GSM2808856", null, "tissue:germ cells|agent:dead end MO|strain:AB|cell type:germ cell|developmental stage:13 hpf", "13hpf PGC   dead end MO  1", "post trimming of remaining adapter sequences and primers with Cutadapt v1.10 Martin  2011  reads were aligned against GRCz10 using STAR v2.5.2b Dobin et al.  2013. Gene level differential expression between the Dnd knockdown sample and the control was assessed using Cufflinks v2.2.1 Trapnell et al.  2012. Results not passing Cuffdiff\u2019s default test criteria were filtered out and a cutoff for the FDR adjusted p value of 0.05 Student's t test\u00a0was chosen. Data were subsequently divided into separate lists containing either up  or downregulated transcripts. For gene ontology GO analysis  a cutoff of 10 FPKM/transcript was applied in the list of upregulated transcripts in this case at least 10 FPKM/transcript in Dnd knockdown condition and downregulated transcripts in this case at least 10 FPKM/transcript in control condition. GO analysis was performed using the PANTHER Overrepresentation test Mi et al.  2013 and the \u201cGO biological process complete\u201d annotation dataset based on the Gene ontology database released 2017 02 28. Subsequently  terms with a minimum of 5 fold enrichment were visualized using REVIGO Supek et al.  2011 Reduce and visualize GO  0.9 similarity large and SimRel as a semantic similarity measure. Genome build: Zv9 Supplementary files format and content: Excel files with Gene Ids and FPKM values for differentially expressed genes between the two conditions  GO terms and REVIGO analysis for each up  or downregulated group of genes", "germ cells", null, "PGCs were FACSed based on germline specific EGFP fluorescence and total RNA extraction was performed using the Arcturus PicoPure RNA isolation kit. DNA was removed using DNAfree Kit of Ambion and mRNA was extracted from total RNA using NEXTflex Bead preparation of BIOO Scientific A cDNA library was prepared using the NEXTflex Rapid Directional RNA Seq kit of BIOO Scientific", null, "agent:dead end MO|strain:AB|cell type:germ cell|developmental stage:13 hpf", "GSM2808856", "GSM2808856: 13hpf PGC   dead end MO  1; Danio rerio; RNA Seq", "GSM2808856", null, "1", "PGCs were FACSed based on germline specific EGFP fluorescence and total RNA extraction was performed using the Arcturus PicoPure RNA isolation kit. DNA was removed using DNAfree Kit of Ambion and mRNA was extracted from total RNA using NEXTflex Bead preparation of BIOO Scientific A cDNA library was prepared using the NEXTflex Rapid Directional RNA Seq kit of BIOO Scientific", "GEO Accession:GSM2808856", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP119825", null, null, "2_SIL443_02_S2_R2_001.fastq.gz 2_SIL443_02_S2_R1_001.fastq.gz", "fastq fastq", 6698714120.0, 44941592.0, "GSM2808856 r1", "0:74.48 1:74.57", "A:1382110759;C:1666182128;G:1762655710;T:1881061600;N:6703923", 74, 74, null, null, 1382110759, 1666182128, 1762655710, 1881061600, 6703923, "SRX3274592", "SRS2585895", "SRA619012", "GEO", "Erez Raz, Institute of Cell Biology, University Clinic Muenster", 2, 0.58574, 0.53597, 0.15277, 0.13856, 0.8226, 0.83169, 0.64247, 0.44471, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2017-10-12", "Segmentation", "Embryo", "Gonad", "Reproductive System"], [43835, "SRR6163069", "SRX3274591", "SRS2585894", "SRP119825", "PRJNA414036", "The vertebrate protein Dead end maintains primordial germ cell fate by inhibiting somatic differentiation", "GSE104855", "Transcriptome Analysis", "Maintaining cell fate relies on robust mechanisms that prevent the differentiation of specified cells into other cell types. This is especially critical during embryogenesis  when extensive cell proliferation  patterning and migration events take place. Here we show that vertebrate primordial germ cells PGCs are protected from reprogramming into other cell types by the RNA binding protein Dead end Dnd. PGCs knocked down for Dnd lose their characteristic morphology and adopt that of various somatic cell types. Concomitantly  they gain a gene expression profile reflecting differentiation into cells of different germ layers  in a process that we could direct by expression of specific cell fate determinants. Importantly  we visualized these events within live zebrafish embryos  which provide temporal information regarding cell reprogramming. Our results shed light on the mechanisms controlling germ cell fate maintenance and are relevant for the formation of teratoma  a tumor class composed of cells from more than one germ layer. Overall design: Transcriptome profiling of 13hpf sorted germ cells of zebrafish embryos injected with either control or dead end Morpholino", null, "pubmed:29257950", null, "13hpf PGC   control MO  1", "GSM2808855", null, "tissue:germ cells|agent:control MO|strain:AB|cell type:germ cell|developmental stage:13 hpf", "13hpf PGC   control MO  1", "post trimming of remaining adapter sequences and primers with Cutadapt v1.10 Martin  2011  reads were aligned against GRCz10 using STAR v2.5.2b Dobin et al.  2013. Gene level differential expression between the Dnd knockdown sample and the control was assessed using Cufflinks v2.2.1 Trapnell et al.  2012. Results not passing Cuffdiff\u2019s default test criteria were filtered out and a cutoff for the