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812 rows where experiment.library_layout = "PAIRED", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation = "Gonad"

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experiment.library_selection 10

devstage_curation 9

technology 7

devstage_curation_coarse 6

experiment.library_strategy 3

experiment.platform 2

tissue_curation_coarse 1

tissue_curation 1

  • Gonad · 812 ✖

experiment.library_source 1

  • TRANSCRIPTOMIC · 812 ✖

experiment.library_layout 1

  • PAIRED · 812 ✖
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
4407 4407 ERR1427376 ERX1497908 ERS1183210 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#48 SAMEA4012100 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012100|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#48|broker name:ArrayExpress|common name:zebrafish|fsc:NaN|gfp:NaN|individual:2|pi:NaN|plate:7|sample name:E MTAB 4617:LCK 7#48|ssc:NaN|tissue:Testes|well:H6                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#48 LCK 7#48 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Testes:tissue|Experimental Factor: NaN:fsc|Experimental Factor: NaN:ssc|Experimental Factor: NaN:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_48_mod.bam LCK_7_48.cram bam cram     E MTAB 4617:LCK 7#48 0:125 1:125 A:84706839;C:81480882;G:75512683;T:89639016;N:40330 125 125     84706839 81480882 75512683 89639016 40330 ERX1497908   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.19405 0.19075 0.02782 0.02779 0.9795 0.98013 0.73205 0.73409 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Gonad Reproductive System
4415 4415 ERR1427368 ERX1497900 ERS1183202 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#40 SAMEA4012092 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012092|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#40|broker name:ArrayExpress|common name:zebrafish|fsc:NaN|gfp:NaN|individual:2|pi:NaN|plate:7|sample name:E MTAB 4617:LCK 7#40|ssc:NaN|tissue:Testes|well:H5                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#40 LCK 7#40 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Testes:tissue|Experimental Factor: NaN:fsc|Experimental Factor: NaN:ssc|Experimental Factor: NaN:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_40_mod.bam LCK_7_40.cram bam cram     E MTAB 4617:LCK 7#40 0:125 1:125 A:98690446;C:95653530;G:87621123;T:105368805;N:43346 125 125     98690446 95653530 87621123 105368805 43346 ERX1497900   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.20112 0.19727 0.01661 0.01621 0.9797 0.9806 0.44206 0.42908 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Gonad Reproductive System
4424 4424 ERR1427359 ERX1497891 ERS1183193 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#32 SAMEA4012083 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012083|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#32|broker name:ArrayExpress|common name:zebrafish|fsc:NaN|gfp:NaN|individual:2|pi:NaN|plate:7|sample name:E MTAB 4617:LCK 7#32|ssc:NaN|tissue:Testes|well:H4                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#32 LCK 7#32 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Testes:tissue|Experimental Factor: NaN:fsc|Experimental Factor: NaN:ssc|Experimental Factor: NaN:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_32_mod.bam LCK_7_32.cram bam cram     E MTAB 4617:LCK 7#32 0:125 1:125 A:102670073;C:105552903;G:96042262;T:111286167;N:48595 125 125     102670073 105552903 96042262 111286167 48595 ERX1497891   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.0367 0.03586 0.00293 0.00297 0.99316 0.99387 0.82316 0.80581 125 125 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Gonad Reproductive System
4433 4433 ERR1427350 ERX1497882 ERS1183184 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#24 SAMEA4012074 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012074|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#24|broker name:ArrayExpress|common name:zebrafish|fsc:NaN|gfp:NaN|individual:2|pi:NaN|plate:7|sample name:E MTAB 4617:LCK 7#24|ssc:NaN|tissue:Testes|well:H3                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#24 LCK 7#24 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Testes:tissue|Experimental Factor: NaN:fsc|Experimental Factor: NaN:ssc|Experimental Factor: NaN:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_24_mod.bam LCK_7_24.cram bam cram     E MTAB 4617:LCK 7#24 0:125 1:125 A:97411995;C:91321821;G:84912221;T:100868660;N:45803 125 125     97411995 91321821 84912221 100868660 45803 ERX1497882   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.25757 0.25144 0.03087 0.02958 0.97642 0.97695 0.71128 0.71145 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Gonad Reproductive System
