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84 rows where devstage_curation = "Larval" and tissue_curation = "Gonad"

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technology 5

experiment.library_selection 4

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Gonad · 84 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

devstage_curation_coarse 1

devstage_curation 1

  • Larval · 84 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.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 selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
29187 29187 SRR8176747 SRX4996876 SRS4031879 SRP480945 PRJNA1055160 Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain PRJNA1055160 Other We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf   pubmed:38529407   Nadia 19dpf ZZ Gonad Single Cell RNA Seq Nadia 19dpf ZZ Gonad Single Cell RNA Seq   strain:Nadia|age:19 dpf provider:John H. Postlethwait University of Oregon|genotype:ZZ|BioSampleModel:Model organism or animal                 scRNA Seq of Danio rerio: Nadia 19dpf ZZ gonad Nadia 19dpf ZZ gonad Nadia 19dpf ZZ gonad A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   SRP480945   loader:fastq load.py     15090036999.0 107021539.0 zz 19NAmale I1 001.fastq.gz 0:8 1:133 A:4154103253;C:3402890354;G:3765557416;T:3755723849;N:11762127 8 133     4154103253 3402890354 3765557416 3755723849 11762127 SRX4996876 SRS4031879 SRA807619 University of Oregon|Institute of Neuroscience University of Oregon                       T B sc-like readlen illumina nextseq unknown poly_a unknown sc single_cell_droplet 10x   United States 2018-11-08 Larval Larval Gonad Reproductive System
29190 29190 SRR8176756 SRX4996867 SRS4031876 SRP480945 PRJNA1055160 Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain PRJNA1055160 Other We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf   pubmed:38529407   Nadia 19dpf ZW Gonad Single Cell RNA Seq Nadia 19dpf ZW Gonad Single Cell RNA Seq   strain:Nadia|age:19 dpf provider:John H. Postlethwait University of Oregon|genotype:ZW|BioSampleModel:Model organism or animal                 scRNA Seq of Danio rerio: Nadia 19dpf ZW gonad Nadia 19dpf ZW gonad Nadia 19dpf ZW gonad A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   SRP480945   loader:fastq load.py     17141425554.0 121570394.0 zw 19NAfem I1 001.fastq.gz 0:8 1:133 A:4656207219;C:3824531650;G:4322736498;T:4324676442;N:13273745 8 133     4656207219 3824531650 4322736498 4324676442 13273745 SRX4996867 SRS4031876 SRA807619 University of Oregon|Institute of Neuroscience University of Oregon                       T B sc-like readlen illumina nextseq unknown poly_a unknown sc single_cell_droplet 10x   United States 2018-11-08 Larval Larval Gonad Reproductive System
29259 29259 SRR27336917 SRX23013778 SRS19977075 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 PaternalKO gonads 31dpf rep2 miR214 PaternalKO gonads 31dpf rep2   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep2|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A11 miR214 PaternalKO gonads 31dpf rep2 miR214 PaternalKO gonads 31dpf rep2 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_PaternalKO_gonads_31dpf_rep2.fastq.gz fastq 2327996832.0 27714248.0 miR214 PaternalKO gonads 31dpf rep2.fastq.gz 0:84 A:602135965;C:552786494;G:537368428;T:635697339;N:8606 84       602135965 552786494 537368428 635697339 8606 SRX23013778 SRS19977075 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95369   0.06146   0.69203   0.47259   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29260 29260 SRR27336918 SRX23013777 SRS19977074 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 PaternalKO gonads 31dpf rep1 miR214 PaternalKO gonads 31dpf rep1   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep1|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A10 miR214 PaternalKO gonads 31dpf rep1 miR214 PaternalKO gonads 31dpf rep1 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_PaternalKO_gonads_31dpf_rep1.fastq.gz fastq 2500978452.0 29773553.0 miR214 PaternalKO gonads 31dpf rep1.fastq.gz 0:84 A:646162933;C:593855971;G:578265372;T:682684551;N:9625 84       646162933 593855971 578265372 682684551 9625 SRX23013777 SRS19977074 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95147   0.05972   0.69071   0.47043   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29261 29261 SRR27336919 SRX23013776 SRS19977073 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 maternalHET gonads 31dpf rep4 miR214 maternalHET gonads 31dpf rep4   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep4|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A9 miR214 maternalHET gonads 31dpf rep4 miR214 maternalHET gonads 31dpf rep4 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_maternalHET_gonads_31dpf_rep4.fastq.gz fastq 2365480908.0 28160487.0 miR214 maternalHET gonads 31dpf rep4.fastq.gz 0:84 A:613121312;C:560582165;G:549338096;T:642429834;N:9501 84       613121312 560582165 549338096 642429834 9501 SRX23013776 SRS19977073 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95304   0.05342   0.7108   0.46822   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29262 29262 SRR27336920 SRX23013775 SRS19977072 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 maternalHET gonads 31dpf rep3 miR214 maternalHET gonads 31dpf rep3   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep3|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A8 miR214 maternalHET gonads 31dpf rep3 miR214 maternalHET gonads 31dpf rep3 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_maternalHET_gonads_31dpf_rep3.fastq.gz fastq 2537794644.0 30211841.0 miR214 maternalHET gonads 31dpf rep3.fastq.gz 0:84 A:658687178;C:600742464;G:585643169;T:692712057;N:9776 84       658687178 600742464 585643169 692712057 9776 SRX23013775 SRS19977072 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95177   0.06701   0.68195   0.47393   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29263 29263 SRR27336921 SRX23013774 SRS19977071 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 maternalHET gonads 31dpf rep2 miR214 maternalHET gonads 31dpf rep2   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep2|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A7 miR214 maternalHET gonads 31dpf rep2 miR214 maternalHET gonads 31dpf rep2 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_maternalHET_gonads_31dpf_rep2.fastq.gz fastq 2417384424.0 28778386.0 miR214 maternalHET gonads 31dpf rep2.fastq.gz 0:84 A:625935186;C:574179061;G:560498085;T:656762980;N:9112 84       625935186 574179061 560498085 656762980 9112 SRX23013774 SRS19977071 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95259   0.05852   0.6981   0.47435   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29264 29264 SRR27336922 SRX23013773 SRS19977070 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 maternalHET gonads 31dpf rep1 miR214 maternalHET gonads 31dpf rep1   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep1|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A6 miR214 maternalHET gonads 31dpf rep1 miR214 maternalHET gonads 31dpf rep1 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_maternalHET_gonads_31dpf_rep1.fastq.gz fastq 2330886180.0 27748645.0 miR214 maternalHET gonads 31dpf rep1.fastq.gz 0:84 A:601589571;C:554105326;G:542789267;T:632393158;N:8858 84       601589571 554105326 542789267 632393158 8858 SRX23013773 SRS19977070 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95338   0.05239   0.71366   0.47291   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29265 29265 SRR27336923 SRX23013772 SRS19977069 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 maternalKO gonads 31dpf rep4 miR214 maternalKO gonads 31dpf rep4   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalKO|biological replicate:rep4|number of gonads:8 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A5 miR214 maternalKO gonads 31dpf rep4 miR214 maternalKO gonads 31dpf rep4 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_maternalKO_gonads_31dpf_rep4.fastq.gz fastq 2340233784.0 27859926.0 miR214 maternalKO gonads 31dpf rep4.fastq.gz 0:84 A:606735187;C:553647808;G:539865459;T:639976430;N:8900 84       606735187 553647808 539865459 639976430 8900 SRX23013772 SRS19977069 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95406   0.06415   0.68225   0.47695   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29266 29266 SRR27336924 SRX23013771 SRS19977068 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 maternalKO gonads 31dpf rep3 miR214 maternalKO gonads 31dpf rep3   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalKO|biological replicate:rep3|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A4 miR214 maternalKO gonads 31dpf rep3 miR214 maternalKO gonads 31dpf rep3 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_maternalKO_gonads_31dpf_rep3.fastq.gz fastq 2058505512.0 24506018.0 miR214 maternalKO gonads 31dpf rep3.fastq.gz 0:84 A:537425814;C:485664494;G:471526682;T:563881213;N:7309 84       537425814 485664494 471526682 563881213 7309 SRX23013771 SRS19977068 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95296   0.06728   0.69266   0.47627   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29267 29267 SRR27336925 SRX23013770 SRS19977067 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 PaternalHET gonads 31dpf rep4 miR214 PaternalHET gonads 31dpf rep4   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep4|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A17 miR214 PaternalHET gonads 31dpf rep4 miR214 PaternalHET gonads 31dpf rep4 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_PaternalHET_gonads_31dpf_rep4.fastq.gz fastq 3001613328.0 35733492.0 miR214 PaternalHET gonads 31dpf rep4.fastq.gz 0:84 A:778860501;C:711155422;G:688784969;T:822801157;N:11279 84       778860501 711155422 688784969 822801157 11279 SRX23013770 SRS19977067 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95361   0.05653   0.7051   0.48382   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29268 29268 SRR27336926 SRX23013769 SRS19977066 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 PaternalHET gonads 31dpf rep3 miR214 PaternalHET gonads 31dpf rep3   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep3|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A16 miR214 PaternalHET gonads 31dpf rep3 miR214 PaternalHET gonads 31dpf rep3 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_PaternalHET_gonads_31dpf_rep3.fastq.gz fastq 3053630664.0 36352746.0 miR214 PaternalHET gonads 31dpf rep3.fastq.gz 0:84 A:785219727;C:726431662;G:713454025;T:828513556;N:11694 84       785219727 726431662 713454025 828513556 11694 SRX23013769 SRS19977066 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95309   0.04588   0.71997   0.46447   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29269 29269 SRR27336927 SRX23013768 SRS19977065 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 PaternalHET gonads 31dpf rep2 miR214 PaternalHET gonads 31dpf rep2   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep2|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A15 miR214 PaternalHET gonads 31dpf rep2 miR214 PaternalHET gonads 31dpf rep2 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_PaternalHET_gonads_31dpf_rep2.fastq.gz fastq 3063695208.0 36472562.0 miR214 PaternalHET gonads 31dpf rep2.fastq.gz 0:84 A:784924646;C:728941687;G:720847462;T:828969510;N:11903 84       784924646 728941687 720847462 828969510 11903 SRX23013768 SRS19977065 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95413   0.04739   0.71936   0.4704   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29270 29270 SRR27336928 SRX23013767 SRS19977064 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 PaternalHET gonads 31dpf rep1 miR214 PaternalHET gonads 31dpf rep1   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep1|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A14 miR214 PaternalHET gonads 31dpf rep1 miR214 PaternalHET gonads 31dpf rep1 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_PaternalHET_gonads_31dpf_rep1.fastq.gz fastq 2699154024.0 32132786.0 miR214 PaternalHET gonads 31dpf rep1.fastq.gz 0:84 A:694174797;C:642049572;G:627991562;T:734927762;N:10331 84       694174797 642049572 627991562 734927762 10331 SRX23013767 SRS19977064 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95518   0.05525   0.70285   0.47695   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29271 29271 SRR27336929 SRX23013766 SRS19977063 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 PaternalKO gonads 31dpf rep4 miR214 PaternalKO gonads 31dpf rep4   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep4|number of gonads:8 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A13 miR214 PaternalKO gonads 31dpf rep4 miR214 PaternalKO gonads 31dpf rep4 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_PaternalKO_gonads_31dpf_rep4.fastq.gz fastq 2514248016.0 29931524.0 miR214 PaternalKO gonads 31dpf rep4.fastq.gz 0:84 A:648908956;C:598837726;G:580002743;T:686488678;N:9913 84       648908956 598837726 580002743 686488678 9913 SRX23013766 SRS19977063 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.94978   0.06951   0.67896   0.47686   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29272 29272 SRR27336930 SRX23013765 SRS19977062 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 PaternalKO gonads 31dpf rep3 miR214 PaternalKO gonads 31dpf rep3   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep3|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A12 miR214 PaternalKO gonads 31dpf rep3 miR214 PaternalKO gonads 31dpf rep3 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_PaternalKO_gonads_31dpf_rep3.fastq.gz fastq 2499529200.0 29756300.0 miR214 PaternalKO gonads 31dpf rep3.fastq.gz 0:84 A:642490769;C:597403823;G:580565141;T:679060154;N:9313 84       642490769 597403823 580565141 679060154 9313 SRX23013765 SRS19977062 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95284   0.05602   0.70289   0.47154   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29273 29273 SRR27336931 SRX23013764 SRS19977061 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 maternalKO gonads 31dpf rep2 miR214 maternalKO gonads 31dpf rep2   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalKO|biological replicate:rep2|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A3 miR214 maternalKO gonads 31dpf rep2 miR214 maternalKO gonads 31dpf rep2 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_maternalKO_gonads_31dpf_rep2.fastq.gz fastq 2529742404.0 30115981.0 miR214 maternalKO gonads 31dpf rep2.fastq.gz 0:84 A:652091166;C:600932059;G:589100617;T:687608862;N:9700 84       652091166 600932059 589100617 687608862 9700 SRX23013764 SRS19977061 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95498   0.05524   0.70366   0.47319   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29274 29274 SRR27336932 SRX23013763 SRS19977060 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 maternalKO gonads 31dpf rep1 miR214 maternalKO gonads 31dpf rep1   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalKO|biological replicate:rep1|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A2 miR214 maternalKO gonads 31dpf rep1 miR214 maternalKO gonads 31dpf rep1 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_maternalKO_gonads_31dpf_rep1.fastq.gz fastq 2310878136.0 27510454.0 miR214 maternalKO gonads 31dpf rep1.fastq.gz 0:84 A:598541924;C:547875391;G:533137786;T:631314274;N:8761 84       598541924 547875391 533137786 631314274 8761 SRX23013763 SRS19977060 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95279   0.06446   0.68757   0.4758   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
30560 30560 SRR27836075 SRX23499416 SRS20351174 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 mutant 4 21 dpf GSM8059034   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing rbpms2 mutant 4 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM GSM8059034 GSM8059034: rbpms2 mutant 4 21 dpf; Danio rerio; RNA Seq GSM8059034 r1 GSM8059034 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-DM_4_S8_L001_R1_001.fastq.gz rbpms2-d21-DM_4_S8_L001_R2_001.fastq.gz fastq fastq 2533252722.0 24835811.0 GSM8059034 r1 0:51 1:51 A:767895104;C:496128064;G:502250517;T:766951391;N:27646 51 51     767895104 496128064 502250517 766951391 27646 SRX23499416 SRS20351174 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
30561 30561 SRR27836076 SRX23499416 SRS20351174 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 mutant 4 21 dpf GSM8059034   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing rbpms2 mutant 4 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM GSM8059034 GSM8059034: rbpms2 mutant 4 21 dpf; Danio rerio; RNA Seq GSM8059034 r1 GSM8059034 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-DM_4_S8_L002_R1_001.fastq.gz rbpms2-d21-DM_4_S8_L002_R2_001.fastq.gz fastq fastq 2500214514.0 24511907.0 GSM8059034 r2 0:51 1:51 A:757980090;C:489633622;G:495839519;T:756737989;N:23294 51 51     757980090 489633622 495839519 756737989 23294 SRX23499416 SRS20351174 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
30562 30562 SRR27836077 SRX23499415 SRS20351173 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 mutant 3 21 dpf GSM8059033   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing rbpms2 mutant 3 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM GSM8059033 GSM8059033: rbpms2 mutant 3 21 dpf; Danio rerio; RNA Seq GSM8059033 r1 GSM8059033 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-DM_3_S7_L001_R1_001.fastq.gz rbpms2-d21-DM_3_S7_L001_R2_001.fastq.gz fastq fastq 2383569354.0 23368327.0 GSM8059033 r1 0:51 1:51 A:705650487;C:468856307;G:473479720;T:735556568;N:26272 51 51     705650487 468856307 473479720 735556568 26272 SRX23499415 SRS20351173 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
30563 30563 SRR27836078 SRX23499415 SRS20351173 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 mutant 3 21 dpf GSM8059033   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing rbpms2 mutant 3 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM GSM8059033 GSM8059033: rbpms2 mutant 3 21 dpf; Danio rerio; RNA Seq GSM8059033 r1 GSM8059033 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-DM_3_S7_L002_R1_001.fastq.gz rbpms2-d21-DM_3_S7_L002_R2_001.fastq.gz fastq fastq 2324856114.0 22792707.0 GSM8059033 r2 0:51 1:51 A:688232198;C:457346277;G:462034541;T:717221485;N:21613 51 51     688232198 457346277 462034541 717221485 21613 SRX23499415 SRS20351173 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
30564 30564 SRR27836079 SRX23499414 SRS20351172 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 mutant 1 21 dpf GSM8059032   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing rbpms2 mutant 1 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM GSM8059032 GSM8059032: rbpms2 mutant 1 21 dpf; Danio rerio; RNA Seq GSM8059032 r1 GSM8059032 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-DM_1_S5_L001_R1_001.fastq.gz rbpms2-d21-DM_1_S5_L001_R2_001.fastq.gz fastq fastq 2412458100.0 23651550.0 GSM8059032 r1 0:51 1:51 A:726246267;C:465733066;G:465377798;T:755071663;N:29306 51 51     726246267 465733066 465377798 755071663 29306 SRX23499414 SRS20351172 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
