metadata: run_metadata: 34 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "RANDOM PCR" and technology = "smartseq"

34 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "RANDOM PCR" and technology = "smartseq"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	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.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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
9775	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
9776	9776	ERR3838753	ERX3851419	ERS4266443	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 rep1	SAMEA6501994	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:SAMEA6501994\|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 rep1\|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 rep1\|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 rep1 p	Soma prim5 wt rep1 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_rep1_R1.fastq.gz Somatic_prim5_rep1_R2.fastq.gz	fastq fastq	1847156504.0	12386853.0	E MTAB 8707:Somatic prim5 rep1 R	0:74.56 1:74.56	A:519724449;C:399975516;G:411702918;T:514818493;N:935128	74	74	519724449	399975516	411702918	514818493	935128	ERX3851419	ERS4266443	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	0.93526	0.93319	0.24244	0.24304	0.75073	0.75201	0.44773	0.44885	76	75	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
9777	9777	ERR3838752	ERX3851418	ERS4266442	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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. 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 Morpholino rep2	SAMEA6501993	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:SAMEA6501993\|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 Morpholino 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 Morpholino 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 Morpholino rep2 p	Soma prim5 Morpholino 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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. 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:Morpholino antisense oligo against Tdrd7 transcript\|Experimental Factor: dose:0.3\|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	S14_R1.fastq.gz S14_R2.fastq.gz	fastq fastq	953947657.0	6389852.0	E MTAB 8707:S14 R	0:74.64 1:74.65	A:271485260;C:204208876;G:210319402;T:267490986;N:443133	74	74	271485260	204208876	210319402	267490986	443133	ERX3851418	ERS4266442	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	0.93577	0.93619	0.1141	0.11516	0.72644	0.72892	0.4694	0.46965	75	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
9778	9778	ERR3838751	ERX3851417	ERS4266441	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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. 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 Morpholino rep1	SAMEA6501992	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:SAMEA6501992\|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 Morpholino rep1\|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 Morpholino rep1\|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 Morpholino rep1 p	Soma prim5 Morpholino rep1 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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. 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:Morpholino antisense oligo against Tdrd7 transcript\|Experimental Factor: dose:0.3\|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	S12_R1.fastq.gz S12_R2.fastq.gz	fastq fastq	753719404.0	5057589.0	E MTAB 8707:S12 R	0:74.51 1:74.52	A:216097326;C:160004832;G:164724356;T:212507268;N:385622	74	74	216097326	160004832	164724356	212507268	385622	ERX3851417	ERS4266441	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	0.93958	0.93943	0.10854	0.1092	0.73267	0.73663	0.45629	0.47862	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
9779	9779	ERR3838750	ERX3851416	ERS4266440	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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. 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 5mismatch Morpholino rep2	SAMEA6501991	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:SAMEA6501991\|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 5mismatch Morpholino 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 5mismatch Morpholino 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 5mismatch Morpholino rep2 p	Soma prim5 5mismatch Morpholino 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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. 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:Control morpholino antisense oligo with 5 mismatches\|Experimental Factor: dose:0.3\|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	S18_R1.fastq.gz S18_R2.fastq.gz	fastq fastq	847966718.0	5668126.0	E MTAB 8707:S18 R	0:74.80 1:74.80	A:230723434;C:191446710;G:197114792;T:228326953;N:354829	74	74	230723434	191446710	197114792	228326953	354829	ERX3851416	ERS4266440	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	0.92436	0.92488	0.08973	0.09012	0.73971	0.74192	0.45291	0.45397	76	73	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
