metadata: run_metadata: 31 rows where experiment.library_selection = "PolyA", technology = "smartseq" and tissue

31 rows where experiment.library_selection = "PolyA", technology = "smartseq" and tissue_curation = "Whole Organism"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.description	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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
55864	55864	SRR10863006	SRX7533063	SRS5972272	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt PGCs 6dpf rep4	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:6dpf\|dev stage:larval\|sex:not applicable\|tissue:germline\|biological replicate:replicate 4\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: PGCs 6dpf	wt PGCs 6dpf S3	wt PGCs 6dpf S3	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 550	SRP241074	wt_PGCs_6dpf_S3.R1.fastq.gz	fastq	7769926725.0	93613575.0	wt PGCs 6dpf S3.R1.fastq.gz	0:83 1:0	A:2066232192;C:1833469023;G:1789669356;T:2080457369;N:98785	83	0	2066232192	1833469023	1789669356	2080457369	98785	SRX7533063	SRS5972272	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	1	0.94606		0.05002		0.68189		0.45731		83		B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Larval	Larval	Whole Organism	All anatomical structures
55865	55865	SRR10863007	SRX7533062	SRS5972271	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt PGCs 3dpf rep4	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:3dpf\|dev stage:protruding mouth\|sex:not applicable\|tissue:germline\|biological replicate:replicate 4\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: PGCs 3dpf	wt PGCs 3dpf S2	wt PGCs 3dpf S2	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 550	SRP241074	wt_PGCs_3dpf_S2.R1.fastq.gz	fastq	7911386779.0	95317913.0	wt PGCs 3dpf S2.R1.fastq.gz	0:83 1:0	A:2123308854;C:1846753353;G:1805771181;T:2135451936;N:101455	83	0	2123308854	1846753353	1805771181	2135451936	101455	SRX7533062	SRS5972271	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	1	0.9461		0.05273		0.67042		0.47729		83		B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Larval	Larval	Whole Organism	All anatomical structures
55866	55866	SRR10863008	SRX7533061	SRS5972270	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt PGCs 1dpf rep4	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:1dpf\|dev stage:Pharyngula period\|sex:not applicable\|tissue:germline\|biological replicate:replicate 4\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: PGCs 1dpf	wt PGCs 1dpf S1	wt PGCs 1dpf S1	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 550	SRP241074	wt_PGCs_1dpf_S1.R1.fastq.gz	fastq	6787337699.0	81775153.0	wt PGCs 1dpf S1.R1.fastq.gz	0:83 1:0	A:1839754910;C:1566044514;G:1538211923;T:1843241243;N:85109	83	0	1839754910	1566044514	1538211923	1843241243	85109	SRX7533061	SRS5972270	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	1	0.94441		0.056		0.68866		0.47945		83		B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Pharyngula	Embryo	Whole Organism	All anatomical structures
55867	55867	SRR10863009	SRX7533060	SRS5972251	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt PGCs 10dpf rep3	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:10dpf\|dev stage:larval\|sex:not applicable\|tissue:germline\|biological replicate:replicate 3\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: PGCs 10dpf	imb ketting 2018 18 redl SmartSeq2 05 10dpf PGCs rep3 S22	imb ketting 2018 18 redl SmartSeq2 05 10dpf PGCs rep3 S22	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_18_redl_SmartSeq2-05_10dpf_PGCs_rep3_S22.R1.fastq.gz imb_ketting_2018_18_redl_SmartSeq2-05_10dpf_PGCs_rep3_S22.R2.fastq.gz	fastq fastq	2398956750.0	15993045.0	imb ketting 2018 18 redl SmartSeq2 05 10dpf PGCs rep3 S22.R1.fastq.gz	0:75 1:75	A:644406123;C:549461993;G:551876029;T:653190800;N:21805	75	75	644406123	549461993	551876029	653190800	21805	SRX7533060	SRS5972251	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.93212	0.93465	0.08119	0.0809	0.64924	0.65273	0.49088	0.48853	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Larval	Larval	Whole Organism	All anatomical structures