4442 4442 ERR1427341 ERX1497873 ERS1183175 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#16 SAMEA4012065 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012065|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#16|broker name:ArrayExpress|common name:zebrafish|fsc:NaN|gfp:NaN|individual:2|pi:NaN|plate:7|sample name:E MTAB 4617:LCK 7#16|ssc:NaN|tissue:Testes|well:H2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#16 LCK 7#16 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Testes:tissue|Experimental Factor: NaN:fsc|Experimental Factor: NaN:ssc|Experimental Factor: NaN:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_16_mod.bam LCK_7_16.cram bam cram     E MTAB 4617:LCK 7#16 0:125 1:125 A:81321616;C:79315899;G:72476597;T:85676964;N:38424 125 125     81321616 79315899 72476597 85676964 38424 ERX1497873   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.20776 0.20306 0.02431 0.02397 0.9654 0.96621 0.66321 0.66592 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Gonad Reproductive System
5793 5793 ERR1955208 ERX2020800 ERS1697077 ERP017053 PRJEB15333 Transposon driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution ena-STUDY-EMBL EUROPEAN BIOINFORMATICS INSTITUTE-07-09-2016-10:25:55:499-247 Other In order to better understand the features associated with male germline transcription we profiled the RNA expression in a number of germline cell types. These include spermatogonial stem cells spermatocytes and round spermatids in mouse and spermatocytes in rat. We also profiled the transcription in zebrafish testes. As a consequence it became apparent that transposable elements are driving considerable lncRNA expression in the later stages of spermatogenesis. This is particularly apparent in the case of endogenous retroviruses in rodents. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 05 08     Transcriptional profiling of zebrafish testes for analysis of conserved repeat element associations SAMEA104033184 EMBL EUROPEAN BIOINFORMATICS INSTITUTE ENA FIRST PUBLIC:2017 05 10T17:01:28Z|ENA LAST UPDATE:2017 04 28T10:34:37Z|External Id:SAMEA104033184|INSDC center name:EMBL EUROPEAN BIOINFORMATICS INSTITUTE|INSDC first public:2017 05 10T17:01:28Z|INSDC last update:2017 04 28T10:34:37Z|INSDC status:public|Submitter Id:Zebrafish.Testis 2|common name:zebrafish|sample name:Zebrafish.Testis 2|scientific name:Danio rerio|strain:AB|tissue type:testis                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 16 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP017053 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 05 10|ENA LAST UPDATE:2018 11 16 zebrafish_testis_2.conserved.1.fastq.gz zebrafish_testis_2.conserved.2.fastq.gz fastq fastq 46555372886.0 230472143.0 ena RUN EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 16 0:101 1:101 A:12260062264;C:10888457642;G:11605642683;T:11637267744;N:163942553 101 101     12260062264 10888457642 11605642683 11637267744 163942553 ERX2020800 ERS1697077 ERA904389 EMBL EUROPEAN BIOINFORMATICS INSTITUTE|European Nucleotide Archive EMBL EUROPEAN BIOINFORMATICS INSTITUTE 2 0.93165 0.92785 0.29822 0.32141 0.71386 0.71971 0.66173 0.63843 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2017-01-31 Undetermined Undetermined Gonad Reproductive System
