{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", experiment.library_selection = \"PolyA\" and technology = \"smartseq\"", "rows": [[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.", null, null, "The vasa:eGFP line Kr\u00f8vel 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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt PGCs 10dpf rep3", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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. 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RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt PGCs 10dpf rep1", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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. 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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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt PGCs 6dpf rep2", null, "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", null, null, null, null, null, null, null, null, "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. 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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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt PGCs 6dpf rep1", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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.", null, null, "The vasa:eGFP line Kr\u00f8vel 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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. 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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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt PGCs 3dpf rep3", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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.", null, null, "The vasa:eGFP line Kr\u00f8vel 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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt PGCs 3dpf rep2", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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.", null, null, "The vasa:eGFP line Kr\u00f8vel 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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt PGCs 3dpf rep1", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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.", null, null, "The vasa:eGFP line Kr\u00f8vel 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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt PGCs 2dpf rep3", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "The vasa:eGFP line Kr\u00f8vel 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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt PGCs 2dpf rep2", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "The vasa:eGFP line Kr\u00f8vel 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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt PGCs 2dpf rep1", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "The vasa:eGFP line Kr\u00f8vel 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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt PGCs 1dpf rep3", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "The vasa:eGFP line Kr\u00f8vel 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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt PGCs 1dpf rep2", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "The vasa:eGFP line Kr\u00f8vel 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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt PGCs 1dpf rep1", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "The vasa:eGFP line Kr\u00f8vel 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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt Fish 10dpf rep2", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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.", null, null, "The vasa:eGFP line Kr\u00f8vel 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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt Fish 10dpf rep1", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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.", null, null, "The vasa:eGFP line Kr\u00f8vel 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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt Fish 6dpf rep2", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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.", null, null, "The vasa:eGFP line Kr\u00f8vel 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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt Fish 6dpf rep1", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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.", null, null, "The vasa:eGFP line Kr\u00f8vel 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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt Fish 3dpf rep2", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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.", null, null, "The vasa:eGFP line Kr\u00f8vel 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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt Fish 3dpf rep1", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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.", null, null, "The vasa:eGFP line Kr\u00f8vel 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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt Fish 2dpf rep2", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "The vasa:eGFP line Kr\u00f8vel 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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt Fish 2dpf rep1", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "The vasa:eGFP line Kr\u00f8vel 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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt Fish 1dpf rep2", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "The vasa:eGFP line Kr\u00f8vel 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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt Fish 1dpf rep1", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "The vasa:eGFP line Kr\u00f8vel 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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt zygote 0hpf rep3", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Zygote", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "The vasa:eGFP line Kr\u00f8vel 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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt zygote 0hpf rep2", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Zygote", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "The vasa:eGFP line Kr\u00f8vel 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 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m 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 85\u00b5m 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\u00b0C until library preparation was done.", null, "wt zygote 0hpf rep1", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "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, null, null, 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", null, "Germany", "2020-01-10", "Zygote", "Embryo", "Whole Organism", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 28, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", 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[experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], 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