9780	9780	ERR3838749	ERX3851415	ERS4266439	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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. 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 5mismatch Morpholino rep1	SAMEA6501990	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:SAMEA6501990\|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 5mismatch Morpholino rep1\|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 5mismatch Morpholino rep1\|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 5mismatch Morpholino rep1 p	Soma prim5 5mismatch Morpholino rep1 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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. 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:Control morpholino antisense oligo with 5 mismatches\|Experimental Factor: dose:0.3\|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	S16_R1.fastq.gz S16_R2.fastq.gz	fastq fastq	444518989.0	2971315.0	E MTAB 8707:S16 R	0:74.80 1:74.80	A:121398448;C:100282796;G:103112415;T:119559792;N:165538	74	74	121398448	100282796	103112415	119559792	165538	ERX3851415	ERS4266439	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	0.92469	0.92438	0.09917	0.10006	0.72279	0.7251	0.45852	0.46016	73	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
9781	9781	ERR3838748	ERX3851414	ERS4266438	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 High rep2	SAMEA6501989	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:SAMEA6501989\|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 High rep2\|age:3.3\|broker name:ArrayExpress\|cell type:whole embryo\|common name:zebrafish\|developmental stage:blastula high\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:Soma High 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 High rep2 p	Soma High 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:blastula high\|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	Fabio_High_rep2_soma_R1.fastq.gz Fabio_High_rep2_soma_R2.fastq.gz	fastq fastq	2072343523.0	13904136.0	E MTAB 8707:Fabio High rep2 soma R	0:74.52 1:74.53	A:596021076;C:439789413;G:451992691;T:583604290;N:936053	74	74	596021076	439789413	451992691	583604290	936053	ERX3851414	ERS4266438	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	0.94263	0.94098	0.04804	0.04844	0.75797	0.76039	0.50847	0.5014	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9782	9782	ERR3838747	ERX3851413	ERS4266437	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 High rep1	SAMEA6501988	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:SAMEA6501988\|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 High rep1\|age:3.3\|broker name:ArrayExpress\|cell type:whole embryo\|common name:zebrafish\|developmental stage:blastula high\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:Soma High rep1\|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 High rep1 p	Soma High rep1 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:blastula high\|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_High_rep1_R1.fastq.gz Somatic_High_rep1_R2.fastq.gz	fastq fastq	6013555644.0	40662218.0	E MTAB 8707:Somatic High rep1 R	0:73.94 1:73.95	A:1821348300;C:1185534582;G:1227848010;T:1774836657;N:3988095	73	73	1821348300	1185534582	1227848010	1774836657	3988095	ERX3851413	ERS4266437	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	0.93539	0.9357	0.07066	0.07028	0.76197	0.76386	0.54301	0.54343	76	75	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9783	9783	ERR3838746	ERX3851412	ERS4266436	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 dome rep2	SAMEA6501987	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 24T08:44:00Z\|External Id:SAMEA6501987\|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 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:Soma dome rep2\|age:4.3\|broker name:ArrayExpress\|cell type:whole embryo\|common name:zebrafish\|developmental stage:blastula dome\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:Soma dome 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 dome rep2 p	Soma dome 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:blastula dome\|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	S10_R1.fastq.gz S10_R2.fastq.gz	fastq fastq	1086124503.0	7272505.0	E MTAB 8707:S10 R	0:74.67 1:74.68	A:305920447;C:235855931;G:243442186;T:300439294;N:466645	74	74	305920447	235855931	243442186	300439294	466645	ERX3851412	ERS4266436	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	0.94089	0.94085	0.04872	0.04916	0.7419	0.74355	0.51209	0.5119	74	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9784	9784	ERR3838745	ERX3851411	ERS4266435	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 dome rep1	SAMEA6501986	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 24T08:44:00Z\|External Id:SAMEA6501986\|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 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:Soma dome rep1\|age:4.3\|broker name:ArrayExpress\|cell type:whole embryo\|common name:zebrafish\|developmental stage:blastula dome\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:Soma dome rep1\|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 dome rep1 p	Soma dome rep1 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:blastula dome\|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	S8_R1.fastq.gz S8_R2.fastq.gz	fastq fastq	336100162.0	2240589.0	E MTAB 8707:S8 R	0:75.00 1:75.00	A:93960580;C:73499585;G:75981355;T:92580945;N:77697	75	75	93960580	73499585	75981355	92580945	77697	ERX3851411	ERS4266435	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	0.93874	0.93856	0.05265	0.0517	0.74188	0.74381	0.51181	0.51086	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9785	9785	ERR3838744	ERX3851410	ERS4266434	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 256 cell rep2	SAMEA6501985	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 24T08:44:00Z\|External Id:SAMEA6501985\|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 