5794 5794 ERR1955207 ERX2020799 ERS1697076 ERP017053 PRJEB15333 Transposon driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution ena-STUDY-EMBL EUROPEAN BIOINFORMATICS INSTITUTE-07-09-2016-10:25:55:499-247 Other In order to better understand the features associated with male germline transcription we profiled the RNA expression in a number of germline cell types. These include spermatogonial stem cells spermatocytes and round spermatids in mouse and spermatocytes in rat. We also profiled the transcription in zebrafish testes. As a consequence it became apparent that transposable elements are driving considerable lncRNA expression in the later stages of spermatogenesis. This is particularly apparent in the case of endogenous retroviruses in rodents. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 05 08     Transcriptional profiling of zebrafish testes for analysis of conserved repeat element associations SAMEA104033183 EMBL EUROPEAN BIOINFORMATICS INSTITUTE ENA FIRST PUBLIC:2017 05 10T17:01:28Z|ENA LAST UPDATE:2017 04 28T10:34:37Z|External Id:SAMEA104033183|INSDC center name:EMBL EUROPEAN BIOINFORMATICS INSTITUTE|INSDC first public:2017 05 10T17:01:28Z|INSDC last update:2017 04 28T10:34:37Z|INSDC status:public|Submitter Id:Zebrafish.Testis 1|common name:zebrafish|sample name:Zebrafish.Testis 1|scientific name:Danio rerio|strain:AB|tissue type:testis                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 15 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP017053 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 05 10|ENA LAST UPDATE:2018 11 16 zebrafish_testis_1.conserved.1.fastq.gz zebrafish_testis_1.conserved.2.fastq.gz fastq fastq 41056086708.0 203247954.0 ena RUN EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 15 0:101 1:101 A:10675591750;C:9672762387;G:10139834713;T:10380949257;N:186948601 101 101     10675591750 9672762387 10139834713 10380949257 186948601 ERX2020799 ERS1697076 ERA904389 EMBL EUROPEAN BIOINFORMATICS INSTITUTE|European Nucleotide Archive EMBL EUROPEAN BIOINFORMATICS INSTITUTE 2 0.92308 0.9157 0.30221 0.31293 0.68276 0.68836 0.56114 0.5857 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2017-01-31 Undetermined Undetermined Gonad Reproductive System
7949 7949 ERR015566 ERX005931 ERS000090 ERP000263 PRJEB2208 Zebrafish gene three prime end pull down for genome annotation E-MTAB-308 Transcriptome Analysis         ZF ovary sample1 SAMEA708832 Wellcome Sanger Institute Alias:ZF ovary sample1|Description:RNA extracted from adult zebrafish ovary|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:24:37Z|INSDC status:public|SRA accession:ERS000090|Sample Name:ERS000090|Sex:female|Strain:Tuebingen|Title:Danio rerio                 Illumina Genome Analyzer II paired end sequencing; Zebrafish gene 3 prime end pull down for genome annotation E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish ovary dpf three prime pull down paired end 250 to 300 bp insert Zebrafish adult ovary mRNA three prime end Zebrafish gene three prime end pull down for genome annotation 20 ug of total RNA was fragmented using RNA Fragmentation Reagent Ambion for 5 minutes at 70 C and ethanol precipitated with glycogen and LiCl. RNA was annealed to the oligo stBPM1polyT22 biotin GGCCAGTCCTGGAGTTTTTTTTTTTTTTTTTTTTTTVN and bound to streptavidin magnetic beads. post washing by pull down on a magnet the bound RNA was reverse transcribed with SuperScript II Invitrogen and a second strand synthesised with DNA polymerase I Promega and RNase H NEB. post further washing the double strand cDNA was released from the beads with BpmI NEB. The cDNA was recovered with the QIAgen PCR Purification Kit and made into a standard Illumina library following the manufacturer's protocol with a fragment size of 250 to 300 bp. Experimental Factor: DEVELOPMENTAL STAGE:adult|Experimental Factor: ORGANISM PART:ovary|Experimental Factor: SEX:female RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina Genome Analyzer II   ERP000263 Illumina Genome Analyzer II paired end sequencing; Zebrafish gene three prime end pull down for genome annotation ENA FIRST PUBLIC:2010 08 19|ENA LAST UPDATE:2018 11 16 3444_6.srf srf 1150193272.0 7567061.0 E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish ovary dpf three prime pull down paired end 250 to 300 bp insert 0:76 1:76 A:280621121;C:291623460;G:285422205;T:273609496;N:18916990 76 76     280621121 291623460 285422205 273609496 18916990 ERX005931 ERS000090 ERA010603 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.96663 0.96605 0.0126 0.01249 0.82272 0.82548 0.45602 0.45286 76 76 B B biological fallback assumption illumina early_illumina 3prime other unknown bulk unknown unknown   United Kingdom 2010-02-26 Adult Adult Gonad Reproductive System
