metadata: run_metadata: 48 rows where devstage_curation = "Pharyngula" and experiment.library

48 rows where devstage_curation = "Pharyngula" and experiment.library_selection = "RANDOM PCR"

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
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
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
64161	64161	SRR14308450	SRX10663886	SRS8758306	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					D1		strain:AB10\|age:24hpf10\|dev stage:24hpf10\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB10	L10	L10	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			D1.raw_1.fastq.gz D1.raw_2.fastq.gz	fastq fastq	6493890000.0	21646300.0	D1.raw 1.fastq.gz	0:150 1:150	A:1744755708;C:1484305355;G:1549325281;T:1715269253;N:234403	150	150	1744755708	1484305355	1549325281	1715269253	234403	SRX10663886	SRS8758306	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.94046	0.93893	0.09092	0.08953	0.69179	0.6957	0.47163	0.4711	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-27	Pharyngula	Embryo	Whole Organism	All anatomical structures
64162	64162	SRR14308451	SRX10663885	SRS8758305	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					C3		strain:AB9\|age:24hpf9\|dev stage:24hpf9\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB9	L9	L9	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			C3.raw_1.fastq.gz C3.raw_2.fastq.gz	fastq fastq	6301176600.0	21003922.0	C3.raw 1.fastq.gz	0:150 1:150	A:1665737962;C:1471580978;G:1530541563;T:1633084943;N:231154	150	150	1665737962	1471580978	1530541563	1633084943	231154	SRX10663885	SRS8758305	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.93548	0.93245	0.07291	0.07262	0.76479	0.76779	0.47781	0.4799	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-27	Pharyngula	Embryo	Cell Line	Cell Line
64163	64163	SRR14308452	SRX10663884	SRS8758304	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					C2		strain:AB8\|age:24hpf8\|dev stage:24hpf8\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB8	L8	L8	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			C2.raw_1.fastq.gz C2.raw_2.fastq.gz	fastq fastq	5887783500.0	19625945.0	C2.raw 1.fastq.gz	0:150 1:150	A:1539979565;C:1392825547;G:1451253488;T:1503541801;N:183099	150	150	1539979565	1392825547	1451253488	1503541801	183099	SRX10663884	SRS8758304	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.94543	0.94466	0.06666	0.06614	0.73342	0.73468	0.46413	0.46432	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-27	Pharyngula	Embryo	Whole Organism	All anatomical structures
64164	64164	SRR14308453	SRX10663883	SRS8758303	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					C1		strain:AB7\|age:24hpf7\|dev stage:24hpf7\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB7	L7	L7	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			C1.raw_1.fastq.gz C1.raw_2.fastq.gz	fastq fastq	5878215900.0	19594053.0	C1.raw 1.fastq.gz	0:150 1:150	A:1567876584;C:1356626287;G:1407943115;T:1545550803;N:219111	150	150	1567876584	1356626287	1407943115	1545550803	219111	SRX10663883	SRS8758303	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.93508	0.93337	0.08056	0.08002	0.74024	0.74276	0.47159	0.47142	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-27	Pharyngula	Embryo	Whole Organism	All anatomical structures
64165	64165	SRR14308454	SRX10663882	SRS8758302	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					B3		strain:AB6\|age:24hpf6\|dev stage:24hpf6\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB6	L6	L6	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			B3.raw_1.fastq.gz B3.raw_2.fastq.gz	fastq fastq	5684530200.0	18948434.0	B3.raw 1.fastq.gz	0:150 1:150	A:1468959527;C:1362254368;G:1409533547;T:1443570573;N:212185	150	150	1468959527	1362254368	1409533547	1443570573	212185	SRX10663882	SRS8758302	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.74739	0.74464	0.07384	0.07335	0.72671	0.72977	0.46742	0.47358	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-27	Pharyngula	Embryo	Whole Organism	All anatomical structures