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:Soma 256 cell rep2\|age:2.5\|broker name:ArrayExpress\|cell type:whole embryo\|common name:zebrafish\|developmental stage:blastula 256 cell\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:Soma 256 cell 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 256 cell rep2 p	Soma 256 cell 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:blastula 256 cell\|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	S2_R1.fastq.gz S2_R2.fastq.gz	fastq fastq	1272080863.0	8551103.0	E MTAB 8707:S2 R	0:74.38 1:74.38	A:364033393;C:268850689;G:276270908;T:362172455;N:753418	74	74	364033393	268850689	276270908	362172455	753418	ERX3851410	ERS4266434	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	0.80562	0.80436	0.23702	0.23786	0.77914	0.77991	0.51225	0.5092	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9786	9786	ERR3838743	ERX3851409	ERS4266433	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 256 cell rep1	SAMEA6501984	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 24T08:44:00Z\|External Id:SAMEA6501984\|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 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:Soma 256 cell rep1\|age:2.5\|broker name:ArrayExpress\|cell type:whole embryo\|common name:zebrafish\|developmental stage:blastula 256 cell\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:Soma 256 cell rep1\|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 256 cell rep1 p	Soma 256 cell rep1 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:blastula 256 cell\|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_256_rep1_R1.fastq.gz Somatic_256_rep1_R2.fastq.gz	fastq fastq	2254901578.0	15144857.0	E MTAB 8707:Somatic 256 rep1 R	0:74.44 1:74.45	A:648357135;C:475813294;G:492914743;T:636658631;N:1157775	74	74	648357135	475813294	492914743	636658631	1157775	ERX3851409	ERS4266433	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	0.92992	0.92787	0.07245	0.07214	0.7599	0.76084	0.53758	0.53839	74	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9787	9787	ERR3838742	ERX3851408	ERS4266432	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 10somites rep2	SAMEA6501983	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 24T08:44:00Z\|External Id:SAMEA6501983\|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 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:Soma 10somites rep2\|age:14\|broker name:ArrayExpress\|cell type:whole embryo\|common name:zebrafish\|developmental stage:10 somites\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:Soma 10somites 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 10somites rep2 p	Soma 10somites 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:10 somites\|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	S6_R1.fastq.gz S6_R2.fastq.gz	fastq fastq	1244080980.0	8338002.0	E MTAB 8707:S6 R	0:74.60 1:74.60	A:356418931;C:263292901;G:270630630;T:353140798;N:597720	74	74	356418931	263292901	270630630	353140798	597720	ERX3851408	ERS4266432	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	0.86791	0.86732	0.20223	0.20398	0.75588	0.75883	0.4862	0.48313	76	75	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Segmentation	Embryo	Whole Organism	All anatomical structures
9788	9788	ERR3838741	ERX3851407	ERS4266431	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 10somites rep1	SAMEA6501982	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 24T08:44:00Z\|External Id:SAMEA6501982\|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 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:Soma 10somites rep1\|age:14\|broker name:ArrayExpress\|cell type:whole embryo\|common name:zebrafish\|developmental stage:10 somites\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:Soma 10somites rep1\|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 10somites rep1 p	Soma 10somites rep1 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:10 somites\|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	S4_R1.fastq.gz S4_R2.fastq.gz	fastq fastq	946153328.0	6354843.0	E MTAB 8707:S4 R	0:74.44 1:74.45	A:268310887;C:203457903;G:208969410;T:264875129;N:539999	74	74	268310887	203457903	208969410	264875129	539999	ERX3851407	ERS4266431	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	0.92415	0.92372	0.12138	0.12268	0.74061	0.74422	0.47246	0.47448	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Segmentation	Embryo	Whole Organism	All anatomical structures
9789	9789	ERR3838740	ERX3851406	ERS4266430	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.	PGC prim5 wt rep2	SAMEA6501981	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 24T08:44:00Z\|External Id:SAMEA6501981\|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 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC prim5 wt rep2\|age:24\|broker name:ArrayExpress\|cell type:primordial germ cell\|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:PGC 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:PGC prim5 wt rep2 p	PGC 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:primordial germ cell	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	PGC_prim5_rep2_R1.fastq.gz PGC_prim5_rep2_R2.fastq.gz	fastq fastq	2236371655.0	15023634.0	E MTAB 8707:PGC prim5 rep2 R	0:74.43 1:74.43	A:619039687;C:495191024;G:509021767;T:611885185;N:1233992	74	74	619039687	495191024	509021767	611885185	1233992	ERX3851406	ERS4266430	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	0.93137	0.92838	0.23991	0.24045	0.71435	0.71591	0.49054	0.49302	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