9357 9357 ERR2983451 ERX2986067 ERS2955655 ERP112513 PRJEB30097 RNA Seq of Danionine species E-MTAB-7476 Transcriptome Analysis Tissues specific transcriptomes of Danio rerio Danio albolineatus and Danio aesculapii Brain Liver and Gonads. ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05   Protocols: Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers. R2wG SAMEA5147910 University of Hamburg, Institute of Zoology, Molecular Animal Physiology ENA FIRST PUBLIC:2018 12 05T17:02:27Z|ENA LAST UPDATE:2018 12 05T10:01:48Z|External Id:SAMEA5147910|INSDC center name:University of Hamburg Institute of Zoology Molecular Animal Physiology|INSDC first public:2018 12 05T17:02:27Z|INSDC last update:2018 12 05T10:01:48Z|INSDC status:public|Submitter Id:E MTAB 7476:R2wG|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|individual:2|organism part:gonad|sample name:E MTAB 7476:R2wG|scientific name:Danio rerio|sex:female|strain:tu                 Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danio9 species E MTAB 7476:R2wG p R2wG p RNA Seq of Danionine species Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers. Experimental Factor: organism:Danio rerio|Experimental Factor: organism part:gonad RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP112513 Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danionine species ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05 FCHNW2WBBXX_L6_HKZEBodsEAAFRAAPEI-209_1.fq.gz FCHNW2WBBXX_L6_HKZEBodsEAAFRAAPEI-209_2.fq.gz fastq fastq 4276100600.0 21380503.0 E MTAB 7476:FCHNW2WBBXX L6 HKZEBodsEAAFRAAPEI 209 0:100 1:100 A:1108098396;C:1033423434;G:1019885778;T:1113782383;N:910609 100 100     1108098396 1033423434 1019885778 1113782383 910609 ERX2986067 ERS2955655 ERA1674470 University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive 2 0.9444 0.94495 0.02624 0.02606 0.74959 0.7512 0.48453 0.48539 100 100 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2018-12-05 Adult Adult Gonad Reproductive System
9359 9359 ERR2983449 ERX2986065 ERS2955653 ERP112513 PRJEB30097 RNA Seq of Danionine species E-MTAB-7476 Transcriptome Analysis Tissues specific transcriptomes of Danio rerio Danio albolineatus and Danio aesculapii Brain Liver and Gonads. ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05   Protocols: Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers. R1wG SAMEA5147908 University of Hamburg, Institute of Zoology, Molecular Animal Physiology ENA FIRST PUBLIC:2018 12 05T17:02:27Z|ENA LAST UPDATE:2018 12 05T10:01:48Z|External Id:SAMEA5147908|INSDC center name:University of Hamburg Institute of Zoology Molecular Animal Physiology|INSDC first public:2018 12 05T17:02:27Z|INSDC last update:2018 12 05T10:01:48Z|INSDC status:public|Submitter Id:E MTAB 7476:R1wG|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|individual:1|organism part:gonad|sample name:E MTAB 7476:R1wG|scientific name:Danio rerio|sex:female|strain:tu                 Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danio9 species E MTAB 7476:R1wG p R1wG p RNA Seq of Danionine species Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers. Experimental Factor: organism:Danio rerio|Experimental Factor: organism part:gonad RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP112513 Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danionine species ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05 FCHNW2WBBXX_L6_HKZEBodsEAAERAAPEI-208_1.fq.gz FCHNW2WBBXX_L6_HKZEBodsEAAERAAPEI-208_2.fq.gz fastq fastq 3574419200.0 17872096.0 E MTAB 7476:FCHNW2WBBXX L6 HKZEBodsEAAERAAPEI 208 0:100 1:100 A:927454175;C:863033369;G:844910972;T:938253904;N:766780 100 100     927454175 863033369 844910972 938253904 766780 ERX2986065 ERS2955653 ERA1674470 University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive 2 0.93851 0.93973 0.02799 0.02809 0.72701 0.72914 0.48827 0.48841 100 100 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2018-12-05 Adult Adult Gonad Reproductive System
