metadata: run_metadata: 605 rows where experiment.library_strategy = "OTHER", tissue_curation = "Whole Organism" and tissue_curation

605 rows where experiment.library_strategy = "OTHER", tissue_curation = "Whole Organism" and tissue_curation_coarse = "All anatomical structures"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
9775	9775	ERR3838754	ERX3851420	ERS4266444	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Soma prim5 wt rep2	SAMEA6501995	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:01Z\|External Id:SAMEA6501995\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:01Z\|INSDC status:public\|Submitter Id:E MTAB 8707:Soma prim5 wt rep2\|age:24\|broker name:ArrayExpress\|cell type:whole embryo\|common name:zebrafish\|developmental stage:pharyngula prim 5\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:Soma prim5 wt rep2\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:Soma prim5 wt rep2 p	Soma prim5 wt rep2 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: compound:n1\|Experimental Factor: cell type:whole embryo	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	Somatic_prim5_rep2_R1.fastq.gz Somatic_prim5_rep2_R2.fastq.gz	fastq fastq	2664555542.0	17942996.0	E MTAB 8707:Somatic prim5 rep2 R	0:74.25 1:74.25	A:757990974;C:568005838;G:586848520;T:749991976;N:1718234	74	74	757990974	568005838	586848520	749991976	1718234	ERX3851420	ERS4266444	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.92034	0.91779	0.22669	0.22761	0.74769	0.74911	0.45866	0.45282	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Pharyngula	Embryo	Whole Organism	All anatomical structures
9776	9776	ERR3838753	ERX3851419	ERS4266443	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Soma prim5 wt rep1	SAMEA6501994	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:01Z\|External Id:SAMEA6501994\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:01Z\|INSDC status:public\|Submitter Id:E MTAB 8707:Soma prim5 wt rep1\|age:24\|broker name:ArrayExpress\|cell type:whole embryo\|common name:zebrafish\|developmental stage:pharyngula prim 5\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:Soma prim5 wt rep1\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:Soma prim5 wt rep1 p	Soma prim5 wt rep1 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: compound:n1\|Experimental Factor: cell type:whole embryo	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	Somatic_prim5_rep1_R1.fastq.gz Somatic_prim5_rep1_R2.fastq.gz	fastq fastq	1847156504.0	12386853.0	E MTAB 8707:Somatic prim5 rep1 R	0:74.56 1:74.56	A:519724449;C:399975516;G:411702918;T:514818493;N:935128	74	74	519724449	399975516	411702918	514818493	935128	ERX3851419	ERS4266443	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.93526	0.93319	0.24244	0.24304	0.75073	0.75201	0.44773	0.44885	76	75	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Pharyngula	Embryo	Whole Organism	All anatomical structures
9777	9777	ERR3838752	ERX3851418	ERS4266442	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Soma prim5 Morpholino rep2	SAMEA6501993	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:01Z\|External Id:SAMEA6501993\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:01Z\|INSDC status:public\|Submitter Id:E MTAB 8707:Soma prim5 Morpholino rep2\|age:24\|broker name:ArrayExpress\|cell type:whole embryo\|common name:zebrafish\|developmental stage:pharyngula prim 5\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:Soma prim5 Morpholino rep2\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:Soma prim5 Morpholino rep2 p	Soma prim5 Morpholino rep2 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: compound:Morpholino antisense oligo against Tdrd7 transcript\|Experimental Factor: dose:0.3\|Experimental Factor: cell type:whole embryo	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	S14_R1.fastq.gz S14_R2.fastq.gz	fastq fastq	953947657.0	6389852.0	E MTAB 8707:S14 R	0:74.64 1:74.65	A:271485260;C:204208876;G:210319402;T:267490986;N:443133	74	74	271485260	204208876	210319402	267490986	443133	ERX3851418	ERS4266442	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.93577	0.93619	0.1141	0.11516	0.72644	0.72892	0.4694	0.46965	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Pharyngula	Embryo	Whole Organism	All anatomical structures
9778	9778	ERR3838751	ERX3851417	ERS4266441	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Soma prim5 Morpholino rep1	SAMEA6501992	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:01Z\|External Id:SAMEA6501992\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:01Z\|INSDC status:public\|Submitter Id:E MTAB 8707:Soma prim5 Morpholino rep1\|age:24\|broker name:ArrayExpress\|cell type:whole embryo\|common name:zebrafish\|developmental stage:pharyngula prim 5\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:Soma prim5 Morpholino rep1\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:Soma prim5 Morpholino rep1 p	Soma prim5 Morpholino rep1 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: compound:Morpholino antisense oligo against Tdrd7 transcript\|Experimental Factor: dose:0.3\|Experimental Factor: cell type:whole embryo	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	S12_R1.fastq.gz S12_R2.fastq.gz	fastq fastq	753719404.0	5057589.0	E MTAB 8707:S12 R	0:74.51 1:74.52	A:216097326;C:160004832;G:164724356;T:212507268;N:385622	74	74	216097326	160004832	164724356	212507268	385622	ERX3851417	ERS4266441	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.93958	0.93943	0.10854	0.1092	0.73267	0.73663	0.45629	0.47862	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Pharyngula	Embryo	Whole Organism	All anatomical structures
9779	9779	ERR3838750	ERX3851416	ERS4266440	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Soma prim5 5mismatch Morpholino rep2	SAMEA6501991	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:01Z\|External Id:SAMEA6501991\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:01Z\|INSDC status:public\|Submitter Id:E MTAB 8707:Soma prim5 5mismatch Morpholino rep2\|age:24\|broker name:ArrayExpress\|cell type:whole embryo\|common name:zebrafish\|developmental stage:pharyngula prim 5\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:Soma prim5 5mismatch Morpholino rep2\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:Soma prim5 5mismatch Morpholino rep2 p	Soma prim5 5mismatch Morpholino rep2 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: compound:Control morpholino antisense oligo with 5 mismatches\|Experimental Factor: dose:0.3\|Experimental Factor: cell type:whole embryo	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	S18_R1.fastq.gz S18_R2.fastq.gz	fastq fastq	847966718.0	5668126.0	E MTAB 8707:S18 R	0:74.80 1:74.80	A:230723434;C:191446710;G:197114792;T:228326953;N:354829	74	74	230723434	191446710	197114792	228326953	354829	ERX3851416	ERS4266440	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.92436	0.92488	0.08973	0.09012	0.73971	0.74192	0.45291	0.45397	76	73	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Pharyngula	Embryo	Whole Organism	All anatomical structures
9780	9780	ERR3838749	ERX3851415	ERS4266439	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Soma prim5 5mismatch Morpholino rep1	SAMEA6501990	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:01Z\|External Id:SAMEA6501990\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:01Z\|INSDC status:public\|Submitter Id:E MTAB 8707:Soma prim5 5mismatch Morpholino rep1\|age:24\|broker name:ArrayExpress\|cell type:whole embryo\|common name:zebrafish\|developmental stage:pharyngula prim 5\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:Soma prim5 5mismatch Morpholino rep1\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:Soma prim5 5mismatch Morpholino rep1 p	Soma prim5 5mismatch Morpholino rep1 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: compound:Control morpholino antisense oligo with 5 mismatches\|Experimental Factor: dose:0.3\|Experimental Factor: cell type:whole embryo	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	S16_R1.fastq.gz S16_R2.fastq.gz	fastq fastq	444518989.0	2971315.0	E MTAB 8707:S16 R	0:74.80 1:74.80	A:121398448;C:100282796;G:103112415;T:119559792;N:165538	74	74	121398448	100282796	103112415	119559792	165538	ERX3851415	ERS4266439	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.92469	0.92438	0.09917	0.10006	0.72279	0.7251	0.45852	0.46016	73	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Pharyngula	Embryo	Whole Organism	All anatomical structures
9781	9781	ERR3838748	ERX3851414	ERS4266438	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Soma High rep2	SAMEA6501989	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:01Z\|External Id:SAMEA6501989\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:01Z\|INSDC status:public\|Submitter Id:E MTAB 8707:Soma High rep2\|age:3.3\|broker name:ArrayExpress\|cell type:whole embryo\|common name:zebrafish\|developmental stage:blastula high\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:Soma High rep2\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:Soma High rep2 p	Soma High rep2 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:blastula high\|Experimental Factor: compound:n1\|Experimental Factor: cell type:whole embryo	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	Fabio_High_rep2_soma_R1.fastq.gz Fabio_High_rep2_soma_R2.fastq.gz	fastq fastq	2072343523.0	13904136.0	E MTAB 8707:Fabio High rep2 soma R	0:74.52 1:74.53	A:596021076;C:439789413;G:451992691;T:583604290;N:936053	74	74	596021076	439789413	451992691	583604290	936053	ERX3851414	ERS4266438	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.94263	0.94098	0.04804	0.04844	0.75797	0.76039	0.50847	0.5014	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9782	9782	ERR3838747	ERX3851413	ERS4266437	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Soma High rep1	SAMEA6501988	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:01Z\|External Id:SAMEA6501988\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:01Z\|INSDC status:public\|Submitter Id:E MTAB 8707:Soma High rep1\|age:3.3\|broker name:ArrayExpress\|cell type:whole embryo\|common name:zebrafish\|developmental stage:blastula high\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:Soma High rep1\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:Soma High rep1 p	Soma High rep1 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:blastula high\|Experimental Factor: compound:n1\|Experimental Factor: cell type:whole embryo	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	Somatic_High_rep1_R1.fastq.gz Somatic_High_rep1_R2.fastq.gz	fastq fastq	6013555644.0	40662218.0	E MTAB 8707:Somatic High rep1 R	0:73.94 1:73.95	A:1821348300;C:1185534582;G:1227848010;T:1774836657;N:3988095	73	73	1821348300	1185534582	1227848010	1774836657	3988095	ERX3851413	ERS4266437	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.93539	0.9357	0.07066	0.07028	0.76197	0.76386	0.54301	0.54343	76	75	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9783	9783	ERR3838746	ERX3851412	ERS4266436	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Soma dome rep2	SAMEA6501987	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:00Z\|External Id:SAMEA6501987\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:Soma dome rep2\|age:4.3\|broker name:ArrayExpress\|cell type:whole embryo\|common name:zebrafish\|developmental stage:blastula dome\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:Soma dome rep2\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:Soma dome rep2 p	Soma dome rep2 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:blastula dome\|Experimental Factor: compound:n1\|Experimental Factor: cell type:whole embryo	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	S10_R1.fastq.gz S10_R2.fastq.gz	fastq fastq	1086124503.0	7272505.0	E MTAB 8707:S10 R	0:74.67 1:74.68	A:305920447;C:235855931;G:243442186;T:300439294;N:466645	74	74	305920447	235855931	243442186	300439294	466645	ERX3851412	ERS4266436	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.94089	0.94085	0.04872	0.04916	0.7419	0.74355	0.51209	0.5119	74	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9784	9784	ERR3838745	ERX3851411	ERS4266435	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Soma dome rep1	SAMEA6501986	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:00Z\|External Id:SAMEA6501986\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:Soma dome rep1\|age:4.3\|broker name:ArrayExpress\|cell type:whole embryo\|common name:zebrafish\|developmental stage:blastula dome\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:Soma dome rep1\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:Soma dome rep1 p	Soma dome rep1 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:blastula dome\|Experimental Factor: compound:n1\|Experimental Factor: cell type:whole embryo	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	S8_R1.fastq.gz S8_R2.fastq.gz	fastq fastq	336100162.0	2240589.0	E MTAB 8707:S8 R	0:75.00 1:75.00	A:93960580;C:73499585;G:75981355;T:92580945;N:77697	75	75	93960580	73499585	75981355	92580945	77697	ERX3851411	ERS4266435	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.93874	0.93856	0.05265	0.0517	0.74188	0.74381	0.51181	0.51086	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9785	9785	ERR3838744	ERX3851410	ERS4266434	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Soma 256 cell rep2	SAMEA6501985	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:00Z\|External Id:SAMEA6501985\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:Soma 256 cell rep2\|age:2.5\|broker name:ArrayExpress\|cell type:whole embryo\|common name:zebrafish\|developmental stage:blastula 256 cell\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:Soma 256 cell rep2\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:Soma 256 cell rep2 p	Soma 256 cell rep2 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:blastula 256 cell\|Experimental Factor: compound:n1\|Experimental Factor: cell type:whole embryo	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	S2_R1.fastq.gz S2_R2.fastq.gz	fastq fastq	1272080863.0	8551103.0	E MTAB 8707:S2 R	0:74.38 1:74.38	A:364033393;C:268850689;G:276270908;T:362172455;N:753418	74	74	364033393	268850689	276270908	362172455	753418	ERX3851410	ERS4266434	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.80562	0.80436	0.23702	0.23786	0.77914	0.77991	0.51225	0.5092	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9786	9786	ERR3838743	ERX3851409	ERS4266433	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Soma 256 cell rep1	SAMEA6501984	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:00Z\|External Id:SAMEA6501984\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:Soma 256 cell rep1\|age:2.5\|broker name:ArrayExpress\|cell type:whole embryo\|common name:zebrafish\|developmental stage:blastula 256 cell\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:Soma 256 cell rep1\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:Soma 256 cell rep1 p	Soma 256 cell rep1 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:blastula 256 cell\|Experimental Factor: compound:n1\|Experimental Factor: cell type:whole embryo	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	Somatic_256_rep1_R1.fastq.gz Somatic_256_rep1_R2.fastq.gz	fastq fastq	2254901578.0	15144857.0	E MTAB 8707:Somatic 256 rep1 R	0:74.44 1:74.45	A:648357135;C:475813294;G:492914743;T:636658631;N:1157775	74	74	648357135	475813294	492914743	636658631	1157775	ERX3851409	ERS4266433	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.92992	0.92787	0.07245	0.07214	0.7599	0.76084	0.53758	0.53839	74	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9787	9787	ERR3838742	ERX3851408	ERS4266432	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Soma 10somites rep2	SAMEA6501983	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:00Z\|External Id:SAMEA6501983\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:Soma 10somites rep2\|age:14\|broker name:ArrayExpress\|cell type:whole embryo\|common name:zebrafish\|developmental stage:10 somites\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:Soma 10somites rep2\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:Soma 10somites rep2 p	Soma 10somites rep2 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:10 somites\|Experimental Factor: compound:n1\|Experimental Factor: cell type:whole embryo	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	S6_R1.fastq.gz S6_R2.fastq.gz	fastq fastq	1244080980.0	8338002.0	E MTAB 8707:S6 R	0:74.60 1:74.60	A:356418931;C:263292901;G:270630630;T:353140798;N:597720	74	74	356418931	263292901	270630630	353140798	597720	ERX3851408	ERS4266432	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.86791	0.86732	0.20223	0.20398	0.75588	0.75883	0.4862	0.48313	76	75	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Segmentation	Embryo	Whole Organism	All anatomical structures