64166	64166	SRR14308455	SRX10663881	SRS8758301	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					B2		strain:AB5\|age:24hpf5\|dev stage:24hpf5\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB5	L5	L5	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			B2.raw_1.fastq.gz B2.raw_2.fastq.gz	fastq fastq	6605542500.0	22018475.0	B2.raw 1.fastq.gz	0:150 1:150	A:1776549620;C:1511937358;G:1570716255;T:1746097273;N:241994	150	150	1776549620	1511937358	1570716255	1746097273	241994	SRX10663881	SRS8758301	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.94479	0.94309	0.09199	0.09117	0.7024	0.70445	0.46871	0.46925	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-27	Pharyngula	Embryo	Whole Organism	All anatomical structures
64167	64167	SRR14308456	SRX10663880	SRS8758300	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					B1		strain:AB4\|age:24hpf4\|dev stage:24hpf4\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB4	L4	L4	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			B1.raw_1.fastq.gz B1.raw_2.fastq.gz	fastq fastq	5853655500.0	19512185.0	B1.raw 1.fastq.gz	0:150 1:150	A:1571488140;C:1342134462;G:1393752149;T:1546065949;N:214800	150	150	1571488140	1342134462	1393752149	1546065949	214800	SRX10663880	SRS8758300	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.94318	0.94153	0.08642	0.08621	0.7024	0.70508	0.46359	0.46397	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-27	Pharyngula	Embryo	Whole Organism	All anatomical structures
64168	64168	SRR14308457	SRX10663879	SRS8758299	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					DD3		strain:AB24\|age:24hpf21\|dev stage:24hpf21\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB24	L24	L24	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			DD3.raw_1.fastq.gz DD3.raw_2.fastq.gz	fastq fastq	7608806100.0	25362687.0	DD3.raw 1.fastq.gz	0:150 1:150	A:2042994601;C:1734375022;G:1812166219;T:2018988826;N:281432	150	150	2042994601	1734375022	1812166219	2018988826	281432	SRX10663879	SRS8758299	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.94225	0.94109	0.10828	0.10717	0.67436	0.6776	0.47781	0.48362	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-27	Pharyngula	Embryo	Whole Organism	All anatomical structures
64169	64169	SRR14308458	SRX10663878	SRS8758298	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					DD2		strain:AB23\|age:24hpf21\|dev stage:24hpf21\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB23	L23	L23	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			DD2.raw_1.fastq.gz DD2.raw_2.fastq.gz	fastq fastq	8917386000.0	29724620.0	DD2.raw 1.fastq.gz	0:150 1:150	A:2348537193;C:2056372655;G:2265284593;T:2246861797;N:329762	150	150	2348537193	2056372655	2265284593	2246861797	329762	SRX10663878	SRS8758298	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.94502	0.94397	0.09162	0.09061	0.67444	0.67718	0.47862	0.47594	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-27	Pharyngula	Embryo	Whole Organism	All anatomical structures
64170	64170	SRR14308459	SRX10663877	SRS8758297	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					DD1		strain:AB22\|age:24hpf21\|dev stage:24hpf21\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB22	L22	L22	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			DD1.raw_1.fastq.gz DD1.raw_2.fastq.gz	fastq fastq	9206423700.0	30688079.0	DD1.raw 1.fastq.gz	0:150 1:150	A:2472225392;C:2105587795;G:2227426250;T:2400846522;N:337741	150	150	2472225392	2105587795	2227426250	2400846522	337741	SRX10663877	SRS8758297	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.94554	0.94388	0.09791	0.09713	0.67176	0.67608	0.47029	0.46751	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-26	Pharyngula	Embryo	Whole Organism	All anatomical structures
64171	64171	SRR14308460	SRX10663876	SRS8758296	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					CC3		strain:AB21\|age:24hpf21\|dev stage:24hpf21\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB21	L21	L21	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			CC3.raw_1.fastq.gz CC3.raw_2.fastq.gz	fastq fastq	7960518600.0	26535062.0	CC3.raw 1.fastq.gz	0:150 1:150	A:2140265475;C:1813420444;G:1929113445;T:2077420579;N:298657	150	150	2140265475	1813420444	1929113445	2077420579	298657	SRX10663876	SRS8758296	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.94251	0.94195	0.10311	0.10286	0.66703	0.66916	0.47505	0.4745	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-27	Pharyngula	Embryo	Whole Organism	All anatomical structures