30565 30565 SRR27836080 SRX23499414 SRS20351172 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 mutant 1 21 dpf GSM8059032   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing rbpms2 mutant 1 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM GSM8059032 GSM8059032: rbpms2 mutant 1 21 dpf; Danio rerio; RNA Seq GSM8059032 r1 GSM8059032 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-DM_1_S5_L002_R1_001.fastq.gz rbpms2-d21-DM_1_S5_L002_R2_001.fastq.gz fastq fastq 2363898144.0 23175472.0 GSM8059032 r2 0:51 1:51 A:711756208;C:456236364;G:456088591;T:739792903;N:24078 51 51     711756208 456236364 456088591 739792903 24078 SRX23499414 SRS20351172 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
30566 30566 SRR27836081 SRX23499413 SRS20351171 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 wildtype 3 21 dpf GSM8059031   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing rbpms2 wildtype 3 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype GSM8059031 GSM8059031: rbpms2 wildtype 3 21 dpf; Danio rerio; RNA Seq GSM8059031 r1 GSM8059031 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-WT_3_S3_L001_R1_001.fastq.gz rbpms2-d21-WT_3_S3_L001_R2_001.fastq.gz fastq fastq 2048418162.0 20082531.0 GSM8059031 r1 0:51 1:51 A:612611264;C:409068349;G:413909657;T:612805097;N:23795 51 51     612611264 409068349 413909657 612805097 23795 SRX23499413 SRS20351171 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
30567 30567 SRR27836082 SRX23499413 SRS20351171 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 wildtype 3 21 dpf GSM8059031   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing rbpms2 wildtype 3 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype GSM8059031 GSM8059031: rbpms2 wildtype 3 21 dpf; Danio rerio; RNA Seq GSM8059031 r1 GSM8059031 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-WT_3_S3_L002_R1_001.fastq.gz rbpms2-d21-WT_3_S3_L002_R2_001.fastq.gz fastq fastq 2018915070.0 19793285.0 GSM8059031 r2 0:51 1:51 A:603776465;C:403221066;G:408169193;T:603728354;N:19992 51 51     603776465 403221066 408169193 603728354 19992 SRX23499413 SRS20351171 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
30568 30568 SRR27836083 SRX23499412 SRS20351179 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 wildtype 2 21 dpf GSM8059030   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing rbpms2 wildtype 2 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype GSM8059030 GSM8059030: rbpms2 wildtype 2 21 dpf; Danio rerio; RNA Seq GSM8059030 r1 GSM8059030 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-WT_2_S2_L001_R1_001.fastq.gz rbpms2-d21-WT_2_S2_L001_R2_001.fastq.gz fastq fastq 1927777866.0 18899783.0 GSM8059030 r1 0:51 1:51 A:589122616;C:372230241;G:374787285;T:591617780;N:19944 51 51     589122616 372230241 374787285 591617780 19944 SRX23499412 SRS20351179 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
30569 30569 SRR27836084 SRX23499412 SRS20351179 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 wildtype 2 21 dpf GSM8059030   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing rbpms2 wildtype 2 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype GSM8059030 GSM8059030: rbpms2 wildtype 2 21 dpf; Danio rerio; RNA Seq GSM8059030 r1 GSM8059030 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-WT_2_S2_L002_R1_001.fastq.gz rbpms2-d21-WT_2_S2_L002_R2_001.fastq.gz fastq fastq 1901436570.0 18641535.0 GSM8059030 r2 0:51 1:51 A:581077435;C:367152917;G:369822980;T:583366137;N:17101 51 51     581077435 367152917 369822980 583366137 17101 SRX23499412 SRS20351179 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
30570 30570 SRR27836085 SRX23499411 SRS20351170 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 wildtype 1 21 dpf GSM8059029   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing rbpms2 wildtype 1 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype GSM8059029 GSM8059029: rbpms2 wildtype 1 21 dpf; Danio rerio; RNA Seq GSM8059029 r1 GSM8059029 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-WT_1_S1_L001_R1_001.fastq.gz rbpms2-d21-WT_1_S1_L001_R2_001.fastq.gz fastq fastq 1878693222.0 18418561.0 GSM8059029 r1 0:51 1:51 A:581058368;C:356028122;G:360378733;T:581204723;N:23276 51 51     581058368 356028122 360378733 581204723 23276 SRX23499411 SRS20351170 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
30571 30571 SRR27836086 SRX23499411 SRS20351170 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 wildtype 1 21 dpf GSM8059029   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing rbpms2 wildtype 1 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype GSM8059029 GSM8059029: rbpms2 wildtype 1 21 dpf; Danio rerio; RNA Seq GSM8059029 r1 GSM8059029 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-WT_1_S1_L002_R1_001.fastq.gz rbpms2-d21-WT_1_S1_L002_R2_001.fastq.gz fastq fastq 1861916160.0 18254080.0 GSM8059029 r2 0:51 1:51 A:575859972;C:352771580;G:357641601;T:575624138;N:18869 51 51     575859972 352771580 357641601 575624138 18869 SRX23499411 SRS20351170 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
36274 36274 SRR298565 SRX079843 SRS212649 SRP007331 PRJNA141525 Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. GSE29418 Transcriptome Analysis RNA libraries from immunoprecipitates of Tdrd1 Ziwi and Zili total testis RNA total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.   pubmed:21743441   WT3WK GSM727522   tissue:3 wpf whole gonads|strain:TL WT3WK three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9. 3 wpf whole gonads   Tissue was homogenized in trizol and total RNA was isolated. RNAs ranging from 18 35 nucleotides were size selected from gel. For cDNA synthesis the RNA molecules in the immunoprecipitated fraction were first poly A tailed using polyApolymerase followed by ligation of synthetic RNA adapter to the five prime phosphate. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.   strain:TL GSM727522 GSM727522: WT3WK GSM727522: WT3WK GSM727522: WT3WK 1   GEO Accession:GSM727522 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP007331   read name barcode proc directive:ignore WT3WK.fastq fastq 365473116.0 10152031.0 GSM727522 1 0:36   36                 SRX079843 SRS212649 SRA039167 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.09055   0.0603   0.97798   0.44571   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2011-05-20 Larval Larval Gonad Reproductive System
36275 36275 SRR298564 SRX079842 SRS212648 SRP007331 PRJNA141525 Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. GSE29418 Transcriptome Analysis RNA libraries from immunoprecipitates of Tdrd1 Ziwi and Zili total testis RNA total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.   pubmed:21743441   TDRD1WK3 GSM727521   tissue:3 wpf tdrd1 mutant gonads|strain:TL TDRD1WK3 three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9. 3 wpf tdrd1 mutant gonads   Tissue was homogenized in trizol and total RNA was isolated. RNAs ranging from 18 35 nucleotides were size selected from gel. For cDNA synthesis the RNA molecules in the immunoprecipitated fraction were first poly A tailed using polyApolymerase followed by ligation of synthetic RNA adapter to the five prime phosphate. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.   strain:TL GSM727521 GSM727521: TDRD1WK3 GSM727521: TDRD1WK3 GSM727521: TDRD1WK3 1   GEO Accession:GSM727521 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP007331   read name barcode proc directive:ignore TDRD1WK3.fastq fastq 369931536.0 10275876.0 GSM727521 1 0:36   36                 SRX079842 SRS212648 SRA039167 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.08303   0.04674   0.97938   0.35673   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2011-05-20 Larval Larval Gonad Reproductive System
40667 40667 SRR3231288 SRX1637086 SRS1342917 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   2wpf wt 1 GSM2090852   tissue:Germ cells|cell line:Primary cells|developmental stage:2wpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 2wpf wt 1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:2wpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090852 GSM2090852: 2wpf wt 1; Danio rerio; RNA Seq GSM2090852   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090852 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     2wpf_wt_1_R1_001.fastq.gz 2wpf_wt_1_R2_001.fastq.gz fastq fastq 899083386.0 8814543.0 GSM2090852 r1 0:51 1:51 A:211455925;C:158092908;G:163752155;T:355377184;N:10405214 51 51     211455925 158092908 163752155 355377184 10405214 SRX1637086 SRS1342917 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.0051 0.10904 0.00468 0.0257 0.99912 0.90145 0.47272 0.47949 51 51 T B mate1 technical by mapping diff illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Larval Larval Gonad Reproductive System
40668 40668 SRR3231289 SRX1637086 SRS1342917 SRP071848 PRJNA315399 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq] GSE79283 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep. parent bioproject:PRJNA315403 pubmed:30086300   2wpf wt 1 GSM2090852   tissue:Germ cells|cell line:Primary cells|developmental stage:2wpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 2wpf wt 1 post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling. Germ cells   mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. Zebrafish were maintained under standard conditions. cell line:Primary cells|developmental stage:2wpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012 GSM2090852 GSM2090852: 2wpf wt 1; Danio rerio; RNA Seq GSM2090852   1 mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing. GEO Accession:GSM2090852 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP071848     2wpf_wt_R1_001.fastq.gz 2wpf_wt_R2_001.fastq.gz fastq fastq 895174134.0 8776217.0 GSM2090852 r2 0:51 1:51 A:210034767;C:157173531;G:162557633;T:353624192;N:11784011 51 51     210034767 157173531 162557633 353624192 11784011 SRX1637086 SRS1342917 SRA385812 GEO Rene Ketting, RNA silencing, IMB 2 0.00514 0.10967 0.00459 0.0262 0.9991 0.90516 0.47887 0.49885 51 51 T B mate1 technical by mapping diff illumina nextseq 3prime cdna_unspecified unknown sc single_cell_plate celseq   Germany 2016-03-16 Larval Larval Gonad Reproductive System
48325 48325 SRR7244607 SRX4149444 SRS3363040 SRP149500 PRJNA473641 Danio rerio strain:Tg vas:EGFP; figla | isolate:WT GFP S/W | breed:F3 generation Transcriptome or Gene expression PRJNA473641 Transcriptome Analysis Explore the function of figla gene in zebrafish gonadal development       Mutant weak GFP MT GFP W 1   strain:Not applicable|isolate:figla / |breed:Not applicable|cultivar:Not applicable|ecotype:Not applicable|age:25 dpf|dev stage:Fish fry|sex:Unknown|tissue:Gonads|replicate:Biological replicate 1 for MT GFP W|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 25 dpf gonad MT GFP W 1 MT GFP W 1 RNA sequencing libraries were generated by extracting 3 g RNA per sample RNA from 25 dpf Danio rerio gonadal tissues. mRNA was then purified from the total RNA and fragmentation was carried out at elevated temperatures. Subsequent cDNA synthesis and size selection steps were carried out to generate fragments of 150 200 bp. PCR purification and quantification was carried out followed by clustering of the libraries. The libraries were then sequenced to generate 150 bp reads.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP149500     MT-GFP-W-1_2.fq.gz MT-GFP-W-1_1.fq.gz fastq fastq 4527981300.0 15093271.0 MT GFP W 1 1.fq.gz 0:150 1:150 A:1164721585;C:1102692407;G:1101191349;T:1158828817;N:547142 150 150     1164721585 1102692407 1101191349 1158828817 547142 SRX4149444 SRS3363040 SRA713582 University of Macau|Faculty of Health Sciences University of Macau 2 0.9286 0.91776 0.03914 0.03918 0.73821 0.74813 0.5081 0.50281 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2018-06-01 Larval Larval Gonad Reproductive System
48326 48326 SRR7244608 SRX4149443 SRS3363039 SRP149500 PRJNA473641 Danio rerio strain:Tg vas:EGFP; figla | isolate:WT GFP S/W | breed:F3 generation Transcriptome or Gene expression PRJNA473641 Transcriptome Analysis Explore the function of figla gene in zebrafish gonadal development       Mutant strong GFP MT GFP S 3   strain:Not applicable|isolate:figla / |breed:Not applicable|cultivar:Not applicable|ecotype:Not applicable|age:25 dpf|dev stage:Fish fry|sex:Unknown|tissue:Gonads|replicate:Biological replicate 3 for MT GFP S|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 25 dpf gonad MT GFP S 3 MT GFP S 3 RNA sequencing libraries were generated by extracting 3 g RNA per sample RNA from 25 dpf Danio rerio gonadal tissues. mRNA was then purified from the total RNA and fragmentation was carried out at elevated temperatures. Subsequent cDNA synthesis and size selection steps were carried out to generate fragments of 150 200 bp. PCR purification and quantification was carried out followed by clustering of the libraries. The libraries were then sequenced to generate 150 bp reads.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP149500     MT-GFP-S-3_2.fq.gz MT-GFP-S-3_1.fq.gz fastq fastq 4581436200.0 15271454.0 MT GFP S 3 2.fq.gz 0:150 1:150 A:1185957730;C:1105792910;G:1107884782;T:1180745199;N:1055579 150 150     1185957730 1105792910 1107884782 1180745199 1055579 SRX4149443 SRS3363039 SRA713582 University of Macau|Faculty of Health Sciences University of Macau 2 0.93304 0.93469 0.0415 0.0413 0.72973 0.73531 0.50584 0.50265 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2018-06-01 Larval Larval Gonad Reproductive System
48327 48327 SRR7244609 SRX4149442 SRS3363038 SRP149500 PRJNA473641 Danio rerio strain:Tg vas:EGFP; figla | isolate:WT GFP S/W | breed:F3 generation Transcriptome or Gene expression PRJNA473641 Transcriptome Analysis Explore the function of figla gene in zebrafish gonadal development       Control strong GFP WT GFP S 2   strain:Not applicable|isolate:figla +/ |breed:Not applicable|cultivar:Not applicable|ecotype:Not applicable|age:25 dpf|dev stage:Fish fry|sex:Unknown|tissue:Gonads|replicate:Biological replicate 2 for WT GFP S|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 25 dpf gonad WT GFP S 2 WT GFP S 2 RNA sequencing libraries were generated by extracting 3 g RNA per sample RNA from 25 dpf Danio rerio gonadal tissues. mRNA was then purified from the total RNA and fragmentation was carried out at elevated temperatures. Subsequent cDNA synthesis and size selection steps were carried out to generate fragments of 150 200 bp. PCR purification and quantification was carried out followed by clustering of the libraries. The libraries were then sequenced to generate 150 bp reads.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP149500     WT-GFP-S-2_2.fq.gz WT-GFP-S-2_1.fq.gz fastq fastq 3925438200.0 13084794.0 WT GFP S 2 1.fq.gz 0:150 1:150 A:1016830066;C:944960672;G:948646826;T:1014965021;N:35615 150 150     1016830066 944960672 948646826 1014965021 35615 SRX4149442 SRS3363038 SRA713582 University of Macau|Faculty of Health Sciences University of Macau 2 0.92519 0.92604 0.0406 0.04153 0.71354 0.72385 0.52506 0.51719 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2018-06-01 Larval Larval Gonad Reproductive System
48328 48328 SRR7244610 SRX4149441 SRS3363037 SRP149500 PRJNA473641 Danio rerio strain:Tg vas:EGFP; figla | isolate:WT GFP S/W | breed:F3 generation Transcriptome or Gene expression PRJNA473641 Transcriptome Analysis Explore the function of figla gene in zebrafish gonadal development       Control strong GFP WT GFP S 1   strain:Not applicable|isolate:figla +/ |breed:Not applicable|cultivar:Not applicable|ecotype:Not applicable|age:25 dpf|dev stage:Fish fry|sex:Unknown|tissue:Gonads|replicate:Biological replicate 1 for WT GFP S|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 25 dpf gonad WT GFP S 1 WT GFP S 1 RNA sequencing libraries were generated by extracting 3 g RNA per sample RNA from 25 dpf Danio rerio gonadal tissues. mRNA was then purified from the total RNA and fragmentation was carried out at elevated temperatures. Subsequent cDNA synthesis and size selection steps were carried out to generate fragments of 150 200 bp. PCR purification and quantification was carried out followed by clustering of the libraries. The libraries were then sequenced to generate 150 bp reads.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP149500     WT-GFP-S-1_2.fq.gz WT-GFP-S-1_1.fq.gz fastq fastq 3853353600.0 12844512.0 WT GFP S 1 2.fq.gz 0:150 1:150 A:995606427;C:930518560;G:933514630;T:993679337;N:34646 150 150     995606427 930518560 933514630 993679337 34646 SRX4149441 SRS3363037 SRA713582 University of Macau|Faculty of Health Sciences University of Macau 2 0.92153 0.92874 0.04217 0.04333 0.71242 0.72017 0.50482 0.51938 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2018-06-01 Larval Larval Gonad Reproductive System
48329 48329 SRR7244614 SRX4149440 SRS3363035 SRP149500 PRJNA473641 Danio rerio strain:Tg vas:EGFP; figla | isolate:WT GFP S/W | breed:F3 generation Transcriptome or Gene expression PRJNA473641 Transcriptome Analysis Explore the function of figla gene in zebrafish gonadal development       Control weak GFP WT GFP W 1   strain:Not applicable|isolate:figla +/ |breed:Not applicable|cultivar:Not applicable|ecotype:Not applicable|age:25 dpf|dev stage:Fish fry|sex:Unknown|tissue:Gonads|replicate:Biological replicate 1 for WT GFP W|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 25 dpf gonad WT GFP W 1 WT GFP W 1 RNA sequencing libraries were generated by extracting 3 g RNA per sample RNA from 25 dpf Danio rerio gonadal tissues. mRNA was then purified from the total RNA and fragmentation was carried out at elevated temperatures. Subsequent cDNA synthesis and size selection steps were carried out to generate fragments of 150 200 bp. PCR purification and quantification was carried out followed by clustering of the libraries. The libraries were then sequenced to generate 150 bp reads.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP149500     WT-GFP-W-1_2.fq.gz WT-GFP-W-1_1.fq.gz fastq fastq 4316037900.0 14386793.0 WT GFP W 1 2.fq.gz 0:150 1:150 A:1113942254;C:1043795560;G:1046264016;T:1111333321;N:702749 150 150     1113942254 1043795560 1046264016 1111333321 702749 SRX4149440 SRS3363035 SRA713582 University of Macau|Faculty of Health Sciences University of Macau 2 0.92927 0.93131 0.04184 0.04197 0.7291 0.73253 0.49518 0.50061 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2018-06-01 Larval Larval Gonad Reproductive System
48330 48330 SRR7244611 SRX4149439 SRS3363036 SRP149500 PRJNA473641 Danio rerio strain:Tg vas:EGFP; figla | isolate:WT GFP S/W | breed:F3 generation Transcriptome or Gene expression PRJNA473641 Transcriptome Analysis Explore the function of figla gene in zebrafish gonadal development       Control strong GFP WT GFP S 3   strain:Not applicable|isolate:figla +/ |breed:Not applicable|cultivar:Not applicable|ecotype:Not applicable|age:25 dpf|dev stage:Fish fry|sex:Unknown|tissue:Gonads|replicate:Biological replicate 3 for WT GFP S|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 25 dpf gonad WT GFP S 3 WT GFP S 3 RNA sequencing libraries were generated by extracting 3 g RNA per sample RNA from 25 dpf Danio rerio gonadal tissues. mRNA was then purified from the total RNA and fragmentation was carried out at elevated temperatures. Subsequent cDNA synthesis and size selection steps were carried out to generate fragments of 150 200 bp. PCR purification and quantification was carried out followed by clustering of the libraries. The libraries were then sequenced to generate 150 bp reads.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP149500     WT-GFP-S-3_2.fq.gz WT-GFP-S-3_1.fq.gz fastq fastq 3729981000.0 12433270.0 WT GFP S 3 2.fq.gz 0:150 1:150 A:965877723;C:899047617;G:901606159;T:962736637;N:712864 150 150     965877723 899047617 901606159 962736637 712864 SRX4149439 SRS3363036 SRA713582 University of Macau|Faculty of Health Sciences University of Macau 2 0.92897 0.93162 0.04099 0.04127 0.71954 0.72728 0.53009 0.51683 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2018-06-01 Larval Larval Gonad Reproductive System