55868	55868	SRR10863010	SRX7533059	SRS5972250	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt PGCs 10dpf rep2	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:10dpf\|dev stage:larval\|sex:not applicable\|tissue:germline\|biological replicate:replicate 2\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: PGCs 10dpf	imb ketting 2018 18 redl SmartSeq2 04 10dpf PGCs rep2 S21	imb ketting 2018 18 redl SmartSeq2 04 10dpf PGCs rep2 S21	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_18_redl_SmartSeq2-04_10dpf_PGCs_rep2_S21.R1.fastq.gz imb_ketting_2018_18_redl_SmartSeq2-04_10dpf_PGCs_rep2_S21.R2.fastq.gz	fastq fastq	1718401350.0	11456009.0	imb ketting 2018 18 redl SmartSeq2 04 10dpf PGCs rep2 S21.R1.fastq.gz	0:75 1:75	A:458124712;C:395812381;G:396455319;T:467992998;N:15940	75	75	458124712	395812381	396455319	467992998	15940	SRX7533059	SRS5972250	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.9304	0.93343	0.06159	0.06103	0.6648	0.66778	0.4903	0.48931	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Larval	Larval	Whole Organism	All anatomical structures
55869	55869	SRR10863011	SRX7533058	SRS5972249	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt PGCs 10dpf rep1	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:10dpf\|dev stage:larval\|sex:not applicable\|tissue:germline\|biological replicate:replicate 1\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: PGCs 10dpf	imb ketting 2018 18 redl SmartSeq2 03 10dpf PGCs rep1 S20	imb ketting 2018 18 redl SmartSeq2 03 10dpf PGCs rep1 S20	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_18_redl_SmartSeq2-03_10dpf_PGCs_rep1_S20.R1.fastq.gz imb_ketting_2018_18_redl_SmartSeq2-03_10dpf_PGCs_rep1_S20.R2.fastq.gz	fastq fastq	2233099350.0	14887329.0	imb ketting 2018 18 redl SmartSeq2 03 10dpf PGCs rep1 S20.R1.fastq.gz	0:75 1:75	A:593248327;C:517482903;G:517558773;T:604789107;N:20240	75	75	593248327	517482903	517558773	604789107	20240	SRX7533058	SRS5972249	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.93341	0.93608	0.06727	0.06743	0.65202	0.65518	0.48494	0.48863	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Larval	Larval	Whole Organism	All anatomical structures
55870	55870	SRR10863012	SRX7533057	SRS5972247	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt PGCs 6dpf rep2	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:6dpf\|dev stage:larval\|sex:not applicable\|tissue:germline\|biological replicate:replicate 2\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: PGCs 6dpf	imb ketting 2018 02 redl SmartSeq 11 16 6dpf PGCs rep2 S11	imb ketting 2018 02 redl SmartSeq 11 16 6dpf PGCs rep2 S11	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_02_redl_SmartSeq_11_16_6dpf_PGCs_rep2_S11.R2.fastq.gz imb_ketting_2018_02_redl_SmartSeq_11_16_6dpf_PGCs_rep2_S11.R1.fastq.gz	fastq fastq	3073587588.0	19453086.0	imb ketting 2018 02 redl SmartSeq 11 16 6dpf PGCs rep2 S11.R1.fastq.gz	0:79 1:79	A:818976238;C:715663048;G:701056981;T:837683663;N:207658	79	79	818976238	715663048	701056981	837683663	207658	SRX7533057	SRS5972247	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.93657	0.93564	0.07313	0.07324	0.66732	0.66927	0.51839	0.51879	79	79	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Larval	Larval	Whole Organism	All anatomical structures
55871	55871	SRR10863014	SRX7533056	SRS5972246	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt PGCs 6dpf rep1	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:6dpf\|dev stage:larval\|sex:not applicable\|tissue:germline\|biological replicate:replicate 1\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: PGCs 6dpf	imb ketting 2018 02 redl SmartSeq 10 15 6dpf PGCs rep1 S10	imb ketting 2018 02 redl SmartSeq 10 15 6dpf PGCs rep1 S10	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_02_redl_SmartSeq_10_15_6dpf_PGCs_rep1_S10.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_10_15_6dpf_PGCs_rep1_S10.R2.fastq.gz	fastq fastq	3659744204.0	23162938.0	imb ketting 2018 02 redl SmartSeq 10 15 6dpf PGCs rep1 S10.R1.fastq.gz	0:79 1:79	A:975611259;C:856115631;G:822696649;T:1005067499;N:253166	79	79	975611259	856115631	822696649	1005067499	253166	SRX7533056	SRS5972246	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.9257	0.92714	0.08263	0.08288	0.66403	0.66606	0.51827	0.51415	79	79	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Larval	Larval	Whole Organism	All anatomical structures