64172	64172	SRR14308461	SRX10663875	SRS8758295	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					A3		strain:AB3\|age:24hpf3\|dev stage:24hpf3\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB3	L3	L3	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			A3.raw_1.fastq.gz A3.raw_2.fastq.gz	fastq fastq	6501644400.0	21672148.0	A3.raw 1.fastq.gz	0:150 1:150	A:1749736007;C:1484391807;G:1544667394;T:1722602072;N:247120	150	150	1749736007	1484391807	1544667394	1722602072	247120	SRX10663875	SRS8758295	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.93166	0.92874	0.09361	0.09274	0.69033	0.69382	0.4671	0.47232	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-27	Pharyngula	Embryo	Whole Organism	All anatomical structures
64173	64173	SRR14308462	SRX10663874	SRS8758294	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					CC2		strain:AB20\|age:24hpf20\|dev stage:24hpf20\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB20	L20	L20	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			CC2.raw_1.fastq.gz CC2.raw_2.fastq.gz	fastq fastq	6983705700.0	23279019.0	CC2.raw 1.fastq.gz	0:150 1:150	A:1893999424;C:1578088530;G:1645506692;T:1865862107;N:248947	150	150	1893999424	1578088530	1645506692	1865862107	248947	SRX10663874	SRS8758294	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.94027	0.93898	0.11339	0.11255	0.66687	0.67044	0.47404	0.47154	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-27	Pharyngula	Embryo	Whole Organism	All anatomical structures
64174	64174	SRR14308463	SRX10663873	SRS8758293	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					CC1		strain:AB19\|age:24hpf19\|dev stage:24hpf19\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB19	L19	L19	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			CC1.raw_1.fastq.gz CC1.raw_2.fastq.gz	fastq fastq	6085625100.0	20285417.0	CC1.raw 1.fastq.gz	0:150 1:150	A:1649108440;C:1377973381;G:1437131820;T:1621215684;N:195775	150	150	1649108440	1377973381	1437131820	1621215684	195775	SRX10663873	SRS8758293	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.93918	0.93804	0.11318	0.11256	0.66754	0.67006	0.4771	0.47662	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-27	Pharyngula	Embryo	Whole Organism	All anatomical structures
64175	64175	SRR14308464	SRX10663872	SRS8758292	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					BB3		strain:AB18\|age:24hpf18\|dev stage:24hpf18\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB18	L18	L18	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			BB3.raw_1.fastq.gz BB3.raw_2.fastq.gz	fastq fastq	7062474600.0	23541582.0	BB3.raw 1.fastq.gz	0:150 1:150	A:1921863301;C:1592284161;G:1655846305;T:1892221736;N:259097	150	150	1921863301	1592284161	1655846305	1892221736	259097	SRX10663872	SRS8758292	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.93889	0.93837	0.11056	0.10986	0.66614	0.66933	0.47318	0.47131	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-27	Pharyngula	Embryo	Whole Organism	All anatomical structures
64176	64176	SRR14308465	SRX10663871	SRS8758291	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					BB2		strain:AB17\|age:24hpf17\|dev stage:24hpf17\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB17	L17	L17	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			BB2.raw_1.fastq.gz BB2.raw_2.fastq.gz	fastq fastq	8811666300.0	29372221.0	BB2.raw 1.fastq.gz	0:150 1:150	A:2397552932;C:1984902811;G:2068491247;T:2360394673;N:324637	150	150	2397552932	1984902811	2068491247	2360394673	324637	SRX10663871	SRS8758291	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.94173	0.9408	0.11119	0.11014	0.66862	0.67361	0.47037	0.47102	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-27	Pharyngula	Embryo	Whole Organism	All anatomical structures