48331 48331 SRR7244612 SRX4149438 SRS3363034 SRP149500 PRJNA473641 Danio rerio strain:Tg vas:EGFP; figla | isolate:WT GFP S/W | breed:F3 generation Transcriptome or Gene expression PRJNA473641 Transcriptome Analysis Explore the function of figla gene in zebrafish gonadal development       Control weak GFP WT GFP W 3   strain:Not applicable|isolate:figla +/ |breed:Not applicable|cultivar:Not applicable|ecotype:Not applicable|age:25 dpf|dev stage:Fish fry|sex:Unknown|tissue:Gonads|replicate:Biological replicate 3 for WT GFP W|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 25 dpf gonad WT GFP W 3 WT GFP W 3 RNA sequencing libraries were generated by extracting 3 g RNA per sample RNA from 25 dpf Danio rerio gonadal tissues. mRNA was then purified from the total RNA and fragmentation was carried out at elevated temperatures. Subsequent cDNA synthesis and size selection steps were carried out to generate fragments of 150 200 bp. PCR purification and quantification was carried out followed by clustering of the libraries. The libraries were then sequenced to generate 150 bp reads.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP149500     WT-GFP-W-3_2.fq.gz WT-GFP-W-3_1.fq.gz fastq fastq 4460555100.0 14868517.0 WT GFP W 3 2.fq.gz 0:150 1:150 A:1151168080;C:1078951831;G:1081169023;T:1148537230;N:728936 150 150     1151168080 1078951831 1081169023 1148537230 728936 SRX4149438 SRS3363034 SRA713582 University of Macau|Faculty of Health Sciences University of Macau 2 0.93283 0.93505 0.04167 0.04245 0.73273 0.73752 0.51474 0.51465 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2018-06-01 Larval Larval Gonad Reproductive System
48332 48332 SRR7244613 SRX4149437 SRS3363033 SRP149500 PRJNA473641 Danio rerio strain:Tg vas:EGFP; figla | isolate:WT GFP S/W | breed:F3 generation Transcriptome or Gene expression PRJNA473641 Transcriptome Analysis Explore the function of figla gene in zebrafish gonadal development       Control weak GFP WT GFP W 2   strain:Not applicable|isolate:figla +/ |breed:Not applicable|cultivar:Not applicable|ecotype:Not applicable|age:25 dpf|dev stage:Fish fry|sex:Unknown|tissue:Gonads|replicate:Biological replicate 2 for WT GFP W|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 25 dpf gonad WT GFP W 2 WT GFP W 2 RNA sequencing libraries were generated by extracting 3 g RNA per sample RNA from 25 dpf Danio rerio gonadal tissues. mRNA was then purified from the total RNA and fragmentation was carried out at elevated temperatures. Subsequent cDNA synthesis and size selection steps were carried out to generate fragments of 150 200 bp. PCR purification and quantification was carried out followed by clustering of the libraries. The libraries were then sequenced to generate 150 bp reads.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP149500     WT-GFP-W-2_2.fq.gz WT-GFP-W-2_1.fq.gz fastq fastq 4411639200.0 14705464.0 WT GFP W 2 2.fq.gz 0:150 1:150 A:1131025272;C:1072829344;G:1075973911;T:1131098315;N:712358 150 150     1131025272 1072829344 1075973911 1131098315 712358 SRX4149437 SRS3363033 SRA713582 University of Macau|Faculty of Health Sciences University of Macau 2 0.93551 0.93638 0.03626 0.03662 0.73866 0.7416 0.50337 0.50374 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2018-06-01 Larval Larval Gonad Reproductive System
48333 48333 SRR7244615 SRX4149436 SRS3363032 SRP149500 PRJNA473641 Danio rerio strain:Tg vas:EGFP; figla | isolate:WT GFP S/W | breed:F3 generation Transcriptome or Gene expression PRJNA473641 Transcriptome Analysis Explore the function of figla gene in zebrafish gonadal development       Mutant strong GFP MT GFP S 2   strain:Not applicable|isolate:figla / |breed:Not applicable|cultivar:Not applicable|ecotype:Not applicable|age:25 dpf|dev stage:Fish fry|sex:Unknown|tissue:Gonads|replicate:Biological replicate 2 for MT GFP S|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 25 dpf gonad MT GFP S 2 MT GFP S 2 RNA sequencing libraries were generated by extracting 3 g RNA per sample RNA from 25 dpf Danio rerio gonadal tissues. mRNA was then purified from the total RNA and fragmentation was carried out at elevated temperatures. Subsequent cDNA synthesis and size selection steps were carried out to generate fragments of 150 200 bp. PCR purification and quantification was carried out followed by clustering of the libraries. The libraries were then sequenced to generate 150 bp reads.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP149500     MT-GFP-S-2_2.fq.gz MT-GFP-S-2_1.fq.gz fastq fastq 5032025400.0 16773418.0 MT GFP S 2 2.fq.gz 0:150 1:150 A:1304328303;C:1213735659;G:1216997071;T:1296429821;N:534546 150 150     1304328303 1213735659 1216997071 1296429821 534546 SRX4149436 SRS3363032 SRA713582 University of Macau|Faculty of Health Sciences University of Macau 2 0.93094 0.93367 0.03923 0.04002 0.73024 0.73486 0.51242 0.51142 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2018-06-01 Larval Larval Gonad Reproductive System
48334 48334 SRR7244616 SRX4149435 SRS3363031 SRP149500 PRJNA473641 Danio rerio strain:Tg vas:EGFP; figla | isolate:WT GFP S/W | breed:F3 generation Transcriptome or Gene expression PRJNA473641 Transcriptome Analysis Explore the function of figla gene in zebrafish gonadal development       Mutant strong GFP MT GFP S 1   strain:Not applicable|isolate:figla / |breed:Not applicable|cultivar:Not applicable|ecotype:Not applicable|age:25 dpf|dev stage:Fish fry|sex:Unknown|tissue:Gonads|replicate:Biological replicate 1 for MT GFP S|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 25 dpf gonad MT GFP S 1 MT GFP S 1 RNA sequencing libraries were generated by extracting 3 g RNA per sample RNA from 25 dpf Danio rerio gonadal tissues. mRNA was then purified from the total RNA and fragmentation was carried out at elevated temperatures. Subsequent cDNA synthesis and size selection steps were carried out to generate fragments of 150 200 bp. PCR purification and quantification was carried out followed by clustering of the libraries. The libraries were then sequenced to generate 150 bp reads.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP149500     MT-GFP-S-1_2.fq.gz MT-GFP-S-1_1.fq.gz fastq fastq 4016382000.0 13387940.0 MT GFP S 1 1.fq.gz 0:150 1:150 A:1041330884;C:965370489;G:969002044;T:1039754515;N:924068 150 150     1041330884 965370489 969002044 1039754515 924068 SRX4149435 SRS3363031 SRA713582 University of Macau|Faculty of Health Sciences University of Macau 2 0.92895 0.93013 0.04034 0.04062 0.74036 0.74541 0.50713 0.52655 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2018-06-01 Larval Larval Gonad Reproductive System
48335 48335 SRR7244617 SRX4149434 SRS3363030 SRP149500 PRJNA473641 Danio rerio strain:Tg vas:EGFP; figla | isolate:WT GFP S/W | breed:F3 generation Transcriptome or Gene expression PRJNA473641 Transcriptome Analysis Explore the function of figla gene in zebrafish gonadal development       Mutant weak GFP MT GFP W 3   strain:Not applicable|isolate:figla / |breed:Not applicable|cultivar:Not applicable|ecotype:Not applicable|age:25 dpf|dev stage:Fish fry|sex:Unknown|tissue:Gonads|replicate:Biological replicate 3 for MT GFP W|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 25 dpf gonad MT GFP W 3 MT GFP W 3 RNA sequencing libraries were generated by extracting 3 g RNA per sample RNA from 25 dpf Danio rerio gonadal tissues. mRNA was then purified from the total RNA and fragmentation was carried out at elevated temperatures. Subsequent cDNA synthesis and size selection steps were carried out to generate fragments of 150 200 bp. PCR purification and quantification was carried out followed by clustering of the libraries. The libraries were then sequenced to generate 150 bp reads.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP149500     MT-GFP-W-3_2.fq.gz MT-GFP-W-3_1.fq.gz fastq fastq 3938295300.0 13127651.0 MT GFP W 3 1.fq.gz 0:150 1:150 A:1014946827;C:955819563;G:955296938;T:1011781397;N:450575 150 150     1014946827 955819563 955296938 1011781397 450575 SRX4149434 SRS3363030 SRA713582 University of Macau|Faculty of Health Sciences University of Macau 2 0.92676 0.9191 0.0449 0.04413 0.74296 0.75854 0.51449 0.50652 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2018-06-01 Larval Larval Gonad Reproductive System
48336 48336 SRR7244618 SRX4149433 SRS3363029 SRP149500 PRJNA473641 Danio rerio strain:Tg vas:EGFP; figla | isolate:WT GFP S/W | breed:F3 generation Transcriptome or Gene expression PRJNA473641 Transcriptome Analysis Explore the function of figla gene in zebrafish gonadal development       Mutant weak GFP MT GFP W 2   strain:Not applicable|isolate:figla / |breed:Not applicable|cultivar:Not applicable|ecotype:Not applicable|age:25 dpf|dev stage:Fish fry|sex:Unknown|tissue:Gonads|replicate:Biological replicate 2 for MT GFP W|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 25 dpf gonad MT GFP W 2 MT GFP W 2 RNA sequencing libraries were generated by extracting 3 g RNA per sample RNA from 25 dpf Danio rerio gonadal tissues. mRNA was then purified from the total RNA and fragmentation was carried out at elevated temperatures. Subsequent cDNA synthesis and size selection steps were carried out to generate fragments of 150 200 bp. PCR purification and quantification was carried out followed by clustering of the libraries. The libraries were then sequenced to generate 150 bp reads.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP149500     MT-GFP-W-2_2.fq.gz MT-GFP-W-2_1.fq.gz fastq fastq 4168599000.0 13895330.0 MT GFP W 2 1.fq.gz 0:150 1:150 A:1073027670;C:1014581587;G:1010948651;T:1069537829;N:503263 150 150     1073027670 1014581587 1010948651 1069537829 503263 SRX4149433 SRS3363029 SRA713582 University of Macau|Faculty of Health Sciences University of Macau 2 0.92168 0.92171 0.03739 0.03743 0.74243 0.75146 0.52723 0.51767 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2018-06-01 Larval Larval Gonad Reproductive System
64217 64217 SRR14343411 SRX10697276 SRS8786690 SRP316710 PRJNA725806 foxl2l regulates female meiotic entry during juvenile gonadal development in zebrafish GSE173480 Transcriptome Analysis Sex determination is distinct from development of other organs for its diversity among species. In zebrafish the sex determination in juvenile stage could be hermaphroditic or gonochoristic. However the detail mechanism is still unclear. Here in this study we found that the transcription factor that belongs to forkhead box family Foxl2l is required for determination of female fate in zebrafish. Foxl2l was expressed from larva stage and became female bias in juvenile stage. The expression was restricted in pre meiotic germ cells. Disruption of Foxl2l function by CRISPR/Cas9 system resulted in all male phenotype in the mutant. Germ cells in foxl2l mutant were arrested in pre meiotic stage at 21 dpf the critical period for female meiotic entry. To further verify the downstream mechanism of Foxl2l on female sex determination wildtype or foxl2l mutant germ cells labeled by foxl2l:egfp at 21 dpf dpf and germ cells labeled by ziwi:egfp at 26 dpf were analyzed by RNA seq and single cell RNA seq respectively Overall design: Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. and RNA sequencing was performed by Illumina NextSeq 500. Each genotype contained triple samples.       HO 3 GSM5268475   tissue:gonad|strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l / |age:21 dpf HO 3 Sequenced data was analyzed by NextSeq Control Software 2.2.0 The de multiplexing adaptor removal and FASTQ file transformation were performed by bcl2fastq Conversion Software 2.17 Illumina Inc. The FASTQ files were imported into CLC Genomics Workbench v.11.0.1 QIAGEN to remove low quality reads including reads with lengths less than 30 nucleotides or with Phred quality score lower than 20 The trimmed reads were mapped to zebrafish genome GRCz11 and TPM were calculated by CLC Genomics Workbench v.11.0.1 QIAGEN Genome build: GRCz11 Supplementary files format and content: txt files contain expression data for all cells gonad   Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols.   strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l / |age:21 dpf GSM5268475 GSM5268475: HO 3; Danio rerio; RNA Seq GSM5268475   1 Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols. GEO Accession:GSM5268475 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP316710     HO_3_run1.R1.fastq HO_3_run1.R2.fastq fastq fastq 3534673132.0 24300429.0 GSM5268475 r1 0:72.72 1:72.74 A:983413722;C:772614472;G:797390978;T:980739251;N:514709 72 72     983413722 772614472 797390978 980739251 514709 SRX10697276 SRS8786690 SRA1224866 GEO Institute of Molecular Biology, Academia Sinica 2 0.92009 0.92081 0.07189 0.07113 0.66176 0.66502 0.48304 0.4818 76 76 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nextera sc_generic single_cell_generic generic-scrnaseq-only   Taiwan 2021-04-28 Larval Larval Gonad Reproductive System
64218 64218 SRR14343412 SRX10697276 SRS8786690 SRP316710 PRJNA725806 foxl2l regulates female meiotic entry during juvenile gonadal development in zebrafish GSE173480 Transcriptome Analysis Sex determination is distinct from development of other organs for its diversity among species. In zebrafish the sex determination in juvenile stage could be hermaphroditic or gonochoristic. However the detail mechanism is still unclear. Here in this study we found that the transcription factor that belongs to forkhead box family Foxl2l is required for determination of female fate in zebrafish. Foxl2l was expressed from larva stage and became female bias in juvenile stage. The expression was restricted in pre meiotic germ cells. Disruption of Foxl2l function by CRISPR/Cas9 system resulted in all male phenotype in the mutant. Germ cells in foxl2l mutant were arrested in pre meiotic stage at 21 dpf the critical period for female meiotic entry. To further verify the downstream mechanism of Foxl2l on female sex determination wildtype or foxl2l mutant germ cells labeled by foxl2l:egfp at 21 dpf dpf and germ cells labeled by ziwi:egfp at 26 dpf were analyzed by RNA seq and single cell RNA seq respectively Overall design: Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. and RNA sequencing was performed by Illumina NextSeq 500. Each genotype contained triple samples.       HO 3 GSM5268475   tissue:gonad|strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l / |age:21 dpf HO 3 Sequenced data was analyzed by NextSeq Control Software 2.2.0 The de multiplexing adaptor removal and FASTQ file transformation were performed by bcl2fastq Conversion Software 2.17 Illumina Inc. The FASTQ files were imported into CLC Genomics Workbench v.11.0.1 QIAGEN to remove low quality reads including reads with lengths less than 30 nucleotides or with Phred quality score lower than 20 The trimmed reads were mapped to zebrafish genome GRCz11 and TPM were calculated by CLC Genomics Workbench v.11.0.1 QIAGEN Genome build: GRCz11 Supplementary files format and content: txt files contain expression data for all cells gonad   Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols.   strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l / |age:21 dpf GSM5268475 GSM5268475: HO 3; Danio rerio; RNA Seq GSM5268475   1 Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols. GEO Accession:GSM5268475 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP316710     HO_3_run2.R1.fastq HO_3_run2.R2.fastq fastq fastq 3789665865.0 25970236.0 GSM5268475 r2 0:72.95 1:72.97 A:1055034390;C:825452326;G:851854221;T:1054834294;N:2490634 72 72     1055034390 825452326 851854221 1054834294 2490634 SRX10697276 SRS8786690 SRA1224866 GEO Institute of Molecular Biology, Academia Sinica 2 0.92122 0.92134 0.07291 0.07232 0.66346 0.66649 0.48355 0.48092 74 74 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nextera sc_generic single_cell_generic generic-scrnaseq-only   Taiwan 2021-04-28 Larval Larval Gonad Reproductive System
64219 64219 SRR14343409 SRX10697275 SRS8786689 SRP316710 PRJNA725806 foxl2l regulates female meiotic entry during juvenile gonadal development in zebrafish GSE173480 Transcriptome Analysis Sex determination is distinct from development of other organs for its diversity among species. In zebrafish the sex determination in juvenile stage could be hermaphroditic or gonochoristic. However the detail mechanism is still unclear. Here in this study we found that the transcription factor that belongs to forkhead box family Foxl2l is required for determination of female fate in zebrafish. Foxl2l was expressed from larva stage and became female bias in juvenile stage. The expression was restricted in pre meiotic germ cells. Disruption of Foxl2l function by CRISPR/Cas9 system resulted in all male phenotype in the mutant. Germ cells in foxl2l mutant were arrested in pre meiotic stage at 21 dpf the critical period for female meiotic entry. To further verify the downstream mechanism of Foxl2l on female sex determination wildtype or foxl2l mutant germ cells labeled by foxl2l:egfp at 21 dpf dpf and germ cells labeled by ziwi:egfp at 26 dpf were analyzed by RNA seq and single cell RNA seq respectively Overall design: Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. and RNA sequencing was performed by Illumina NextSeq 500. Each genotype contained triple samples.       HO 2 GSM5268474   tissue:gonad|strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l / |age:21 dpf HO 2 Sequenced data was analyzed by NextSeq Control Software 2.2.0 The de multiplexing adaptor removal and FASTQ file transformation were performed by bcl2fastq Conversion Software 2.17 Illumina Inc. The FASTQ files were imported into CLC Genomics Workbench v.11.0.1 QIAGEN to remove low quality reads including reads with lengths less than 30 nucleotides or with Phred quality score lower than 20 The trimmed reads were mapped to zebrafish genome GRCz11 and TPM were calculated by CLC Genomics Workbench v.11.0.1 QIAGEN Genome build: GRCz11 Supplementary files format and content: txt files contain expression data for all cells gonad   Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols.   strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l / |age:21 dpf GSM5268474 GSM5268474: HO 2; Danio rerio; RNA Seq GSM5268474   1 Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols. GEO Accession:GSM5268474 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP316710     HO_2_run1.R1.fastq HO_2_run1.R2.fastq fastq fastq 3972958992.0 27776809.0 GSM5268474 r1 0:71.50 1:71.53 A:1124808892;C:846395118;G:875350364;T:1125141364;N:1263254 71 71     1124808892 846395118 875350364 1125141364 1263254 SRX10697275 SRS8786689 SRA1224866 GEO Institute of Molecular Biology, Academia Sinica 2 0.89819 0.89964 0.11368 0.11314 0.65052 0.65387 0.49509 0.49244 76 76 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nextera sc_generic single_cell_generic generic-scrnaseq-only   Taiwan 2021-04-28 Larval Larval Gonad Reproductive System