9788	9788	ERR3838741	ERX3851407	ERS4266431	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Soma 10somites rep1	SAMEA6501982	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:00Z\|External Id:SAMEA6501982\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:Soma 10somites rep1\|age:14\|broker name:ArrayExpress\|cell type:whole embryo\|common name:zebrafish\|developmental stage:10 somites\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:Soma 10somites rep1\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:Soma 10somites rep1 p	Soma 10somites rep1 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:10 somites\|Experimental Factor: compound:n1\|Experimental Factor: cell type:whole embryo	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	S4_R1.fastq.gz S4_R2.fastq.gz	fastq fastq	946153328.0	6354843.0	E MTAB 8707:S4 R	0:74.44 1:74.45	A:268310887;C:203457903;G:208969410;T:264875129;N:539999	74	74	268310887	203457903	208969410	264875129	539999	ERX3851407	ERS4266431	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.92415	0.92372	0.12138	0.12268	0.74061	0.74422	0.47246	0.47448	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Segmentation	Embryo	Whole Organism	All anatomical structures
9789	9789	ERR3838740	ERX3851406	ERS4266430	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	PGC prim5 wt rep2	SAMEA6501981	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:00Z\|External Id:SAMEA6501981\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC prim5 wt rep2\|age:24\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:pharyngula prim 5\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:PGC prim5 wt rep2\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:PGC prim5 wt rep2 p	PGC prim5 wt rep2 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: compound:n1\|Experimental Factor: cell type:primordial germ cell	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	PGC_prim5_rep2_R1.fastq.gz PGC_prim5_rep2_R2.fastq.gz	fastq fastq	2236371655.0	15023634.0	E MTAB 8707:PGC prim5 rep2 R	0:74.43 1:74.43	A:619039687;C:495191024;G:509021767;T:611885185;N:1233992	74	74	619039687	495191024	509021767	611885185	1233992	ERX3851406	ERS4266430	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.93137	0.92838	0.23991	0.24045	0.71435	0.71591	0.49054	0.49302	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Pharyngula	Embryo	Whole Organism	All anatomical structures
9790	9790	ERR3838739	ERX3851405	ERS4266429	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	PGC prim5 wt rep1	SAMEA6501980	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:00Z\|External Id:SAMEA6501980\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC prim5 wt rep1\|age:24\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:pharyngula prim 5\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:PGC prim5 wt rep1\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:PGC prim5 wt rep1 p	PGC prim5 wt rep1 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: compound:n1\|Experimental Factor: cell type:primordial germ cell	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	PGC_prim5_rep1_R1.fastq.gz PGC_prim5_rep1_R2.fastq.gz	fastq fastq	1619398294.0	10873533.0	E MTAB 8707:PGC prim5 rep1 R	0:74.46 1:74.47	A:450612629;C:355178930;G:365650222;T:447083613;N:872900	74	74	450612629	355178930	365650222	447083613	872900	ERX3851405	ERS4266429	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.92755	0.92901	0.22893	0.22952	0.71131	0.71372	0.49829	0.50019	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Pharyngula	Embryo	Whole Organism	All anatomical structures
9791	9791	ERR3838738	ERX3851404	ERS4266428	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	PGC prim5 Morpholino rep2	SAMEA6501979	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:00Z\|External Id:SAMEA6501979\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC prim5 Morpholino rep2\|age:24\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:pharyngula prim 5\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:PGC prim5 Morpholino rep2\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:PGC prim5 Morpholino rep2 p	PGC prim5 Morpholino rep2 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: compound:Morpholino antisense oligo against Tdrd7 transcript\|Experimental Factor: dose:0.3\|Experimental Factor: cell type:primordial germ cell	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	S13_R1.fastq.gz S13_R2.fastq.gz	fastq fastq	906443913.0	6069224.0	E MTAB 8707:S13 R	0:74.67 1:74.68	A:256935983;C:195137600;G:200975999;T:253026767;N:367564	74	74	256935983	195137600	200975999	253026767	367564	ERX3851404	ERS4266428	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.93468	0.93605	0.09793	0.09817	0.71163	0.71291	0.48766	0.48921	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Pharyngula	Embryo	Whole Organism	All anatomical structures
9792	9792	ERR3838737	ERX3851403	ERS4266427	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	PGC prim5 Morpholino rep1	SAMEA6501978	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:00Z\|External Id:SAMEA6501978\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC prim5 Morpholino rep1\|age:24\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:pharyngula prim 5\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:PGC prim5 Morpholino rep1\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:PGC prim5 Morpholino rep1 p	PGC prim5 Morpholino rep1 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: compound:Morpholino antisense oligo against Tdrd7 transcript\|Experimental Factor: dose:0.3\|Experimental Factor: cell type:primordial germ cell	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	Fabio_cat_11_R1.fastq.gz Fabio_cat_11_R2.fastq.gz	fastq fastq	1078919524.0	7241200.0	E MTAB 8707:Fabio cat 11 R	0:74.50 1:74.50	A:308200726;C:229836659;G:236649504;T:303673221;N:559414	74	74	308200726	229836659	236649504	303673221	559414	ERX3851403	ERS4266427	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.93808	0.93753	0.10449	0.10446	0.70733	0.71017	0.48103	0.48247	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Pharyngula	Embryo	Whole Organism	All anatomical structures
9793	9793	ERR3838736	ERX3851402	ERS4266426	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	PGC prim5 5mismatch Morpholino rep2	SAMEA6501977	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:00Z\|External Id:SAMEA6501977\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC prim5 5mismatch Morpholino rep2\|age:24\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:pharyngula prim 5\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:PGC prim5 5mismatch Morpholino rep2\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:PGC prim5 5mismatch Morpholino rep2 p	PGC prim5 5mismatch Morpholino rep2 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: compound:Control morpholino antisense oligo with 5 mismatches\|Experimental Factor: dose:0.3\|Experimental Factor: cell type:primordial germ cell	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	S17_R1.fastq.gz S17_R2.fastq.gz	fastq fastq	673911944.0	4501723.0	E MTAB 8707:S17 R	0:74.85 1:74.85	A:184466911;C:150779527;G:155693395;T:182720480;N:251631	74	74	184466911	150779527	155693395	182720480	251631	ERX3851402	ERS4266426	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.9199	0.92023	0.08791	0.08923	0.70132	0.70378	0.49183	0.49425	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Pharyngula	Embryo	Whole Organism	All anatomical structures
9794	9794	ERR3838735	ERX3851401	ERS4266425	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	PGC prim5 5mismatch Morpholino rep1	SAMEA6501976	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:00Z\|External Id:SAMEA6501976\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC prim5 5mismatch Morpholino rep1\|age:24\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:pharyngula prim 5\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:PGC prim5 5mismatch Morpholino rep1\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:PGC prim5 5mismatch Morpholino rep1 p	PGC prim5 5mismatch Morpholino rep1 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: compound:Control morpholino antisense oligo with 5 mismatches\|Experimental Factor: dose:0.3\|Experimental Factor: cell type:primordial germ cell	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	S15_R1.fastq.gz S15_R2.fastq.gz	fastq fastq	565636692.0	3782000.0	E MTAB 8707:S15 R	0:74.78 1:74.78	A:157353454;C:124504476;G:128260137;T:155314004;N:204621	74	74	157353454	124504476	128260137	155314004	204621	ERX3851401	ERS4266425	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.91956	0.91996	0.08306	0.08458	0.69982	0.70203	0.48525	0.48771	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Pharyngula	Embryo	Whole Organism	All anatomical structures
9795	9795	ERR3838734	ERX3851400	ERS4266424	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	PGC High rep2	SAMEA6501975	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:00Z\|External Id:SAMEA6501975\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC High rep2\|age:3.3\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:blastula high\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:PGC High rep2\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:PGC High rep2 p	PGC High rep2 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:blastula high\|Experimental Factor: compound:n1\|Experimental Factor: cell type:primordial germ cell	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	PGC_High_rep2_R1.fastq.gz PGC_High_rep2_R2.fastq.gz	fastq fastq	2491013839.0	16740632.0	E MTAB 8707:PGC High rep2 R	0:74.40 1:74.40	A:715637079;C:527451931;G:545855323;T:700774175;N:1295331	74	74	715637079	527451931	545855323	700774175	1295331	ERX3851400	ERS4266424	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.93381	0.93556	0.06095	0.06172	0.76094	0.76364	0.52942	0.53118	74	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9796	9796	ERR3838733	ERX3851399	ERS4266423	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	PGC High rep1	SAMEA6501974	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:00Z\|External Id:SAMEA6501974\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC High rep1\|age:3.3\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:blastula high\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:PGC High rep1\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:PGC High rep1 p	PGC High rep1 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:blastula high\|Experimental Factor: compound:n1\|Experimental Factor: cell type:primordial germ cell	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	PGC_High_rep1_R1.fastq.gz PGC_High_rep1_R2.fastq.gz	fastq fastq	2055218051.0	13801653.0	E MTAB 8707:PGC High rep1 R	0:74.45 1:74.46	A:594747301;C:431446277;G:445665283;T:582330624;N:1028566	74	74	594747301	431446277	445665283	582330624	1028566	ERX3851399	ERS4266423	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.93644	0.93494	0.06937	0.07015	0.76353	0.7653	0.45909	0.44979	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9797	9797	ERR3838732	ERX3851398	ERS4266422	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	PGC dome rep2	SAMEA6501973	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:00Z\|External Id:SAMEA6501973\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC dome rep2\|age:4.3\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:blastula dome\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:PGC dome rep2\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:PGC dome rep2 p	PGC dome rep2 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:blastula dome\|Experimental Factor: compound:n1\|Experimental Factor: cell type:primordial germ cell	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	S9_R1.fastq.gz S9_R2.fastq.gz	fastq fastq	882858901.0	5912255.0	E MTAB 8707:S9 R	0:74.66 1:74.67	A:246639630;C:193554406;G:199940889;T:242369366;N:354610	74	74	246639630	193554406	199940889	242369366	354610	ERX3851398	ERS4266422	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.94045	0.9404	0.04635	0.04658	0.74582	0.74777	0.4915	0.49248	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9798	9798	ERR3838731	ERX3851397	ERS4266421	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	PGC dome rep1	SAMEA6501972	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:00Z\|External Id:SAMEA6501972\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC dome rep1\|age:4.3\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:blastula dome\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:PGC dome rep1\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:PGC dome rep1 p	PGC dome rep1 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:blastula dome\|Experimental Factor: compound:n1\|Experimental Factor: cell type:primordial germ cell	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	S7_R1.fastq.gz S7_R2.fastq.gz	fastq fastq	592299285.0	3961989.0	E MTAB 8707:S7 R	0:74.75 1:74.75	A:166664600;C:128421892;G:132787149;T:164189412;N:236232	74	74	166664600	128421892	132787149	164189412	236232	ERX3851397	ERS4266421	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.93981	0.94032	0.04868	0.04843	0.74627	0.74722	0.49243	0.48872	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9799	9799	ERR3838730	ERX3851396	ERS4266420	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	PGC 256 cell rep2	SAMEA6501971	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:00Z\|External Id:SAMEA6501971\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC 256 cell rep2\|age:2.5\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:blastula 256 cell\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:PGC 256 cell rep2\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:PGC 256 cell rep2 p	PGC 256 cell rep2 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:blastula 256 cell\|Experimental Factor: compound:n1\|Experimental Factor: cell type:primordial germ cell	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	S1_R1.fastq.gz S1_R2.fastq.gz	fastq fastq	745277323.0	4983607.0	E MTAB 8707:S1 R	0:74.77 1:74.77	A:208352741;C:163024343;G:168234953;T:205391192;N:274094	74	74	208352741	163024343	168234953	205391192	274094	ERX3851396	ERS4266420	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.9393	0.9395	0.03941	0.03941	0.75473	0.75708	0.51338	0.51754	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9800	9800	ERR3838729	ERX3851395	ERS4266419	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	PGC 256 cell rep1	SAMEA6501970	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:00Z\|External Id:SAMEA6501970\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC 256 cell rep1\|age:2.5\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:blastula 256 cell\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:PGC 256 cell rep1\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:PGC 256 cell rep1 p	PGC 256 cell rep1 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:blastula 256 cell\|Experimental Factor: compound:n1\|Experimental Factor: cell type:primordial germ cell	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	PGC_256_rep1_R1.fastq.gz PGC_256_rep1_R2.fastq.gz	fastq fastq	1876891175.0	12625794.0	E MTAB 8707:PGC 256 rep1 R	0:74.32 1:74.33	A:539140549;C:396392844;G:411568412;T:528672735;N:1116635	74	74	539140549	396392844	411568412	528672735	1116635	ERX3851395	ERS4266419	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.92251	0.92173	0.06705	0.06723	0.76059	0.76374	0.54467	0.54135	76	75	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Blastula	Embryo	Whole Organism	All anatomical structures