55873	55873	SRR10863013	SRX7533054	SRS5972248	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt PGCs 6dpf rep3	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:6dpf\|dev stage:larval\|sex:not applicable\|tissue:germline\|biological replicate:replicate 3\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: PGCs 6dpf	imb ketting 2018 02 redl SmartSeq 12 57 6dpf PGCs rep3 S12	imb ketting 2018 02 redl SmartSeq 12 57 6dpf PGCs rep3 S12	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_02_redl_SmartSeq_12_57_6dpf_PGCs_rep3_S12.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_12_57_6dpf_PGCs_rep3_S12.R2.fastq.gz	fastq fastq	3238333398.0	20495781.0	imb ketting 2018 02 redl SmartSeq 12 57 6dpf PGCs rep3 S12.R1.fastq.gz	0:79 1:79	A:863266932;C:756411819;G:730470194;T:887962716;N:221737	79	79	863266932	756411819	730470194	887962716	221737	SRX7533054	SRS5972248	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.93352	0.93414	0.07865	0.07846	0.6619	0.66365	0.50442	0.5037	79	79	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Larval	Larval	Whole Organism	All anatomical structures
55874	55874	SRR10863016	SRX7533053	SRS5972245	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt PGCs 3dpf rep3	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:3dpf\|dev stage:protruding mouth\|sex:not applicable\|tissue:germline\|biological replicate:replicate 3\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: PGCs 3dpf	imb ketting 2018 02 redl SmartSeq 09 52 3dpf PGCs rep3 S9	imb ketting 2018 02 redl SmartSeq 09 52 3dpf PGCs rep3 S9	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_02_redl_SmartSeq_09_52_3dpf_PGCs_rep3_S9.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_09_52_3dpf_PGCs_rep3_S9.R2.fastq.gz	fastq fastq	3249954930.0	20569335.0	imb ketting 2018 02 redl SmartSeq 09 52 3dpf PGCs rep3 S9.R1.fastq.gz	0:79 1:79	A:869000041;C:756586733;G:737450634;T:886691114;N:226408	79	79	869000041	756586733	737450634	886691114	226408	SRX7533053	SRS5972245	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.93775	0.93746	0.05915	0.05925	0.66559	0.66813	0.4987	0.49658	79	79	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Larval	Larval	Whole Organism	All anatomical structures
55875	55875	SRR10863017	SRX7533052	SRS5972243	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt PGCs 3dpf rep2	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:3dpf\|dev stage:protruding mouth\|sex:not applicable\|tissue:germline\|biological replicate:replicate 2\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: PGCs 3dpf	imb ketting 2018 02 redl SmartSeq 08 46 3dpf PGCs rep2 S8	imb ketting 2018 02 redl SmartSeq 08 46 3dpf PGCs rep2 S8	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_02_redl_SmartSeq_08_46_3dpf_PGCs_rep2_S8.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_08_46_3dpf_PGCs_rep2_S8.R2.fastq.gz	fastq fastq	2750070738.0	17405511.0	imb ketting 2018 02 redl SmartSeq 08 46 3dpf PGCs rep2 S8.R1.fastq.gz	0:79 1:79	A:733848756;C:641808995;G:625301352;T:748928086;N:183549	79	79	733848756	641808995	625301352	748928086	183549	SRX7533052	SRS5972243	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.93969	0.94099	0.07298	0.07296	0.6591	0.6608	0.46537	0.46521	79	79	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Larval	Larval	Whole Organism	All anatomical structures
55876	55876	SRR10863018	SRX7533051	SRS5972242	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt PGCs 3dpf rep1	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:3dpf\|dev stage:protruding mouth\|sex:not applicable\|tissue:germline\|biological replicate:replicate 1\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: PGCs 3dpf	imb ketting 2018 02 redl SmartSeq 07 32 3dpf PGCs rep1 S7	imb ketting 2018 02 redl SmartSeq 07 32 3dpf PGCs rep1 S7	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_02_redl_SmartSeq_07_32_3dpf_PGCs_rep1_S7.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_07_32_3dpf_PGCs_rep1_S7.R2.fastq.gz	fastq fastq	3579619086.0	22655817.0	imb ketting 2018 02 redl SmartSeq 07 32 3dpf PGCs rep1 S7.R1.fastq.gz	0:79 1:79	A:953705275;C:837082021;G:815003971;T:973585384;N:242435	79	79	953705275	837082021	815003971	973585384	242435	SRX7533051	SRS5972242	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.94105	0.94076	0.07884	0.07956	0.66046	0.66188	0.46606	0.46734	79	79	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Larval	Larval	Whole Organism	All anatomical structures