64220 64220 SRR14343410 SRX10697275 SRS8786689 SRP316710 PRJNA725806 foxl2l regulates female meiotic entry during juvenile gonadal development in zebrafish GSE173480 Transcriptome Analysis Sex determination is distinct from development of other organs for its diversity among species. In zebrafish the sex determination in juvenile stage could be hermaphroditic or gonochoristic. However the detail mechanism is still unclear. Here in this study we found that the transcription factor that belongs to forkhead box family Foxl2l is required for determination of female fate in zebrafish. Foxl2l was expressed from larva stage and became female bias in juvenile stage. The expression was restricted in pre meiotic germ cells. Disruption of Foxl2l function by CRISPR/Cas9 system resulted in all male phenotype in the mutant. Germ cells in foxl2l mutant were arrested in pre meiotic stage at 21 dpf the critical period for female meiotic entry. To further verify the downstream mechanism of Foxl2l on female sex determination wildtype or foxl2l mutant germ cells labeled by foxl2l:egfp at 21 dpf dpf and germ cells labeled by ziwi:egfp at 26 dpf were analyzed by RNA seq and single cell RNA seq respectively Overall design: Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. and RNA sequencing was performed by Illumina NextSeq 500. Each genotype contained triple samples.       HO 2 GSM5268474   tissue:gonad|strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l / |age:21 dpf HO 2 Sequenced data was analyzed by NextSeq Control Software 2.2.0 The de multiplexing adaptor removal and FASTQ file transformation were performed by bcl2fastq Conversion Software 2.17 Illumina Inc. The FASTQ files were imported into CLC Genomics Workbench v.11.0.1 QIAGEN to remove low quality reads including reads with lengths less than 30 nucleotides or with Phred quality score lower than 20 The trimmed reads were mapped to zebrafish genome GRCz11 and TPM were calculated by CLC Genomics Workbench v.11.0.1 QIAGEN Genome build: GRCz11 Supplementary files format and content: txt files contain expression data for all cells gonad   Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols.   strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l / |age:21 dpf GSM5268474 GSM5268474: HO 2; Danio rerio; RNA Seq GSM5268474   1 Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols. GEO Accession:GSM5268474 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP316710     HO_2_run2.R2.fastq HO_2_run2.R1.fastq fastq fastq 4396792493.0 30653836.0 GSM5268474 r2 0:71.70 1:71.73 A:1244672283;C:933954952;G:965736051;T:1248628688;N:3800519 71 71     1244672283 933954952 965736051 1248628688 3800519 SRX10697275 SRS8786689 SRA1224866 GEO Institute of Molecular Biology, Academia Sinica 2 0.89957 0.90042 0.11576 0.11485 0.64985 0.65348 0.48847 0.48933 76 76 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nextera sc_generic single_cell_generic generic-scrnaseq-only   Taiwan 2021-04-28 Larval Larval Gonad Reproductive System
64221 64221 SRR14343407 SRX10697274 SRS8786688 SRP316710 PRJNA725806 foxl2l regulates female meiotic entry during juvenile gonadal development in zebrafish GSE173480 Transcriptome Analysis Sex determination is distinct from development of other organs for its diversity among species. In zebrafish the sex determination in juvenile stage could be hermaphroditic or gonochoristic. However the detail mechanism is still unclear. Here in this study we found that the transcription factor that belongs to forkhead box family Foxl2l is required for determination of female fate in zebrafish. Foxl2l was expressed from larva stage and became female bias in juvenile stage. The expression was restricted in pre meiotic germ cells. Disruption of Foxl2l function by CRISPR/Cas9 system resulted in all male phenotype in the mutant. Germ cells in foxl2l mutant were arrested in pre meiotic stage at 21 dpf the critical period for female meiotic entry. To further verify the downstream mechanism of Foxl2l on female sex determination wildtype or foxl2l mutant germ cells labeled by foxl2l:egfp at 21 dpf dpf and germ cells labeled by ziwi:egfp at 26 dpf were analyzed by RNA seq and single cell RNA seq respectively Overall design: Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. and RNA sequencing was performed by Illumina NextSeq 500. Each genotype contained triple samples.       HO 1 GSM5268473   tissue:gonad|strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l / |age:21 dpf HO 1 Sequenced data was analyzed by NextSeq Control Software 2.2.0 The de multiplexing adaptor removal and FASTQ file transformation were performed by bcl2fastq Conversion Software 2.17 Illumina Inc. The FASTQ files were imported into CLC Genomics Workbench v.11.0.1 QIAGEN to remove low quality reads including reads with lengths less than 30 nucleotides or with Phred quality score lower than 20 The trimmed reads were mapped to zebrafish genome GRCz11 and TPM were calculated by CLC Genomics Workbench v.11.0.1 QIAGEN Genome build: GRCz11 Supplementary files format and content: txt files contain expression data for all cells gonad   Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols.   strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l / |age:21 dpf GSM5268473 GSM5268473: HO 1; Danio rerio; RNA Seq GSM5268473   1 Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols. GEO Accession:GSM5268473 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP316710     HO_1_run1.R1.fastq HO_1_run1.R2.fastq fastq fastq 3833739891.0 26806927.0 GSM5268473 r1 0:71.49 1:71.52 A:1084861861;C:818381943;G:845191898;T:1084121864;N:1182325 71 71     1084861861 818381943 845191898 1084121864 1182325 SRX10697274 SRS8786688 SRA1224866 GEO Institute of Molecular Biology, Academia Sinica 2 0.90273 0.90247 0.09672 0.09556 0.6565 0.65932 0.48356 0.49197 74 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nextera sc_generic single_cell_generic generic-scrnaseq-only   Taiwan 2021-04-28 Larval Larval Gonad Reproductive System
64222 64222 SRR14343408 SRX10697274 SRS8786688 SRP316710 PRJNA725806 foxl2l regulates female meiotic entry during juvenile gonadal development in zebrafish GSE173480 Transcriptome Analysis Sex determination is distinct from development of other organs for its diversity among species. In zebrafish the sex determination in juvenile stage could be hermaphroditic or gonochoristic. However the detail mechanism is still unclear. Here in this study we found that the transcription factor that belongs to forkhead box family Foxl2l is required for determination of female fate in zebrafish. Foxl2l was expressed from larva stage and became female bias in juvenile stage. The expression was restricted in pre meiotic germ cells. Disruption of Foxl2l function by CRISPR/Cas9 system resulted in all male phenotype in the mutant. Germ cells in foxl2l mutant were arrested in pre meiotic stage at 21 dpf the critical period for female meiotic entry. To further verify the downstream mechanism of Foxl2l on female sex determination wildtype or foxl2l mutant germ cells labeled by foxl2l:egfp at 21 dpf dpf and germ cells labeled by ziwi:egfp at 26 dpf were analyzed by RNA seq and single cell RNA seq respectively Overall design: Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. and RNA sequencing was performed by Illumina NextSeq 500. Each genotype contained triple samples.       HO 1 GSM5268473   tissue:gonad|strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l / |age:21 dpf HO 1 Sequenced data was analyzed by NextSeq Control Software 2.2.0 The de multiplexing adaptor removal and FASTQ file transformation were performed by bcl2fastq Conversion Software 2.17 Illumina Inc. The FASTQ files were imported into CLC Genomics Workbench v.11.0.1 QIAGEN to remove low quality reads including reads with lengths less than 30 nucleotides or with Phred quality score lower than 20 The trimmed reads were mapped to zebrafish genome GRCz11 and TPM were calculated by CLC Genomics Workbench v.11.0.1 QIAGEN Genome build: GRCz11 Supplementary files format and content: txt files contain expression data for all cells gonad   Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols.   strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l / |age:21 dpf GSM5268473 GSM5268473: HO 1; Danio rerio; RNA Seq GSM5268473   1 Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols. GEO Accession:GSM5268473 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP316710     HO_1_run2.R2.fastq HO_1_run2.R1.fastq fastq fastq 4251914417.0 29647144.0 GSM5268473 r2 0:71.69 1:71.72 A:1202985882;C:905068322;G:934722262;T:1205490290;N:3647661 71 71     1202985882 905068322 934722262 1205490290 3647661 SRX10697274 SRS8786688 SRA1224866 GEO Institute of Molecular Biology, Academia Sinica 2 0.90347 0.9046 0.09694 0.09634 0.65662 0.66131 0.49104 0.48825 76 76 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nextera sc_generic single_cell_generic generic-scrnaseq-only   Taiwan 2021-04-28 Larval Larval Gonad Reproductive System
64223 64223 SRR14343405 SRX10697273 SRS8786687 SRP316710 PRJNA725806 foxl2l regulates female meiotic entry during juvenile gonadal development in zebrafish GSE173480 Transcriptome Analysis Sex determination is distinct from development of other organs for its diversity among species. In zebrafish the sex determination in juvenile stage could be hermaphroditic or gonochoristic. However the detail mechanism is still unclear. Here in this study we found that the transcription factor that belongs to forkhead box family Foxl2l is required for determination of female fate in zebrafish. Foxl2l was expressed from larva stage and became female bias in juvenile stage. The expression was restricted in pre meiotic germ cells. Disruption of Foxl2l function by CRISPR/Cas9 system resulted in all male phenotype in the mutant. Germ cells in foxl2l mutant were arrested in pre meiotic stage at 21 dpf the critical period for female meiotic entry. To further verify the downstream mechanism of Foxl2l on female sex determination wildtype or foxl2l mutant germ cells labeled by foxl2l:egfp at 21 dpf dpf and germ cells labeled by ziwi:egfp at 26 dpf were analyzed by RNA seq and single cell RNA seq respectively Overall design: Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. and RNA sequencing was performed by Illumina NextSeq 500. Each genotype contained triple samples.       WT 3 GSM5268472   tissue:gonad|strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l+/+|age:21 dpf WT 3 Sequenced data was analyzed by NextSeq Control Software 2.2.0 The de multiplexing adaptor removal and FASTQ file transformation were performed by bcl2fastq Conversion Software 2.17 Illumina Inc. The FASTQ files were imported into CLC Genomics Workbench v.11.0.1 QIAGEN to remove low quality reads including reads with lengths less than 30 nucleotides or with Phred quality score lower than 20 The trimmed reads were mapped to zebrafish genome GRCz11 and TPM were calculated by CLC Genomics Workbench v.11.0.1 QIAGEN Genome build: GRCz11 Supplementary files format and content: txt files contain expression data for all cells gonad   Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols.   strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l+/+|age:21 dpf GSM5268472 GSM5268472: WT 3; Danio rerio; RNA Seq GSM5268472   1 Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols. GEO Accession:GSM5268472 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP316710     WT_3_run1.R1.fastq WT_3_run1.R2.fastq fastq fastq 3615402373.0 25312788.0 GSM5268472 r1 0:71.39 1:71.44 A:1078168256;C:699509937;G:739078497;T:1097303558;N:1342125 71 71     1078168256 699509937 739078497 1097303558 1342125 SRX10697273 SRS8786687 SRA1224866 GEO Institute of Molecular Biology, Academia Sinica 2 0.7144 0.71612 0.09852 0.09708 0.70027 0.70331 0.49157 0.49119 75 76 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nextera sc_generic single_cell_generic generic-scrnaseq-only   Taiwan 2021-04-28 Larval Larval Gonad Reproductive System
64224 64224 SRR14343406 SRX10697273 SRS8786687 SRP316710 PRJNA725806 foxl2l regulates female meiotic entry during juvenile gonadal development in zebrafish GSE173480 Transcriptome Analysis Sex determination is distinct from development of other organs for its diversity among species. In zebrafish the sex determination in juvenile stage could be hermaphroditic or gonochoristic. However the detail mechanism is still unclear. Here in this study we found that the transcription factor that belongs to forkhead box family Foxl2l is required for determination of female fate in zebrafish. Foxl2l was expressed from larva stage and became female bias in juvenile stage. The expression was restricted in pre meiotic germ cells. Disruption of Foxl2l function by CRISPR/Cas9 system resulted in all male phenotype in the mutant. Germ cells in foxl2l mutant were arrested in pre meiotic stage at 21 dpf the critical period for female meiotic entry. To further verify the downstream mechanism of Foxl2l on female sex determination wildtype or foxl2l mutant germ cells labeled by foxl2l:egfp at 21 dpf dpf and germ cells labeled by ziwi:egfp at 26 dpf were analyzed by RNA seq and single cell RNA seq respectively Overall design: Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. and RNA sequencing was performed by Illumina NextSeq 500. Each genotype contained triple samples.       WT 3 GSM5268472   tissue:gonad|strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l+/+|age:21 dpf WT 3 Sequenced data was analyzed by NextSeq Control Software 2.2.0 The de multiplexing adaptor removal and FASTQ file transformation were performed by bcl2fastq Conversion Software 2.17 Illumina Inc. The FASTQ files were imported into CLC Genomics Workbench v.11.0.1 QIAGEN to remove low quality reads including reads with lengths less than 30 nucleotides or with Phred quality score lower than 20 The trimmed reads were mapped to zebrafish genome GRCz11 and TPM were calculated by CLC Genomics Workbench v.11.0.1 QIAGEN Genome build: GRCz11 Supplementary files format and content: txt files contain expression data for all cells gonad   Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols.   strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l+/+|age:21 dpf GSM5268472 GSM5268472: WT 3; Danio rerio; RNA Seq GSM5268472   1 Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols. GEO Accession:GSM5268472 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP316710     WT_3_run2.R1.fastq WT_3_run2.R2.fastq fastq fastq 4010245556.0 27994253.0 GSM5268472 r2 0:71.60 1:71.65 A:1193569082;C:773024546;G:816013849;T:1223955095;N:3682984 71 71     1193569082 773024546 816013849 1223955095 3682984 SRX10697273 SRS8786687 SRA1224866 GEO Institute of Molecular Biology, Academia Sinica 2 0.71057 0.71162 0.09984 0.09845 0.70102 0.70435 0.4941 0.48909 74 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nextera sc_generic single_cell_generic generic-scrnaseq-only   Taiwan 2021-04-28 Larval Larval Gonad Reproductive System
64225 64225 SRR14343403 SRX10697272 SRS8786686 SRP316710 PRJNA725806 foxl2l regulates female meiotic entry during juvenile gonadal development in zebrafish GSE173480 Transcriptome Analysis Sex determination is distinct from development of other organs for its diversity among species. In zebrafish the sex determination in juvenile stage could be hermaphroditic or gonochoristic. However the detail mechanism is still unclear. Here in this study we found that the transcription factor that belongs to forkhead box family Foxl2l is required for determination of female fate in zebrafish. Foxl2l was expressed from larva stage and became female bias in juvenile stage. The expression was restricted in pre meiotic germ cells. Disruption of Foxl2l function by CRISPR/Cas9 system resulted in all male phenotype in the mutant. Germ cells in foxl2l mutant were arrested in pre meiotic stage at 21 dpf the critical period for female meiotic entry. To further verify the downstream mechanism of Foxl2l on female sex determination wildtype or foxl2l mutant germ cells labeled by foxl2l:egfp at 21 dpf dpf and germ cells labeled by ziwi:egfp at 26 dpf were analyzed by RNA seq and single cell RNA seq respectively Overall design: Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. and RNA sequencing was performed by Illumina NextSeq 500. Each genotype contained triple samples.       WT 2 GSM5268471   tissue:gonad|strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l+/+|age:21 dpf WT 2 Sequenced data was analyzed by NextSeq Control Software 2.2.0 The de multiplexing adaptor removal and FASTQ file transformation were performed by bcl2fastq Conversion Software 2.17 Illumina Inc. The FASTQ files were imported into CLC Genomics Workbench v.11.0.1 QIAGEN to remove low quality reads including reads with lengths less than 30 nucleotides or with Phred quality score lower than 20 The trimmed reads were mapped to zebrafish genome GRCz11 and TPM were calculated by CLC Genomics Workbench v.11.0.1 QIAGEN Genome build: GRCz11 Supplementary files format and content: txt files contain expression data for all cells gonad   Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols.   strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l+/+|age:21 dpf GSM5268471 GSM5268471: WT 2; Danio rerio; RNA Seq GSM5268471   1 Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols. GEO Accession:GSM5268471 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP316710     WT_2_run1.R1.fastq WT_2_run1.R2.fastq fastq fastq 4242860973.0 29911182.0 GSM5268471 r1 0:70.91 1:70.94 A:1225861906;C:877846427;G:910477747;T:1227170958;N:1503935 70 70     1225861906 877846427 910477747 1227170958 1503935 SRX10697272 SRS8786686 SRA1224866 GEO Institute of Molecular Biology, Academia Sinica 2 0.88249 0.8846 0.12426 0.12254 0.67568 0.67777 0.49104 0.49087 76 76 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nextera sc_generic single_cell_generic generic-scrnaseq-only   Taiwan 2021-04-28 Larval Larval Gonad Reproductive System