FDR adjusted p value of 0.05 Student's t test\u00a0was chosen. Data were subsequently divided into separate lists containing either up  or downregulated transcripts. For gene ontology GO analysis  a cutoff of 10 FPKM/transcript was applied in the list of upregulated transcripts in this case at least 10 FPKM/transcript in Dnd knockdown condition and downregulated transcripts in this case at least 10 FPKM/transcript in control condition. GO analysis was performed using the PANTHER Overrepresentation test Mi et al.  2013 and the \u201cGO biological process complete\u201d annotation dataset based on the Gene ontology database released 2017 02 28. Subsequently  terms with a minimum of 5 fold enrichment were visualized using REVIGO Supek et al.  2011 Reduce and visualize GO  0.9 similarity large and SimRel as a semantic similarity measure. Genome build: Zv9 Supplementary files format and content: Excel files with Gene Ids and FPKM values for differentially expressed genes between the two conditions  GO terms and REVIGO analysis for each up  or downregulated group of genes", "germ cells", null, "PGCs were FACSed based on germline specific EGFP fluorescence and total RNA extraction was performed using the Arcturus PicoPure RNA isolation kit. DNA was removed using DNAfree Kit of Ambion and mRNA was extracted from total RNA using NEXTflex Bead preparation of BIOO Scientific A cDNA library was prepared using the NEXTflex Rapid Directional RNA Seq kit of BIOO Scientific", null, "agent:control MO|strain:AB|cell type:germ cell|developmental stage:13 hpf", "GSM2808855", "GSM2808855: 13hpf PGC   control MO  1; Danio rerio; RNA Seq", "GSM2808855", null, "1", "PGCs were FACSed based on germline specific EGFP fluorescence and total RNA extraction was performed using the Arcturus PicoPure RNA isolation kit. DNA was removed using DNAfree Kit of Ambion and mRNA was extracted from total RNA using NEXTflex Bead preparation of BIOO Scientific A cDNA library was prepared using the NEXTflex Rapid Directional RNA Seq kit of BIOO Scientific", "GEO Accession:GSM2808855", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP119825", null, null, "1_SIL443_01_S1_R1_001.fastq.gz 1_SIL443_01_S1_R2_001.fastq.gz", "fastq fastq", 5496482855.0, 36876415.0, "GSM2808855 r1", "0:74.48 1:74.57", "A:1211902681;C:1356435115;G:1443569780;T:1478848150;N:5727129", 74, 74, null, null, 1211902681, 1356435115, 1443569780, 1478848150, 5727129, "SRX3274591", "SRS2585894", "SRA619012", "GEO", "Erez Raz, Institute of Cell Biology, University Clinic Muenster", 2, 0.66316, 0.5871, 0.16838, 0.14743, 0.7824, 0.79511, 0.63777, 0.50198, 74, 74, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2017-10-12", "Segmentation", "Embryo", "Gonad", "Reproductive System"], [60889, "SRR12628232", "SRX9110495", "SRS7353478", "SRP282187", "PRJNA663091", "Characterization of small RNAs in early zebrafish PGCs", "GSE157865", "Transcriptome Analysis", "Microscale small RNA high throughput sequencing was used to study small RNA distribution in early zebrafish PGCs primordial germ cells. We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected  miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition  miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. 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We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected  miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition  miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. 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[experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"devstage_curation\" = :p0 and \"tissue_curation\" = :p1 order by rowid limit 101", "params": {"p0": "Segmentation", "p1": "Gonad"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Segmentation&tissue_curation=Gonad", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation&tissue_curation=Gonad&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "miRNA-Seq", "label": "miRNA-Seq", "count": 2, "toggle_url": 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"http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation&tissue_curation=Gonad&experiment.library_selection=cDNA", "selected": false}, {"value": "size fractionation", "label": "size fractionation", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation&tissue_curation=Gonad&experiment.library_selection=size+fractionation", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Segmentation&tissue_curation=Gonad", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation&tissue_curation=Gonad&experiment.library_layout=PAIRED", "selected": false}, {"value": "SINGLE", "label": "SINGLE", "count": 2, "toggle_url": 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"http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation&tissue_curation=Gonad&tissue_curation_coarse=Reproductive+System", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Segmentation&tissue_curation=Gonad", "results": [{"value": "Gonad", "label": "Gonad", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Segmentation&tissue_curation=Gonad", "results": [{"value": "unknown", "label": "unknown", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation&tissue_curation=Gonad&technology=unknown", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 86.43818000564352}