55877	55877	SRR10863019	SRX7533050	SRS5972252	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt PGCs 2dpf rep3	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:2dpf\|dev stage:Long pec stage\|sex:not applicable\|tissue:germline\|biological replicate:replicate 3\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: PGCs 2dpf	imb ketting 2018 02 redl SmartSeq 06 61 2dpf PGCs rep3 S6	imb ketting 2018 02 redl SmartSeq 06 61 2dpf PGCs rep3 S6	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_02_redl_SmartSeq_06_61_2dpf_PGCs_rep3_S6.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_06_61_2dpf_PGCs_rep3_S6.R2.fastq.gz	fastq fastq	3108720942.0	19675449.0	imb ketting 2018 02 redl SmartSeq 06 61 2dpf PGCs rep3 S6.R1.fastq.gz	0:79 1:79	A:837919918;C:714812252;G:702998193;T:852776390;N:214189	79	79	837919918	714812252	702998193	852776390	214189	SRX7533050	SRS5972252	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.93952	0.93945	0.07277	0.07278	0.66983	0.67221	0.50192	0.50133	79	79	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Hatching	Embryo	Whole Organism	All anatomical structures
55878	55878	SRR10863020	SRX7533049	SRS5972244	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt PGCs 2dpf rep2	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:2dpf\|dev stage:Long pec stage\|sex:not applicable\|tissue:germline\|biological replicate:replicate 2\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: PGCs 2dpf	imb ketting 2018 02 redl SmartSeq 05 22 2dpf PGCs rep2 S5	imb ketting 2018 02 redl SmartSeq 05 22 2dpf PGCs rep2 S5	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_02_redl_SmartSeq_05_22_2dpf_PGCs_rep2_S5.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_05_22_2dpf_PGCs_rep2_S5.R2.fastq.gz	fastq fastq	3241530370.0	20516015.0	imb ketting 2018 02 redl SmartSeq 05 22 2dpf PGCs rep2 S5.R1.fastq.gz	0:79 1:79	A:861911078;C:762577918;G:730686512;T:886132359;N:222503	79	79	861911078	762577918	730686512	886132359	222503	SRX7533049	SRS5972244	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.93797	0.93734	0.06416	0.06415	0.67004	0.67251	0.50367	0.50353	79	79	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Hatching	Embryo	Whole Organism	All anatomical structures
55879	55879	SRR10863021	SRX7533048	SRS5972269	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt PGCs 2dpf rep1	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:2dpf\|dev stage:Long pec stage\|sex:not applicable\|tissue:germline\|biological replicate:replicate 1\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: PGCs 2dpf	imb ketting 2018 02 redl SmartSeq 04 07 2dpf PGCs rep1 S4	imb ketting 2018 02 redl SmartSeq 04 07 2dpf PGCs rep1 S4	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_02_redl_SmartSeq_04_07_2dpf_PGCs_rep1_S4.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_04_07_2dpf_PGCs_rep1_S4.R2.fastq.gz	fastq fastq	3363342524.0	21286978.0	imb ketting 2018 02 redl SmartSeq 04 07 2dpf PGCs rep1 S4.R1.fastq.gz	0:79 1:79	A:906938869;C:772810568;G:756589497;T:926768184;N:235406	79	79	906938869	772810568	756589497	926768184	235406	SRX7533048	SRS5972269	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.93588	0.93667	0.11457	0.11483	0.66663	0.66799	0.4795	0.4762	79	79	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Hatching	Embryo	Whole Organism	All anatomical structures
55880	55880	SRR10863022	SRX7533047	SRS5972268	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt PGCs 1dpf rep3	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:1dpf\|dev stage:Pharyngula period\|sex:not applicable\|tissue:germline\|biological replicate:replicate 3\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: PGCs 1dpf	imb ketting 2018 02 redl SmartSeq 03 20 1dpf PGCs rep3 S3	imb ketting 2018 02 redl SmartSeq 03 20 1dpf PGCs rep3 S3	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_02_redl_SmartSeq_03_20_1dpf_PGCs_rep3_S3.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_03_20_1dpf_PGCs_rep3_S3.R2.fastq.gz	fastq fastq	3406105382.0	21557629.0	imb ketting 2018 02 redl SmartSeq 03 20 1dpf PGCs rep3 S3.R1.fastq.gz	0:79 1:79	A:914561772;C:790081165;G:768217890;T:933018206;N:226349	79	79	914561772	790081165	768217890	933018206	226349	SRX7533047	SRS5972268	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.93859	0.93927	0.06346	0.06362	0.68467	0.68665	0.51016	0.44765	79	79	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Pharyngula	Embryo	Whole Organism	All anatomical structures