9790	9790	ERR3838739	ERX3851405	ERS4266429	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.	PGC prim5 wt rep1	SAMEA6501980	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 24T08:44:00Z\|External Id:SAMEA6501980\|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 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC prim5 wt rep1\|age:24\|broker name:ArrayExpress\|cell type:primordial germ cell\|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:PGC prim5 wt rep1\|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:PGC prim5 wt rep1 p	PGC prim5 wt rep1 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:primordial germ cell	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	PGC_prim5_rep1_R1.fastq.gz PGC_prim5_rep1_R2.fastq.gz	fastq fastq	1619398294.0	10873533.0	E MTAB 8707:PGC prim5 rep1 R	0:74.46 1:74.47	A:450612629;C:355178930;G:365650222;T:447083613;N:872900	74	74	450612629	355178930	365650222	447083613	872900	ERX3851405	ERS4266429	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	0.92755	0.92901	0.22893	0.22952	0.71131	0.71372	0.49829	0.50019	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
9791	9791	ERR3838738	ERX3851404	ERS4266428	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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. 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.	PGC prim5 Morpholino rep2	SAMEA6501979	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 24T08:44:00Z\|External Id:SAMEA6501979\|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 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC prim5 Morpholino rep2\|age:24\|broker name:ArrayExpress\|cell type:primordial germ cell\|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:PGC prim5 Morpholino 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:PGC prim5 Morpholino rep2 p	PGC prim5 Morpholino 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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. 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:Morpholino antisense oligo against Tdrd7 transcript\|Experimental Factor: dose:0.3\|Experimental Factor: cell type:primordial germ cell	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	S13_R1.fastq.gz S13_R2.fastq.gz	fastq fastq	906443913.0	6069224.0	E MTAB 8707:S13 R	0:74.67 1:74.68	A:256935983;C:195137600;G:200975999;T:253026767;N:367564	74	74	256935983	195137600	200975999	253026767	367564	ERX3851404	ERS4266428	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	0.93468	0.93605	0.09793	0.09817	0.71163	0.71291	0.48766	0.48921	75	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
9792	9792	ERR3838737	ERX3851403	ERS4266427	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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. 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.	PGC prim5 Morpholino rep1	SAMEA6501978	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 24T08:44:00Z\|External Id:SAMEA6501978\|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 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC prim5 Morpholino rep1\|age:24\|broker name:ArrayExpress\|cell type:primordial germ cell\|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:PGC prim5 Morpholino rep1\|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:PGC prim5 Morpholino rep1 p	PGC prim5 Morpholino rep1 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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. 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:Morpholino antisense oligo against Tdrd7 transcript\|Experimental Factor: dose:0.3\|Experimental Factor: cell type:primordial germ cell	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	Fabio_cat_11_R1.fastq.gz Fabio_cat_11_R2.fastq.gz	fastq fastq	1078919524.0	7241200.0	E MTAB 8707:Fabio cat 11 R	0:74.50 1:74.50	A:308200726;C:229836659;G:236649504;T:303673221;N:559414	74	74	308200726	229836659	236649504	303673221	559414	ERX3851403	ERS4266427	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	0.93808	0.93753	0.10449	0.10446	0.70733	0.71017	0.48103	0.48247	75	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
9793	9793	ERR3838736	ERX3851402	ERS4266426	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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. 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.	PGC prim5 5mismatch Morpholino rep2	SAMEA6501977	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 24T08:44:00Z\|External Id:SAMEA6501977\|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 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC prim5 5mismatch Morpholino rep2\|age:24\|broker name:ArrayExpress\|cell type:primordial germ cell\|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:PGC prim5 5mismatch Morpholino 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:PGC prim5 5mismatch Morpholino rep2 p	PGC prim5 5mismatch Morpholino 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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. 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:Control morpholino antisense oligo with 5 mismatches\|Experimental Factor: dose:0.3\|Experimental Factor: cell type:primordial germ cell	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	S17_R1.fastq.gz S17_R2.fastq.gz	fastq fastq	673911944.0	4501723.0	E MTAB 8707:S17 R	0:74.85 1:74.85	A:184466911;C:150779527;G:155693395;T:182720480;N:251631	74	74	184466911	150779527	155693395	182720480	251631	ERX3851402	ERS4266426	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	0.9199	0.92023	0.08791	0.08923	0.70132	0.70378	0.49183	0.49425	75	75	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