64226 64226 SRR14343404 SRX10697272 SRS8786686 SRP316710 PRJNA725806 foxl2l regulates female meiotic entry during juvenile gonadal development in zebrafish GSE173480 Transcriptome Analysis Sex determination is distinct from development of other organs for its diversity among species. In zebrafish the sex determination in juvenile stage could be hermaphroditic or gonochoristic. However the detail mechanism is still unclear. Here in this study we found that the transcription factor that belongs to forkhead box family Foxl2l is required for determination of female fate in zebrafish. Foxl2l was expressed from larva stage and became female bias in juvenile stage. The expression was restricted in pre meiotic germ cells. Disruption of Foxl2l function by CRISPR/Cas9 system resulted in all male phenotype in the mutant. Germ cells in foxl2l mutant were arrested in pre meiotic stage at 21 dpf the critical period for female meiotic entry. To further verify the downstream mechanism of Foxl2l on female sex determination wildtype or foxl2l mutant germ cells labeled by foxl2l:egfp at 21 dpf dpf and germ cells labeled by ziwi:egfp at 26 dpf were analyzed by RNA seq and single cell RNA seq respectively Overall design: Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. and RNA sequencing was performed by Illumina NextSeq 500. Each genotype contained triple samples.       WT 2 GSM5268471   tissue:gonad|strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l+/+|age:21 dpf WT 2 Sequenced data was analyzed by NextSeq Control Software 2.2.0 The de multiplexing adaptor removal and FASTQ file transformation were performed by bcl2fastq Conversion Software 2.17 Illumina Inc. The FASTQ files were imported into CLC Genomics Workbench v.11.0.1 QIAGEN to remove low quality reads including reads with lengths less than 30 nucleotides or with Phred quality score lower than 20 The trimmed reads were mapped to zebrafish genome GRCz11 and TPM were calculated by CLC Genomics Workbench v.11.0.1 QIAGEN Genome build: GRCz11 Supplementary files format and content: txt files contain expression data for all cells gonad   Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols.   strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l+/+|age:21 dpf GSM5268471 GSM5268471: WT 2; Danio rerio; RNA Seq GSM5268471   1 Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols. GEO Accession:GSM5268471 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP316710     WT_2_run2.R2.fastq WT_2_run2.R1.fastq fastq fastq 4702850600.0 33040042.0 GSM5268471 r2 0:71.15 1:71.19 A:1357977487;C:969603630;G:1005776160;T:1365277602;N:4215721 71 71     1357977487 969603630 1005776160 1365277602 4215721 SRX10697272 SRS8786686 SRA1224866 GEO Institute of Molecular Biology, Academia Sinica 2 0.88141 0.88412 0.12385 0.12227 0.67805 0.68156 0.48576 0.49354 76 76 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nextera sc_generic single_cell_generic generic-scrnaseq-only   Taiwan 2021-04-28 Larval Larval Gonad Reproductive System
64227 64227 SRR14343401 SRX10697271 SRS8786685 SRP316710 PRJNA725806 foxl2l regulates female meiotic entry during juvenile gonadal development in zebrafish GSE173480 Transcriptome Analysis Sex determination is distinct from development of other organs for its diversity among species. In zebrafish the sex determination in juvenile stage could be hermaphroditic or gonochoristic. However the detail mechanism is still unclear. Here in this study we found that the transcription factor that belongs to forkhead box family Foxl2l is required for determination of female fate in zebrafish. Foxl2l was expressed from larva stage and became female bias in juvenile stage. The expression was restricted in pre meiotic germ cells. Disruption of Foxl2l function by CRISPR/Cas9 system resulted in all male phenotype in the mutant. Germ cells in foxl2l mutant were arrested in pre meiotic stage at 21 dpf the critical period for female meiotic entry. To further verify the downstream mechanism of Foxl2l on female sex determination wildtype or foxl2l mutant germ cells labeled by foxl2l:egfp at 21 dpf dpf and germ cells labeled by ziwi:egfp at 26 dpf were analyzed by RNA seq and single cell RNA seq respectively Overall design: Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. and RNA sequencing was performed by Illumina NextSeq 500. Each genotype contained triple samples.       WT 1 GSM5268470   tissue:gonad|strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l+/+|age:21 dpf WT 1 Sequenced data was analyzed by NextSeq Control Software 2.2.0 The de multiplexing adaptor removal and FASTQ file transformation were performed by bcl2fastq Conversion Software 2.17 Illumina Inc. The FASTQ files were imported into CLC Genomics Workbench v.11.0.1 QIAGEN to remove low quality reads including reads with lengths less than 30 nucleotides or with Phred quality score lower than 20 The trimmed reads were mapped to zebrafish genome GRCz11 and TPM were calculated by CLC Genomics Workbench v.11.0.1 QIAGEN Genome build: GRCz11 Supplementary files format and content: txt files contain expression data for all cells gonad   Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols.   strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l+/+|age:21 dpf GSM5268470 GSM5268470: WT 1; Danio rerio; RNA Seq GSM5268470   1 Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols. GEO Accession:GSM5268470 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP316710     WT_1_run1.R2.fastq WT_1_run1.R1.fastq fastq fastq 3768759279.0 26193297.0 GSM5268470 r1 0:71.93 1:71.95 A:1068721513;C:803440242;G:829244956;T:1066480466;N:872102 71 71     1068721513 803440242 829244956 1066480466 872102 SRX10697271 SRS8786685 SRA1224866 GEO Institute of Molecular Biology, Academia Sinica 2 0.90907 0.91124 0.10338 0.1029 0.67054 0.67343 0.48963 0.49025 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nextera sc_generic single_cell_generic generic-scrnaseq-only   Taiwan 2021-04-28 Larval Larval Gonad Reproductive System
64228 64228 SRR14343402 SRX10697271 SRS8786685 SRP316710 PRJNA725806 foxl2l regulates female meiotic entry during juvenile gonadal development in zebrafish GSE173480 Transcriptome Analysis Sex determination is distinct from development of other organs for its diversity among species. In zebrafish the sex determination in juvenile stage could be hermaphroditic or gonochoristic. However the detail mechanism is still unclear. Here in this study we found that the transcription factor that belongs to forkhead box family Foxl2l is required for determination of female fate in zebrafish. Foxl2l was expressed from larva stage and became female bias in juvenile stage. The expression was restricted in pre meiotic germ cells. Disruption of Foxl2l function by CRISPR/Cas9 system resulted in all male phenotype in the mutant. Germ cells in foxl2l mutant were arrested in pre meiotic stage at 21 dpf the critical period for female meiotic entry. To further verify the downstream mechanism of Foxl2l on female sex determination wildtype or foxl2l mutant germ cells labeled by foxl2l:egfp at 21 dpf dpf and germ cells labeled by ziwi:egfp at 26 dpf were analyzed by RNA seq and single cell RNA seq respectively Overall design: Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. and RNA sequencing was performed by Illumina NextSeq 500. Each genotype contained triple samples.       WT 1 GSM5268470   tissue:gonad|strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l+/+|age:21 dpf WT 1 Sequenced data was analyzed by NextSeq Control Software 2.2.0 The de multiplexing adaptor removal and FASTQ file transformation were performed by bcl2fastq Conversion Software 2.17 Illumina Inc. The FASTQ files were imported into CLC Genomics Workbench v.11.0.1 QIAGEN to remove low quality reads including reads with lengths less than 30 nucleotides or with Phred quality score lower than 20 The trimmed reads were mapped to zebrafish genome GRCz11 and TPM were calculated by CLC Genomics Workbench v.11.0.1 QIAGEN Genome build: GRCz11 Supplementary files format and content: txt files contain expression data for all cells gonad   Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols.   strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l+/+|age:21 dpf GSM5268470 GSM5268470: WT 1; Danio rerio; RNA Seq GSM5268470   1 Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols. GEO Accession:GSM5268470 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP316710     WT_1_run2.R2.fastq WT_1_run2.R1.fastq fastq fastq 4100200544.0 28410131.0 GSM5268470 r2 0:72.15 1:72.17 A:1163123243;C:871020431;G:898995203;T:1163892058;N:3169609 72 72     1163123243 871020431 898995203 1163892058 3169609 SRX10697271 SRS8786685 SRA1224866 GEO Institute of Molecular Biology, Academia Sinica 2 0.90943 0.91044 0.10346 0.103 0.66914 0.67004 0.48705 0.49202 76 76 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nextera sc_generic single_cell_generic generic-scrnaseq-only   Taiwan 2021-04-28 Larval Larval Gonad Reproductive System
64474 64474 SRR14710790 SRX11048789 SRS9116824 SRP322308 PRJNA734487 polyA+ RNA seq of zebrafish gonad at 25 dpf and 30dpf GSE175979 Transcriptome Analysis In this study we explored the biological process of zebrafish gonad differentiation through PolyA enriched RNA sequencing and found that the differences in the gonads differentiating towards testis or ovary were represented through types and expression levels of different genes. Using the GO enrichment classification it is found that in the differentiating ovary the differentially expressed genes are enriched in processes of material synthesis and metabolic pathway indicating that oocyte requires the accumulation of maternal RNA protein sugar lipids vitamins and other substances which is consistent with its basic function of providing primary materials for early development of fertilized embryo. In addition during ovarian differentiation the biological processes associated with the nucleus mitochondria and cytoplasmic particles are more active and the genes associated with sperm egg recognition are also expressed during this period. Unlike the differentiating ovary when the gonad differentiates into testis the differentially expressed genes are more enriched in biological regulation and development processes including morphogenesis cell proliferation etc.The cytometers adapted to these biological processes are associated with cell membrane such as membrane receptors extra cellular regions extra cellular matrix and cell connections and also associated with nuclear chromatin. In addition we enriched 14 signaling pathways involved in testis differentiation and showed the expression heat map of every differentially expressed gene of each pathway. Overall the study reveals the different biological processes existing in the differentiation of the zebrafish gonads into ovary or testis helping us to get a comprehensive understanding of the basis on biological events and molecules during this process. Overall design: Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads. Each gonad is placed under a microscope to identify either the testis or the ovary. Six 25 d…   pubmed:36257818   25dpf testis rep4 GSM5352293   source name:Gonad|strain:AB|tissue:testis|age:post fertilization day 25|genotype:Tgpiwil1 egfp nos3UTRihb327Tg 25dpf testis rep4 High throughput sequencing raw image data files were converted to reads using fqtools plus analysis and using FastqC v0.11.8 and sequencing report tool of MultiQC v0.9to evaluate the raw read quality statistics. Reads were mapped to the corresponding reference genome Ensembl v96 with the parameters " dta x rna strandness RF" and " known spliceset infile" using Hisat2 v2.0.5 and gene annotation was performed in GTF format Ensembl 96. Hisat2 converts the data into BAM format sorted by Samtools v1.5 and removed duplicates using the Picard MarkDuplicates v2.18.15 tool. HTSeq v0.9.1 was used to read and count the parameter " t exon i gene id r pos s reverse". Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Gonad   Gonads were removed and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample 5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit N711 Vazyme and 5ng of amplified cDNA was used for construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502. The zebrafish were maintained  raised  and staged according to zebrafish book. The rearing density is 50 larvae/L for age from 5 dpf to 15 dpf  20 fish/L for age 15 dpf to 1 mpf. strain:AB|tissue:testis|age:post fertilization day 25|genotype:Tgpiwil1 egfp nos3UTRihb327Tg GSM5352293 GSM5352293: 25dpf testis rep4; Danio rerio; RNA Seq GSM5352293   1 Gonads were removed and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample 5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit N711 Vazyme and 5ng of amplified cDNA was used for construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502. GEO Accession:GSM5352293 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP322308     25d_small_4_r1.fastq.gz 25d_small_4_r2.fastq.gz fastq fastq 6890175600.0 22967252.0 GSM5352293 r1 0:150 1:150 A:1847152438;C:1592967055;G:1612263138;T:1837718440;N:74529 150 150     1847152438 1592967055 1612263138 1837718440 74529 SRX11048789 SRS9116824 SRA1239593 GEO College of Life Science and Technology, Huazhong Agricultural University 2 0.94233 0.942 0.03417 0.03432 0.67758 0.68274 0.49361 0.49141 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-06-02 Larval Larval Gonad Reproductive System
64475 64475 SRR14710789 SRX11048788 SRS9116823 SRP322308 PRJNA734487 polyA+ RNA seq of zebrafish gonad at 25 dpf and 30dpf GSE175979 Transcriptome Analysis In this study we explored the biological process of zebrafish gonad differentiation through PolyA enriched RNA sequencing and found that the differences in the gonads differentiating towards testis or ovary were represented through types and expression levels of different genes. Using the GO enrichment classification it is found that in the differentiating ovary the differentially expressed genes are enriched in processes of material synthesis and metabolic pathway indicating that oocyte requires the accumulation of maternal RNA protein sugar lipids vitamins and other substances which is consistent with its basic function of providing primary materials for early development of fertilized embryo. In addition during ovarian differentiation the biological processes associated with the nucleus mitochondria and cytoplasmic particles are more active and the genes associated with sperm egg recognition are also expressed during this period. Unlike the differentiating ovary when the gonad differentiates into testis the differentially expressed genes are more enriched in biological regulation and development processes including morphogenesis cell proliferation etc.The cytometers adapted to these biological processes are associated with cell membrane such as membrane receptors extra cellular regions extra cellular matrix and cell connections and also associated with nuclear chromatin. In addition we enriched 14 signaling pathways involved in testis differentiation and showed the expression heat map of every differentially expressed gene of each pathway. Overall the study reveals the different biological processes existing in the differentiation of the zebrafish gonads into ovary or testis helping us to get a comprehensive understanding of the basis on biological events and molecules during this process. Overall design: Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads. Each gonad is placed under a microscope to identify either the testis or the ovary. Six 25 d…   pubmed:36257818   25dpf testis rep3 GSM5352292   source name:Gonad|strain:AB|tissue:testis|age:post fertilization day 25|genotype:Tgpiwil1 egfp nos3UTRihb327Tg 25dpf testis rep3 High throughput sequencing raw image data files were converted to reads using fqtools plus analysis and using FastqC v0.11.8 and sequencing report tool of MultiQC v0.9to evaluate the raw read quality statistics. Reads were mapped to the corresponding reference genome Ensembl v96 with the parameters " dta x rna strandness RF" and " known spliceset infile" using Hisat2 v2.0.5 and gene annotation was performed in GTF format Ensembl 96. Hisat2 converts the data into BAM format sorted by Samtools v1.5 and removed duplicates using the Picard MarkDuplicates v2.18.15 tool. HTSeq v0.9.1 was used to read and count the parameter " t exon i gene id r pos s reverse". Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Gonad   Gonads were removed and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample 5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit N711 Vazyme and 5ng of amplified cDNA was used for construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502. The zebrafish were maintained  raised  and staged according to zebrafish book. The rearing density is 50 larvae/L for age from 5 dpf to 15 dpf  20 fish/L for age 15 dpf to 1 mpf. strain:AB|tissue:testis|age:post fertilization day 25|genotype:Tgpiwil1 egfp nos3UTRihb327Tg GSM5352292 GSM5352292: 25dpf testis rep3; Danio rerio; RNA Seq GSM5352292   1 Gonads were removed and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample 5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit N711 Vazyme and 5ng of amplified cDNA was used for construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502. GEO Accession:GSM5352292 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP322308     25d_small_3_r1.fastq.gz 25d_small_3_r2.fastq.gz fastq fastq 5831956159.0 19798606.0 GSM5352292 r1 0:148.29 1:146.28 A:1579100295;C:1335743387;G:1350943242;T:1566138991;N:30244 148 146     1579100295 1335743387 1350943242 1566138991 30244 SRX11048788 SRS9116823 SRA1239593 GEO College of Life Science and Technology, Huazhong Agricultural University 2 0.93585 0.9374 0.05188 0.05233 0.67732 0.68087 0.4849 0.48409 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-06-02 Larval Larval Gonad Reproductive System
64476 64476 SRR14710788 SRX11048787 SRS9116822 SRP322308 PRJNA734487 polyA+ RNA seq of zebrafish gonad at 25 dpf and 30dpf GSE175979 Transcriptome Analysis In this study we explored the biological process of zebrafish gonad differentiation through PolyA enriched RNA sequencing and found that the differences in the gonads differentiating towards testis or ovary were represented through types and expression levels of different genes. Using the GO enrichment classification it is found that in the differentiating ovary the differentially expressed genes are enriched in processes of material synthesis and metabolic pathway indicating that oocyte requires the accumulation of maternal RNA protein sugar lipids vitamins and other substances which is consistent with its basic function of providing primary materials for early development of fertilized embryo. In addition during ovarian differentiation the biological processes associated with the nucleus mitochondria and cytoplasmic particles are more active and the genes associated with sperm egg recognition are also expressed during this period. Unlike the differentiating ovary when the gonad differentiates into testis the differentially expressed genes are more enriched in biological regulation and development processes including morphogenesis cell proliferation etc.The cytometers adapted to these biological processes are associated with cell membrane such as membrane receptors extra cellular regions extra cellular matrix and cell connections and also associated with nuclear chromatin. In addition we enriched 14 signaling pathways involved in testis differentiation and showed the expression heat map of every differentially expressed gene of each pathway. Overall the study reveals the different biological processes existing in the differentiation of the zebrafish gonads into ovary or testis helping us to get a comprehensive understanding of the basis on biological events and molecules during this process. Overall design: Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads. Each gonad is placed under a microscope to identify either the testis or the ovary. Six 25 d…   pubmed:36257818   25dpf testis rep2 GSM5352291   source name:Gonad|strain:AB|tissue:testis|age:post fertilization day 25|genotype:Tgpiwil1 egfp nos3UTRihb327Tg 25dpf testis rep2 High throughput sequencing raw image data files were converted to reads using fqtools plus analysis and using FastqC v0.11.8 and sequencing report tool of MultiQC v0.9to evaluate the raw read quality statistics. Reads were mapped to the corresponding reference genome Ensembl v96 with the parameters " dta x rna strandness RF" and " known spliceset infile" using Hisat2 v2.0.5 and gene annotation was performed in GTF format Ensembl 96. Hisat2 converts the data into BAM format sorted by Samtools v1.5 and removed duplicates using the Picard MarkDuplicates v2.18.15 tool. HTSeq v0.9.1 was used to read and count the parameter " t exon i gene id r pos s reverse". Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Gonad   Gonads were removed and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample 5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit N711 Vazyme and 5ng of amplified cDNA was used for construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502. The zebrafish were maintained  raised  and staged according to zebrafish book. The rearing density is 50 larvae/L for age from 5 dpf to 15 dpf  20 fish/L for age 15 dpf to 1 mpf. strain:AB|tissue:testis|age:post fertilization day 25|genotype:Tgpiwil1 egfp nos3UTRihb327Tg GSM5352291 GSM5352291: 25dpf testis rep2; Danio rerio; RNA Seq GSM5352291   1 Gonads were removed and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample 5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit N711 Vazyme and 5ng of amplified cDNA was used for construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502. GEO Accession:GSM5352291 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP322308     25d_small_2_r1.fastq.gz 25d_small_2_r2.fastq.gz fastq fastq 6680102886.0 22669793.0 GSM5352291 r1 0:148.36 1:146.31 A:1795760462;C:1540640290;G:1558598345;T:1785066434;N:37355 148 146     1795760462 1540640290 1558598345 1785066434 37355 SRX11048787 SRS9116822 SRA1239593 GEO College of Life Science and Technology, Huazhong Agricultural University 2 0.93171 0.93413 0.05866 0.0592 0.68233 0.68682 0.493 0.48934 148 136 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-06-02 Larval Larval Gonad Reproductive System