9801	9801	ERR3838728	ERX3851394	ERS4266418	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	PGC 10somites rep2	SAMEA6501969	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:00Z\|External Id:SAMEA6501969\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC 10somites rep2\|age:14\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:10 somites\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:PGC 10somites rep2\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:PGC 10somites rep2 p	PGC 10somites rep2 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:10 somites\|Experimental Factor: compound:n1\|Experimental Factor: cell type:primordial germ cell	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	S5_R1.fastq.gz S5_R2.fastq.gz	fastq fastq	1186993033.0	7958634.0	E MTAB 8707:S5 R	0:74.57 1:74.58	A:332263881;C:259239478;G:267014990;T:327946611;N:528073	74	74	332263881	259239478	267014990	327946611	528073	ERX3851394	ERS4266418	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.90713	0.9062	0.10071	0.1016	0.73058	0.73279	0.48458	0.48038	74	75	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Segmentation	Embryo	Whole Organism	All anatomical structures
9802	9802	ERR3838727	ERX3851393	ERS4266417	ERP119601	PRJEB36411	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E-MTAB-8707	Transcriptome Analysis	Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24		Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	PGC 10somites rep1	SAMEA6501968	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK	ENA FIRST PUBLIC:2020 04 30T04:03:48Z\|ENA LAST UPDATE:2020 01 24T08:44:00Z\|External Id:SAMEA6501968\|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK\|INSDC first public:2020 04 30T04:03:48Z\|INSDC last update:2020 01 24T08:44:00Z\|INSDC status:public\|Submitter Id:E MTAB 8707:PGC 10somites rep1\|age:14\|broker name:ArrayExpress\|cell type:primordial germ cell\|common name:zebrafish\|developmental stage:10 somites\|genotype:tgbuc:egfp\|phenotype:fluorescent PGCs due to germ plasm localised GFP\|sample name:E MTAB 8707:PGC 10somites rep1\|scientific name:Danio rerio\|strain:AB									NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	E MTAB 8707:PGC 10somites rep1 p	PGC 10somites rep1 p	RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA.	Experimental Factor: developmental stage:10 somites\|Experimental Factor: compound:n1\|Experimental Factor: cell type:primordial germ cell	OTHER	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	NextSeq 550	ERP119601	NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis	ENA FIRST PUBLIC:2020 12 24\|ENA LAST UPDATE:2020 01 24	S3_R1.fastq.gz S3_R2.fastq.gz	fastq fastq	1230551446.0	8251644.0	E MTAB 8707:S3 R	0:74.56 1:74.57	A:345409587;C:267720436;G:275626594;T:341185818;N:609011	74	74	345409587	267720436	275626594	341185818	609011	ERX3851393	ERS4266417	ERA2354529	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK\|European Nucleotide Archive	2	0.90983	0.90985	0.1005	0.10037	0.72622	0.72825	0.49116	0.49135	76	75	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	United Kingdom	2020-01-24	Segmentation	Embryo	Whole Organism	All anatomical structures
9803	9803	ERR3909553	ERX3918377	ERS4309135	ERP120006	PRJEB36776	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E-MTAB-8795	Transcriptome Analysis	The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 13		Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Total3	SAMEA6544760	UNIVERSITY OF BIRMINGHAM	ENA FIRST PUBLIC:2020 06 19T17:05:18Z\|ENA LAST UPDATE:2020 02 13T15:36:56Z\|External Id:SAMEA6544760\|INSDC center name:UNIVERSITY OF BIRMINGHAM\|INSDC first public:2020 06 19T17:05:18Z\|INSDC last update:2020 02 13T15:36:56Z\|INSDC status:public\|Submitter Id:E MTAB 8795:Total3\|age:14\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|fraction:unsorted whole organism\|organism part:whole organism\|sample name:E MTAB 8795:Total3\|scientific name:Danio rerio\|sex:not available\|strain:Dual FUCCI									Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E MTAB 8795:Total3 s	Total3 s	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Experimental Factor: fraction:unsorted whole organism	OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP120006	Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 25	14SomiteTotal3_TCGACG_L003_R1_001.fastq.gz	fastq	652379310.0	14497318.0	E MTAB 8795:Total3	0:45 1:0	A:150840591;C:135992123;G:240098326;T:125390188;N:58082	45	0	150840591	135992123	240098326	125390188	58082	ERX3918377	ERS4309135	ERA2381432	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	1	0.00539		0.00111		0.99582		0.74079		45		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	United Kingdom	2020-02-13	Segmentation	Embryo	Whole Organism	All anatomical structures
9804	9804	ERR3909552	ERX3918376	ERS4309134	ERP120006	PRJEB36776	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E-MTAB-8795	Transcriptome Analysis	The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 13		Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Total2	SAMEA6544759	UNIVERSITY OF BIRMINGHAM	ENA FIRST PUBLIC:2020 06 19T17:05:18Z\|ENA LAST UPDATE:2020 02 13T15:36:56Z\|External Id:SAMEA6544759\|INSDC center name:UNIVERSITY OF BIRMINGHAM\|INSDC first public:2020 06 19T17:05:18Z\|INSDC last update:2020 02 13T15:36:56Z\|INSDC status:public\|Submitter Id:E MTAB 8795:Total2\|age:14\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|fraction:unsorted whole organism\|organism part:whole organism\|sample name:E MTAB 8795:Total2\|scientific name:Danio rerio\|sex:not available\|strain:Dual FUCCI									Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E MTAB 8795:Total2 s	Total2 s	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Experimental Factor: fraction:unsorted whole organism	OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP120006	Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 25	14SomiteTotal2_TATAGC_L003_R1_001.fastq.gz	fastq	457981740.0	10177372.0	E MTAB 8795:Total2	0:45 1:0	A:108846441;C:95327665;G:163111561;T:90654528;N:41545	45	0	108846441	95327665	163111561	90654528	41545	ERX3918376	ERS4309134	ERA2381432	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	1	0.00612		0.00144		0.99387		0.66666		45		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	United Kingdom	2020-02-13	Segmentation	Embryo	Whole Organism	All anatomical structures
9805	9805	ERR3909551	ERX3918375	ERS4309133	ERP120006	PRJEB36776	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E-MTAB-8795	Transcriptome Analysis	The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 13		Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Total1	SAMEA6544758	UNIVERSITY OF BIRMINGHAM	ENA FIRST PUBLIC:2020 06 19T17:05:18Z\|ENA LAST UPDATE:2020 02 13T15:36:56Z\|External Id:SAMEA6544758\|INSDC center name:UNIVERSITY OF BIRMINGHAM\|INSDC first public:2020 06 19T17:05:18Z\|INSDC last update:2020 02 13T15:36:56Z\|INSDC status:public\|Submitter Id:E MTAB 8795:Total1\|age:14\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|fraction:unsorted whole organism\|organism part:whole organism\|sample name:E MTAB 8795:Total1\|scientific name:Danio rerio\|sex:not available\|strain:Dual FUCCI									Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E MTAB 8795:Total1 s	Total1 s	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Experimental Factor: fraction:unsorted whole organism	OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP120006	Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 25	14SomiteTotal1_GTATAC_L003_R1_001.fastq.gz	fastq	778934655.0	17309659.0	E MTAB 8795:Total1	0:45 1:0	A:175694794;C:165046556;G:285795545;T:152324198;N:73562	45	0	175694794	165046556	285795545	152324198	73562	ERX3918375	ERS4309133	ERA2381432	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	1	0.0048		0.00098		0.99492		0.69892		45		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	United Kingdom	2020-02-13	Segmentation	Embryo	Whole Organism	All anatomical structures
9806	9806	ERR3909550	ERX3918374	ERS4309132	ERP120006	PRJEB36776	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E-MTAB-8795	Transcriptome Analysis	The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 13		Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Red3	SAMEA6544757	UNIVERSITY OF BIRMINGHAM	ENA FIRST PUBLIC:2020 06 19T17:05:18Z\|ENA LAST UPDATE:2020 02 13T15:36:56Z\|External Id:SAMEA6544757\|INSDC center name:UNIVERSITY OF BIRMINGHAM\|INSDC first public:2020 06 19T17:05:18Z\|INSDC last update:2020 02 13T15:36:56Z\|INSDC status:public\|Submitter Id:E MTAB 8795:Red3\|age:14\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|fraction:G1 slow cycling\|organism part:whole organism\|sample name:E MTAB 8795:Red3\|scientific name:Danio rerio\|sex:not available\|strain:Dual FUCCI									Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E MTAB 8795:Red3 s	Red3 s	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Experimental Factor: fraction:G1 slow cycling	OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP120006	Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 25	14SomiteRed3_CACGAT_L003_R1_001.fastq.gz	fastq	980271990.0	21783822.0	E MTAB 8795:Red3	0:45 1:0	A:231772782;C:201265416;G:341867307;T:205267905;N:98580	45	0	231772782	201265416	341867307	205267905	98580	ERX3918374	ERS4309132	ERA2381432	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	1	0.0047		0.00138		0.99366		0.64343		45		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	United Kingdom	2020-02-13	Segmentation	Embryo	Whole Organism	All anatomical structures
9807	9807	ERR3909549	ERX3918373	ERS4309131	ERP120006	PRJEB36776	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E-MTAB-8795	Transcriptome Analysis	The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 13		Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Red2	SAMEA6544756	UNIVERSITY OF BIRMINGHAM	ENA FIRST PUBLIC:2020 06 19T17:05:18Z\|ENA LAST UPDATE:2020 02 13T15:36:56Z\|External Id:SAMEA6544756\|INSDC center name:UNIVERSITY OF BIRMINGHAM\|INSDC first public:2020 06 19T17:05:18Z\|INSDC last update:2020 02 13T15:36:56Z\|INSDC status:public\|Submitter Id:E MTAB 8795:Red2\|age:14\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|fraction:G1 slow cycling\|organism part:whole organism\|sample name:E MTAB 8795:Red2\|scientific name:Danio rerio\|sex:not available\|strain:Dual FUCCI									Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E MTAB 8795:Red2 s	Red2 s	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Experimental Factor: fraction:G1 slow cycling	OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP120006	Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 25	14SomiteRed2_ATCGTG_L003_R1_001.fastq.gz	fastq	755095185.0	16779893.0	E MTAB 8795:Red2	0:45 1:0	A:173488674;C:161696782;G:267896203;T:151943387;N:70139	45	0	173488674	161696782	267896203	151943387	70139	ERX3918373	ERS4309131	ERA2381432	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	1	0.00548		0.00113		0.99415		0.65826		45		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	United Kingdom	2020-02-13	Segmentation	Embryo	Whole Organism	All anatomical structures
9808	9808	ERR3909548	ERX3918372	ERS4309130	ERP120006	PRJEB36776	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E-MTAB-8795	Transcriptome Analysis	The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 13		Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Red1	SAMEA6544755	UNIVERSITY OF BIRMINGHAM	ENA FIRST PUBLIC:2020 06 19T17:05:18Z\|ENA LAST UPDATE:2020 02 13T15:36:56Z\|External Id:SAMEA6544755\|INSDC center name:UNIVERSITY OF BIRMINGHAM\|INSDC first public:2020 06 19T17:05:18Z\|INSDC last update:2020 02 13T15:36:56Z\|INSDC status:public\|Submitter Id:E MTAB 8795:Red1\|age:14\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|fraction:G1 slow cycling\|organism part:whole organism\|sample name:E MTAB 8795:Red1\|scientific name:Danio rerio\|sex:not available\|strain:Dual FUCCI									Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E MTAB 8795:Red1 s	Red1 s	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Experimental Factor: fraction:G1 slow cycling	OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP120006	Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 25	14SomiteRed1_ACAGAT_L003_R1_001.fastq.gz	fastq	755180370.0	16781786.0	E MTAB 8795:Red1	0:45 1:0	A:179369537;C:157573419;G:260889303;T:157277751;N:70360	45	0	179369537	157573419	260889303	157277751	70360	ERX3918372	ERS4309130	ERA2381432	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	1	0.00451		0.00099		0.99314		0.66248		45		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	United Kingdom	2020-02-13	Segmentation	Embryo	Whole Organism	All anatomical structures
9809	9809	ERR3909547	ERX3918371	ERS4309129	ERP120006	PRJEB36776	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E-MTAB-8795	Transcriptome Analysis	The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 13		Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Green3	SAMEA6544754	UNIVERSITY OF BIRMINGHAM	ENA FIRST PUBLIC:2020 06 19T17:05:18Z\|ENA LAST UPDATE:2020 02 13T15:36:56Z\|External Id:SAMEA6544754\|INSDC center name:UNIVERSITY OF BIRMINGHAM\|INSDC first public:2020 06 19T17:05:18Z\|INSDC last update:2020 02 13T15:36:56Z\|INSDC status:public\|Submitter Id:E MTAB 8795:Green3\|age:14\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|fraction:S/G2/M rapid cycling\|organism part:whole organism\|sample name:E MTAB 8795:Green3\|scientific name:Danio rerio\|sex:not available\|strain:Dual FUCCI									Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E MTAB 8795:Green3 s	Green3 s	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Experimental Factor: fraction:S/G2/M rapid cycling	OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP120006	Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 25	14SomiteGreen3_GAGTGA_L003_R1_001.fastq.gz	fastq	819288855.0	18206419.0	E MTAB 8795:Green3	0:45 1:0	A:189173618;C:170597494;G:286250625;T:173188944;N:78174	45	0	189173618	170597494	286250625	173188944	78174	ERX3918371	ERS4309129	ERA2381432	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	1	0.00439		0.001		0.99377		0.68367		45		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	United Kingdom	2020-02-13	Segmentation	Embryo	Whole Organism	All anatomical structures
