run_metadata: 9775

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
9775	ERR3838754	ERX3851420	ERS4266444	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Soma prim5 wt rep2	SAMEA6501995	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:01Z\|External Id:SAMEA6501995\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:01Z\|INSDC status:public\|Submitter Id:E MTAB 8707:Soma prim5 wt rep2\|age:24\|broker name:ArrayExpress\|cell type:whole embryo\|common name:zebrafish\|developmental stage:pharyngula prim 5\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:Soma prim5 wt rep2\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:Soma prim5 wt rep2 p	Soma prim5 wt rep2 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: compound:n1\|Experimental Factor: cell type:whole embryo	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550		ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	Somatic_prim5_rep2_R1.fastq.gz Somatic_prim5_rep2_R2.fastq.gz	fastq fastq	2664555542.0	17942996.0	E MTAB 8707:Somatic prim5 rep2 R	0:74.25 1:74.25	A:757990974;C:568005838;G:586848520;T:749991976;N:1718234	74	74			757990974	568005838	586848520	749991976	1718234	ERX3851420	ERS4266444	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.92034	0.91779	0.22669	0.22761	0.74769	0.74911	0.45866	0.45282	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq		United Kingdom	2020-01-24	Pharyngula	Embryo	Whole Organism	All anatomical structures