24582 24582 SRR25462250 SRX21195051 SRS18453977 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG HE 8mpf 3 GSM7669027   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing PG HE 8mpf 3 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ GSM7669027 GSM7669027: PG HE 8mpf 3; Danio rerio; RNA Seq GSM7669027 r1 GSM7669027 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     HE_PG_8mpf_3_S11_L003_R1_001.fastq.gz HE_PG_8mpf_3_S11_L003_R2_001.fastq.gz fastq fastq 7161373434.0 60309247.0 GSM7669027 r1 0:59.39 1:59.35 A:1783731260;C:1744025029;G:1733970346;T:1880173306;N:19473493 59 59     1783731260 1744025029 1733970346 1880173306 19473493 SRX21195051 SRS18453977     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.94187 0.94592 0.01475 0.01464 0.77447 0.77498 0.45855 0.4635 60 60 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Adult Adult Gonad Reproductive System
24583 24583 SRR25462251 SRX21195050 SRS18453976 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG HE 8mpf 2 GSM7669026   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing PG HE 8mpf 2 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ GSM7669026 GSM7669026: PG HE 8mpf 2; Danio rerio; RNA Seq GSM7669026 r1 GSM7669026 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     HE_PG_8mpf_2_S7_L003_R1_001.fastq.gz HE_PG_8mpf_2_S7_L003_R2_001.fastq.gz fastq fastq 3176994053.0 26828357.0 GSM7669026 r1 0:59.22 1:59.20 A:793619267;C:767135191;G:764404567;T:830643823;N:21191205 59 59     793619267 767135191 764404567 830643823 21191205 SRX21195050 SRS18453976     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.93822 0.94226 0.01596 0.0161 0.77684 0.77772 0.47008 0.46904 59 60 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Adult Adult Gonad Reproductive System
24584 24584 SRR25462252 SRX21195049 SRS18453975 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG HE 8mpf 1 GSM7669025   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing PG HE 8mpf 1 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ GSM7669025 GSM7669025: PG HE 8mpf 1; Danio rerio; RNA Seq GSM7669025 r1 GSM7669025 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     HE_PG_8mpf_1_S6_L003_R1_001.fastq.gz HE_PG_8mpf_1_S6_L003_R2_001.fastq.gz fastq fastq 4587580737.0 38590260.0 GSM7669025 r1 0:59.45 1:59.43 A:1149031944;C:1121086335;G:1106925902;T:1203970839;N:6565717 59 59     1149031944 1121086335 1106925902 1203970839 6565717 SRX21195049 SRS18453975     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.94032 0.9437 0.01481 0.01462 0.77682 0.77774 0.45843 0.4699 58 60 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Adult Adult Gonad Reproductive System
24585 24585 SRR25462253 SRX21195048 SRS18453974 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG WT 8mpf 3 GSM7669024   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing PG WT 8mpf 3 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+ GSM7669024 GSM7669024: PG WT 8mpf 3; Danio rerio; RNA Seq GSM7669024 r1 GSM7669024 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     WT_PG_8mpf_3_S8_L003_R2_001.fastq.gz WT_PG_8mpf_3_S8_L003_R1_001.fastq.gz fastq fastq 3920821867.0 33089226.0 GSM7669024 r1 0:59.26 1:59.23 A:977738236;C:951999354;G:944769809;T:1023828622;N:22485846 59 59     977738236 951999354 944769809 1023828622 22485846 SRX21195048 SRS18453974     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.94193 0.94555 0.01657 0.01646 0.76784 0.76919 0.47238 0.47016 60 60 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Adult Adult Gonad Reproductive System
24586 24586 SRR25462254 SRX21195047 SRS18453973 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG WT 8mpf 2 GSM7669023   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing PG WT 8mpf 2 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+ GSM7669023 GSM7669023: PG WT 8mpf 2; Danio rerio; RNA Seq GSM7669023 r1 GSM7669023 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     WT_PG_8mpf_2_S10_L003_R2_001.fastq.gz WT_PG_8mpf_2_S10_L003_R1_001.fastq.gz fastq fastq 4917868553.0 41430484.0 GSM7669023 r1 0:59.37 1:59.33 A:1231173294;C:1195692797;G:1182545852;T:1292018757;N:16437853 59 59     1231173294 1195692797 1182545852 1292018757 16437853 SRX21195047 SRS18453973     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.94048 0.94432 0.0178 0.0178 0.75645 0.7569 0.46332 0.46812 59 57 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Adult Adult Gonad Reproductive System