9810	9810	ERR3909546	ERX3918370	ERS4309128	ERP120006	PRJEB36776	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E-MTAB-8795	Transcriptome Analysis	The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 13		Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Green2	SAMEA6544753	UNIVERSITY OF BIRMINGHAM	ENA FIRST PUBLIC:2020 06 19T17:05:18Z\|ENA LAST UPDATE:2020 02 13T15:36:56Z\|External Id:SAMEA6544753\|INSDC center name:UNIVERSITY OF BIRMINGHAM\|INSDC first public:2020 06 19T17:05:18Z\|INSDC last update:2020 02 13T15:36:56Z\|INSDC status:public\|Submitter Id:E MTAB 8795:Green2\|age:14\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|fraction:S/G2/M rapid cycling\|organism part:whole organism\|sample name:E MTAB 8795:Green2\|scientific name:Danio rerio\|sex:not available\|strain:Dual FUCCI									Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E MTAB 8795:Green2 s	Green2 s	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Experimental Factor: fraction:S/G2/M rapid cycling	OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP120006	Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 25	14SomiteGreen2_CTGACG_L003_R1_001.fastq.gz	fastq	697971375.0	15510475.0	E MTAB 8795:Green2	0:45 1:0	A:160028926;C:147075253;G:245773112;T:145025474;N:68610	45	0	160028926	147075253	245773112	145025474	68610	ERX3918370	ERS4309128	ERA2381432	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	1	0.00489		0.00085		0.99586		0.80163		45		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	United Kingdom	2020-02-13	Segmentation	Embryo	Whole Organism	All anatomical structures
9811	9811	ERR3909545	ERX3918369	ERS4309127	ERP120006	PRJEB36776	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E-MTAB-8795	Transcriptome Analysis	The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 13		Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Green1	SAMEA6544752	UNIVERSITY OF BIRMINGHAM	ENA FIRST PUBLIC:2020 06 19T17:05:18Z\|ENA LAST UPDATE:2020 02 13T15:36:56Z\|External Id:SAMEA6544752\|INSDC center name:UNIVERSITY OF BIRMINGHAM\|INSDC first public:2020 06 19T17:05:18Z\|INSDC last update:2020 02 13T15:36:56Z\|INSDC status:public\|Submitter Id:E MTAB 8795:Green1\|age:14\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|fraction:S/G2/M rapid cycling\|organism part:whole organism\|sample name:E MTAB 8795:Green1\|scientific name:Danio rerio\|sex:not available\|strain:Dual FUCCI									Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E MTAB 8795:Green1 s	Green1 s	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Experimental Factor: fraction:S/G2/M rapid cycling	OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP120006	Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 25	14SomiteGreen1_CACTGA_L003_R1_001.fastq.gz	fastq	826595640.0	18368792.0	E MTAB 8795:Green1	0:45 1:0	A:193728088;C:171605661;G:287824557;T:173352680;N:84654	45	0	193728088	171605661	287824557	173352680	84654	ERX3918369	ERS4309127	ERA2381432	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	1	0.00505		0.00101		0.99287		0.58198		45		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	United Kingdom	2020-02-13	Segmentation	Embryo	Whole Organism	All anatomical structures
25295	25295	SRR25764045	SRX21486723	SRS18719024	SRP457105	PRJNA1009809	Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [Ribo Seq]	GSE241753	Other	Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.	parent bioproject:PRJNA1009800	pubmed:39402326		WT bud 10 hpf Ribo seq rep1	GSM7734770		source name:Gastrula\|strain:TLAB strain\|tissue:Gastrula\|developmental stage:Bud 10 hpf\|treatment:100 µg/ml CHX 100 µg/ml TIG\|geo loc name:missing\|collection date:missing	WT bud 10 hpf Ribo seq rep1	We identified the A site location in each mapped read with Scikit ribo [Fang et al. 2018] which uses a random forest with recursive feature selection and a generalized linear model for accurate A site prediction based on matched ribosome profiling and RNA Seq datasets. Kallisto 0.44.0 with parameters b 100 single l 180 s 20 t 40 was used to quantify transcript abundances in Transcripts Per Million TPM from RNA Seq data based on the reference set of MANE annotated transcripts see Codon usage analysis for description of this annotation. To avoid memory errors due to the large size of the human genome and the presence of multiple transcript isoforms all RNAfold dependencies in Scikit ribo were omitted and the index was built separately for each chromosome. To make the hg38 GTF compatible with Scikit ribo transcript/UTR annotations were removed. For each transcript the start codon in the first exon and the stop codon in the last exon were adjusted to represent transcript start and end coordinates taking into account the gene strand. To estimate codon dwell times short 20 23 nt and long 28 33 nt ribosome footprints were analyzed separately. rRNA filtered reads were aligned to GRCz11.108 using STAR v2.6.1c [Dobin et al. 2013] the following options: outFilterMultimapNmax 1 seedSearchStartLmax 15 outSAMtype BAM SortedByCoordinate outFilterMismatchNmax 2 alignEndsType EndToEnd quantMode TranscriptomeSAM outSAMattributes NH HI AS nM NM MD We identified the A site location in each mapped read with Scikit ribo [Fang et al. 2018] which uses a random forest with recursive feature selection and a generalized linear model for accurate A site prediction based on matched ribosome profiling and RNA Seq datasets. Kallisto 0.44.0 with parameters b 100 single l 180 s 20 t 40 was used to quantify transcript abundances in Transcripts Per Million TPM from RNA Seq data based on the reference set of MANE annotated transcripts see Codon usage analysis for description of this annotation. To avoid memory err…	Gastrula	unperturbed growth conditions in E3 medium for zebrafish embryos.	200 whole embryos were flash frozen in liquid nitrogen and subsequently lysed in footprint lysis buffer containing 100 µg/ml CHX and 100 µg/ml TIG 0.1% NP 40 10 µg/ml aprotinin 20 µM leupeptin 2.5 µM pepstatin A 0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously triturated through a 26G gauge needle and spun down for 7 minutes at 16 000xg/ 4°C. Supernatant was transferred to a new tube. 20 µg RNA in 200 µl polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2 000 rpm/22°C. post incubation on ice for 5 minutes extracts were pre cleared by centrifugation for 5 minutes at 3 000 g/ 4°C. Ribosomes were pelleted through 3 ml of a sucrose cushion 1 M sucrose 20 mM Tris pH=8.0 140 mM KCl 5 mM MgCl2 1 mM DTT by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50 000 rpm/ 4°C. Ribosome pellets were rinsed once dissolved in 200 µl drug free polysome lysis buffer and incubated with 200 U hiPSC or 300 U NPC RNase I for 45 minutes at 2 000 rpm/22°C. Ribosome footprint libraries were prepared essentially as described McGlincy and Ingolia 2017; Wu 2019 with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 µl LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection with T4 PNK and ligated to pre adenylated adapters containing 5 random nucleotides at their 5’ ends McGlinzy 2017 with T4 RNA Ligase 2 truncated KQ. Adapter ligated RNA was subjected to rRNA depletion using the Ribo Seq riboPOOL h/m/r depletion kit siTOOLs for CHX only samples and legacy RiboZero Gold kit Illumina for CHX+TIG samples The rRNA depleted footprints were reverse transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 commercially available as CircLigase. Libraries were constructed from circularized cDNA with KAP…	Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.	strain:TLAB strain\|tissue:Gastrula\|developmental stage:Bud 10 hpf\|treatment:100 µg/ml CHX 100 µg/ml TIG	GSM7734770	GSM7734770: WT bud 10 hpf Ribo seq rep1; Danio rerio; OTHER	GSM7734770 r1	GSM7734770	1	200 whole embryos were flash frozen in liquid nitrogen and subsequently lysed in footprint lysis buffer containing 100 µg/ml CHX and 100 µg/ml TIG 0.1% NP 40 10 µg/ml aprotinin 20 µM leupeptin 2.5 µM pepstatin A 0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously triturated through a 26G gauge needle and spun down for 7 minutes at 16 000xg/ 4°C. Supernatant was transferred to a new tube. 20 µg RNA in 200 µl polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2 000 rpm/22°C. post incubation on ice for 5 minutes extracts were pre cleared by centrifugation for 5 minutes at 3 000 g/ 4°C. Ribosomes were pelleted through 3 ml of a sucrose cushion 1 M sucrose 20 mM Tris pH=8.0 140 mM KCl 5 mM MgCl2 1 mM DTT by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50 000 rpm/ 4°C. Ribosome pellets were rinsed once dissolved in 200 µl drug free polysome lysis buffer and incubated with 200 U hiPSC or 300 U NPC RNase I for 45 minutes at 2 000 rpm/22°C. Ribosome footprint libraries were prepared essentially as described McGlincy and Ingolia 2017; Wu 2019 with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 µl LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection with T4 PNK and ligated to pre adenylated adapters containing 5 random nucleotides at their five prime ends McGlinzy 2017 with T4 RNA Ligase 2 truncated KQ. Adapter ligated RNA was subjected to rRNA depletion using the Ribo Seq riboPOOL h/m/r depletion kit siTOOLs for CHX only samples and legacy RiboZero Gold kit Illumina for CHX+TIG samples The rRNA depleted footprints were reverse transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 commercially available as CircLigase. Libraries were constructed from circularized cDNA …		OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	SRP457105			WT_ribo_bud_1.fastq.gz	fastq	1476985703.0	55745002.0	GSM7734770 r1	0:26.50	A:266369385;C:466461341;G:473469631;T:270671671;N:13675	26		266369385	466461341	473469631	270671671	13675	SRX21486723	SRS18719024	SRA1700409	Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry	Max Planck Institute of Biochemistry	1	0.773		0.14121		0.82242		0.78464		30		B		usable mapping rate	illumina	nextseq	5prime	rrna_depletion	ribozero	bulk	unknown	unknown	Germany	2023-08-28	Gastrula	Embryo	Whole Organism	All anatomical structures
25296	25296	SRR25764046	SRX21486722	SRS18719023	SRP457105	PRJNA1009809	Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [Ribo Seq]	GSE241753	Other	Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.	parent bioproject:PRJNA1009800	pubmed:39402326		WT sphere 4 hpf Ribo seq rep1	GSM7734769		source name:Blastula\|strain:TLAB strain\|tissue:Blastula\|developmental stage:Sphere 4 hpf\|treatment:100 µg/ml CHX 100 µg/ml TIG\|geo loc name:missing\|collection date:missing	WT sphere 4 hpf Ribo seq rep1	We identified the A site location in each mapped read with Scikit ribo [Fang et al. 2018] which uses a random forest with recursive feature selection and a generalized linear model for accurate A site prediction based on matched ribosome profiling and RNA Seq datasets. Kallisto 0.44.0 with parameters b 100 single l 180 s 20 t 40 was used to quantify transcript abundances in Transcripts Per Million TPM from RNA Seq data based on the reference set of MANE annotated transcripts see Codon usage analysis for description of this annotation. To avoid memory errors due to the large size of the human genome and the presence of multiple transcript isoforms all RNAfold dependencies in Scikit ribo were omitted and the index was built separately for each chromosome. To make the hg38 GTF compatible with Scikit ribo transcript/UTR annotations were removed. For each transcript the start codon in the first exon and the stop codon in the last exon were adjusted to represent transcript start and end coordinates taking into account the gene strand. To estimate codon dwell times short 20 23 nt and long 28 33 nt ribosome footprints were analyzed separately. rRNA filtered reads were aligned to GRCz11.108 using STAR v2.6.1c [Dobin et al. 2013] the following options: outFilterMultimapNmax 1 seedSearchStartLmax 15 outSAMtype BAM SortedByCoordinate outFilterMismatchNmax 2 alignEndsType EndToEnd quantMode TranscriptomeSAM outSAMattributes NH HI AS nM NM MD We identified the A site location in each mapped read with Scikit ribo [Fang et al. 2018] which uses a random forest with recursive feature selection and a generalized linear model for accurate A site prediction based on matched ribosome profiling and RNA Seq datasets. Kallisto 0.44.0 with parameters b 100 single l 180 s 20 t 40 was used to quantify transcript abundances in Transcripts Per Million TPM from RNA Seq data based on the reference set of MANE annotated transcripts see Codon usage analysis for description of this annotation. To avoid memory err…	Blastula	unperturbed growth conditions in E3 medium for zebrafish embryos.	200 whole embryos were flash frozen in liquid nitrogen and subsequently lysed in footprint lysis buffer containing 100 µg/ml CHX and 100 µg/ml TIG 0.1% NP 40 10 µg/ml aprotinin 20 µM leupeptin 2.5 µM pepstatin A 0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously triturated through a 26G gauge needle and spun down for 7 minutes at 16 000xg/ 4°C. Supernatant was transferred to a new tube. 20 µg RNA in 200 µl polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2 000 rpm/22°C. post incubation on ice for 5 minutes extracts were pre cleared by centrifugation for 5 minutes at 3 000 g/ 4°C. Ribosomes were pelleted through 3 ml of a sucrose cushion 1 M sucrose 20 mM Tris pH=8.0 140 mM KCl 5 mM MgCl2 1 mM DTT by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50 000 rpm/ 4°C. Ribosome pellets were rinsed once dissolved in 200 µl drug free polysome lysis buffer and incubated with 200 U hiPSC or 300 U NPC RNase I for 45 minutes at 2 000 rpm/22°C. Ribosome footprint libraries were prepared essentially as described McGlincy and Ingolia 2017; Wu 2019 with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 µl LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection with T4 PNK and ligated to pre adenylated adapters containing 5 random nucleotides at their 5’ ends McGlinzy 2017 with T4 RNA Ligase 2 truncated KQ. Adapter ligated RNA was subjected to rRNA depletion using the Ribo Seq riboPOOL h/m/r depletion kit siTOOLs for CHX only samples and legacy RiboZero Gold kit Illumina for CHX+TIG samples The rRNA depleted footprints were reverse transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 commercially available as CircLigase. Libraries were constructed from circularized cDNA with KAP…	Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.	strain:TLAB strain\|tissue:Blastula\|developmental stage:Sphere 4 hpf\|treatment:100 µg/ml CHX 100 µg/ml TIG	GSM7734769	GSM7734769: WT sphere 4 hpf Ribo seq rep1; Danio rerio; OTHER	GSM7734769 r1	GSM7734769	1	200 whole embryos were flash frozen in liquid nitrogen and subsequently lysed in footprint lysis buffer containing 100 µg/ml CHX and 100 µg/ml TIG 0.1% NP 40 10 µg/ml aprotinin 20 µM leupeptin 2.5 µM pepstatin A 0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously triturated through a 26G gauge needle and spun down for 7 minutes at 16 000xg/ 4°C. Supernatant was transferred to a new tube. 20 µg RNA in 200 µl polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2 000 rpm/22°C. post incubation on ice for 5 minutes extracts were pre cleared by centrifugation for 5 minutes at 3 000 g/ 4°C. Ribosomes were pelleted through 3 ml of a sucrose cushion 1 M sucrose 20 mM Tris pH=8.0 140 mM KCl 5 mM MgCl2 1 mM DTT by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50 000 rpm/ 4°C. Ribosome pellets were rinsed once dissolved in 200 µl drug free polysome lysis buffer and incubated with 200 U hiPSC or 300 U NPC RNase I for 45 minutes at 2 000 rpm/22°C. Ribosome footprint libraries were prepared essentially as described McGlincy and Ingolia 2017; Wu 2019 with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 µl LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection with T4 PNK and ligated to pre adenylated adapters containing 5 random nucleotides at their five prime ends McGlinzy 2017 with T4 RNA Ligase 2 truncated KQ. Adapter ligated RNA was subjected to rRNA depletion using the Ribo Seq riboPOOL h/m/r depletion kit siTOOLs for CHX only samples and legacy RiboZero Gold kit Illumina for CHX+TIG samples The rRNA depleted footprints were reverse transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 commercially available as CircLigase. Libraries were constructed from circularized cDNA …		OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 500	SRP457105			WT_ribo_sphere_1.fastq.gz	fastq	1336027898.0	47907512.0	GSM7734769 r1	0:27.89	A:229038284;C:439455963;G:429428292;T:238088512;N:16847	27		229038284	439455963	429428292	238088512	16847	SRX21486722	SRS18719023	SRA1700409	Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry	Max Planck Institute of Biochemistry	1	0.85867		0.20418		0.8776		0.79481		24		B		usable mapping rate	illumina	nextseq	5prime	rrna_depletion	ribozero	bulk	unknown	unknown	Germany	2023-08-28	Blastula	Embryo	Whole Organism	All anatomical structures