9794	9794	ERR3838735	ERX3851401	ERS4266425	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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. 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.	PGC prim5 5mismatch Morpholino rep1	SAMEA6501976	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 24T08:44:00Z\|External Id:SAMEA6501976\|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 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC prim5 5mismatch Morpholino rep1\|age:24\|broker name:ArrayExpress\|cell type:primordial germ cell\|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:PGC prim5 5mismatch Morpholino rep1\|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:PGC prim5 5mismatch Morpholino rep1 p	PGC prim5 5mismatch Morpholino rep1 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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. 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:Control morpholino antisense oligo with 5 mismatches\|Experimental Factor: dose:0.3\|Experimental Factor: cell type:primordial germ cell	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	S15_R1.fastq.gz S15_R2.fastq.gz	fastq fastq	565636692.0	3782000.0	E MTAB 8707:S15 R	0:74.78 1:74.78	A:157353454;C:124504476;G:128260137;T:155314004;N:204621	74	74	157353454	124504476	128260137	155314004	204621	ERX3851401	ERS4266425	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	0.91956	0.91996	0.08306	0.08458	0.69982	0.70203	0.48525	0.48771	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
9795	9795	ERR3838734	ERX3851400	ERS4266424	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.	PGC High rep2	SAMEA6501975	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 24T08:44:00Z\|External Id:SAMEA6501975\|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 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC High rep2\|age:3.3\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:blastula high\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:PGC High 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:PGC High rep2 p	PGC High 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:blastula high\|Experimental Factor: compound:n1\|Experimental Factor: cell type:primordial germ cell	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	PGC_High_rep2_R1.fastq.gz PGC_High_rep2_R2.fastq.gz	fastq fastq	2491013839.0	16740632.0	E MTAB 8707:PGC High rep2 R	0:74.40 1:74.40	A:715637079;C:527451931;G:545855323;T:700774175;N:1295331	74	74	715637079	527451931	545855323	700774175	1295331	ERX3851400	ERS4266424	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	0.93381	0.93556	0.06095	0.06172	0.76094	0.76364	0.52942	0.53118	74	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9796	9796	ERR3838733	ERX3851399	ERS4266423	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.	PGC High rep1	SAMEA6501974	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 24T08:44:00Z\|External Id:SAMEA6501974\|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 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC High rep1\|age:3.3\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:blastula high\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:PGC High rep1\|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:PGC High rep1 p	PGC High rep1 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:blastula high\|Experimental Factor: compound:n1\|Experimental Factor: cell type:primordial germ cell	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	PGC_High_rep1_R1.fastq.gz PGC_High_rep1_R2.fastq.gz	fastq fastq	2055218051.0	13801653.0	E MTAB 8707:PGC High rep1 R	0:74.45 1:74.46	A:594747301;C:431446277;G:445665283;T:582330624;N:1028566	74	74	594747301	431446277	445665283	582330624	1028566	ERX3851399	ERS4266423	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	0.93644	0.93494	0.06937	0.07015	0.76353	0.7653	0.45909	0.44979	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9797	9797	ERR3838732	ERX3851398	ERS4266422	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.	PGC dome rep2	SAMEA6501973	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 24T08:44:00Z\|External Id:SAMEA6501973\|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 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC dome rep2\|age:4.3\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:blastula dome\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:PGC dome 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:PGC dome rep2 p	PGC dome 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:blastula dome\|Experimental Factor: compound:n1\|Experimental Factor: cell type:primordial germ cell	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	S9_R1.fastq.gz S9_R2.fastq.gz	fastq fastq	882858901.0	5912255.0	E MTAB 8707:S9 R	0:74.66 1:74.67	A:246639630;C:193554406;G:199940889;T:242369366;N:354610	74	74	246639630	193554406	199940889	242369366	354610	ERX3851398	ERS4266422	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	0.94045	0.9404	0.04635	0.04658	0.74582	0.74777	0.4915	0.49248	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9798	9798	ERR3838731	ERX3851397	ERS4266421	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.	