55881	55881	SRR10863023	SRX7533046	SRS5972267	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt PGCs 1dpf rep2	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:1dpf\|dev stage:Pharyngula period\|sex:not applicable\|tissue:germline\|biological replicate:replicate 2\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: PGCs 1dpf	imb ketting 2018 02 redl SmartSeq 02 30 1dpf PGCs rep2 S2	imb ketting 2018 02 redl SmartSeq 02 30 1dpf PGCs rep2 S2	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_02_redl_SmartSeq_02_30_1dpf_PGCs_rep2_S2.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_02_30_1dpf_PGCs_rep2_S2.R2.fastq.gz	fastq fastq	3126220074.0	19786203.0	imb ketting 2018 02 redl SmartSeq 02 30 1dpf PGCs rep2 S2.R1.fastq.gz	0:79 1:79	A:835660285;C:727271703;G:711392935;T:851683391;N:211760	79	79	835660285	727271703	711392935	851683391	211760	SRX7533046	SRS5972267	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.93836	0.93845	0.05796	0.0579	0.67805	0.68002	0.49555	0.49733	79	79	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Pharyngula	Embryo	Whole Organism	All anatomical structures
55885	55885	SRR10863024	SRX7533042	SRS5972265	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt PGCs 1dpf rep1	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:1dpf\|dev stage:Pharyngula period\|sex:not applicable\|tissue:germline\|biological replicate:replicate 1\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: PGCs 1dpf	imb ketting 2018 02 redl SmartSeq 01 24 1dpf PGCs rep1 S1	imb ketting 2018 02 redl SmartSeq 01 24 1dpf PGCs rep1 S1	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_02_redl_SmartSeq_01_24_1dpf_PGCs_rep1_S1.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_01_24_1dpf_PGCs_rep1_S1.R2.fastq.gz	fastq fastq	3512354852.0	22230094.0	imb ketting 2018 02 redl SmartSeq 01 24 1dpf PGCs rep1 S1.R1.fastq.gz	0:79 1:79	A:937439392;C:820724988;G:797835842;T:956108725;N:245905	79	79	937439392	820724988	797835842	956108725	245905	SRX7533042	SRS5972265	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.94053	0.94062	0.05733	0.05792	0.6801	0.68174	0.49423	0.49408	79	79	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Pharyngula	Embryo	Whole Organism	All anatomical structures
55886	55886	SRR10863027	SRX7533041	SRS5972266	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt Fish 10dpf rep2	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:10dpf\|dev stage:larval\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 2\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: Fish 10dpf	imb ketting 2018 18 redl SmartSeq2 02 10dpf fish rep2 S19	imb ketting 2018 18 redl SmartSeq2 02 10dpf fish rep2 S19	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_18_redl_SmartSeq2-02_10dpf_fish_rep2_S19.R1.fastq.gz imb_ketting_2018_18_redl_SmartSeq2-02_10dpf_fish_rep2_S19.R2.fastq.gz	fastq fastq	2625890700.0	17505938.0	imb ketting 2018 18 redl SmartSeq2 02 10dpf fish rep2 S19.R1.fastq.gz	0:75 1:75	A:702642659;C:603804487;G:604515055;T:714904148;N:24351	75	75	702642659	603804487	604515055	714904148	24351	SRX7533041	SRS5972266	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.93546	0.93678	0.11349	0.11316	0.67829	0.68217	0.45966	0.46585	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Larval	Larval	Whole Organism	All anatomical structures