29210	29210	SRR27489726	SRX23160983	SRS20111140	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	80S fraction 6hpf replica A	MPRA repA fractions 4 5 6hpf		strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:10\|replicate:replicate A\|BioSampleModel:Model organism or animal									80S fraction 6hpf replica A	Library 10	Library 10	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206645_HGWLYDSX3_3_MPRA_repA_fractions_4_5_6hpf_CTCTCGTC_TATAACCT_S10_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206645_HGWLYDSX3_3_MPRA_repA_fractions_4_5_6hpf_CTCTCGTC_TATAACCT_S10_L003_R2_001_MM_1.fastq.gz	fastq fastq	13762167482.0	45570091.0	BSSE QGF 206645 HGWLYDSX3 3 MPRA repA fractions 4 5 6hpf CTCTCGTC TATAACCT S10 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3449173111;C:3620318973;G:3412595233;T:3279391764;N:688401	151	151	3449173111	3620318973	3412595233	3279391764	688401	SRX23160983	SRS20111140	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01348	9e-05	0.00033	1e-05	0.99151	0.99973	0.41104	0.57142	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29211	29211	SRR27489727	SRX23160982	SRS20111139	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			input sample	Total 6hpf replica A	MPRA repA input 6hpf		strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:9\|replicate:replicate A\|BioSampleModel:Model organism or animal									Total 6hpf replica A	Library 9	Library 9	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206644_HGWLYDSX3_3_MPRA_repA_input_6hpf_TCTCTACT_CGCGGTTC_S9_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206644_HGWLYDSX3_3_MPRA_repA_input_6hpf_TCTCTACT_CGCGGTTC_S9_L003_R1_001_MM_1.fastq.gz	fastq fastq	13570263998.0	44934649.0	BSSE QGF 206644 HGWLYDSX3 3 MPRA repA input 6hpf TCTCTACT CGCGGTTC S9 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3444180060;C:3577051220;G:3264051077;T:3284343514;N:638127	151	151	3444180060	3577051220	3264051077	3284343514	638127	SRX23160982	SRS20111139	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01809	5e-05	0.00042	0.0	0.99013	0.99985	0.41794	0.57142	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29212	29212	SRR27489728	SRX23160981	SRS20111138	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	HMW fraction 4hpf replica A	MPRA repA fractions 8 9 4hpf		strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:8\|replicate:replicate A\|BioSampleModel:Model organism or animal									HMW fraction 4hpf replica A	Library 8	Library 8	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206643_HGWLYDSX3_3_MPRA_repA_fractions_8_9_4hpf_GACCTGAA_TTGGTGAG_S8_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206643_HGWLYDSX3_3_MPRA_repA_fractions_8_9_4hpf_GACCTGAA_TTGGTGAG_S8_L003_R1_001_MM_1.fastq.gz	fastq fastq	12066108000.0	39954000.0	BSSE QGF 206643 HGWLYDSX3 3 MPRA repA fractions 8 9 4hpf GACCTGAA TTGGTGAG S8 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3060316371;C:3136678983;G:2965588104;T:2902920606;N:603936	151	151	3060316371	3136678983	2965588104	2902920606	603936	SRX23160981	SRS20111138	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01336	5e-05	0.00027	0.0	0.99143	0.99983	0.40418	0.125	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29213	29213	SRR27489729	SRX23160980	SRS20111142	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	LMW fraction 4hpf replica A	MPRA repA fractions 6 7 4hpf		strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:7\|replicate:replicate A\|BioSampleModel:Model organism or animal									LMW fraction 4hpf replica A	Library 7	Library 7	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206642_HGWLYDSX3_3_MPRA_repA_fractions_6_7_4hpf_AGTTCAGG_CCAACAGA_S7_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206642_HGWLYDSX3_3_MPRA_repA_fractions_6_7_4hpf_AGTTCAGG_CCAACAGA_S7_L003_R1_001_MM_1.fastq.gz	fastq fastq	11998643314.0	39730607.0	BSSE QGF 206642 HGWLYDSX3 3 MPRA repA fractions 6 7 4hpf AGTTCAGG CCAACAGA S7 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3044270548;C:3145201016;G:2907229129;T:2901344613;N:598008	151	151	3044270548	3145201016	2907229129	2901344613	598008	SRX23160980	SRS20111142	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01631	0.00013	0.00035	1e-05	0.99101	0.99965	0.40542	0.33333	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29214	29214	SRR27489730	SRX23160979	SRS20111137	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	80S fraction 4hpf replica A	MPRA repA fractions 4 5 4hpf		strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:6\|replicate:replicate A\|BioSampleModel:Model organism or animal									80S fraction 4hpf replica A	Library 6	Library 6	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206641_HGWLYDSX3_3_MPRA_repA_fractions_4_5_4hpf_TGGATCGA_GTGCGATA_S6_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206641_HGWLYDSX3_3_MPRA_repA_fractions_4_5_4hpf_TGGATCGA_GTGCGATA_S6_L003_R2_001_MM_1.fastq.gz	fastq fastq	12838157410.0	42510455.0	BSSE QGF 206641 HGWLYDSX3 3 MPRA repA fractions 4 5 4hpf TGGATCGA GTGCGATA S6 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3238698530;C:3377705608;G:3143460419;T:3077655243;N:637610	151	151	3238698530	3377705608	3143460419	3077655243	637610	SRX23160979	SRS20111137	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01549	3e-05	0.00042	1e-05	0.99097	0.99995	0.42138	0.5	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29216	29216	SRR27489733	SRX23160976	SRS20111134	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	HMW fraction 10hpf replica C	MPRA repC fractions 8 9 10hpf		strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:48\|replicate:replicate C\|BioSampleModel:Model organism or animal									HMW fraction 10hpf replica C	Library 48	Library 48	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206683_HGWLYDSX3_3_MPRA_repC_fractions_8_9_10hpf_CAACAATG_CTTCACGG_S48_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206683_HGWLYDSX3_3_MPRA_repC_fractions_8_9_10hpf_CAACAATG_CTTCACGG_S48_L003_R2_001_MM_1.fastq.gz	fastq fastq	16074911568.0	53228184.0	BSSE QGF 206683 HGWLYDSX3 3 MPRA repC fractions 8 9 10hpf CAACAATG CTTCACGG S48 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:4029048727;C:4167204709;G:4036912991;T:3840941866;N:803275	151	151	4029048727	4167204709	4036912991	3840941866	803275	SRX23160976	SRS20111134	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.00795	0.00021	0.00019	2e-05	0.99263	0.99935	0.45247	0.62857	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29217	29217	SRR27489734	SRX23160975	SRS20111132	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	LMW fraction 10hpf replica C	MPRA repC fractions 6 7 10hpf		strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:47\|replicate:replicate C\|BioSampleModel:Model organism or animal									LMW fraction 10hpf replica C	Library 47	Library 47	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206682_HGWLYDSX3_3_MPRA_repC_fractions_6_7_10hpf_GGTGAACC_GCGTTGGA_S47_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206682_HGWLYDSX3_3_MPRA_repC_fractions_6_7_10hpf_GGTGAACC_GCGTTGGA_S47_L003_R2_001_MM_1.fastq.gz	fastq fastq	16211925948.0	53681874.0	BSSE QGF 206682 HGWLYDSX3 3 MPRA repC fractions 6 7 10hpf GGTGAACC GCGTTGGA S47 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:4078470905;C:4239434649;G:4000426230;T:3892801664;N:792500	151	151	4078470905	4239434649	4000426230	3892801664	792500	SRX23160975	SRS20111132	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01232	0.00028	0.00027	5e-05	0.99166	0.99926	0.4522	0.61904	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29218	29218	SRR27489735	SRX23160974	SRS20111131	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	80S fraction 10hpf replica C	MPRA repC fractions 4 5 10hpf		strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:46\|replicate:replicate C\|BioSampleModel:Model organism or animal									80S fraction 10hpf replica C	Library 46	Library 46	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206681_HGWLYDSX3_3_MPRA_repC_fractions_4_5_10hpf_AACAGGTT_ATACCAAG_S46_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206681_HGWLYDSX3_3_MPRA_repC_fractions_4_5_10hpf_AACAGGTT_ATACCAAG_S46_L003_R2_001_MM_1.fastq.gz	fastq fastq	18761117310.0	62122905.0	BSSE QGF 206681 HGWLYDSX3 3 MPRA repC fractions 4 5 10hpf AACAGGTT ATACCAAG S46 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:4746221682;C:4940258209;G:4549993563;T:4523714877;N:928979	151	151	4746221682	4940258209	4549993563	4523714877	928979	SRX23160974	SRS20111131	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01785	0.0002	0.00043	3e-05	0.9908	0.99951	0.45866	0.6	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29219	29219	SRR27489736	SRX23160973	SRS20111130	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			input sample	Total 10hpf replica C	MPRA repC input 10hpf		strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:45\|replicate:replicate C\|BioSampleModel:Model organism or animal									Total 10hpf replica C	Library 45	Library 45	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206680_HGWLYDSX3_3_MPRA_repC_input_10hpf_GCGCTCTA_GCTCCGAC_S45_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206680_HGWLYDSX3_3_MPRA_repC_input_10hpf_GCGCTCTA_GCTCCGAC_S45_L003_R2_001_MM_1.fastq.gz	fastq fastq	15148053334.0	50159117.0	BSSE QGF 206680 HGWLYDSX3 3 MPRA repC input 10hpf GCGCTCTA GCTCCGAC S45 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3877492548;C:4007711111;G:3560735163;T:3701356537;N:757975	151	151	3877492548	4007711111	3560735163	3701356537	757975	SRX23160973	SRS20111130	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.02196	3e-05	0.00062	1e-05	0.98944	0.99993	0.4404	0.66666	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29220	29220	SRR27489737	SRX23160972	SRS20111129	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	HMW fraction 6hpf replica C	MPRA repC fractions 8 9 6hpf		strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:44\|replicate:replicate C\|BioSampleModel:Model organism or animal									HMW fraction 6hpf replica C	Library 44	Library 44	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206679_HGWLYDSX3_3_MPRA_repC_fractions_8_9_6hpf_ATATCTCG_ATCTTAGT_S44_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206679_HGWLYDSX3_3_MPRA_repC_fractions_8_9_6hpf_ATATCTCG_ATCTTAGT_S44_L003_R1_001_MM_1.fastq.gz	fastq fastq	14506315716.0	48034158.0	BSSE QGF 206679 HGWLYDSX3 3 MPRA repC fractions 8 9 6hpf ATATCTCG ATCTTAGT S44 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3655344763;C:3770081597;G:3599601074;T:3480562617;N:725665	151	151	3655344763	3770081597	3599601074	3480562617	725665	SRX23160972	SRS20111129	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01152	0.00012	0.00021	1e-05	0.99204	0.99963	0.40859	0.47368	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29221	29221	SRR27489738	SRX23160971	SRS20111128	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	LMW fraction 6hpf replica C	MPRA repC fractions 6 7 6hpf		strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:43\|replicate:replicate C\|BioSampleModel:Model organism or animal									LMW fraction 6hpf replica C	Library 43	Library 43	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206678_HGWLYDSX3_3_MPRA_repC_fractions_6_7_6hpf_ACCTTGGC_GGCCTCAT_S43_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206678_HGWLYDSX3_3_MPRA_repC_fractions_6_7_6hpf_ACCTTGGC_GGCCTCAT_S43_L003_R2_001_MM_1.fastq.gz	fastq fastq	14912162946.0	49378023.0	BSSE QGF 206678 HGWLYDSX3 3 MPRA repC fractions 6 7 6hpf ACCTTGGC GGCCTCAT S43 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3752402181;C:3897191999;G:3682100517;T:3579734634;N:733615	151	151	3752402181	3897191999	3682100517	3579734634	733615	SRX23160971	SRS20111128	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01301	0.0001	0.00023	0.0	0.99131	0.99963	0.41128	0.44444	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29222	29222	SRR27489739	SRX23160970	SRS20111127	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	80S fraction 6hpf replica C	MPRA repC fractions 4 5 6hpf		strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:42\|replicate:replicate C\|BioSampleModel:Model organism or animal									80S fraction 6hpf replica C	Library 42	Library 42	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206677_HGWLYDSX3_3_MPRA_repC_fractions_4_5_6hpf_GTTCCAAT_AATTCTGC_S42_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206677_HGWLYDSX3_3_MPRA_repC_fractions_4_5_6hpf_GTTCCAAT_AATTCTGC_S42_L003_R1_001_MM_1.fastq.gz	fastq fastq	16464627468.0	54518634.0	BSSE QGF 206677 HGWLYDSX3 3 MPRA repC fractions 4 5 6hpf GTTCCAAT AATTCTGC S42 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:4169088631;C:4342123158;G:3994621055;T:3957976348;N:818276	151	151	4169088631	4342123158	3994621055	3957976348	818276	SRX23160970	SRS20111127	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01689	8e-05	0.00051	0.0	0.99107	0.99973	0.40071	0.53846	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29223	29223	SRR27489740	SRX23160969	SRS20111125	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			input sample	Total 6hpf replica C	MPRA repC input 6hpf		strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:41\|replicate:replicate C\|BioSampleModel:Model organism or animal									Total 6hpf replica C	Library 41	Library 41	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206676_HGWLYDSX3_3_MPRA_repC_input_6hpf_GCAATGCA_GGAACGTT_S41_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206676_HGWLYDSX3_3_MPRA_repC_input_6hpf_GCAATGCA_GGAACGTT_S41_L003_R2_001_MM_1.fastq.gz	fastq fastq	10859083158.0	35957229.0	BSSE QGF 206676 HGWLYDSX3 3 MPRA repC input 6hpf GCAATGCA GGAACGTT S41 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:2762807814;C:2857106152;G:2613305234;T:2625327901;N:536057	151	151	2762807814	2857106152	2613305234	2625327901	536057	SRX23160969	SRS20111125	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01753	0.0	0.00047	0.0	0.9907	1.0	0.40097		