PGC dome rep1	SAMEA6501972	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 24T08:44:00Z\|External Id:SAMEA6501972\|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 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC dome rep1\|age:4.3\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:blastula dome\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:PGC dome rep1\|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:PGC dome rep1 p	PGC dome rep1 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:blastula dome\|Experimental Factor: compound:n1\|Experimental Factor: cell type:primordial germ cell	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	S7_R1.fastq.gz S7_R2.fastq.gz	fastq fastq	592299285.0	3961989.0	E MTAB 8707:S7 R	0:74.75 1:74.75	A:166664600;C:128421892;G:132787149;T:164189412;N:236232	74	74	166664600	128421892	132787149	164189412	236232	ERX3851397	ERS4266421	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	0.93981	0.94032	0.04868	0.04843	0.74627	0.74722	0.49243	0.48872	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9799	9799	ERR3838730	ERX3851396	ERS4266420	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.	PGC 256 cell rep2	SAMEA6501971	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 24T08:44:00Z\|External Id:SAMEA6501971\|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 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC 256 cell rep2\|age:2.5\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:blastula 256 cell\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:PGC 256 cell 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:PGC 256 cell rep2 p	PGC 256 cell 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:blastula 256 cell\|Experimental Factor: compound:n1\|Experimental Factor: cell type:primordial germ cell	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	S1_R1.fastq.gz S1_R2.fastq.gz	fastq fastq	745277323.0	4983607.0	E MTAB 8707:S1 R	0:74.77 1:74.77	A:208352741;C:163024343;G:168234953;T:205391192;N:274094	74	74	208352741	163024343	168234953	205391192	274094	ERX3851396	ERS4266420	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	0.9393	0.9395	0.03941	0.03941	0.75473	0.75708	0.51338	0.51754	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9800	9800	ERR3838729	ERX3851395	ERS4266419	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.	PGC 256 cell rep1	SAMEA6501970	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 24T08:44:00Z\|External Id:SAMEA6501970\|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 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC 256 cell rep1\|age:2.5\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:blastula 256 cell\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:PGC 256 cell rep1\|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:PGC 256 cell rep1 p	PGC 256 cell rep1 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:blastula 256 cell\|Experimental Factor: compound:n1\|Experimental Factor: cell type:primordial germ cell	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	PGC_256_rep1_R1.fastq.gz PGC_256_rep1_R2.fastq.gz	fastq fastq	1876891175.0	12625794.0	E MTAB 8707:PGC 256 rep1 R	0:74.32 1:74.33	A:539140549;C:396392844;G:411568412;T:528672735;N:1116635	74	74	539140549	396392844	411568412	528672735	1116635	ERX3851395	ERS4266419	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	0.92251	0.92173	0.06705	0.06723	0.76059	0.76374	0.54467	0.54135	76	75	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9801	9801	ERR3838728	ERX3851394	ERS4266418	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.	PGC 10somites rep2	SAMEA6501969	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 24T08:44:00Z\|External Id:SAMEA6501969\|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 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC 10somites rep2\|age:14\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:10 somites\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:PGC 10somites 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:PGC 10somites rep2 p	PGC 10somites 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:10 somites\|Experimental Factor: compound:n1\|Experimental Factor: cell type:primordial germ cell	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	S5_R1.fastq.gz S5_R2.fastq.gz	fastq fastq	1186993033.0	7958634.0	E MTAB 8707:S5 R	0:74.57 1:74.58	A:332263881;C:259239478;G:267014990;T:327946611;N:528073	74	74	332263881	259239478	267014990	327946611	528073	ERX3851394	ERS4266418	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	0.90713	0.9062	0.10071	0.1016	0.73058	0.73279	0.48458	0.48038	74	75	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Segmentation	Embryo	Whole Organism	All anatomical structures
9802	9802	ERR3838727	ERX3851393	ERS4266417	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.	PGC 10somites rep1	SAMEA6501968	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 24T08:44:00Z\|External Id:SAMEA6501968\|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 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC 10somites rep1\|age:14\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:10 somites\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:PGC 10somites rep1\|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:PGC 10somites rep1 p	PGC 10somites rep1 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:10 somites\|Experimental Factor: compound:n1\|Experimental Factor: cell type:primordial germ cell	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	S3_R1.fastq.gz S3_R2.fastq.gz	fastq fastq	1230551446.0	8251644.0	E MTAB 8707:S3 R	0:74.56 1:74.57	A:345409587;C:267720436;G:275626594;T:341185818;N:609011	74	74	345409587	267720436	275626594	341185818	609011	ERX3851393	ERS4266417	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	0.90983	0.90985	0.1005	0.10037	0.72622	0.72825	0.49116	0.49135	76	75	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Segmentation	Embryo	Whole Organism	All anatomical structures