55888	55888	SRR10863029	SRX7533039	SRS5972264	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt Fish 10dpf rep1	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:10dpf\|dev stage:larval\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 1\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: Fish 10dpf	imb ketting 2018 18 redl SmartSeq2 01 10dpf fish rep1 S18	imb ketting 2018 18 redl SmartSeq2 01 10dpf fish rep1 S18	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_18_redl_SmartSeq2-01_10dpf_fish_rep1_S18.R1.fastq.gz imb_ketting_2018_18_redl_SmartSeq2-01_10dpf_fish_rep1_S18.R2.fastq.gz	fastq fastq	2317008450.0	15446723.0	imb ketting 2018 18 redl SmartSeq2 01 10dpf fish rep1 S18.R1.fastq.gz	0:75 1:75	A:616522892;C:537227364;G:538867346;T:624369327;N:21521	75	75	616522892	537227364	538867346	624369327	21521	SRX7533039	SRS5972264	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.94141	0.94282	0.09767	0.09803	0.67771	0.68081	0.46229	0.46273	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Larval	Larval	Whole Organism	All anatomical structures
55889	55889	SRR10863030	SRX7533038	SRS5972263	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt Fish 6dpf rep2	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:6dpf\|dev stage:larval\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 2\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: Fish 6dpf	imb ketting 2018 02 redl SmartSeq 20 67 6dpf Fish rep2 S20	imb ketting 2018 02 redl SmartSeq 20 67 6dpf Fish rep2 S20	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_02_redl_SmartSeq_20_67_6dpf_Fish_rep2_S20.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_20_67_6dpf_Fish_rep2_S20.R2.fastq.gz	fastq fastq	3141146018.0	19880671.0	imb ketting 2018 02 redl SmartSeq 20 67 6dpf Fish rep2 S20.R1.fastq.gz	0:79 1:79	A:838842352;C:731410784;G:716864447;T:853811876;N:216559	79	79	838842352	731410784	716864447	853811876	216559	SRX7533038	SRS5972263	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.94189	0.94199	0.11104	0.11083	0.68787	0.68976	0.4417	0.44175	79	79	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Larval	Larval	Whole Organism	All anatomical structures
55890	55890	SRR10863031	SRX7533037	SRS5972262	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt Fish 6dpf rep1	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:6dpf\|dev stage:larval\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 1\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: Fish 6dpf	imb ketting 2018 02 redl SmartSeq 19 66 6dpf Fish rep1 S19	imb ketting 2018 02 redl SmartSeq 19 66 6dpf Fish rep1 S19	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_02_redl_SmartSeq_19_66_6dpf_Fish_rep1_S19.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_19_66_6dpf_Fish_rep1_S19.R2.fastq.gz	fastq fastq	3208247986.0	20305367.0	imb ketting 2018 02 redl SmartSeq 19 66 6dpf Fish rep1 S19.R1.fastq.gz	0:79 1:79	A:854547229;C:748854314;G:732176934;T:872455301;N:214208	79	79	854547229	748854314	732176934	872455301	214208	SRX7533037	SRS5972262	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.9405	0.94167	0.1138	0.1145	0.67858	0.683	0.46082	0.42095	79	79	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Larval	Larval	Whole Organism	All anatomical structures
55891	55891	SRR10863032	SRX7533036	SRS5972261	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt Fish 3dpf rep2	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:3dpf\|dev stage:protruding mouth\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 2\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: Fish 3dpf	imb ketting 2018 02 redl SmartSeq 18 68 3dpf Fish rep2 S18	imb ketting 2018 02 redl SmartSeq 18 68 3dpf Fish rep2 S18	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_02_redl_SmartSeq_18_68_3dpf_Fish_rep2_S18.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_18_68_3dpf_Fish_rep2_S18.R2.fastq.gz	fastq fastq	3473912978.0	21986791.0	imb ketting 2018 02 redl SmartSeq 18 68 3dpf Fish rep2 S18.R1.fastq.gz	0:79 1:79	A:926028590;C:808989307;G:800996495;T:937660664;N:237922	79	79	926028590	808989307	800996495	937660664	237922	SRX7533036	SRS5972261	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.94661	0.94606	0.09208	0.09205	0.67896	0.68105	0.43418	0.44149	79	79	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Larval	Larval	Whole Organism	All anatomical structures