151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29224	29224	SRR27489741	SRX23160968	SRS20111133	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			input sample	Total 4hpf replica A	MPRA repA input 4hpf		strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:5\|replicate:replicate A\|BioSampleModel:Model organism or animal									Total 4hpf replica A	Library 5	Library 5	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206640_HGWLYDSX3_3_MPRA_repA_input_4hpf_CAAGCTAG_ACATAGCG_S5_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206640_HGWLYDSX3_3_MPRA_repA_input_4hpf_CAAGCTAG_ACATAGCG_S5_L003_R2_001_MM_1.fastq.gz	fastq fastq	13631534966.0	45137533.0	BSSE QGF 206640 HGWLYDSX3 3 MPRA repA input 4hpf CAAGCTAG ACATAGCG S5 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3486253250;C:3611078376;G:3219396920;T:3314128840;N:677580	151	151	3486253250	3611078376	3219396920	3314128840	677580	SRX23160968	SRS20111133	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.02225	2e-05	0.00066	0.0	0.98975	0.99993	0.40257	0.33333	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29225	29225	SRR27489742	SRX23160967	SRS20111126	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	HMW fraction 4hpf replica C	MPRA repC fractions 8 9 4hpf		strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:40\|replicate:replicate C\|BioSampleModel:Model organism or animal									HMW fraction 4hpf replica C	Library 40	Library 40	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206675_HGWLYDSX3_3_MPRA_repC_fractions_8_9_4hpf_ATGGCATG_AAGGTACC_S40_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206675_HGWLYDSX3_3_MPRA_repC_fractions_8_9_4hpf_ATGGCATG_AAGGTACC_S40_L003_R2_001_MM_1.fastq.gz	fastq fastq	16854209582.0	55808641.0	BSSE QGF 206675 HGWLYDSX3 3 MPRA repC fractions 8 9 4hpf ATGGCATG AAGGTACC S40 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:4270727222;C:4383022813;G:4143081915;T:4056541855;N:835777	151	151	4270727222	4383022813	4143081915	4056541855	835777	SRX23160967	SRS20111126	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01329	0.00015	0.00029	2e-05	0.99141	0.99953	0.4263	0.47826	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29226	29226	SRR27489743	SRX23160966	SRS20111124	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	LMW fraction 4hpf replica C	MPRA repC fractions 6 7 4hpf		strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:39\|replicate:replicate C\|BioSampleModel:Model organism or animal									LMW fraction 4hpf replica C	Library 39	Library 39	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206674_HGWLYDSX3_3_MPRA_repC_fractions_6_7_4hpf_GGAGCGTC_GTCCGTGC_S39_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206674_HGWLYDSX3_3_MPRA_repC_fractions_6_7_4hpf_GGAGCGTC_GTCCGTGC_S39_L003_R2_001_MM_1.fastq.gz	fastq fastq	12146174844.0	40219122.0	BSSE QGF 206674 HGWLYDSX3 3 MPRA repC fractions 6 7 4hpf GGAGCGTC GTCCGTGC S39 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3060215849;C:3176615755;G:3002666854;T:2906066243;N:610143	151	151	3060215849	3176615755	3002666854	2906066243	610143	SRX23160966	SRS20111124	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01309	0.0002	0.00031	0.0	0.99164	0.99939	0.40018	0.57142	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29227	29227	SRR27489744	SRX23160965	SRS20111123	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	80S fraction 4hpf replica C	MPRA repC fractions 4 5 4hpf		strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:38\|replicate:replicate C\|BioSampleModel:Model organism or animal									80S fraction 4hpf replica C	Library 38	Library 38	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206673_HGWLYDSX3_3_MPRA_repC_fractions_4_5_4hpf_AAGATACT_ACTTACAT_S38_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206673_HGWLYDSX3_3_MPRA_repC_fractions_4_5_4hpf_AAGATACT_ACTTACAT_S38_L003_R1_001_MM_1.fastq.gz	fastq fastq	14100203330.0	46689415.0	BSSE QGF 206673 HGWLYDSX3 3 MPRA repC fractions 4 5 4hpf AAGATACT ACTTACAT S38 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3544539088;C:3702795841;G:3493240125;T:3358929671;N:698605	151	151	3544539088	3702795841	3493240125	3358929671	698605	SRX23160965	SRS20111123	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01368	0.00016	0.00037	0.0	0.99107	0.99951	0.40864	0.5	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29228	29228	SRR27489745	SRX23160964	SRS20111120	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			input sample	Total 4hpf replica C	MPRA repC input 4hpf		strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:37\|replicate:replicate C\|BioSampleModel:Model organism or animal									Total 4hpf replica C	Library 37	Library 37	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206672_HGWLYDSX3_3_MPRA_repC_input_4hpf_GCGCAAGC_TCACGCCG_S37_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206672_HGWLYDSX3_3_MPRA_repC_input_4hpf_GCGCAAGC_TCACGCCG_S37_L003_R2_001_MM_1.fastq.gz	fastq fastq	10925301792.0	36176496.0	BSSE QGF 206672 HGWLYDSX3 3 MPRA repC input 4hpf GCGCAAGC TCACGCCG S37 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:2802490901;C:2878602103;G:2592316062;T:2651349641;N:543085	151	151	2802490901	2878602103	2592316062	2651349641	543085	SRX23160964	SRS20111120	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.02108	3e-05	0.0006	0.0	0.98981	0.99991	0.42181	0.0	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29229	29229	SRR27489746	SRX23160963	SRS20111121	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	HMW fraction 2hpf replica C	MPRA repC fractions 8 9 2hpf		strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:36\|replicate:replicate C\|BioSampleModel:Model organism or animal									HMW fraction 2hpf replica C	Library 36	Library 36	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206671_HGWLYDSX3_3_MPRA_repC_fractions_8_9_2hpf_ATATGGAT_CTGTATTA_S36_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206671_HGWLYDSX3_3_MPRA_repC_fractions_8_9_2hpf_ATATGGAT_CTGTATTA_S36_L003_R2_001_MM_1.fastq.gz	fastq fastq	13085558528.0	43329664.0	BSSE QGF 206671 HGWLYDSX3 3 MPRA repC fractions 8 9 2hpf ATATGGAT CTGTATTA S36 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3305413622;C:3391845548;G:3249932870;T:3137708503;N:657985	151	151	3305413622	3391845548	3249932870	3137708503	657985	SRX23160963	SRS20111121	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01098	8e-05	0.00025	0.0	0.99216	0.99973	0.4317	0.61538	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
29230	29230	SRR27489747	SRX23160962	SRS20111119	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	LMW fraction 2hpf replica C	MPRA repC fractions 6 7 2hpf		strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:35\|replicate:replicate C\|BioSampleModel:Model organism or animal									LMW fraction 2hpf replica C	Library 35	Library 35	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206670_HGWLYDSX3_3_MPRA_repC_fractions_6_7_2hpf_CGGACAAC_TCCGGATT_S35_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206670_HGWLYDSX3_3_MPRA_repC_fractions_6_7_2hpf_CGGACAAC_TCCGGATT_S35_L003_R1_001_MM_1.fastq.gz	fastq fastq	16647721914.0	55124907.0	BSSE QGF 206670 HGWLYDSX3 3 MPRA repC fractions 6 7 2hpf CGGACAAC TCCGGATT S35 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:4231542934;C:4348688006;G:4050131444;T:4016534422;N:825108	151	151	4231542934	4348688006	4050131444	4016534422	825108	SRX23160962	SRS20111119	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01514	0.00017	0.00035	3e-05	0.99109	0.99955	0.4372	0.30434	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
29231	29231	SRR27489748	SRX23160961	SRS20111118	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	80S fraction 2hpf replica C	MPRA repC fractions 4 5 2hpf		strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:34\|replicate:replicate C\|BioSampleModel:Model organism or animal									80S fraction 2hpf replica C	Library 34	Library 34	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206669_HGWLYDSX3_3_MPRA_repC_fractions_4_5_2hpf_TAAGTGGT_CTTAAGCC_S34_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206669_HGWLYDSX3_3_MPRA_repC_fractions_4_5_2hpf_TAAGTGGT_CTTAAGCC_S34_L003_R2_001_MM_1.fastq.gz	fastq fastq	15431181052.0	51096626.0	BSSE QGF 206669 HGWLYDSX3 3 MPRA repC fractions 4 5 2hpf TAAGTGGT CTTAAGCC S34 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3856018869;C:4036338306;G:3877988553;T:3660059325;N:775999	151	151	3856018869	4036338306	3877988553	3660059325	775999	SRX23160961	SRS20111118	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01114	8e-05	0.00028	0.0	0.99192	0.99975	0.42956	0.5	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
29232	29232	SRR27489749	SRX23160960	SRS20111117	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			input sample	Total 2hpf replica C	MPRA repC input 2hpf		strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:33\|replicate:replicate C\|BioSampleModel:Model organism or animal									Total 2hpf replica C	Library 33	Library 33	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206668_HGWLYDSX3_3_MPRA_repC_input_2hpf_CTACGACA_GAGTCCAA_S33_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206668_HGWLYDSX3_3_MPRA_repC_input_2hpf_CTACGACA_GAGTCCAA_S33_L003_R1_001_MM_1.fastq.gz	fastq fastq	11771229160.0	38977580.0	BSSE QGF 206668 HGWLYDSX3 3 MPRA repC input 2hpf CTACGACA GAGTCCAA S33 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:2999574420;C:3115525474;G:2806539264;T:2849003922;N:586080	151	151	2999574420	3115525474	2806539264	2849003922	586080	SRX23160960	SRS20111117	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01997	2e-05	0.00054	0.0	0.99022	0.99993	0.41853	0.33333	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
29233	29233	SRR27489750	SRX23160959	SRS20111116	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	HMW fraction 10hpf replica B	MPRA repB fractions 8 9 10hpf		strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:32\|replicate:replicate B\|BioSampleModel:Model organism or animal									HMW fraction 10hpf replica B	Library 32	Library 32	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206667_HGWLYDSX3_3_MPRA_repB_fractions_8_9_10hpf_TCGTAGTG_AGACTTGG_S32_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206667_HGWLYDSX3_3_MPRA_repB_fractions_8_9_10hpf_TCGTAGTG_AGACTTGG_S32_L003_R2_001_MM_1.fastq.gz	fastq fastq	12683073766.0	41996933.0	BSSE QGF 206667 HGWLYDSX3 3 MPRA repB fractions 8 9 10hpf TCGTAGTG AGACTTGG S32 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3165850297;C:3286094227;G:3205853472;T:3024640146;N:635624	151	151	3165850297	3286094227	3205853472	3024640146	635624	SRX23160959	SRS20111116	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.00973	0.00093	0.00036	0.00015	0.99265	0.99819	0.4701	0.61111	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29234	29234	SRR27489751	SRX23160958	SRS20111115	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	LMW fraction 10hpf replica B	MPRA repB fractions 6 7 10hpf		strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:31\|replicate:replicate B\|BioSampleModel:Model organism or animal									LMW fraction 10hpf replica B	Library 31	Library 31	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206666_HGWLYDSX3_3_MPRA_repB_fractions_6_7_10hpf_GATTCTGC_GACGAGAG_S31_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206666_HGWLYDSX3_3_MPRA_repB_fractions_6_7_10hpf_GATTCTGC_GACGAGAG_S31_L003_R2_001_MM_1.fastq.gz	fastq fastq	11187950286.0	37046193.0	BSSE QGF 206666 HGWLYDSX3 3 MPRA repB fractions 6 7 10hpf GATTCTGC GACGAGAG S31 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:2805602272;C:2927866458;G:2773076846;T:2680845208;N:559502	151	151	2805602272	2927866458	2773076846	2680845208	559502	SRX23160958	SRS20111115	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01142	0.0002	0.00018	2e-05	0.99243	0.99943	0.45894	0.54838	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29235	29235	SRR27489752	SRX23160957	SRS20111114	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	HMW fraction 2hpf replica A	MPRA repA fractions 8 9 2hpf		strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:4\|replicate:replicate A\|BioSampleModel:Model organism or animal									HMW fraction 2hpf replica A	Library 4	Library 4	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206639_HGWLYDSX3_3_MPRA_repA_fractions_8_9_2hpf_GCTTGTCA_GAACATAC_S4_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206639_HGWLYDSX3_3_MPRA_repA_fractions_8_9_2hpf_GCTTGTCA_GAACATAC_S4_L003_R1_001_MM_1.fastq.gz	fastq fastq	12108626278.0	40094789.0	BSSE QGF 206639 HGWLYDSX3 3 MPRA repA fractions 8 9 2hpf GCTTGTCA GAACATAC S4 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3079403604;C:3149095123;G:2953175005;T:2926352278;N:600268	151	151	3079403604	3149095123	2953175005	2926352278	600268	SRX23160957	SRS20111114	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.014	5e-05	0.00032	0.0	0.99137	0.99987	0.45127	0.28571	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
29236	29236	SRR27489753	SRX23160956	SRS20111113	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	80S fraction 10hpf replica B	MPRA repB fractions 4 5 10hpf		strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:30\|replicate:replicate B\|BioSampleModel:Model organism or animal									80S fraction 10hpf replica B	Library 30	Library 30	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206665_HGWLYDSX3_3_MPRA_repB_fractions_4_5_10hpf_AGCCTCAT_AGTAGAGA_S30_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206665_HGWLYDSX3_3_MPRA_repB_fractions_4_5_10hpf_AGCCTCAT_AGTAGAGA_S30_L003_R2_001_MM_1.fastq.gz	fastq fastq	15465851256.0	51211428.0	BSSE QGF 206665 HGWLYDSX3 3 MPRA repB fractions 4 5 10hpf AGCCTCAT AGTAGAGA S30 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3889753740;C:4075740540;G:3791174754;T:3708409198;N:773024	151	151	3889753740	4075740540	3791174754	3708409198	773024	SRX23160956	SRS20111113	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01609	0.00014	0.0003	3e-05	0.99139	0.99959	0.4335	0.5	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29237	29237	SRR27489754	SRX23160955	SRS20111112	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			input sample	Total 10hpf replica B	MPRA repB input 10hpf		strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:29\|replicate:replicate B\|BioSampleModel:Model organism or animal									Total 10hpf replica B	Library 29	Library 29	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206664_HGWLYDSX3_3_MPRA_repB_input_10hpf_CGTTAGAA_TTCAGGTC_S29_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206664_HGWLYDSX3_3_MPRA_repB_input_10hpf_CGTTAGAA_TTCAGGTC_S29_L003_R2_001_MM_1.fastq.gz	fastq fastq	12592035866.0	41695483.0	BSSE QGF 206664 HGWLYDSX3 3 MPRA repB input 10hpf CGTTAGAA TTCAGGTC S29 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3220865280;C:3326103488;G:2978281202;T:3066156448;N:629448	151	151	3220865280	3326103488	2978281202	3066156448	629448	SRX23160955	SRS20111112	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.02168	1e-05	0.0006	0.0	0.98993	0.99997	0.41273	1.0	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29238	29238	SRR27489755	SRX23160954	SRS20111122	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	HMW fraction 6hpf replica B	MPRA repB fractions 8 9 6hpf		strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:28\|replicate:replicate B\|BioSampleModel:Model organism or animal									HMW fraction 6hpf replica B	Library 28	Library 28	