24587 24587 SRR25462255 SRX21195046 SRS18453972 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG WT 8mpf 1 GSM7669022   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing PG WT 8mpf 1 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+ GSM7669022 GSM7669022: PG WT 8mpf 1; Danio rerio; RNA Seq GSM7669022 r1 GSM7669022 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     WT_PG_8mpf_1_S9_L003_R1_001.fastq.gz WT_PG_8mpf_1_S9_L003_R2_001.fastq.gz fastq fastq 3375380667.0 28408784.0 GSM7669022 r1 0:59.42 1:59.40 A:842316103;C:825987175;G:818715765;T:881225528;N:7136096 59 59     842316103 825987175 818715765 881225528 7136096 SRX21195046 SRS18453972     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.94039 0.9444 0.0162 0.01617 0.7697 0.76986 0.47132 0.46938 60 60 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Adult Adult Gonad Reproductive System
24588 24588 SRR25462256 SRX21195045 SRS18453971 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG HE 50dpf 3 GSM7669021   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing PG HE 50dpf 3 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ GSM7669021 GSM7669021: PG HE 50dpf 3; Danio rerio; RNA Seq GSM7669021 r1 GSM7669021 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     PG_HE_3_S26_L003_R1_001.fastq.gz PG_HE_3_S26_L003_R2_001.fastq.gz fastq fastq 4520051001.0 22984712.0 GSM7669021 r1 0:98.32 1:98.33 A:1134815259;C:1102592573;G:1104475707;T:1160918938;N:17248524 98 98     1134815259 1102592573 1104475707 1160918938 17248524 SRX21195045 SRS18453971     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.93438 0.93937 0.01237 0.01252 0.78208 0.78192 0.48454 0.49474 99 99 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Juvenile Juvenile Gonad Reproductive System
24589 24589 SRR25462257 SRX21195044 SRS18453970 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG HE 50dpf 2 GSM7669020   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing PG HE 50dpf 2 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ GSM7669020 GSM7669020: PG HE 50dpf 2; Danio rerio; RNA Seq GSM7669020 r1 GSM7669020 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     PG_HE_2_S25_L003_R2_001.fastq.gz PG_HE_2_S25_L003_R1_001.fastq.gz fastq fastq 3915471868.0 19847479.0 GSM7669020 r1 0:98.64 1:98.64 A:982714666;C:957212118;G:961590362;T:1003408448;N:10546274 98 98     982714666 957212118 961590362 1003408448 10546274 SRX21195044 SRS18453970     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.93184 0.93552 0.01275 0.01275 0.78356 0.7835 0.49472 0.48841 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Juvenile Juvenile Gonad Reproductive System
24590 24590 SRR25462258 SRX21195043 SRS18453969 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG HE 50dpf 1 GSM7669019   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing PG HE 50dpf 1 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ GSM7669019 GSM7669019: PG HE 50dpf 1; Danio rerio; RNA Seq GSM7669019 r1 GSM7669019 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     PG_HE_1_S24_L003_R1_001.fastq.gz PG_HE_1_S24_L003_R2_001.fastq.gz fastq fastq 4764998144.0 24264412.0 GSM7669019 r1 0:98.18 1:98.20 A:1194676445;C:1161648051;G:1165061360;T:1221860864;N:21751424 98 98     1194676445 1161648051 1165061360 1221860864 21751424 SRX21195043 SRS18453969     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.91864 0.92247 0.01213 0.01245 0.7949 0.79584 0.50422 0.50318 100 98 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Juvenile Juvenile Gonad Reproductive System
24591 24591 SRR25462259 SRX21195042 SRS18453968 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG WT 50dpf 3 GSM7669018   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing PG WT 50dpf 3 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+ GSM7669018 GSM7669018: PG WT 50dpf 3; Danio rerio; RNA Seq GSM7669018 r1 GSM7669018 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     PG_WT_3_S23_L003_R1_001.fastq.gz PG_WT_3_S23_L003_R2_001.fastq.gz fastq fastq 6204452412.0 31480139.0 GSM7669018 r1 0:98.55 1:98.54 A:1567898375;C:1505755791;G:1512895523;T:1599284546;N:18618177 98 98     1567898375 1505755791 1512895523 1599284546 18618177 SRX21195042 SRS18453968     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.9312 0.93599 0.01692 0.01686 0.76426 0.76439 0.46519 0.47751 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Juvenile Juvenile Gonad Reproductive System