55892	55892	SRR10863033	SRX7533035	SRS5972260	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt Fish 3dpf rep1	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:3dpf\|dev stage:protruding mouth\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 1\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: Fish 3dpf	imb ketting 2018 02 redl SmartSeq 17 03 3dpf Fish rep1 S17	imb ketting 2018 02 redl SmartSeq 17 03 3dpf Fish rep1 S17	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_02_redl_SmartSeq_17_03_3dpf_Fish_rep1_S17.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_17_03_3dpf_Fish_rep1_S17.R2.fastq.gz	fastq fastq	3383193960.0	21412620.0	imb ketting 2018 02 redl SmartSeq 17 03 3dpf Fish rep1 S17.R1.fastq.gz	0:79 1:79	A:903658559;C:789740630;G:763902271;T:925656543;N:235957	79	79	903658559	789740630	763902271	925656543	235957	SRX7533035	SRS5972260	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.94068	0.94162	0.11921	0.11989	0.67377	0.67572	0.45353	0.44698	79	79	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Larval	Larval	Whole Organism	All anatomical structures
55893	55893	SRR10863034	SRX7533034	SRS5972259	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt Fish 2dpf rep2	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:2dpf\|dev stage:Long pec stage\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 2\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: Fish 2dpf	imb ketting 2018 02 redl SmartSeq 16 63 2dpf Fish rep2 S16	imb ketting 2018 02 redl SmartSeq 16 63 2dpf Fish rep2 S16	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_02_redl_SmartSeq_16_63_2dpf_Fish_rep2_S16.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_16_63_2dpf_Fish_rep2_S16.R2.fastq.gz	fastq fastq	3091658206.0	19567457.0	imb ketting 2018 02 redl SmartSeq 16 63 2dpf Fish rep2 S16.R1.fastq.gz	0:79 1:79	A:818837054;C:727836511;G:707557580;T:837216941;N:210120	79	79	818837054	727836511	707557580	837216941	210120	SRX7533034	SRS5972259	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.94667	0.94646	0.08702	0.08692	0.69804	0.70138	0.43628	0.43409	79	79	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Hatching	Embryo	Whole Organism	All anatomical structures
55894	55894	SRR10863035	SRX7533033	SRS5972258	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt Fish 2dpf rep1	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:2dpf\|dev stage:Long pec stage\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 1\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: Fish 2dpf	imb ketting 2018 02 redl SmartSeq 15 02 2dpf Fish rep1 S15	imb ketting 2018 02 redl SmartSeq 15 02 2dpf Fish rep1 S15	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_02_redl_SmartSeq_15_02_2dpf_Fish_rep1_S15.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_15_02_2dpf_Fish_rep1_S15.R2.fastq.gz	fastq fastq	3499876328.0	22151116.0	imb ketting 2018 02 redl SmartSeq 15 02 2dpf Fish rep1 S15.R1.fastq.gz	0:79 1:79	A:931187812;C:820606968;G:796104654;T:951733888;N:243006	79	79	931187812	820606968	796104654	951733888	243006	SRX7533033	SRS5972258	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.94532	0.94537	0.10394	0.10459	0.69489	0.69727	0.4345	0.43676	79	79	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Hatching	Embryo	Whole Organism	All anatomical structures
55895	55895	SRR10863036	SRX7533032	SRS5972257	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt Fish 1dpf rep2	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:1dpf\|dev stage:Pharyngula period\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 2\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: Fish 1dpf	imb ketting 2018 02 redl SmartSeq 14 69 1dpf Fish rep2 S14	imb ketting 2018 02 redl SmartSeq 14 69 1dpf Fish rep2 S14	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_02_redl_SmartSeq_14_69_1dpf_Fish_rep2_S14.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_14_69_1dpf_Fish_rep2_S14.R2.fastq.gz	fastq fastq	3173577572.0	20085934.0	imb ketting 2018 02 redl SmartSeq 14 69 1dpf Fish rep2 S14.R1.fastq.gz	0:79 1:79	A:851665093;C:736131084;G:718748661;T:866816699;N:216035	79	79	851665093	736131084	718748661	866816699	216035	SRX7533032	SRS5972257	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.94469	0.9439	0.08631	0.08612	0.71062	0.71204	0.46629	0.46237	79	79	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Pharyngula	Embryo	Whole Organism	All anatomical structures
