run_metadata: 43832

This data as json

rowid	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	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
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		pubmed:29257950		13hpf PGC dead end MO 2	GSM2808858		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’s default test criteria were filtered out and a cutoff for the FDR adjusted p value of 0.05 Student's t test was 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 “GO biological process complete” 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		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		agent:dead end MO\|strain:AB\|cell type:germ cell\|developmental stage:13 hpf	GSM2808858	GSM2808858: 13hpf PGC dead end MO 2; Danio rerio; RNA Seq	GSM2808858		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:GSM2808858	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP119825			4_SIL443_04_S4_R1_001.fastq.gz 4_SIL443_04_S4_R2_001.fastq.gz	fastq fastq	8437981102.0	56604234.0	GSM2808858 r1	0:74.50 1:74.57	A:1860341053;C:1941389948;G:2080153476;T:2547414135;N:8682490	74	74			1860341053	1941389948	2080153476	2547414135	8682490	SRX3274594	SRS2585897	SRA619012	GEO	Erez Raz, Institute of Cell Biology, University Clinic Muenster	2	0.51323	0.44439	0.09069	0.07858	0.81278	0.8254	0.55336	0.55973	74	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		Germany	2017-10-12	Segmentation	Embryo	Gonad	Reproductive System