64477 64477 SRR14710787 SRX11048786 SRS9116821 SRP322308 PRJNA734487 polyA+ RNA seq of zebrafish gonad at 25 dpf and 30dpf GSE175979 Transcriptome Analysis In this study we explored the biological process of zebrafish gonad differentiation through PolyA enriched RNA sequencing and found that the differences in the gonads differentiating towards testis or ovary were represented through types and expression levels of different genes. Using the GO enrichment classification it is found that in the differentiating ovary the differentially expressed genes are enriched in processes of material synthesis and metabolic pathway indicating that oocyte requires the accumulation of maternal RNA protein sugar lipids vitamins and other substances which is consistent with its basic function of providing primary materials for early development of fertilized embryo. In addition during ovarian differentiation the biological processes associated with the nucleus mitochondria and cytoplasmic particles are more active and the genes associated with sperm egg recognition are also expressed during this period. Unlike the differentiating ovary when the gonad differentiates into testis the differentially expressed genes are more enriched in biological regulation and development processes including morphogenesis cell proliferation etc.The cytometers adapted to these biological processes are associated with cell membrane such as membrane receptors extra cellular regions extra cellular matrix and cell connections and also associated with nuclear chromatin. In addition we enriched 14 signaling pathways involved in testis differentiation and showed the expression heat map of every differentially expressed gene of each pathway. Overall the study reveals the different biological processes existing in the differentiation of the zebrafish gonads into ovary or testis helping us to get a comprehensive understanding of the basis on biological events and molecules during this process. Overall design: Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads. Each gonad is placed under a microscope to identify either the testis or the ovary. Six 25 d…   pubmed:36257818   25dpf testis rep1 GSM5352290   source name:Gonad|strain:AB|tissue:testis|age:post fertilization day 25|genotype:Tgpiwil1 egfp nos3UTRihb327Tg 25dpf testis rep1 High throughput sequencing raw image data files were converted to reads using fqtools plus analysis and using FastqC v0.11.8 and sequencing report tool of MultiQC v0.9to evaluate the raw read quality statistics. Reads were mapped to the corresponding reference genome Ensembl v96 with the parameters " dta x rna strandness RF" and " known spliceset infile" using Hisat2 v2.0.5 and gene annotation was performed in GTF format Ensembl 96. Hisat2 converts the data into BAM format sorted by Samtools v1.5 and removed duplicates using the Picard MarkDuplicates v2.18.15 tool. HTSeq v0.9.1 was used to read and count the parameter " t exon i gene id r pos s reverse". Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Gonad   Gonads were removed and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample 5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit N711 Vazyme and 5ng of amplified cDNA was used for construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502. The zebrafish were maintained  raised  and staged according to zebrafish book. The rearing density is 50 larvae/L for age from 5 dpf to 15 dpf  20 fish/L for age 15 dpf to 1 mpf. strain:AB|tissue:testis|age:post fertilization day 25|genotype:Tgpiwil1 egfp nos3UTRihb327Tg GSM5352290 GSM5352290: 25dpf testis rep1; Danio rerio; RNA Seq GSM5352290   1 Gonads were removed and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample 5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit N711 Vazyme and 5ng of amplified cDNA was used for construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502. GEO Accession:GSM5352290 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP322308     25d_small_1_r1.fastq.gz 25d_small_1_r2.fastq.gz fastq fastq 6376264134.0 21620713.0 GSM5352290 r1 0:148.28 1:146.63 A:1681014759;C:1506515258;G:1528740404;T:1659966778;N:26935 148 146     1681014759 1506515258 1528740404 1659966778 26935 SRX11048786 SRS9116821 SRA1239593 GEO College of Life Science and Technology, Huazhong Agricultural University 2 0.94285 0.94253 0.03594 0.03655 0.69049 0.6953 0.4631 0.45347 150 149 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-06-02 Larval Larval Gonad Reproductive System
64481 64481 SRR14710783 SRX11048782 SRS9116817 SRP322308 PRJNA734487 polyA+ RNA seq of zebrafish gonad at 25 dpf and 30dpf GSE175979 Transcriptome Analysis In this study we explored the biological process of zebrafish gonad differentiation through PolyA enriched RNA sequencing and found that the differences in the gonads differentiating towards testis or ovary were represented through types and expression levels of different genes. Using the GO enrichment classification it is found that in the differentiating ovary the differentially expressed genes are enriched in processes of material synthesis and metabolic pathway indicating that oocyte requires the accumulation of maternal RNA protein sugar lipids vitamins and other substances which is consistent with its basic function of providing primary materials for early development of fertilized embryo. In addition during ovarian differentiation the biological processes associated with the nucleus mitochondria and cytoplasmic particles are more active and the genes associated with sperm egg recognition are also expressed during this period. Unlike the differentiating ovary when the gonad differentiates into testis the differentially expressed genes are more enriched in biological regulation and development processes including morphogenesis cell proliferation etc.The cytometers adapted to these biological processes are associated with cell membrane such as membrane receptors extra cellular regions extra cellular matrix and cell connections and also associated with nuclear chromatin. In addition we enriched 14 signaling pathways involved in testis differentiation and showed the expression heat map of every differentially expressed gene of each pathway. Overall the study reveals the different biological processes existing in the differentiation of the zebrafish gonads into ovary or testis helping us to get a comprehensive understanding of the basis on biological events and molecules during this process. Overall design: Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads. Each gonad is placed under a microscope to identify either the testis or the ovary. Six 25 d…   pubmed:36257818   25dpf ovary rep2 GSM5352286   source name:Gonad|strain:AB|tissue:ovary|age:post fertilization day 25|genotype:Tgpiwil1 egfp nos3UTRihb327Tg 25dpf ovary rep2 High throughput sequencing raw image data files were converted to reads using fqtools plus analysis and using FastqC v0.11.8 and sequencing report tool of MultiQC v0.9to evaluate the raw read quality statistics. Reads were mapped to the corresponding reference genome Ensembl v96 with the parameters " dta x rna strandness RF" and " known spliceset infile" using Hisat2 v2.0.5 and gene annotation was performed in GTF format Ensembl 96. Hisat2 converts the data into BAM format sorted by Samtools v1.5 and removed duplicates using the Picard MarkDuplicates v2.18.15 tool. HTSeq v0.9.1 was used to read and count the parameter " t exon i gene id r pos s reverse". Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Gonad   Gonads were removed and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample 5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit N711 Vazyme and 5ng of amplified cDNA was used for construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502. The zebrafish were maintained  raised  and staged according to zebrafish book. The rearing density is 50 larvae/L for age from 5 dpf to 15 dpf  20 fish/L for age 15 dpf to 1 mpf. strain:AB|tissue:ovary|age:post fertilization day 25|genotype:Tgpiwil1 egfp nos3UTRihb327Tg GSM5352286 GSM5352286: 25dpf ovary rep2; Danio rerio; RNA Seq GSM5352286   1 Gonads were removed and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample 5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit N711 Vazyme and 5ng of amplified cDNA was used for construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502. GEO Accession:GSM5352286 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP322308     25d_big_2_r1.fastq.gz 25d_big_2_r2.fastq.gz fastq fastq 6848830500.0 22829435.0 GSM5352286 r1 0:150 1:150 A:1816129601;C:1604382405;G:1622927432;T:1805308096;N:82966 150 150     1816129601 1604382405 1622927432 1805308096 82966 SRX11048782 SRS9116817 SRA1239593 GEO College of Life Science and Technology, Huazhong Agricultural University 2 0.94216 0.94259 0.02756 0.02746 0.6996 0.70506 0.49444 0.49308 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-06-02 Larval Larval Gonad Reproductive System
64482 64482 SRR14710782 SRX11048781 SRS9116816 SRP322308 PRJNA734487 polyA+ RNA seq of zebrafish gonad at 25 dpf and 30dpf GSE175979 Transcriptome Analysis In this study we explored the biological process of zebrafish gonad differentiation through PolyA enriched RNA sequencing and found that the differences in the gonads differentiating towards testis or ovary were represented through types and expression levels of different genes. Using the GO enrichment classification it is found that in the differentiating ovary the differentially expressed genes are enriched in processes of material synthesis and metabolic pathway indicating that oocyte requires the accumulation of maternal RNA protein sugar lipids vitamins and other substances which is consistent with its basic function of providing primary materials for early development of fertilized embryo. In addition during ovarian differentiation the biological processes associated with the nucleus mitochondria and cytoplasmic particles are more active and the genes associated with sperm egg recognition are also expressed during this period. Unlike the differentiating ovary when the gonad differentiates into testis the differentially expressed genes are more enriched in biological regulation and development processes including morphogenesis cell proliferation etc.The cytometers adapted to these biological processes are associated with cell membrane such as membrane receptors extra cellular regions extra cellular matrix and cell connections and also associated with nuclear chromatin. In addition we enriched 14 signaling pathways involved in testis differentiation and showed the expression heat map of every differentially expressed gene of each pathway. Overall the study reveals the different biological processes existing in the differentiation of the zebrafish gonads into ovary or testis helping us to get a comprehensive understanding of the basis on biological events and molecules during this process. Overall design: Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads. Each gonad is placed under a microscope to identify either the testis or the ovary. Six 25 d…   pubmed:36257818   25dpf ovary rep1 GSM5352285   source name:Gonad|strain:AB|tissue:ovary|age:post fertilization day 25|genotype:Tgpiwil1 egfp nos3UTRihb327Tg 25dpf ovary rep1 High throughput sequencing raw image data files were converted to reads using fqtools plus analysis and using FastqC v0.11.8 and sequencing report tool of MultiQC v0.9to evaluate the raw read quality statistics. Reads were mapped to the corresponding reference genome Ensembl v96 with the parameters " dta x rna strandness RF" and " known spliceset infile" using Hisat2 v2.0.5 and gene annotation was performed in GTF format Ensembl 96. Hisat2 converts the data into BAM format sorted by Samtools v1.5 and removed duplicates using the Picard MarkDuplicates v2.18.15 tool. HTSeq v0.9.1 was used to read and count the parameter " t exon i gene id r pos s reverse". Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Gonad   Gonads were removed and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample 5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit N711 Vazyme and 5ng of amplified cDNA was used for construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502. The zebrafish were maintained  raised  and staged according to zebrafish book. The rearing density is 50 larvae/L for age from 5 dpf to 15 dpf  20 fish/L for age 15 dpf to 1 mpf. strain:AB|tissue:ovary|age:post fertilization day 25|genotype:Tgpiwil1 egfp nos3UTRihb327Tg GSM5352285 GSM5352285: 25dpf ovary rep1; Danio rerio; RNA Seq GSM5352285   1 Gonads were removed and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample 5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit N711 Vazyme and 5ng of amplified cDNA was used for construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502. GEO Accession:GSM5352285 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP322308     25d_big_1_r1.fastq.gz 25d_big_1_r2.fastq.gz fastq fastq 6699368196.0 22701560.0 GSM5352285 r1 0:148.41 1:146.69 A:1788695477;C:1561375723;G:1579986364;T:1769263423;N:47209 148 146     1788695477 1561375723 1579986364 1769263423 47209 SRX11048781 SRS9116816 SRA1239593 GEO College of Life Science and Technology, Huazhong Agricultural University 2 0.93284 0.93388 0.03454 0.03469 0.68911 0.69382 0.46265 0.50354 150 142 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-06-02 Larval Larval Gonad Reproductive System
68610 68610 SRR18053106 SRX14205166 SRS12027307 SRP360188 PRJNA807685 Zebrafish establish female germ cell identity by advancing cell proliferation and meiosis GSE196899 Transcriptome Analysis In this study we utilize the RNA seq of germ cell to uncover the early germ cell development. To obtain fish with defined sex we crossed domesticated zebrafish with the Nadia strain that has a female dominant W segment. These fish were placed on a ziwi:GFP background to facilitate sorting of fluorescent germ cells for transcriptomic analysis. We analyzed the transcriptomes of germ cells at 10 dpf to 14 dpf dpf when sex dimorphic changes started to appear. Overall design: Germ cells mRNA of 10 12 and 14 dpf in W hybrid ZW*Tupfel long fin and Z hybrid ZZ*Tupfel long fin       ZGC 14 S2 GSM5904419   source name:Germ cells|strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:14 dpf ZGC 14 S2 Sequencing was performed on an Illumina NextSeq500 platform in a 75 base paired end mode.Illumina NextSeq Control software and RTA used for basecalling. sequenced reads were trimmed and mapped to GRCz11 by STAR v2.7.7a expected count TPM and FPKM were calculated by RSEM v1.3.1 Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene id transcript id expected count TPM and FPKM for each sample Germ cells   Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:14 dpf GSM5904419 GSM5904419: ZGC 14 S2; Danio rerio; RNA Seq GSM5904419 r1 GSM5904419 1 Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP360188     ZGC-14d_S2_R1_001.fastq.gz ZGC-14d_S2_R2_001.fastq.gz fastq fastq 8772065329.0 58086157.0 GSM5904419 r1 0:75.50 1:75.52 A:2411951416;C:1868366714;G:1884143678;T:2606412427;N:1191094 75 75     2411951416 1868366714 1884143678 2606412427 1191094 SRX14205166 SRS12027307 SRA1374254 Institute of Molecular Biology, Academia Sinica Institute of Molecular Biology, Academia Sinica 2 0.91301 0.85113 0.12019 0.11193 0.74073 0.75357 0.46933 0.46403 76 74 B B biological fallback assumption illumina nextseq full_length cdna_unspecified nextera bulk unknown unknown   Taiwan 2022-02-16 Larval Larval Gonad Reproductive System
68611 68611 SRR18053107 SRX14205165 SRS12027306 SRP360188 PRJNA807685 Zebrafish establish female germ cell identity by advancing cell proliferation and meiosis GSE196899 Transcriptome Analysis In this study we utilize the RNA seq of germ cell to uncover the early germ cell development. To obtain fish with defined sex we crossed domesticated zebrafish with the Nadia strain that has a female dominant W segment. These fish were placed on a ziwi:GFP background to facilitate sorting of fluorescent germ cells for transcriptomic analysis. We analyzed the transcriptomes of germ cells at 10 dpf to 14 dpf dpf when sex dimorphic changes started to appear. Overall design: Germ cells mRNA of 10 12 and 14 dpf in W hybrid ZW*Tupfel long fin and Z hybrid ZZ*Tupfel long fin       WGC 14d 2 S5 GSM5904418   source name:Germ cells|strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:14 dpf WGC 14d 2 S5 Sequencing was performed on an Illumina NextSeq500 platform in a 75 base paired end mode.Illumina NextSeq Control software and RTA used for basecalling. sequenced reads were trimmed and mapped to GRCz11 by STAR v2.7.7a expected count TPM and FPKM were calculated by RSEM v1.3.1 Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene id transcript id expected count TPM and FPKM for each sample Germ cells   Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:14 dpf GSM5904418 GSM5904418: WGC 14d 2 S5; Danio rerio; RNA Seq GSM5904418 r1 GSM5904418 1 Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP360188     WGC-14d-2_S5_R1_001.fastq.gz WGC-14d-2_S5_R2_001.fastq.gz fastq fastq 8849339495.0 58595861.0 GSM5904418 r1 0:75.51 1:75.51 A:2359117522;C:1984584571;G:1986239530;T:2518617243;N:780629 75 75     2359117522 1984584571 1986239530 2518617243 780629 SRX14205165 SRS12027306 SRA1374254 Institute of Molecular Biology, Academia Sinica Institute of Molecular Biology, Academia Sinica 2 0.94001 0.89251 0.08641 0.08088 0.69885 0.7119 0.48052 0.48199 76 75 B B biological fallback assumption illumina nextseq full_length cdna_unspecified nextera bulk unknown unknown   Taiwan 2022-02-16 Larval Larval Gonad Reproductive System