24592 24592 SRR25462260 SRX21195041 SRS18453967 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG WT 50dpf 2 GSM7669017   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing PG WT 50dpf 2 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+ GSM7669017 GSM7669017: PG WT 50dpf 2; Danio rerio; RNA Seq GSM7669017 r1 GSM7669017 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     PG_WT_2_S22_L003_R1_001.fastq.gz PG_WT_2_S22_L003_R2_001.fastq.gz fastq fastq 3907759829.0 19906505.0 GSM7669017 r1 0:98.15 1:98.15 A:991973983;C:940499355;G:946342572;T:1011476708;N:17467211 98 98     991973983 940499355 946342572 1011476708 17467211 SRX21195041 SRS18453967     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.91435 0.9186 0.02035 0.02032 0.764 0.76321 0.48743 0.48644 97 99 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Juvenile Juvenile Gonad Reproductive System
24593 24593 SRR25462261 SRX21195040 SRS18453966 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG WT 50dpf 1 GSM7669016   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing PG WT 50dpf 1 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+ GSM7669016 GSM7669016: PG WT 50dpf 1; Danio rerio; RNA Seq GSM7669016 r1 GSM7669016 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     PG_WT_1_S21_L003_R2_001.fastq.gz PG_WT_1_S21_L003_R1_001.fastq.gz fastq fastq 7395136401.0 37752582.0 GSM7669016 r1 0:97.94 1:97.94 A:1865709287;C:1789949400;G:1796311820;T:1908470411;N:34695483 97 97     1865709287 1789949400 1796311820 1908470411 34695483 SRX21195040 SRS18453966     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.9216 0.92737 0.01817 0.01802 0.76601 0.76593 0.48894 0.4975 100 99 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Juvenile Juvenile Gonad Reproductive System
24594 24594 SRR25462243 SRX21195038 SRS18453964 SRP452269 PRJNA1000446 Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish GSE239623 Transcriptome Analysis Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.       PV M3 GSM7669033   source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing PV M3 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / GSM7669033 GSM7669033: PV M3; Danio rerio; RNA Seq GSM7669033 r1 GSM7669033 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452269     PV_M3_R1.fastq.gz PV_M3_R2.fastq.gz fastq fastq 4644457090.0 23465750.0 GSM7669033 r1 0:98.98 1:98.94 A:1196567358;C:1114203322;G:1109379777;T:1223156356;N:1150277 98 98     1196567358 1114203322 1109379777 1223156356 1150277 SRX21195038 SRS18453964     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.94849 0.95248 0.02727 0.02708 0.73602 0.73718 0.48396 0.4855 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Undetermined Embryo Gonad Reproductive System
24595 24595 SRR25462244 SRX21195037 SRS18453963 SRP452269 PRJNA1000446 Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish GSE239623 Transcriptome Analysis Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.       PV M2 GSM7669032   source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing PV M2 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / GSM7669032 GSM7669032: PV M2; Danio rerio; RNA Seq GSM7669032 r1 GSM7669032 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452269     PV_M2_R1.fastq.gz PV_M2_R2.fastq.gz fastq fastq 2464506276.0 12449948.0 GSM7669032 r1 0:98.99 1:98.96 A:632587002;C:593372099;G:591579950;T:646214108;N:753117 98 98     632587002 593372099 591579950 646214108 753117 SRX21195037 SRS18453963     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.94889 0.9522 0.02585 0.02585 0.73669 0.73841 0.48398 0.48486 100 99 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Undetermined Embryo Gonad Reproductive System
24596 24596 SRR25462245 SRX21195036 SRS18453962 SRP452269 PRJNA1000446 Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish GSE239623 Transcriptome Analysis Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.       PV M1 GSM7669031   source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing PV M1 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / GSM7669031 GSM7669031: PV M1; Danio rerio; RNA Seq GSM7669031 r1 GSM7669031 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452269     PV_M1_R1.fastq.gz PV_M1_R2.fastq.gz fastq fastq 3634173229.0 18461903.0 GSM7669031 r1 0:98.44 1:98.41 A:930322973;C:875929476;G:875710056;T:948595199;N:3615525 98 98     930322973 875929476 875710056 948595199 3615525 SRX21195036 SRS18453962     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.94787 0.95134 0.02457 0.02445 0.73762 0.73843 0.48244 0.48069 100 98 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Undetermined Embryo Gonad Reproductive System