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206663_HGWLYDSX3_3_MPRA_repB_fractions_8_9_6hpf_TACCGAGG_CCTGAACT_S28_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206663_HGWLYDSX3_3_MPRA_repB_fractions_8_9_6hpf_TACCGAGG_CCTGAACT_S28_L003_R2_001_MM_1.fastq.gz	fastq fastq	12606651156.0	41743878.0	BSSE QGF 206663 HGWLYDSX3 3 MPRA repB fractions 8 9 6hpf TACCGAGG CCTGAACT S28 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3184687427;C:3283680489;G:3107570485;T:3030085619;N:627136	151	151	3184687427	3283680489	3107570485	3030085619	627136	SRX23160954	SRS20111122	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01219	7e-05	0.00028	0.0	0.99182	0.99977	0.42217	0.45454	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29239	29239	SRR27489756	SRX23160953	SRS20111110	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	LMW fraction 6hpf replica B	MPRA repB fractions 6 7 6hpf		strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:27\|replicate:replicate B\|BioSampleModel:Model organism or animal									LMW fraction 6hpf replica B	Library 27	Library 27	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206662_HGWLYDSX3_3_MPRA_repB_fractions_6_7_6hpf_AATGCCTC_TCGATCCA_S27_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206662_HGWLYDSX3_3_MPRA_repB_fractions_6_7_6hpf_AATGCCTC_TCGATCCA_S27_L003_R1_001_MM_1.fastq.gz	fastq fastq	13738263880.0	45490940.0	BSSE QGF 206662 HGWLYDSX3 3 MPRA repB fractions 6 7 6hpf AATGCCTC TCGATCCA S27 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3463772316;C:3608023656;G:3363805269;T:3301974573;N:688066	151	151	3463772316	3608023656	3363805269	3301974573	688066	SRX23160953	SRS20111110	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01443	0.00014	0.00028	1e-05	0.99117	0.99957	0.38916	0.45833	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29240	29240	SRR27489757	SRX23160952	SRS20111111	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	80S fraction 6hpf replica B	MPRA repB fractions 4 5 6hpf		strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:26\|replicate:replicate B\|BioSampleModel:Model organism or animal									80S fraction 6hpf replica B	Library 26	Library 26	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206661_HGWLYDSX3_3_MPRA_repB_fractions_4_5_6hpf_GGCATTCT_CTAGCTTG_S26_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206661_HGWLYDSX3_3_MPRA_repB_fractions_4_5_6hpf_GGCATTCT_CTAGCTTG_S26_L003_R1_001_MM_1.fastq.gz	fastq fastq	10624262152.0	35179676.0	BSSE QGF 206661 HGWLYDSX3 3 MPRA repB fractions 4 5 6hpf GGCATTCT CTAGCTTG S26 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:2680084455;C:2804915710;G:2592024460;T:2546707250;N:530277	151	151	2680084455	2804915710	2592024460	2546707250	530277	SRX23160952	SRS20111111	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01636	0.00013	0.00046	0.0	0.99088	0.99959	0.39222	0.40909	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29241	29241	SRR27489758	SRX23160951	SRS20111109	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			input sample	Total 6hpf replica B	MPRA repB input 6hpf		strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:25\|replicate:replicate B\|BioSampleModel:Model organism or animal									Total 6hpf replica B	Library 25	Library 25	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206660_HGWLYDSX3_3_MPRA_repB_input_6hpf_TTACAGGA_TGACAAGC_S25_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206660_HGWLYDSX3_3_MPRA_repB_input_6hpf_TTACAGGA_TGACAAGC_S25_L003_R2_001_MM_1.fastq.gz	fastq fastq	10153888998.0	33622149.0	BSSE QGF 206660 HGWLYDSX3 3 MPRA repB input 6hpf TTACAGGA TGACAAGC S25 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:2587160061;C:2673241688;G:2432503358;T:2460478928;N:504963	151	151	2587160061	2673241688	2432503358	2460478928	504963	SRX23160951	SRS20111109	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01911	2e-05	0.00061	0.0	0.99064	0.99995	0.42802	0.0	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29242	29242	SRR27489759	SRX23160950	SRS20111107	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	HMW fraction 4hpf replica B	MPRA repB fractions 8 9 4hpf		strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:24\|replicate:replicate B\|BioSampleModel:Model organism or animal									HMW fraction 4hpf replica B	Library 24	Library 24	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206659_HGWLYDSX3_3_MPRA_repB_fractions_8_9_4hpf_CCGTGAAG_CAGTGGAT_S24_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206659_HGWLYDSX3_3_MPRA_repB_fractions_8_9_4hpf_CCGTGAAG_CAGTGGAT_S24_L003_R2_001_MM_1.fastq.gz	fastq fastq	11600767978.0	38413139.0	BSSE QGF 206659 HGWLYDSX3 3 MPRA repB fractions 8 9 4hpf CCGTGAAG CAGTGGAT S24 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:2943303855;C:3024500200;G:2833306086;T:2799077405;N:580432	151	151	2943303855	3024500200	2833306086	2799077405	580432	SRX23160950	SRS20111107	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01371	0.00013	0.00031	1e-05	0.99143	0.99955	0.41912	0.5909	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29243	29243	SRR27489760	SRX23160949	SRS20111106	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	LMW fraction 4hpf replica B	MPRA repB fractions 6 7 4hpf		strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:23\|replicate:replicate B\|BioSampleModel:Model organism or animal									LMW fraction 4hpf replica B	Library 23	Library 23	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206658_HGWLYDSX3_3_MPRA_repB_fractions_6_7_4hpf_CTTGGTAT_CCAAGTCC_S23_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206658_HGWLYDSX3_3_MPRA_repB_fractions_6_7_4hpf_CTTGGTAT_CCAAGTCC_S23_L003_R2_001_MM_1.fastq.gz	fastq fastq	13216553444.0	43763422.0	BSSE QGF 206658 HGWLYDSX3 3 MPRA repB fractions 6 7 4hpf CTTGGTAT CCAAGTCC S23 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3339016083;C:3457419680;G:3233764657;T:3185687490;N:665534	151	151	3339016083	3457419680	3233764657	3185687490	665534	SRX23160949	SRS20111106	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01431	0.00024	0.00034	1e-05	0.99135	0.99924	0.41915	0.45238	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29244	29244	SRR27489761	SRX23160948	SRS20111105	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	80S fraction 4hpf replica B	MPRA repB fractions 4 5 4hpf		strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:22\|replicate:replicate B\|BioSampleModel:Model organism or animal									80S fraction 4hpf replica B	Library 22	Library 22	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206657_HGWLYDSX3_3_MPRA_repB_fractions_4_5_4hpf_ATGAGGCC_GTTAATTG_S22_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206657_HGWLYDSX3_3_MPRA_repB_fractions_4_5_4hpf_ATGAGGCC_GTTAATTG_S22_L003_R2_001_MM_1.fastq.gz	fastq fastq	11938250562.0	39530631.0	BSSE QGF 206657 HGWLYDSX3 3 MPRA repB fractions 4 5 4hpf ATGAGGCC GTTAATTG S22 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3040684418;C:3144238599;G:2873359599;T:2879374531;N:593415	151	151	3040684418	3144238599	2873359599	2879374531	593415	SRX23160948	SRS20111105	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.0185	8e-05	0.00056	0.0	0.9903	0.99969	0.4376	0.4	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29245	29245	SRR27489762	SRX23160947	SRS20111104	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			input sample	Total 4hpf replica B	MPRA repB input 4hpf		strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:21\|replicate:replicate B\|BioSampleModel:Model organism or animal									Total 4hpf replica B	Library 21	Library 21	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206656_HGWLYDSX3_3_MPRA_repB_input_4hpf_GCAGAATT_ACCGGCCA_S21_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206656_HGWLYDSX3_3_MPRA_repB_input_4hpf_GCAGAATT_ACCGGCCA_S21_L003_R1_001_MM_1.fastq.gz	fastq fastq	14482326346.0	47954723.0	BSSE QGF 206656 HGWLYDSX3 3 MPRA repB input 4hpf GCAGAATT ACCGGCCA S21 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3697691325;C:3838972714;G:3432418300;T:3512522230;N:721777	151	151	3697691325	3838972714	3432418300	3512522230	721777	SRX23160947	SRS20111104	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.0211	2e-05	0.00055	0.0	0.9903	0.99993	0.42543	0.0	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29246	29246	SRR27489763	SRX23160946	SRS20111108	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	LMW fraction 2hpf replica A	MPRA repA fractions 6 7 2hpf		strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:3\|replicate:replicate A\|BioSampleModel:Model organism or animal									LMW fraction 2hpf replica A	Library 3	Library 3	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206638_HGWLYDSX3_3_MPRA_repA_fractions_6_7_2hpf_ATCCACTG_AGGTGCGT_S3_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206638_HGWLYDSX3_3_MPRA_repA_fractions_6_7_2hpf_ATCCACTG_AGGTGCGT_S3_L003_R1_001_MM_1.fastq.gz	fastq fastq	12524202136.0	41470868.0	BSSE QGF 206638 HGWLYDSX3 3 MPRA repA fractions 6 7 2hpf ATCCACTG AGGTGCGT S3 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3168466372;C:3269998328;G:3075956662;T:3009160932;N:619842	151	151	3168466372	3269998328	3075956662	3009160932	619842	SRX23160946	SRS20111108	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01351	7e-05	0.00028	0.0	0.99168	0.99977	0.43472	0.54545	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
29247	29247	SRR27489764	SRX23160945	SRS20111103	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	HMW fraction 2hpf replica B	MPRA repB fractions 8 9 2hpf		strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:20\|replicate:replicate B\|BioSampleModel:Model organism or animal									HMW fraction 2hpf replica B	Library 20	Library 20	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206655_HGWLYDSX3_3_MPRA_repB_fractions_8_9_2hpf_AACGTTCC_GGAGTACT_S20_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206655_HGWLYDSX3_3_MPRA_repB_fractions_8_9_2hpf_AACGTTCC_GGAGTACT_S20_L003_R2_001_MM_1.fastq.gz	fastq fastq	12514444214.0	41438557.0	BSSE QGF 206655 HGWLYDSX3 3 MPRA repB fractions 8 9 2hpf AACGTTCC GGAGTACT S20 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3174354240;C:3246812350;G:3082021359;T:3010633962;N:622303	151	151	3174354240	3246812350	3082021359	3010633962	622303	SRX23160945	SRS20111103	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01121	0.00016	0.00027	1e-05	0.99204	0.99953	0.43533	0.5	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
29248	29248	SRR27489765	SRX23160944	SRS20111102	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	LMW fraction 2hpf replica B	MPRA repB fractions 6 7 2hpf		strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:19\|replicate:replicate B\|BioSampleModel:Model organism or animal									LMW fraction 2hpf replica B	Library 19	Library 19	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206654_HGWLYDSX3_3_MPRA_repB_fractions_6_7_2hpf_GGTACCTT_AAGACGTC_S19_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206654_HGWLYDSX3_3_MPRA_repB_fractions_6_7_2hpf_GGTACCTT_AAGACGTC_S19_L003_R1_001_MM_1.fastq.gz	fastq fastq	16535129670.0	54752085.0	BSSE QGF 206654 HGWLYDSX3 3 MPRA repB fractions 6 7 2hpf GGTACCTT AAGACGTC S19 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:4184643114;C:4312135767;G:4051628900;T:3985895468;N:826421	151	151	4184643114	4312135767	4051628900	3985895468	826421	SRX23160944	SRS20111102	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01416	0.00017	0.00031	1e-05	0.9917	0.99941	0.40732	0.6	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
29249	29249	SRR27489766	SRX23160943	SRS20111101	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	80S fraction 2hpf replica B	MPRA repB fractions 4 5 2hpf		strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:18\|replicate:replicate B\|BioSampleModel:Model organism or animal									80S fraction 2hpf replica B	Library 18	Library 18	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206653_HGWLYDSX3_3_MPRA_repB_fractions_4_5_2hpf_GCACGGAC_GTCTCGCA_S18_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206653_HGWLYDSX3_3_MPRA_repB_fractions_4_5_2hpf_GCACGGAC_GTCTCGCA_S18_L003_R2_001_MM_1.fastq.gz	fastq fastq	12692870042.0	42029371.0	BSSE QGF 206653 HGWLYDSX3 3 MPRA repB fractions 4 5 2hpf GCACGGAC GTCTCGCA S18 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3179006274;C:3325152682;G:3173386021;T:3014687781;N:637284	151	151	3179006274	3325152682	3173386021	3014687781	637284	SRX23160943	SRS20111101	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01199	8e-05	0.0003	1e-05	0.99145	0.99979	0.40897	0.36363	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
29250	29250	SRR27489767	SRX23160942	SRS20111100	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			input sample	Total 2hpf replica B	MPRA repB input 2hpf		strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:17\|replicate:replicate B\|BioSampleModel:Model organism or animal									Total 2hpf replica B	Library 17	Library 17	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206652_HGWLYDSX3_3_MPRA_repB_input_2hpf_ATGTAAGT_ACTCTATG_S17_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206652_HGWLYDSX3_3_MPRA_repB_input_2hpf_ATGTAAGT_ACTCTATG_S17_L003_R2_001_MM_1.fastq.gz	fastq fastq	13169436008.0	43607404.0	BSSE QGF 206652 HGWLYDSX3 3 MPRA repB input 2hpf ATGTAAGT ACTCTATG S17 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3341908647;C:3485072739;G:3171200836;T:3170595031;N:658755	151	151	3341908647	3485072739	3171200836	3170595031	658755	SRX23160942	SRS20111100	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01868	5e-05	0.0006	0.0	0.99038	0.99983	0.41955	0.125	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