68612 68612 SRR18053108 SRX14205164 SRS12027305 SRP360188 PRJNA807685 Zebrafish establish female germ cell identity by advancing cell proliferation and meiosis GSE196899 Transcriptome Analysis In this study we utilize the RNA seq of germ cell to uncover the early germ cell development. To obtain fish with defined sex we crossed domesticated zebrafish with the Nadia strain that has a female dominant W segment. These fish were placed on a ziwi:GFP background to facilitate sorting of fluorescent germ cells for transcriptomic analysis. We analyzed the transcriptomes of germ cells at 10 dpf to 14 dpf dpf when sex dimorphic changes started to appear. Overall design: Germ cells mRNA of 10 12 and 14 dpf in W hybrid ZW*Tupfel long fin and Z hybrid ZZ*Tupfel long fin       WGC 14d S4 GSM5904417   source name:Germ cells|strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:14 dpf WGC 14d S4 Sequencing was performed on an Illumina NextSeq500 platform in a 75 base paired end mode.Illumina NextSeq Control software and RTA used for basecalling. sequenced reads were trimmed and mapped to GRCz11 by STAR v2.7.7a expected count TPM and FPKM were calculated by RSEM v1.3.1 Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene id transcript id expected count TPM and FPKM for each sample Germ cells   Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:14 dpf GSM5904417 GSM5904417: WGC 14d S4; Danio rerio; RNA Seq GSM5904417 r1 GSM5904417 1 Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP360188     WGC-14d_S4_R1_001.fastq.gz WGC-14d_S4_R2_001.fastq.gz fastq fastq 9088917585.0 60180495.0 GSM5904417 r1 0:75.51 1:75.52 A:2446403695;C:2007845322;G:2019822658;T:2613990716;N:855194 75 75     2446403695 2007845322 2019822658 2613990716 855194 SRX14205164 SRS12027305 SRA1374254 Institute of Molecular Biology, Academia Sinica Institute of Molecular Biology, Academia Sinica 2 0.93036 0.8827 0.13916 0.13339 0.71283 0.72851 0.48205 0.47214 74 75 B B biological fallback assumption illumina nextseq full_length cdna_unspecified nextera bulk unknown unknown   Taiwan 2022-02-16 Larval Larval Gonad Reproductive System
68613 68613 SRR18053109 SRX14205163 SRS12027304 SRP360188 PRJNA807685 Zebrafish establish female germ cell identity by advancing cell proliferation and meiosis GSE196899 Transcriptome Analysis In this study we utilize the RNA seq of germ cell to uncover the early germ cell development. To obtain fish with defined sex we crossed domesticated zebrafish with the Nadia strain that has a female dominant W segment. These fish were placed on a ziwi:GFP background to facilitate sorting of fluorescent germ cells for transcriptomic analysis. We analyzed the transcriptomes of germ cells at 10 dpf to 14 dpf dpf when sex dimorphic changes started to appear. Overall design: Germ cells mRNA of 10 12 and 14 dpf in W hybrid ZW*Tupfel long fin and Z hybrid ZZ*Tupfel long fin       ZGC 12d S1 GSM5904416   source name:Germ cells|strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf ZGC 12d S1 Sequencing was performed on an Illumina NextSeq500 platform in a 75 base paired end mode.Illumina NextSeq Control software and RTA used for basecalling. sequenced reads were trimmed and mapped to GRCz11 by STAR v2.7.7a expected count TPM and FPKM were calculated by RSEM v1.3.1 Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene id transcript id expected count TPM and FPKM for each sample Germ cells   Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf GSM5904416 GSM5904416: ZGC 12d S1; Danio rerio; RNA Seq GSM5904416 r1 GSM5904416 1 Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP360188     ZGC-12d_S1_R1_001.fastq.gz ZGC-12d_S1_R2_001.fastq.gz fastq fastq 8722159635.0 57761505.0 GSM5904416 r1 0:75.49 1:75.51 A:2572149639;C:1718706987;G:1732875524;T:2697159696;N:1267789 75 75     2572149639 1718706987 1732875524 2697159696 1267789 SRX14205163 SRS12027304 SRA1374254 Institute of Molecular Biology, Academia Sinica Institute of Molecular Biology, Academia Sinica 2 0.86521 0.83888 0.47276 0.46969 0.74089 0.75574 0.46986 0.47701 76 75 B B biological fallback assumption illumina nextseq full_length cdna_unspecified nextera bulk unknown unknown   Taiwan 2022-02-16 Larval Larval Gonad Reproductive System
68614 68614 SRR18053110 SRX14205162 SRS12027303 SRP360188 PRJNA807685 Zebrafish establish female germ cell identity by advancing cell proliferation and meiosis GSE196899 Transcriptome Analysis In this study we utilize the RNA seq of germ cell to uncover the early germ cell development. To obtain fish with defined sex we crossed domesticated zebrafish with the Nadia strain that has a female dominant W segment. These fish were placed on a ziwi:GFP background to facilitate sorting of fluorescent germ cells for transcriptomic analysis. We analyzed the transcriptomes of germ cells at 10 dpf to 14 dpf dpf when sex dimorphic changes started to appear. Overall design: Germ cells mRNA of 10 12 and 14 dpf in W hybrid ZW*Tupfel long fin and Z hybrid ZZ*Tupfel long fin       WGC 12d 2 S6 GSM5904415   source name:Germ cells|strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf WGC 12d 2 S6 Sequencing was performed on an Illumina NextSeq500 platform in a 75 base paired end mode.Illumina NextSeq Control software and RTA used for basecalling. sequenced reads were trimmed and mapped to GRCz11 by STAR v2.7.7a expected count TPM and FPKM were calculated by RSEM v1.3.1 Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene id transcript id expected count TPM and FPKM for each sample Germ cells   Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf GSM5904415 GSM5904415: WGC 12d 2 S6; Danio rerio; RNA Seq GSM5904415 r1 GSM5904415 1 Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP360188     WGC-12d-2_S6_R1_001.fastq.gz WGC-12d-2_S6_R2_001.fastq.gz fastq fastq 9263385431.0 61336656.0 GSM5904415 r1 0:75.51 1:75.52 A:2474480015;C:2069771470;G:2074616387;T:2643692210;N:825349 75 75     2474480015 2069771470 2074616387 2643692210 825349 SRX14205162 SRS12027303 SRA1374254 Institute of Molecular Biology, Academia Sinica Institute of Molecular Biology, Academia Sinica 2 0.93793 0.89386 0.09513 0.09067 0.71096 0.72634 0.48198 0.47513 75 75 B B biological fallback assumption illumina nextseq full_length cdna_unspecified nextera bulk unknown unknown   Taiwan 2022-02-16 Larval Larval Gonad Reproductive System
68615 68615 SRR18053111 SRX14205161 SRS12027302 SRP360188 PRJNA807685 Zebrafish establish female germ cell identity by advancing cell proliferation and meiosis GSE196899 Transcriptome Analysis In this study we utilize the RNA seq of germ cell to uncover the early germ cell development. To obtain fish with defined sex we crossed domesticated zebrafish with the Nadia strain that has a female dominant W segment. These fish were placed on a ziwi:GFP background to facilitate sorting of fluorescent germ cells for transcriptomic analysis. We analyzed the transcriptomes of germ cells at 10 dpf to 14 dpf dpf when sex dimorphic changes started to appear. Overall design: Germ cells mRNA of 10 12 and 14 dpf in W hybrid ZW*Tupfel long fin and Z hybrid ZZ*Tupfel long fin       WGC 12d S3 GSM5904414   source name:Germ cells|strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf WGC 12d S3 Sequencing was performed on an Illumina NextSeq500 platform in a 75 base paired end mode.Illumina NextSeq Control software and RTA used for basecalling. sequenced reads were trimmed and mapped to GRCz11 by STAR v2.7.7a expected count TPM and FPKM were calculated by RSEM v1.3.1 Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene id transcript id expected count TPM and FPKM for each sample Germ cells   Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf GSM5904414 GSM5904414: WGC 12d S3; Danio rerio; RNA Seq GSM5904414 r1 GSM5904414 1 Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP360188     WGC-12d_S3_R1_001.fastq.gz WGC-12d_S3_R2_001.fastq.gz fastq fastq 8254221483.0 54653772.0 GSM5904414 r1 0:75.51 1:75.52 A:2262599449;C:1792236979;G:1799631634;T:2398932437;N:820984 75 75     2262599449 1792236979 1799631634 2398932437 820984 SRX14205161 SRS12027302 SRA1374254 Institute of Molecular Biology, Academia Sinica Institute of Molecular Biology, Academia Sinica 2 0.90409 0.86227 0.23283 0.23002 0.72111 0.73677 0.4701 0.47989 76 75 B B biological fallback assumption illumina nextseq full_length cdna_unspecified nextera bulk unknown unknown   Taiwan 2022-02-16 Larval Larval Gonad Reproductive System
68616 68616 SRR18053112 SRX14205160 SRS12027301 SRP360188 PRJNA807685 Zebrafish establish female germ cell identity by advancing cell proliferation and meiosis GSE196899 Transcriptome Analysis In this study we utilize the RNA seq of germ cell to uncover the early germ cell development. To obtain fish with defined sex we crossed domesticated zebrafish with the Nadia strain that has a female dominant W segment. These fish were placed on a ziwi:GFP background to facilitate sorting of fluorescent germ cells for transcriptomic analysis. We analyzed the transcriptomes of germ cells at 10 dpf to 14 dpf dpf when sex dimorphic changes started to appear. Overall design: Germ cells mRNA of 10 12 and 14 dpf in W hybrid ZW*Tupfel long fin and Z hybrid ZZ*Tupfel long fin       ZGC 12d 4 GSM5904413   source name:Germ cells|strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf ZGC 12d 4 Sequencing was performed on an Illumina NextSeq500 platform in a 75 base paired end mode.Illumina NextSeq Control software and RTA used for basecalling. sequenced reads were trimmed and mapped to GRCz11 by STAR v2.7.7a expected count TPM and FPKM were calculated by RSEM v1.3.1 Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene id transcript id expected count TPM and FPKM for each sample Germ cells   Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf GSM5904413 GSM5904413: ZGC 12d 4; Danio rerio; RNA Seq GSM5904413 r1 GSM5904413 1 Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP360188   loader:fastq load.py ZGC-12d-4_S8_R1_001.fastq.gz ZGC-12d-4_S8_R2_001.fastq.gz fastq fastq 6330329001.0 45706640.0 GSM5904413 r1 0:69.24 1:69.26 A:1836315265;C:1317627281;G:1350410243;T:1822990911;N:2985301 69 69     1836315265 1317627281 1350410243 1822990911 2985301 SRX14205160 SRS12027301 SRA1374254 Institute of Molecular Biology, Academia Sinica Institute of Molecular Biology, Academia Sinica 2 0.90991 0.91123 0.10112 0.10038 0.66758 0.66851 0.4944 0.5031 74 74 B B biological fallback assumption illumina nextseq full_length cdna_unspecified nextera bulk unknown unknown   Taiwan 2022-02-16 Larval Larval Gonad Reproductive System
68617 68617 SRR18053113 SRX14205159 SRS12027300 SRP360188 PRJNA807685 Zebrafish establish female germ cell identity by advancing cell proliferation and meiosis GSE196899 Transcriptome Analysis In this study we utilize the RNA seq of germ cell to uncover the early germ cell development. To obtain fish with defined sex we crossed domesticated zebrafish with the Nadia strain that has a female dominant W segment. These fish were placed on a ziwi:GFP background to facilitate sorting of fluorescent germ cells for transcriptomic analysis. We analyzed the transcriptomes of germ cells at 10 dpf to 14 dpf dpf when sex dimorphic changes started to appear. Overall design: Germ cells mRNA of 10 12 and 14 dpf in W hybrid ZW*Tupfel long fin and Z hybrid ZZ*Tupfel long fin       ZGC 12d 3 GSM5904412   source name:Germ cells|strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf ZGC 12d 3 Sequencing was performed on an Illumina NextSeq500 platform in a 75 base paired end mode.Illumina NextSeq Control software and RTA used for basecalling. sequenced reads were trimmed and mapped to GRCz11 by STAR v2.7.7a expected count TPM and FPKM were calculated by RSEM v1.3.1 Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene id transcript id expected count TPM and FPKM for each sample Germ cells   Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf GSM5904412 GSM5904412: ZGC 12d 3; Danio rerio; RNA Seq GSM5904412 r1 GSM5904412 1 Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP360188   loader:fastq load.py ZGC-12d-3_S7_R1_001.fastq.gz ZGC-12d-3_S7_R2_001.fastq.gz fastq fastq 7295566549.0 51840671.0 GSM5904412 r1 0:70.36 1:70.37 A:2107135730;C:1526622299;G:1568277083;T:2090864804;N:2666633 70 70     2107135730 1526622299 1568277083 2090864804 2666633 SRX14205159 SRS12027300 SRA1374254 Institute of Molecular Biology, Academia Sinica Institute of Molecular Biology, Academia Sinica 2 0.90924 0.90939 0.10127 0.10121 0.6716 0.67535 0.48934 0.50815 76 74 B B biological fallback assumption illumina nextseq full_length cdna_unspecified nextera bulk unknown unknown   Taiwan 2022-02-16 Larval Larval Gonad Reproductive System
68618 68618 SRR18053114 SRX14205158 SRS12027299 SRP360188 PRJNA807685 Zebrafish establish female germ cell identity by advancing cell proliferation and meiosis GSE196899 Transcriptome Analysis In this study we utilize the RNA seq of germ cell to uncover the early germ cell development. To obtain fish with defined sex we crossed domesticated zebrafish with the Nadia strain that has a female dominant W segment. These fish were placed on a ziwi:GFP background to facilitate sorting of fluorescent germ cells for transcriptomic analysis. We analyzed the transcriptomes of germ cells at 10 dpf to 14 dpf dpf when sex dimorphic changes started to appear. Overall design: Germ cells mRNA of 10 12 and 14 dpf in W hybrid ZW*Tupfel long fin and Z hybrid ZZ*Tupfel long fin       ZGC 12d 2 GSM5904411   source name:Germ cells|strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf ZGC 12d 2 Sequencing was performed on an Illumina NextSeq500 platform in a 75 base paired end mode.Illumina NextSeq Control software and RTA used for basecalling. sequenced reads were trimmed and mapped to GRCz11 by STAR v2.7.7a expected count TPM and FPKM were calculated by RSEM v1.3.1 Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene id transcript id expected count TPM and FPKM for each sample Germ cells   Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf GSM5904411 GSM5904411: ZGC 12d 2; Danio rerio; RNA Seq GSM5904411 r1 GSM5904411 1 Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP360188   loader:fastq load.py ZGC-12d-2_S6_R1_001.fastq.gz ZGC-12d-2_S6_R2_001.fastq.gz fastq fastq 6547690177.0 47132355.0 GSM5904411 r1 0:69.45 1:69.47 A:1871218137;C:1391116965;G:1426144072;T:1856318670;N:2892333 69 69     1871218137 1391116965 1426144072 1856318670 2892333 SRX14205158 SRS12027299 SRA1374254 Institute of Molecular Biology, Academia Sinica Institute of Molecular Biology, Academia Sinica 2 0.91159 0.91257 0.09408 0.09442 0.68416 0.68643 0.49982 0.50278 73 76 B B biological fallback assumption illumina nextseq full_length cdna_unspecified nextera bulk unknown unknown   Taiwan 2022-02-16 Larval Larval Gonad Reproductive System
68619 68619 SRR18053115 SRX14205157 SRS12027298 SRP360188 PRJNA807685 Zebrafish establish female germ cell identity by advancing cell proliferation and meiosis GSE196899 Transcriptome Analysis In this study we utilize the RNA seq of germ cell to uncover the early germ cell development. To obtain fish with defined sex we crossed domesticated zebrafish with the Nadia strain that has a female dominant W segment. These fish were placed on a ziwi:GFP background to facilitate sorting of fluorescent germ cells for transcriptomic analysis. We analyzed the transcriptomes of germ cells at 10 dpf to 14 dpf dpf when sex dimorphic changes started to appear. Overall design: Germ cells mRNA of 10 12 and 14 dpf in W hybrid ZW*Tupfel long fin and Z hybrid ZZ*Tupfel long fin       ZGC 12d 1 GSM5904410   source name:Germ cells|strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf ZGC 12d 1 Sequencing was performed on an Illumina NextSeq500 platform in a 75 base paired end mode.Illumina NextSeq Control software and RTA used for basecalling. sequenced reads were trimmed and mapped to GRCz11 by STAR v2.7.7a expected count TPM and FPKM were calculated by RSEM v1.3.1 Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene id transcript id expected count TPM and FPKM for each sample Germ cells   Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf GSM5904410 GSM5904410: ZGC 12d 1; Danio rerio; RNA Seq GSM5904410 r1 GSM5904410 1 Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP360188   loader:fastq load.py ZGC-12d-1_S5_R1_001.fastq.gz ZGC-12d-1_S5_R2_001.fastq.gz fastq fastq 6922463414.0 49745983.0 GSM5904410 r1 0:69.57 1:69.59 A:1950215328;C:1495914205;G:1534891861;T:1938211177;N:3230843 69 69     1950215328 1495914205 1534891861 1938211177 3230843 SRX14205157 SRS12027298 SRA1374254 Institute of Molecular Biology, Academia Sinica Institute of Molecular Biology, Academia Sinica 2 0.91439 0.91479 0.08718 0.08691 0.66671 0.66837 0.49932 0.50205 76 76 B B biological fallback assumption illumina nextseq full_length cdna_unspecified nextera bulk unknown unknown   Taiwan 2022-02-16 Larval Larval Gonad Reproductive System
68620 68620 SRR18053116 SRX14205156 SRS12027297 SRP360188 PRJNA807685 Zebrafish establish female germ cell identity by advancing cell proliferation and meiosis GSE196899 Transcriptome Analysis In this study we utilize the RNA seq of germ cell to uncover the early germ cell development. To obtain fish with defined sex we crossed domesticated zebrafish with the Nadia strain that has a female dominant W segment. These fish were placed on a ziwi:GFP background to facilitate sorting of fluorescent germ cells for transcriptomic analysis. We analyzed the transcriptomes of germ cells at 10 dpf to 14 dpf dpf when sex dimorphic changes started to appear. Overall design: Germ cells mRNA of 10 12 and 14 dpf in W hybrid ZW*Tupfel long fin and Z hybrid ZZ*Tupfel long fin       WGC 12d 4 GSM5904409   source name:Germ cells|strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf WGC 12d 4 Sequencing was performed on an Illumina NextSeq500 platform in a 75 base paired end mode.Illumina NextSeq Control software and RTA used for basecalling. sequenced reads were trimmed and mapped to GRCz11 by STAR v2.7.7a expected count TPM and FPKM were calculated by RSEM v1.3.1 Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene id transcript id expected count TPM and FPKM for each sample Germ cells   Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf GSM5904409 GSM5904409: WGC 12d 4; Danio rerio; RNA Seq GSM5904409 r1 GSM5904409 1 Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP360188   loader:fastq load.py WGC-12d-4_S4_R1_001.fastq.gz WGC-12d-4_S4_R2_001.fastq.gz fastq fastq 6359260156.0 45475594.0 GSM5904409 r1 0:69.91 1:69.93 A:1809337849;C:1356748319;G:1393608207;T:1796993266;N:2572515 69 69     1809337849 1356748319 1393608207 1796993266 2572515 SRX14205156 SRS12027297 SRA1374254 Institute of Molecular Biology, Academia Sinica Institute of Molecular Biology, Academia Sinica 2 0.90486 0.90498 0.10907 0.10859 0.66531 0.66667 0.49946 0.50298 75 76 B B biological fallback assumption illumina nextseq full_length cdna_unspecified nextera bulk unknown unknown   Taiwan 2022-02-16 Larval Larval Gonad Reproductive System