10111	10111	ERR4911024	ERX4777847	ERS5435613	ERP125516	PRJEB41701	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-9857	Transcriptome Analysis	In this rescue experiment embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 12 02	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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. 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.	PGC Rescue rep2	SAMEA7678632	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA first public:2020 12 24\|ENA last update:2020 12 02\|External Id:SAMEA7678632\|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 12 24T04:05:28Z\|INSDC last update:2020 12 02T17:13:26Z\|INSDC status:public\|Submitter Id:E MTAB 9857:PGC Rescue rep2\|age:24\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:pharyngula prim 5\|genotype:tgbuc:gfp\|sample name:E MTAB 9857:PGC Rescue rep2\|strain:AB	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 9857:PGC Rescue rep2 p	PGC Rescue 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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. 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: compound:tdrd7 MO + tdrd7 rescue RNA	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP125516	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 12 09	Tdrd7_Rescue_PGC_rep2_R1.fastq.gz Tdrd7_Rescue_PGC_rep2_R2.fastq.gz	fastq fastq	6487121744.0	43103086.0	E MTAB 9857:Tdrd7 Rescue PGC rep2 R	0:75.26 1:75.24	A:1769293880;C:1469053016;G:1516553427;T:1729496045;N:2725376	75	75	1769293880	1469053016	1516553427	1729496045	2725376	ERX4777847	ERS5435613	ERA3184570	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	0.95185	0.95349	0.04302	0.04315	0.72829	0.73022	0.47176	0.47104	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-12-02	Pharyngula	Embryo	Whole Organism	All anatomical structures
10112	10112	ERR4911023	ERX4777846	ERS5435612	ERP125516	PRJEB41701	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-9857	Transcriptome Analysis	In this rescue experiment embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 12 02	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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. 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.	PGC Rescue rep1	SAMEA7678631	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA first public:2020 12 24\|ENA last update:2020 12 02\|External Id:SAMEA7678631\|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 12 24T04:05:28Z\|INSDC last update:2020 12 02T17:13:26Z\|INSDC status:public\|Submitter Id:E MTAB 9857:PGC Rescue rep1\|age:24\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:pharyngula prim 5\|genotype:tgbuc:gfp\|sample name:E MTAB 9857:PGC Rescue rep1\|strain:AB	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 9857:PGC Rescue rep1 p	PGC Rescue rep1 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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. 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: compound:tdrd7 MO + tdrd7 rescue RNA	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP125516	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 12 09	Tdrd7_Rescue_PGC_rep1_R1.fastq.gz Tdrd7_Rescue_PGC_rep1_R2.fastq.gz	fastq fastq	5952473889.0	39454929.0	E MTAB 9857:Tdrd7 Rescue PGC rep1 R	0:75.44 1:75.43	A:1640467527;C:1332668425;G:1380033115;T:1597665169;N:1639653	75	75	1640467527	1332668425	1380033115	1597665169	1639653	ERX4777846	ERS5435612	ERA3184570	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	0.95086	0.95226	0.06292	0.0629	0.70341	0.70579	0.46524	0.46691	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-12-02	Pharyngula	Embryo	Whole Organism	All anatomical structures
10113	10113	ERR4911022	ERX4777845	ERS5435611	ERP125516	PRJEB41701	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-9857	Transcriptome Analysis	In this rescue experiment embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 12 02	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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. 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.	PGC MO rep2	SAMEA7678630	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA first public:2020 12 24\|ENA last update:2020 12 02\|External Id:SAMEA7678630\|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 12 24T04:05:28Z\|INSDC last update:2020 12 02T17:13:26Z\|INSDC status:public\|Submitter Id:E MTAB 9857:PGC MO rep2\|age:24\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:pharyngula prim 5\|genotype:tgbuc:gfp\|sample name:E MTAB 9857:PGC MO rep2\|strain:AB	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 9857:PGC MO rep2 p	PGC MO 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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. 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: compound:tdrd7 targeting MO	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP125516	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 12 09	Tdrd7_MO_PGC_rep2_R1.fastq.gz Tdrd7_MO_PGC_rep2_R2.fastq.gz	fastq fastq	906443913.0	6069224.0	E MTAB 9857:Tdrd7 MO PGC rep2 R	0:74.67 1:74.68	A:256935983;C:195137600;G:200975999;T:253026767;N:367564	74	74	256935983	195137600	200975999	253026767	367564	ERX4777845	ERS5435611	ERA3184570	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	0.93468	0.93603	0.09796	0.09848	0.7119	0.71439	0.48682	0.48933	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-12-02	Pharyngula	Embryo	Whole Organism	All anatomical structures