55896	55896	SRR10863037	SRX7533031	SRS5972256	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt Fish 1dpf rep1	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:1dpf\|dev stage:Pharyngula period\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 1\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: Fish 1dpf	imb ketting 2018 02 redl SmartSeq 13 01 1dpf Fish rep1 S13	imb ketting 2018 02 redl SmartSeq 13 01 1dpf Fish rep1 S13	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_02_redl_SmartSeq_13_01_1dpf_Fish_rep1_S13.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_13_01_1dpf_Fish_rep1_S13.R2.fastq.gz	fastq fastq	3241792492.0	20517674.0	imb ketting 2018 02 redl SmartSeq 13 01 1dpf Fish rep1 S13.R1.fastq.gz	0:79 1:79	A:865936682;C:756362974;G:735614291;T:883655547;N:222998	79	79	865936682	756362974	735614291	883655547	222998	SRX7533031	SRS5972256	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.94544	0.94715	0.08154	0.0819	0.70928	0.71011	0.45932	0.46165	79	79	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Pharyngula	Embryo	Whole Organism	All anatomical structures
55897	55897	SRR10863038	SRX7533030	SRS5972255	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt zygote 0hpf rep3	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:0hpf\|dev stage:zygote\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 3\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: zygotes 0hpf	imb ketting 2018 18 redl SmartSeq2 08 0hpf zygotes rep3 S25	imb ketting 2018 18 redl SmartSeq2 08 0hpf zygotes rep3 S25	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_18_redl_SmartSeq2-08_0hpf_zygotes_rep3_S25.R1.fastq.gz imb_ketting_2018_18_redl_SmartSeq2-08_0hpf_zygotes_rep3_S25.R2.fastq.gz	fastq fastq	2254742850.0	15031619.0	imb ketting 2018 18 redl SmartSeq2 08 0hpf zygotes rep3 S25.R1.fastq.gz	0:75 1:75	A:601169757;C:521134633;G:522514682;T:609902670;N:21108	75	75	601169757	521134633	522514682	609902670	21108	SRX7533030	SRS5972255	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.94461	0.94575	0.01803	0.01807	0.76751	0.76883	0.49585	0.49808	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Zygote	Embryo	Whole Organism	All anatomical structures
55899	55899	SRR10863040	SRX7533028	SRS5972254	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt zygote 0hpf rep2	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:0hpf\|dev stage:zygote\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 2\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: zygotes 0hpf	imb ketting 2018 18 redl SmartSeq2 07 0hpf zygotes rep2 S24	imb ketting 2018 18 redl SmartSeq2 07 0hpf zygotes rep2 S24	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_18_redl_SmartSeq2-07_0hpf_zygotes_rep2_S24.R1.fastq.gz imb_ketting_2018_18_redl_SmartSeq2-07_0hpf_zygotes_rep2_S24.R2.fastq.gz	fastq fastq	2415051600.0	16100344.0	imb ketting 2018 18 redl SmartSeq2 07 0hpf zygotes rep2 S24.R1.fastq.gz	0:75 1:75	A:644001016;C:558385744;G:560491907;T:652150600;N:22333	75	75	644001016	558385744	560491907	652150600	22333	SRX7533028	SRS5972254	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.9462	0.94755	0.02097	0.02075	0.76694	0.76909	0.4948	0.49938	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Zygote	Embryo	Whole Organism	All anatomical structures
55900	55900	SRR10863041	SRX7533027	SRS5972253	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.	The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.	wt zygote 0hpf rep1	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:0hpf\|dev stage:zygote\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 1\|BioSampleModel:Model organism or animal	mRNA of Zebrafish: zygotes 0hpf	imb ketting 2018 18 redl SmartSeq2 06 0hpf zygotes rep1 S23	imb ketting 2018 18 redl SmartSeq2 06 0hpf zygotes rep1 S23	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074	imb_ketting_2018_18_redl_SmartSeq2-06_0hpf_zygotes_rep1_S23.R1.fastq.gz imb_ketting_2018_18_redl_SmartSeq2-06_0hpf_zygotes_rep1_S23.R2.fastq.gz	fastq fastq	2621759100.0	17478394.0	imb ketting 2018 18 redl SmartSeq2 06 0hpf zygotes rep1 S23.R1.fastq.gz	0:75 1:75	A:697302326;C:607756156;G:612217195;T:704460378;N:23045	75	75	697302326	607756156	612217195	704460378	23045	SRX7533027	SRS5972253	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.94882	0.95052	0.02124	0.02139	0.77082	0.7724	0.49237	0.49259	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Zygote	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");;