68621 68621 SRR18053117 SRX14205155 SRS12027296 SRP360188 PRJNA807685 Zebrafish establish female germ cell identity by advancing cell proliferation and meiosis GSE196899 Transcriptome Analysis In this study we utilize the RNA seq of germ cell to uncover the early germ cell development. To obtain fish with defined sex we crossed domesticated zebrafish with the Nadia strain that has a female dominant W segment. These fish were placed on a ziwi:GFP background to facilitate sorting of fluorescent germ cells for transcriptomic analysis. We analyzed the transcriptomes of germ cells at 10 dpf to 14 dpf dpf when sex dimorphic changes started to appear. Overall design: Germ cells mRNA of 10 12 and 14 dpf in W hybrid ZW*Tupfel long fin and Z hybrid ZZ*Tupfel long fin       WGC 12d 3 GSM5904408   source name:Germ cells|strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf WGC 12d 3 Sequencing was performed on an Illumina NextSeq500 platform in a 75 base paired end mode.Illumina NextSeq Control software and RTA used for basecalling. sequenced reads were trimmed and mapped to GRCz11 by STAR v2.7.7a expected count TPM and FPKM were calculated by RSEM v1.3.1 Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene id transcript id expected count TPM and FPKM for each sample Germ cells   Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf GSM5904408 GSM5904408: WGC 12d 3; Danio rerio; RNA Seq GSM5904408 r1 GSM5904408 1 Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP360188   loader:fastq load.py WGC-12d-3_S3_R1_001.fastq.gz WGC-12d-3_S3_R2_001.fastq.gz fastq fastq 6013942017.0 43331055.0 GSM5904408 r1 0:69.39 1:69.40 A:1723789351;C:1270513233;G:1307399719;T:1709606441;N:2633273 69 69     1723789351 1270513233 1307399719 1709606441 2633273 SRX14205155 SRS12027296 SRA1374254 Institute of Molecular Biology, Academia Sinica Institute of Molecular Biology, Academia Sinica 2 0.8887 0.88991 0.12692 0.12629 0.6618 0.66231 0.50592 0.50436 76 76 B B biological fallback assumption illumina nextseq full_length cdna_unspecified nextera bulk unknown unknown   Taiwan 2022-02-16 Larval Larval Gonad Reproductive System
68622 68622 SRR18053118 SRX14205154 SRS12027295 SRP360188 PRJNA807685 Zebrafish establish female germ cell identity by advancing cell proliferation and meiosis GSE196899 Transcriptome Analysis In this study we utilize the RNA seq of germ cell to uncover the early germ cell development. To obtain fish with defined sex we crossed domesticated zebrafish with the Nadia strain that has a female dominant W segment. These fish were placed on a ziwi:GFP background to facilitate sorting of fluorescent germ cells for transcriptomic analysis. We analyzed the transcriptomes of germ cells at 10 dpf to 14 dpf dpf when sex dimorphic changes started to appear. Overall design: Germ cells mRNA of 10 12 and 14 dpf in W hybrid ZW*Tupfel long fin and Z hybrid ZZ*Tupfel long fin       WGC 12d 2 GSM5904407   source name:Germ cells|strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf WGC 12d 2 Sequencing was performed on an Illumina NextSeq500 platform in a 75 base paired end mode.Illumina NextSeq Control software and RTA used for basecalling. sequenced reads were trimmed and mapped to GRCz11 by STAR v2.7.7a expected count TPM and FPKM were calculated by RSEM v1.3.1 Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene id transcript id expected count TPM and FPKM for each sample Germ cells   Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf GSM5904407 GSM5904407: WGC 12d 2; Danio rerio; RNA Seq GSM5904407 r1 GSM5904407 1 Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP360188   loader:fastq load.py WGC-12d-2_S2_R1_001.fastq.gz WGC-12d-2_S2_R2_001.fastq.gz fastq fastq 6849433930.0 48624193.0 GSM5904407 r1 0:70.42 1:70.44 A:1965504915;C:1446185564;G:1486794623;T:1948393472;N:2555356 70 70     1965504915 1446185564 1486794623 1948393472 2555356 SRX14205154 SRS12027295 SRA1374254 Institute of Molecular Biology, Academia Sinica Institute of Molecular Biology, Academia Sinica 2 0.89086 0.89097 0.12682 0.12701 0.66194 0.66344 0.49164 0.49551 76 76 B B biological fallback assumption illumina nextseq full_length cdna_unspecified nextera bulk unknown unknown   Taiwan 2022-02-16 Larval Larval Gonad Reproductive System
68623 68623 SRR18053119 SRX14205153 SRS12027294 SRP360188 PRJNA807685 Zebrafish establish female germ cell identity by advancing cell proliferation and meiosis GSE196899 Transcriptome Analysis In this study we utilize the RNA seq of germ cell to uncover the early germ cell development. To obtain fish with defined sex we crossed domesticated zebrafish with the Nadia strain that has a female dominant W segment. These fish were placed on a ziwi:GFP background to facilitate sorting of fluorescent germ cells for transcriptomic analysis. We analyzed the transcriptomes of germ cells at 10 dpf to 14 dpf dpf when sex dimorphic changes started to appear. Overall design: Germ cells mRNA of 10 12 and 14 dpf in W hybrid ZW*Tupfel long fin and Z hybrid ZZ*Tupfel long fin       WGC 12d 1 GSM5904406   source name:Germ cells|strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf WGC 12d 1 Sequencing was performed on an Illumina NextSeq500 platform in a 75 base paired end mode.Illumina NextSeq Control software and RTA used for basecalling. sequenced reads were trimmed and mapped to GRCz11 by STAR v2.7.7a expected count TPM and FPKM were calculated by RSEM v1.3.1 Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene id transcript id expected count TPM and FPKM for each sample Germ cells   Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf GSM5904406 GSM5904406: WGC 12d 1; Danio rerio; RNA Seq GSM5904406 r1 GSM5904406 1 Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP360188   loader:fastq load.py WGC-12d-1_S1_R1_001.fastq.gz WGC-12d-1_S1_R2_001.fastq.gz fastq fastq 7142014082.0 51431842.0 GSM5904406 r1 0:69.42 1:69.44 A:2020588707;C:1536219895;G:1574729406;T:2007273434;N:3202640 69 69     2020588707 1536219895 1574729406 2007273434 3202640 SRX14205153 SRS12027294 SRA1374254 Institute of Molecular Biology, Academia Sinica Institute of Molecular Biology, Academia Sinica 2 0.88974 0.88943 0.08794 0.08766 0.67284 0.67353 0.49125 0.49137 76 75 B B biological fallback assumption illumina nextseq full_length cdna_unspecified nextera bulk unknown unknown   Taiwan 2022-02-16 Larval Larval Gonad Reproductive System
68624 68624 SRR18053120 SRX14205152 SRS12027293 SRP360188 PRJNA807685 Zebrafish establish female germ cell identity by advancing cell proliferation and meiosis GSE196899 Transcriptome Analysis In this study we utilize the RNA seq of germ cell to uncover the early germ cell development. To obtain fish with defined sex we crossed domesticated zebrafish with the Nadia strain that has a female dominant W segment. These fish were placed on a ziwi:GFP background to facilitate sorting of fluorescent germ cells for transcriptomic analysis. We analyzed the transcriptomes of germ cells at 10 dpf to 14 dpf dpf when sex dimorphic changes started to appear. Overall design: Germ cells mRNA of 10 12 and 14 dpf in W hybrid ZW*Tupfel long fin and Z hybrid ZZ*Tupfel long fin       ZGC 10d 3 GSM5904405   source name:Germ cells|strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:10 dpf ZGC 10d 3 Sequencing was performed on an Illumina NextSeq500 platform in a 75 base paired end mode.Illumina NextSeq Control software and RTA used for basecalling. sequenced reads were trimmed and mapped to GRCz11 by STAR v2.7.7a expected count TPM and FPKM were calculated by RSEM v1.3.1 Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene id transcript id expected count TPM and FPKM for each sample Germ cells   Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:10 dpf GSM5904405 GSM5904405: ZGC 10d 3; Danio rerio; RNA Seq GSM5904405 r1 GSM5904405 1 Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP360188   loader:fastq load.py ZGC-10d-3_S14_R1_001.fastq.gz ZGC-10d-3_S14_R2_001.fastq.gz fastq fastq 7454901016.0 53103891.0 GSM5904405 r1 0:70.18 1:70.20 A:2106408530;C:1605407370;G:1648344530;T:2091876333;N:2864253 70 70     2106408530 1605407370 1648344530 2091876333 2864253 SRX14205152 SRS12027293 SRA1374254 Institute of Molecular Biology, Academia Sinica Institute of Molecular Biology, Academia Sinica 2 0.9099 0.91056 0.10008 0.09968 0.66953 0.6702 0.50389 0.50387 76 76 B B biological fallback assumption illumina nextseq full_length cdna_unspecified nextera bulk unknown unknown   Taiwan 2022-02-16 Larval Larval Gonad Reproductive System
68625 68625 SRR18053121 SRX14205151 SRS12027292 SRP360188 PRJNA807685 Zebrafish establish female germ cell identity by advancing cell proliferation and meiosis GSE196899 Transcriptome Analysis In this study we utilize the RNA seq of germ cell to uncover the early germ cell development. To obtain fish with defined sex we crossed domesticated zebrafish with the Nadia strain that has a female dominant W segment. These fish were placed on a ziwi:GFP background to facilitate sorting of fluorescent germ cells for transcriptomic analysis. We analyzed the transcriptomes of germ cells at 10 dpf to 14 dpf dpf when sex dimorphic changes started to appear. Overall design: Germ cells mRNA of 10 12 and 14 dpf in W hybrid ZW*Tupfel long fin and Z hybrid ZZ*Tupfel long fin       ZGC 10d 2 GSM5904404   source name:Germ cells|strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:10 dpf ZGC 10d 2 Sequencing was performed on an Illumina NextSeq500 platform in a 75 base paired end mode.Illumina NextSeq Control software and RTA used for basecalling. sequenced reads were trimmed and mapped to GRCz11 by STAR v2.7.7a expected count TPM and FPKM were calculated by RSEM v1.3.1 Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene id transcript id expected count TPM and FPKM for each sample Germ cells   Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:10 dpf GSM5904404 GSM5904404: ZGC 10d 2; Danio rerio; RNA Seq GSM5904404 r1 GSM5904404 1 Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP360188   loader:fastq load.py ZGC-10d-2_S13_R1_001.fastq.gz ZGC-10d-2_S13_R2_001.fastq.gz fastq fastq 7030544986.0 49888238.0 GSM5904404 r1 0:70.46 1:70.47 A:1971780065;C:1528134150;G:1570010020;T:1958005642;N:2615109 70 70     1971780065 1528134150 1570010020 1958005642 2615109 SRX14205151 SRS12027292 SRA1374254 Institute of Molecular Biology, Academia Sinica Institute of Molecular Biology, Academia Sinica 2 0.91039 0.91005 0.09561 0.0955 0.66994 0.67091 0.48935 0.49281 76 73 B B biological fallback assumption illumina nextseq full_length cdna_unspecified nextera bulk unknown unknown   Taiwan 2022-02-16 Larval Larval Gonad Reproductive System
68626 68626 SRR18053122 SRX14205150 SRS12027291 SRP360188 PRJNA807685 Zebrafish establish female germ cell identity by advancing cell proliferation and meiosis GSE196899 Transcriptome Analysis In this study we utilize the RNA seq of germ cell to uncover the early germ cell development. To obtain fish with defined sex we crossed domesticated zebrafish with the Nadia strain that has a female dominant W segment. These fish were placed on a ziwi:GFP background to facilitate sorting of fluorescent germ cells for transcriptomic analysis. We analyzed the transcriptomes of germ cells at 10 dpf to 14 dpf dpf when sex dimorphic changes started to appear. Overall design: Germ cells mRNA of 10 12 and 14 dpf in W hybrid ZW*Tupfel long fin and Z hybrid ZZ*Tupfel long fin       ZGC 10d 1 GSM5904403   source name:Germ cells|strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:10 dpf ZGC 10d 1 Sequencing was performed on an Illumina NextSeq500 platform in a 75 base paired end mode.Illumina NextSeq Control software and RTA used for basecalling. sequenced reads were trimmed and mapped to GRCz11 by STAR v2.7.7a expected count TPM and FPKM were calculated by RSEM v1.3.1 Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene id transcript id expected count TPM and FPKM for each sample Germ cells   Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:10 dpf GSM5904403 GSM5904403: ZGC 10d 1; Danio rerio; RNA Seq GSM5904403 r1 GSM5904403 1 Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP360188   loader:fastq load.py ZGC-10d-1_S12_R1_001.fastq.gz ZGC-10d-1_S12_R2_001.fastq.gz fastq fastq 6639003469.0 47061345.0 GSM5904403 r1 0:70.53 1:70.54 A:1868084396;C:1438823645;G:1475994376;T:1853571640;N:2529412 70 70     1868084396 1438823645 1475994376 1853571640 2529412 SRX14205150 SRS12027291 SRA1374254 Institute of Molecular Biology, Academia Sinica Institute of Molecular Biology, Academia Sinica 2 0.87395 0.8743 0.07625 0.07628 0.67405 0.67521 0.49366 0.49298 51 51 B B biological fallback assumption illumina nextseq full_length cdna_unspecified nextera bulk unknown unknown   Taiwan 2022-02-16 Larval Larval Gonad Reproductive System
68627 68627 SRR18053123 SRX14205149 SRS12027290 SRP360188 PRJNA807685 Zebrafish establish female germ cell identity by advancing cell proliferation and meiosis GSE196899 Transcriptome Analysis In this study we utilize the RNA seq of germ cell to uncover the early germ cell development. To obtain fish with defined sex we crossed domesticated zebrafish with the Nadia strain that has a female dominant W segment. These fish were placed on a ziwi:GFP background to facilitate sorting of fluorescent germ cells for transcriptomic analysis. We analyzed the transcriptomes of germ cells at 10 dpf to 14 dpf dpf when sex dimorphic changes started to appear. Overall design: Germ cells mRNA of 10 12 and 14 dpf in W hybrid ZW*Tupfel long fin and Z hybrid ZZ*Tupfel long fin       WGC 10d 3 GSM5904402   source name:Germ cells|strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:10 dpf WGC 10d 3 Sequencing was performed on an Illumina NextSeq500 platform in a 75 base paired end mode.Illumina NextSeq Control software and RTA used for basecalling. sequenced reads were trimmed and mapped to GRCz11 by STAR v2.7.7a expected count TPM and FPKM were calculated by RSEM v1.3.1 Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene id transcript id expected count TPM and FPKM for each sample Germ cells   Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:10 dpf GSM5904402 GSM5904402: WGC 10d 3; Danio rerio; RNA Seq GSM5904402 r1 GSM5904402 1 Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP360188   loader:fastq load.py WGC-10d-3_S11_R1_001.fastq.gz WGC-10d-3_S11_R2_001.fastq.gz fastq fastq 6867212328.0 48529139.0 GSM5904402 r1 0:70.75 1:70.76 A:1952427816;C:1467373674;G:1507248503;T:1937765716;N:2396619 70 70     1952427816 1467373674 1507248503 1937765716 2396619 SRX14205149 SRS12027290 SRA1374254 Institute of Molecular Biology, Academia Sinica Institute of Molecular Biology, Academia Sinica 2 0.91481 0.91559 0.0877 0.08809 0.67288 0.67572 0.49249 0.49104 72 72 B B biological fallback assumption illumina nextseq full_length cdna_unspecified nextera bulk unknown unknown   Taiwan 2022-02-16 Larval Larval Gonad Reproductive System
68628 68628 SRR18053124 SRX14205148 SRS12027289 SRP360188 PRJNA807685 Zebrafish establish female germ cell identity by advancing cell proliferation and meiosis GSE196899 Transcriptome Analysis In this study we utilize the RNA seq of germ cell to uncover the early germ cell development. To obtain fish with defined sex we crossed domesticated zebrafish with the Nadia strain that has a female dominant W segment. These fish were placed on a ziwi:GFP background to facilitate sorting of fluorescent germ cells for transcriptomic analysis. We analyzed the transcriptomes of germ cells at 10 dpf to 14 dpf dpf when sex dimorphic changes started to appear. Overall design: Germ cells mRNA of 10 12 and 14 dpf in W hybrid ZW*Tupfel long fin and Z hybrid ZZ*Tupfel long fin       WGC 10d 2 GSM5904401   source name:Germ cells|strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:10 dpf WGC 10d 2 Sequencing was performed on an Illumina NextSeq500 platform in a 75 base paired end mode.Illumina NextSeq Control software and RTA used for basecalling. sequenced reads were trimmed and mapped to GRCz11 by STAR v2.7.7a expected count TPM and FPKM were calculated by RSEM v1.3.1 Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene id transcript id expected count TPM and FPKM for each sample Germ cells   Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:10 dpf GSM5904401 GSM5904401: WGC 10d 2; Danio rerio; RNA Seq GSM5904401 r1 GSM5904401 1 Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP360188   loader:fastq load.py WGC-10d-2_S10_R1_001.fastq.gz WGC-10d-2_S10_R2_001.fastq.gz fastq fastq 7002154175.0 49314839.0 GSM5904401 r1 0:70.99 1:71.00 A:2016866979;C:1471190152;G:1513128865;T:1998734540;N:2233639 70 71     2016866979 1471190152 1513128865 1998734540 2233639 SRX14205148 SRS12027289 SRA1374254 Institute of Molecular Biology, Academia Sinica Institute of Molecular Biology, Academia Sinica 2 0.90876 0.90767 0.10283 0.10244 0.67671 0.68043 0.50783 0.5055 76 76 B B biological fallback assumption illumina nextseq full_length cdna_unspecified nextera bulk unknown unknown   Taiwan 2022-02-16 Larval Larval Gonad Reproductive System
68629 68629 SRR18053125 SRX14205147 SRS12027288 SRP360188 PRJNA807685 Zebrafish establish female germ cell identity by advancing cell proliferation and meiosis GSE196899 Transcriptome Analysis In this study we utilize the RNA seq of germ cell to uncover the early germ cell development. To obtain fish with defined sex we crossed domesticated zebrafish with the Nadia strain that has a female dominant W segment. These fish were placed on a ziwi:GFP background to facilitate sorting of fluorescent germ cells for transcriptomic analysis. We analyzed the transcriptomes of germ cells at 10 dpf to 14 dpf dpf when sex dimorphic changes started to appear. Overall design: Germ cells mRNA of 10 12 and 14 dpf in W hybrid ZW*Tupfel long fin and Z hybrid ZZ*Tupfel long fin       WGC 10d 1 GSM5904400   source name:Germ cells|strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:10 dpf WGC 10d 1 Sequencing was performed on an Illumina NextSeq500 platform in a 75 base paired end mode.Illumina NextSeq Control software and RTA used for basecalling. sequenced reads were trimmed and mapped to GRCz11 by STAR v2.7.7a expected count TPM and FPKM were calculated by RSEM v1.3.1 Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene id transcript id expected count TPM and FPKM for each sample Germ cells   Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:10 dpf GSM5904400 GSM5904400: WGC 10d 1; Danio rerio; RNA Seq GSM5904400 r1 GSM5904400 1 Gonads were dissected Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification. In SMART seq HT full length cDNA was synthesized in one step and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP360188   loader:fastq load.py WGC-10d-1_S9_R1_001.fastq.gz WGC-10d-1_S9_R2_001.fastq.gz fastq fastq 6769640776.0 48285302.0 GSM5904400 r1 0:70.09 1:70.11 A:1949281558;C:1423988202;G:1460614800;T:1933246530;N:2509686 70 70     1949281558 1423988202 1460614800 1933246530 2509686 SRX14205147 SRS12027288 SRA1374254 Institute of Molecular Biology, Academia Sinica Institute of Molecular Biology, Academia Sinica 2 0.91141 0.91158 0.0926 0.09301 0.67097 0.6729 0.49222 0.48458 73 76 B B biological fallback assumption illumina nextseq full_length cdna_unspecified nextera bulk unknown unknown   Taiwan 2022-02-16 Larval Larval Gonad Reproductive System

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