64177	64177	SRR14308466	SRX10663870	SRS8758290	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					BB1		strain:AB16\|age:24hpf16\|dev stage:24hpf16\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB16	L16	L16	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			BB1.raw_1.fastq.gz BB1.raw_2.fastq.gz	fastq fastq	7443202800.0	24810676.0	BB1.raw 1.fastq.gz	0:150 1:150	A:2006371139;C:1694257851;G:1793398929;T:1948895527;N:279354	150	150	2006371139	1694257851	1793398929	1948895527	279354	SRX10663870	SRS8758290	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.94595	0.94447	0.09854	0.09761	0.66947	0.67308	0.47022	0.46692	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-27	Pharyngula	Embryo	Whole Organism	All anatomical structures
64178	64178	SRR14308467	SRX10663869	SRS8758289	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					AA3		strain:AB15\|age:24hpf15\|dev stage:24hpf15\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB15	L15	L15	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			AA3.raw_2.fastq.gz AA3.raw_1.fastq.gz	fastq fastq	9615009600.0	32050032.0	AA3.raw 1.fastq.gz	0:150 1:150	A:2582591269;C:2196606474;G:2311586967;T:2523869435;N:355455	150	150	2582591269	2196606474	2311586967	2523869435	355455	SRX10663869	SRS8758289	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.94626	0.94544	0.10279	0.10177	0.6607	0.66409	0.47416	0.46877	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-26	Pharyngula	Embryo	Whole Organism	All anatomical structures
64179	64179	SRR14308468	SRX10663868	SRS8758288	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					AA2		strain:AB14\|age:24hpf14\|dev stage:24hpf14\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB14	L14	L14	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			AA2.raw_1.fastq.gz AA2.raw_2.fastq.gz	fastq fastq	9362109300.0	31207031.0	AA2.raw 1.fastq.gz	0:150 1:150	A:2520201597;C:2134760126;G:2243935064;T:2462866543;N:345970	150	150	2520201597	2134760126	2243935064	2462866543	345970	SRX10663868	SRS8758288	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.94556	0.94456	0.10681	0.10604	0.66235	0.6647	0.4763	0.47399	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-26	Pharyngula	Embryo	Whole Organism	All anatomical structures
64180	64180	SRR14308469	SRX10663867	SRS8758287	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					AA1		strain:AB13\|age:24hpf13\|dev stage:24hpf13\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB13	L13	L13	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			AA1.raw_1.fastq.gz AA1.raw_2.fastq.gz	fastq fastq	7908833100.0	26362777.0	AA1.raw 1.fastq.gz	0:150 1:150	A:2160066191;C:1780834262;G:1851117381;T:2116551054;N:264212	150	150	2160066191	1780834262	1851117381	2116551054	264212	SRX10663867	SRS8758287	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.9396	0.93706	0.12075	0.11997	0.6619	0.66429	0.46569	0.46809	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-27	Pharyngula	Embryo	Whole Organism	All anatomical structures
64181	64181	SRR14308470	SRX10663866	SRS8758286	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					D3		strain:AB12\|age:24hpf12\|dev stage:24hpf12\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB12	L12	L12	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			D3.raw_1.fastq.gz D3.raw_2.fastq.gz	fastq fastq	6923319900.0	23077733.0	D3.raw 1.fastq.gz	0:150 1:150	A:1863150654;C:1581723494;G:1644468748;T:1833723008;N:253996	150	150	1863150654	1581723494	1644468748	1833723008	253996	SRX10663866	SRS8758286	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.94206	0.94012	0.09084	0.08963	0.69158	0.69587	0.46957	0.46928	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-27	Pharyngula	Embryo	Whole Organism	All anatomical structures
64182	64182	SRR14308471	SRX10663865	SRS8758285	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					D2		strain:AB11\|age:24hpf11\|dev stage:24hpf11\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB11	L11	L11	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			D2.raw_1.fastq.gz D2.raw_2.fastq.gz	fastq fastq	5966531700.0	19888439.0	D2.raw 1.fastq.gz	0:150 1:150	A:1618527031;C:1354948721;G:1407570126;T:1585294636;N:191186	150	150	1618527031	1354948721	1407570126	1585294636	191186	SRX10663865	SRS8758285	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.93817	0.93656	0.09919	0.09832	0.69633	0.69873	0.46752	0.46677	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-27	Pharyngula	Embryo	Whole Organism	All anatomical structures