29251	29251	SRR27489768	SRX23160941	SRS20111099	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	HMW fraction 10hpf replica A	MPRA repA fractions 8 9 10hpf		strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:16\|replicate:replicate A\|BioSampleModel:Model organism or animal									HMW fraction 10hpf replica A	Library 16	Library 16	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206651_HGWLYDSX3_3_MPRA_repA_fractions_8_9_10hpf_CGGCGTGA_GCGCCTGT_S16_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206651_HGWLYDSX3_3_MPRA_repA_fractions_8_9_10hpf_CGGCGTGA_GCGCCTGT_S16_L003_R2_001_MM_1.fastq.gz	fastq fastq	13501095730.0	44705615.0	BSSE QGF 206651 HGWLYDSX3 3 MPRA repA fractions 8 9 10hpf CGGCGTGA GCGCCTGT S16 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3386778587;C:3499255836;G:3382745292;T:3231634315;N:681700	151	151	3386778587	3499255836	3382745292	3231634315	681700	SRX23160941	SRS20111099	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.00829	0.00016	0.00011	0.0	0.99265	0.99949	0.49527	0.48275	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29252	29252	SRR27489769	SRX23160940	SRS20111096	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	LMW fraction 10hpf replica A	MPRA repA fractions 6 7 10hpf		strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:15\|replicate:replicate A\|BioSampleModel:Model organism or animal									LMW fraction 10hpf replica A	Library 15	Library 15	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206650_HGWLYDSX3_3_MPRA_repA_fractions_6_7_10hpf_TAATACAG_ATATTCAC_S15_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206650_HGWLYDSX3_3_MPRA_repA_fractions_6_7_10hpf_TAATACAG_ATATTCAC_S15_L003_R2_001_MM_1.fastq.gz	fastq fastq	13046767232.0	43201216.0	BSSE QGF 206650 HGWLYDSX3 3 MPRA repA fractions 6 7 10hpf TAATACAG ATATTCAC S15 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3290688159;C:3400409529;G:3214905336;T:3140115501;N:648707	151	151	3290688159	3400409529	3214905336	3140115501	648707	SRX23160940	SRS20111096	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01093	0.0001	0.00011	0.0	0.99249	0.99967	0.43443	0.77777	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29253	29253	SRR27489770	SRX23160939	SRS20111097	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	80S fraction 10hpf replica A	MPRA repA fractions 4 5 10hpf		strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:14\|replicate:replicate A\|BioSampleModel:Model organism or animal									80S fraction 10hpf replica A	Library 14	Library 14	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206649_HGWLYDSX3_3_MPRA_repA_fractions_4_5_10hpf_AATCCGGA_CTACAGTT_S14_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206649_HGWLYDSX3_3_MPRA_repA_fractions_4_5_10hpf_AATCCGGA_CTACAGTT_S14_L003_R2_001_MM_1.fastq.gz	fastq fastq	13986764580.0	46313790.0	BSSE QGF 206649 HGWLYDSX3 3 MPRA repA fractions 4 5 10hpf AATCCGGA CTACAGTT S14 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3536884918;C:3676313944;G:3410122661;T:3362749616;N:693441	151	151	3536884918	3676313944	3410122661	3362749616	693441	SRX23160939	SRS20111097	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01503	7e-05	0.00035	0.0	0.99141	0.99983	0.43326	0.77777	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29254	29254	SRR27489771	SRX23160938	SRS20111095	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			input sample	Total 10hpf replica A	MPRA repA input 10hpf		strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:13\|replicate:replicate A\|BioSampleModel:Model organism or animal									Total 10hpf replica A	Library 13	Library 13	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206648_HGWLYDSX3_3_MPRA_repA_input_10hpf_GGCTTAAG_TCGTGACC_S13_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206648_HGWLYDSX3_3_MPRA_repA_input_10hpf_GGCTTAAG_TCGTGACC_S13_L003_R2_001_MM_1.fastq.gz	fastq fastq	11263507666.0	37296383.0	BSSE QGF 206648 HGWLYDSX3 3 MPRA repA input 10hpf GGCTTAAG TCGTGACC S13 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:2881851385;C:2968960112;G:2663338223;T:2748794775;N:563171	151	151	2881851385	2968960112	2663338223	2748794775	563171	SRX23160938	SRS20111095	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.02096	1e-05	0.00058	0.0	0.99022	0.99997	0.43837	1.0	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29255	29255	SRR27489772	SRX23160937	SRS20111098	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	HMW fraction 6hpf replica A	MPRA repA fractions 8 9 6hpf		strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:12\|replicate:replicate A\|BioSampleModel:Model organism or animal									HMW fraction 6hpf replica A	Library 12	Library 12	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206647_HGWLYDSX3_3_MPRA_repA_fractions_8_9_6hpf_TTGGACTC_GGAAGCAG_S12_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206647_HGWLYDSX3_3_MPRA_repA_fractions_8_9_6hpf_TTGGACTC_GGAAGCAG_S12_L003_R2_001_MM_1.fastq.gz	fastq fastq	14724761980.0	48757490.0	BSSE QGF 206647 HGWLYDSX3 3 MPRA repA fractions 8 9 6hpf TTGGACTC GGAAGCAG S12 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3711442998;C:3830334531;G:3642299006;T:3539948266;N:737179	151	151	3711442998	3830334531	3642299006	3539948266	737179	SRX23160937	SRS20111098	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01161	8e-05	0.0002	1e-05	0.99214	0.99985	0.4529	0.3	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29256	29256	SRR27489773	SRX23160936	SRS20111094	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	LMW fraction 6hpf replica A	MPRA repA fractions 6 7 6hpf		strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:11\|replicate:replicate A\|BioSampleModel:Model organism or animal									LMW fraction 6hpf replica A	Library 11	Library 11	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206646_HGWLYDSX3_3_MPRA_repA_fractions_6_7_6hpf_CCAAGTCT_AAGGATGA_S11_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206646_HGWLYDSX3_3_MPRA_repA_fractions_6_7_6hpf_CCAAGTCT_AAGGATGA_S11_L003_R2_001_MM_1.fastq.gz	fastq fastq	16713361312.0	55342256.0	BSSE QGF 206646 HGWLYDSX3 3 MPRA repA fractions 6 7 6hpf CCAAGTCT AAGGATGA S11 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:4183339886;C:4365661507;G:4181177026;T:3982339731;N:843162	151	151	4183339886	4365661507	4181177026	3982339731	843162	SRX23160936	SRS20111094	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01132	0.00011	0.00024	0.0	0.99174	0.99965	0.40968	0.47368	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29257	29257	SRR27489774	SRX23160935	SRS20111093	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	80S fraction 2hpf replica A	MPRA repA fractions 4 5 2hpf		strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:2\|replicate:replicate A\|BioSampleModel:Model organism or animal									80S fraction 2hpf replica A	Library 2	Library 2	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206637_HGWLYDSX3_3_MPRA_repA_fractions_4_5_2hpf_TTGGACTT_TATGAGTA_S2_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206637_HGWLYDSX3_3_MPRA_repA_fractions_4_5_2hpf_TTGGACTT_TATGAGTA_S2_L003_R2_001_MM_1.fastq.gz	fastq fastq	16111078182.0	53347941.0	BSSE QGF 206637 HGWLYDSX3 3 MPRA repA fractions 4 5 2hpf TTGGACTT TATGAGTA S2 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:4069536779;C:4222816450;G:3957789955;T:3860129964;N:805034	151	151	4069536779	4222816450	3957789955	3860129964	805034	SRX23160935	SRS20111093	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01511	5e-05	0.00034	0.0	0.99135	0.99985	0.41564	0.42857	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
29258	29258	SRR27489775	SRX23160934	SRS20111092	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			input sample	Total 2hpf replica A	MPRA repA input 2hpf		strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:1\|replicate:replicate A\|BioSampleModel:Model organism or animal									Total 2hpf replica A	Library 1	Library 1	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP483112			BSSE_QGF_206636_HGWLYDSX3_3_MPRA_repA_input_2hpf_GGACTTGG_CGCAGACG_S1_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206636_HGWLYDSX3_3_MPRA_repA_input_2hpf_GGACTTGG_CGCAGACG_S1_L003_R2_001_MM_1.fastq.gz	fastq fastq	9769305890.0	32348695.0	BSSE QGF 206636 HGWLYDSX3 3 MPRA repA input 2hpf GGACTTGG CGCAGACG S1 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:2477269774;C:2598109179;G:2338444856;T:2354997596;N:484485	151	151	2477269774	2598109179	2338444856	2354997596	484485	SRX23160934	SRS20111092	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.0205	4e-05	0.00059	0.0	0.99013	0.99987	0.41957	0.33333	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
29739	29739	SRR27467672	SRX23139234	SRS20090275	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						Dome mock R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:5 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 5 hpf mock rep2	EV04009	EV04009	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP482074			EV04009.R1.fastq.gz	fastq	609590940.0	4354221.0	EV04009.R1.fastq.gz	0:140	A:155062144;C:147628702;G:168099121;T:138772205;N:28768	140		155062144	147628702	168099121	138772205	28768	SRX23139234	SRS20090275	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Blastula	Embryo	Whole Organism	All anatomical structures
29740	29740	SRR27467673	SRX23139233	SRS20090278	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						1K cell BS R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:3 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 3 hpf BS rep2	EV04008	EV04008	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP482074			EV04008.R1.fastq.gz	fastq	675505180.0	4825037.0	EV04008.R1.fastq.gz	0:140	A:178823976;C:121648962;G:198428643;T:176572292;N:31307	140		178823976	121648962	198428643	176572292	31307	SRX23139233	SRS20090278	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Blastula	Embryo	Whole Organism	All anatomical structures
29741	29741	SRR27467674	SRX23139232	SRS20090272	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						1K cell DM R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:3 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 3 hpf DM rep2	EV04007	EV04007	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP482074			EV04007.R1.fastq.gz	fastq	702064440.0	5014746.0	EV04007.R1.fastq.gz	0:140	A:176719694;C:166467163;G:207893965;T:150951950;N:31668	140		176719694	166467163	207893965	150951950	31668	SRX23139232	SRS20090272	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	2e-05		0.0		0.99997		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Blastula	Embryo	Whole Organism	All anatomical structures
29742	29742	SRR27467675	SRX23139231	SRS20090271	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						1K cell mock R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:3 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 3 hpf mock rep2	EV04006	EV04006	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP482074			EV04006.R1.fastq.gz	fastq	664790700.0	4748505.0	EV04006.R1.fastq.gz	0:140	A:172014219;C:146545691;G:200358431;T:145840649;N:31710	140		172014219	146545691	200358431	145840649	31710	SRX23139231	SRS20090271	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	3e-05		0.0		0.99993		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Blastula	Embryo	Whole Organism	All anatomical structures
29743	29743	SRR27467676	SRX23139230	SRS20090273	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						4 cell DM R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:1 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 1 hpf DM rep2	EV04004	EV04004	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP482074			EV04004.R1.fastq.gz	fastq	895671560.0	6397654.0	EV04004.R1.fastq.gz	0:140	A:206443066;C:147067097;G:365386937;T:176734600;N:39860	140		206443066	147067097	365386937	176734600	39860	SRX23139230	SRS20090273	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Cleavage	Embryo	Whole Organism	All anatomical structures
29744	29744	SRR27467677	SRX23139229	SRS20090274	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						4 cell mock R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:1 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 1 hpf mock rep2	EV04003	EV04003	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP482074			EV04003.R1.fastq.gz	fastq	664112120.0	4743658.0	EV04003.R1.fastq.gz	0:140	A:163711695;C:142612940;G:211194350;T:146562626;N:30509	140		163711695	142612940	211194350	146562626	30509	SRX23139229	SRS20090274	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	2e-05		0.0		0.99997		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Cleavage	Embryo	Whole Organism	All anatomical structures
29747	29747	SRR27467680	SRX23139226	SRS20090267	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						24h BS R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:24 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 24 hpf BS rep2	EV03009	EV03009	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP482074			EV03009.R1.fastq.gz	fastq	168931280.0	2222780.0	EV03009.R1.fastq.gz	0:76	A:49803604;C:36479774;G:37758990;T:44874154;N:14758	76		49803604	36479774	37758990	44874154	14758	SRX23139226	SRS20090267	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00034		0.0002		0.99965		0.5		76		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Pharyngula	Embryo	Whole Organism	All anatomical structures
29748	29748	SRR27467681	SRX23139225	SRS20090266	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						24h DM R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:24 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 24 hpf DM rep2	EV03008	EV03008	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP482074			EV03008.R1.fastq.gz	fastq	200878792.0	2643142.0	EV03008.R1.fastq.gz	0:76	A:46955288;C:54746275;G:55887832;T:43270561;N:18836	76		46955288	54746275	55887832	43270561	18836	SRX23139225	SRS20090266	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.29408		0.00737		0.91823		0.54549		76		B		usable mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Pharyngula	Embryo	Whole Organism	All anatomical structures
29749	29749	SRR27467682	SRX23139224	SRS20090269	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						24h mock R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:24 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 24 hpf mock rep2	EV03007	EV03007	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP482074			EV03007.R1.fastq.gz	fastq	175642840.0	2311090.0	EV03007.R1.fastq.gz	0:76	A:44745275;C:48908904;G:44862157;T:37111895;N:14609	76		44745275	48908904	44862157	37111895	14609	SRX23139224	SRS20090269	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.06887		0.00273		0.96623		0.48721		76		B		usable mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Pharyngula	Embryo	Whole Organism	All anatomical structures
29750	29750	SRR27467683	SRX23139223	SRS20090265	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						Bud BS R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:10 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 10 hpf BS rep2	EV04014	EV04014	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP482074			EV04014.R1.fastq.gz	fastq	774901260.0	5535009.0	EV04014.R1.fastq.gz	0:140	A:193865579;C:138861953;G:251102013;T:191036071;N:35644	140		193865579	138861953	251102013	191036071	35644	SRX23139223	SRS20090265	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Gastrula	Embryo	Whole Organism	All anatomical structures
29751	29751	SRR27467684	SRX23139222	SRS20090264	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						Bud DM R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:10 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 10 hpf DM rep2	EV04013	EV04013	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP482074			EV04013.R1.fastq.gz	fastq	666372840.0	4759806.0	EV04013.R1.fastq.gz	0:140	A:172923134;C:142243998;G:211584978;T:139591020;N:29710	140		172923134	142243998	211584978	139591020	29710	SRX23139222	SRS20090264	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	3e-05		0.0		0.99991		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Gastrula	Embryo	Whole Organism	All anatomical structures
29752	29752	SRR27467685	SRX23139221	SRS20090262	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						Bud mock R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:10 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 10 hpf mock rep2	EV04012	EV04012	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP482074			EV04012.R1.fastq.gz	fastq	628769540.0	4491211.0	EV04012.R1.fastq.gz	0:140	A:160925901;C:143204697;G:183224867;T:141385307;N:28768	140		160925901	143204697	183224867	141385307	28768	SRX23139221	SRS20090262	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	1e-05		0.0		0.99997		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Gastrula	Embryo	Whole Organism	All anatomical structures
29753	29753	SRR27467686	SRX23139220	SRS20090263	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						Dome BS R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:5 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 5 hpf BS rep2	EV04011	EV04011	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP482074			EV04011.R1.fastq.gz	fastq	720913200.0	5149380.0	EV04011.R1.fastq.gz	0:140	A:185414155;C:126110104;G:238649631;T:170706590;N:32720	140		185414155	126110104	238649631	170706590	32720	SRX23139220	SRS20090263	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Blastula	Embryo	Whole Organism	All anatomical structures

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