10114	10114	ERR4911021	ERX4777844	ERS5435610	ERP125516	PRJEB41701	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-9857	Transcriptome Analysis	In this rescue experiment embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 12 02	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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. 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.	PGC MO rep1	SAMEA7678629	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA first public:2020 12 24\|ENA last update:2020 12 02\|External Id:SAMEA7678629\|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 12 24T04:05:28Z\|INSDC last update:2020 12 02T17:13:26Z\|INSDC status:public\|Submitter Id:E MTAB 9857:PGC MO rep1\|age:24\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:pharyngula prim 5\|genotype:tgbuc:gfp\|sample name:E MTAB 9857:PGC MO rep1\|strain:AB	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 9857:PGC MO rep1 p	PGC MO rep1 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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. 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: compound:tdrd7 targeting MO	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP125516	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 12 09	Tdrd7_MO_PGC_rep1_R1.fastq.gz Tdrd7_MO_PGC_rep1_R2.fastq.gz	fastq fastq	1078919524.0	7241200.0	E MTAB 9857:Tdrd7 MO PGC rep1 R	0:74.50 1:74.50	A:308200726;C:229836659;G:236649504;T:303673221;N:559414	74	74	308200726	229836659	236649504	303673221	559414	ERX4777844	ERS5435610	ERA3184570	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	0.938	0.93748	0.10463	0.10431	0.7077	0.70999	0.48098	0.48239	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-12-02	Pharyngula	Embryo	Whole Organism	All anatomical structures
10115	10115	ERR4911020	ERX4777843	ERS5435609	ERP125516	PRJEB41701	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-9857	Transcriptome Analysis	In this rescue experiment embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 12 02	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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. 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.	PGC 5mm rep2	SAMEA7678628	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA first public:2020 12 24\|ENA last update:2020 12 02\|External Id:SAMEA7678628\|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 12 24T04:05:28Z\|INSDC last update:2020 12 02T17:13:26Z\|INSDC status:public\|Submitter Id:E MTAB 9857:PGC 5mm rep2\|age:24\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:pharyngula prim 5\|genotype:tgbuc:gfp\|sample name:E MTAB 9857:PGC 5mm rep2\|strain:AB	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 9857:PGC 5mm rep2 p	PGC 5mm 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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. 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: compound:tdrd7 5mismatch MO	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP125516	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 12 09	Tdrd7_5mm_PGC_rep2_R1.fastq.gz Tdrd7_5mm_PGC_rep2_R2.fastq.gz	fastq fastq	673911944.0	4501723.0	E MTAB 9857:Tdrd7 5mm PGC rep2 R	0:74.85 1:74.85	A:184466911;C:150779527;G:155693395;T:182720480;N:251631	74	74	184466911	150779527	155693395	182720480	251631	ERX4777843	ERS5435609	ERA3184570	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	0.91989	0.92025	0.08795	0.08919	0.70096	0.70416	0.49184	0.49415	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-12-02	Pharyngula	Embryo	Whole Organism	All anatomical structures
10116	10116	ERR4911019	ERX4777842	ERS5435608	ERP125516	PRJEB41701	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-9857	Transcriptome Analysis	In this rescue experiment embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 12 02	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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. 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.	PGC 5mm rep1	SAMEA7678627	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA first public:2020 12 24\|ENA last update:2020 12 02\|External Id:SAMEA7678627\|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 12 24T04:05:28Z\|INSDC last update:2020 12 02T17:13:26Z\|INSDC status:public\|Submitter Id:E MTAB 9857:PGC 5mm rep1\|age:24\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:pharyngula prim 5\|genotype:tgbuc:gfp\|sample name:E MTAB 9857:PGC 5mm rep1\|strain:AB	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 9857:PGC 5mm rep1 p	PGC 5mm rep1 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. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. 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: compound:tdrd7 5mismatch MO	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP125516	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 12 09	Tdrd7_5mm_PGC_rep1_R1.fastq.gz Tdrd7_5mm_PGC_rep1_R2.fastq.gz	fastq fastq	565636692.0	3782000.0	E MTAB 9857:Tdrd7 5mm PGC rep1 R	0:74.78 1:74.78	A:157353454;C:124504476;G:128260137;T:155314004;N:204621	74	74	157353454	124504476	128260137	155314004	204621	ERX4777842	ERS5435608	ERA3184570	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	0.91957	0.91995	0.08301	0.0845	0.69929	0.70195	0.48544	0.4877	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-12-02	Pharyngula	Embryo	Whole Organism	All anatomical structures

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;