64183	64183	SRR14308472	SRX10663864	SRS8758284	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					A2		strain:AB2\|age:24hpf2\|dev stage:24hpf2\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB2	L2	L2	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			A2.raw_1.fastq.gz A2.raw_2.fastq.gz	fastq fastq	6898409700.0	22994699.0	A2.raw 1.fastq.gz	0:150 1:150	A:1853201809;C:1578196914;G:1644192208;T:1822563946;N:254823	150	150	1853201809	1578196914	1644192208	1822563946	254823	SRX10663864	SRS8758284	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.92689	0.92559	0.09274	0.092	0.69449	0.698	0.47398	0.47458	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-27	Pharyngula	Embryo	Whole Organism	All anatomical structures
64184	64184	SRR14308473	SRX10663863	SRS8758283	SRP315996	PRJNA724011	BDE 47 zebrafish 24hpf 4dpf	PRJNA724011	Other					A1		strain:AB1\|age:24hpf1\|dev stage:24hpf1\|sex:pooled male and female\|tissue:wholefish\|BioSampleModel:Model organism or animal	AB1	L1	L1	paried end seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina MiSeq	SRP315996			A1.raw_1.fastq.gz A1.raw_2.fastq.gz	fastq fastq	6969096000.0	23230320.0	A1.raw 1.fastq.gz	0:150 1:150	A:1873420822;C:1595222195;G:1663575945;T:1836625430;N:251608	150	150	1873420822	1595222195	1663575945	1836625430	251608	SRX10663863	SRS8758283	SRA1222808	Shantou University\|Medical Colleg	Shantou University	2	0.92862	0.92691	0.09367	0.09313	0.69203	0.69603	0.47678	0.47455	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-04-27	Pharyngula	Embryo	Whole Organism	All anatomical structures
71549	71549	SRR21700247	SRX17697774	SRS15228561	SRP399479	PRJNA884084	RNA Seq data of gmfg morphants and their control siblings	PRJNA884084	Other	To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.			biological replicate 3	gmfg atgMO 3		strain:not applicable\|isolate:not applicable\|dev stage:26 hpf\|sex:not applicable\|tissue:the dissected trunk and tail\|collection date:2021 02 26\|geo loc name:China:Shenzhen Guangdong\|sample type:mo3\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio	MO3 20210214	MO3 20210214	RNA seq of Danio rerio in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500	SRP399479			MO_3_1.fq.gz	fastq	1194263900.0	23885278.0	MO 3 1.fq.gz	0:50 1:0	A:315714579;C:274130504;G:282488713;T:321930104;N:0	50	0	315714579	274130504	282488713	321930104	0	SRX17697774	SRS15228561	SRA1506658	the First Affiliated Hospital, School of Medicine, Zhejiang University\|BoneMarrow Transplantation Center	the First Affiliated Hospital, School of Medicine, Zhejiang University	1	0.9415		0.07261		0.70701		0.47029		50		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-09-25	Pharyngula	Embryo	Multi-tissue	Multi-system
71550	71550	SRR21700248	SRX17697773	SRS15228560	SRP399479	PRJNA884084	RNA Seq data of gmfg morphants and their control siblings	PRJNA884084	Other	To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.			biological replicate 2	gmfg atgMO 2		strain:not applicable\|isolate:not applicable\|dev stage:26 hpf\|sex:not applicable\|tissue:the dissected trunk and tail\|collection date:2021 02 26\|geo loc name:China:Shenzhen Guangdong\|sample type:mo2\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio	MO2 20210213	MO2 20210213	RNA seq of Danio rerio in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500	SRP399479			MO_2_1.fq.gz	fastq	1193697300.0	23873946.0	MO 2 1.fq.gz	0:50 1:0	A:316188077;C:272941933;G:282559962;T:322007328;N:0	50	0	316188077	272941933	282559962	322007328	0	SRX17697773	SRS15228560	SRA1506658	the First Affiliated Hospital, School of Medicine, Zhejiang University\|BoneMarrow Transplantation Center	the First Affiliated Hospital, School of Medicine, Zhejiang University	1	0.94144		0.07426		0.70715		0.47856		50		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-09-25	Pharyngula	Embryo	Multi-tissue	Multi-system
71551	71551	SRR21700249	SRX17697772	SRS15228559	SRP399479	PRJNA884084	RNA Seq data of gmfg morphants and their control siblings	PRJNA884084	Other	To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.			biological replicate 1	gmfg atgMO 1		strain:not applicable\|isolate:not applicable\|dev stage:26 hpf\|sex:not applicable\|tissue:the dissected trunk and tail\|collection date:2021 02 26\|geo loc name:China:Shenzhen Guangdong\|sample type:mo1\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio	MO1 20210212	MO1 20210212	RNA seq of Danio rerio in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500	SRP399479			MO_1_1.fq.gz	fastq	1194311300.0	23886226.0	MO 1 1.fq.gz	0:50 1:0	A:317344841;C:272348188;G:281111904;T:323506367;N:0	50	0	317344841	272348188	281111904	323506367	0	SRX17697772	SRS15228559	SRA1506658	the First Affiliated Hospital, School of Medicine, Zhejiang University\|BoneMarrow Transplantation Center	the First Affiliated Hospital, School of Medicine, Zhejiang University	1	0.94366		0.07701		0.70274		0.47929		50		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-09-25	Pharyngula	Embryo	Multi-tissue	Multi-system
71552	71552	SRR21700250	SRX17697771	SRS15228558	SRP399479	PRJNA884084	RNA Seq data of gmfg morphants and their control siblings	PRJNA884084	Other	To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.			biological replicate 3	ctl 3		strain:not applicable\|isolate:not applicable\|dev stage:26 hpf\|sex:not applicable\|tissue:the dissected trunk and tail\|collection date:2021 02 26\|geo loc name:China:Shenzhen Guangdong\|sample type:ctl3\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio	ctl3 20210211	ctl3 20210211	RNA seq of Danio rerio in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500	SRP399479			ctl_3_1.fq.gz	fastq	1190502850.0	23810057.0	ctl 3 1.fq.gz	0:50 1:0	A:314168919;C:272277792;G:283249731;T:320806408;N:0	50	0	314168919	272277792	283249731	320806408	0	SRX17697771	SRS15228558	SRA1506658	the First Affiliated Hospital, School of Medicine, Zhejiang University\|BoneMarrow Transplantation Center	the First Affiliated Hospital, School of Medicine, Zhejiang University	1	0.94354		0.08493		0.70228		0.48147		50		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-09-25	Pharyngula	Embryo	Multi-tissue	Multi-system
71553	71553	SRR21700251	SRX17697770	SRS15228557	SRP399479	PRJNA884084	RNA Seq data of gmfg morphants and their control siblings	PRJNA884084	Other	To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.			biological replicate 2	ctl 2		strain:not applicable\|isolate:not applicable\|dev stage:26 hpf\|sex:not applicable\|tissue:the dissected trunk and tail\|collection date:2021 02 26\|geo loc name:China:Shenzhen Guangdong\|sample type:ctl2\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio	ctl2 20210210	ctl2 20210210	RNA seq of Danio rerio in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500	SRP399479			ctl_2_1.fq.gz	fastq	1193941900.0	23878838.0	ctl 2 1.fq.gz	0:50 1:0	A:315521033;C:273947671;G:281554279;T:322918917;N:0	50	0	315521033	273947671	281554279	322918917	0	SRX17697770	SRS15228557	SRA1506658	the First Affiliated Hospital, School of Medicine, Zhejiang University\|BoneMarrow Transplantation Center	the First Affiliated Hospital, School of Medicine, Zhejiang University	1	0.94073		0.08514		0.70281		0.4767		50		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-09-25	Pharyngula	Embryo	Multi-tissue	Multi-system
71554	71554	SRR21700252	SRX17697769	SRS15228556	SRP399479	PRJNA884084	RNA Seq data of gmfg morphants and their control siblings	PRJNA884084	Other	To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.			biological replicate 1	ctl 1		strain:not applicable\|isolate:not applicable\|dev stage:26 hpf\|sex:not applicable\|tissue:the dissected trunk and tail\|collection date:2021 02 26\|geo loc name:China:Shenzhen Guangdong\|sample type:ctl1\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio	ctl1 20210209	ctl1 20210209	RNA seq of Danio rerio in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500	SRP399479			ctl_1_1.fq.gz	fastq	1194196300.0	23883926.0	ctl 1 1.fq.gz	0:50 1:0	A:315050496;C:273915045;G:282252071;T:322978688;N:0	50	0	315050496	273915045	282252071	322978688	0	SRX17697769	SRS15228556	SRA1506658	the First Affiliated Hospital, School of Medicine, Zhejiang University\|BoneMarrow Transplantation Center	the First Affiliated Hospital, School of Medicine, Zhejiang University	1	0.94272		0.08675		0.70234		0.47397		50		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-09-25	Pharyngula	Embryo	Multi-tissue	Multi-system

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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");;