24597 24597 SRR25462246 SRX21195035 SRS18453961 SRP452269 PRJNA1000446 Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish GSE239623 Transcriptome Analysis Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.       PV WT3 GSM7669030   source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing PV WT3 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+ GSM7669030 GSM7669030: PV WT3; Danio rerio; RNA Seq GSM7669030 r1 GSM7669030 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452269     PV_WT3_R2.fastq PV_WT3_R1.fastq fastq fastq 2965772270.0 14976621.0 GSM7669030 r1 0:99.03 1:98.99 A:759343389;C:716154246;G:713466520;T:775995980;N:812135 99 98     759343389 716154246 713466520 775995980 812135 SRX21195035 SRS18453961     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.95027 0.95485 0.02356 0.02292 0.74422 0.74554 0.47974 0.48267 100 98 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Undetermined Embryo Gonad Reproductive System
24598 24598 SRR25462247 SRX21195034 SRS18453960 SRP452269 PRJNA1000446 Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish GSE239623 Transcriptome Analysis Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.       PV WT2 GSM7669029   source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing PV WT2 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+ GSM7669029 GSM7669029: PV WT2; Danio rerio; RNA Seq GSM7669029 r1 GSM7669029 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452269     PV_WT2_R2.fastq PV_WT2_R1.fastq fastq fastq 2021387268.0 10195384.0 GSM7669029 r1 0:99.15 1:99.12 A:517788644;C:487363563;G:485168383;T:530550229;N:516449 99 99     517788644 487363563 485168383 530550229 516449 SRX21195034 SRS18453960     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.95113 0.9544 0.02394 0.02364 0.74168 0.74363 0.47881 0.47499 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Undetermined Embryo Gonad Reproductive System
24599 24599 SRR25462248 SRX21195033 SRS18453959 SRP452269 PRJNA1000446 Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish GSE239623 Transcriptome Analysis Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.       PV WT1 GSM7669028   source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing PV WT1 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+ GSM7669028 GSM7669028: PV WT1; Danio rerio; RNA Seq GSM7669028 r1 GSM7669028 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452269     PV_WT1_R1.fastq PV_WT1_R2.fastq fastq fastq 3244660111.0 16481925.0 GSM7669028 r1 0:98.44 1:98.42 A:831426044;C:781489498;G:779991004;T:848549246;N:3204319 98 98     831426044 781489498 779991004 848549246 3204319 SRX21195033 SRS18453959     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.94779 0.95185 0.02328 0.02298 0.74294 0.74391 0.48052 0.47966 95 95 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Undetermined Embryo Gonad Reproductive System
25267 25267 SRR25744342 SRX21467662 SRS18702380 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad eif4e1b 3 GSM7730282   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / |geo loc name:missing|collection date:missing Gonad eif4e1b 3 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / GSM7730282 GSM7730282: Gonad eif4e1b 3; Danio rerio; ssRNA seq GSM7730282 r1 GSM7730282 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_HOM3_1.fastq.gz Ovary_HOM3_2.fastq.gz fastq fastq 2170738056.0 10746228.0 GSM7730282 r1 0:101 1:101 A:531993767;C:520631008;G:565772072;T:552334154;N:7055 101 101     531993767 520631008 565772072 552334154 7055 SRX21467662 SRS18702380 SRA1698764 IMP IMP 2 0.77665 0.7702 0.14988 0.14284 0.66716 0.66957 0.49991 0.47425 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25268 25268 SRR25744343 SRX21467661 SRS18702379 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad eif4e1b 2 GSM7730281   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / |geo loc name:missing|collection date:missing Gonad eif4e1b 2 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / GSM7730281 GSM7730281: Gonad eif4e1b 2; Danio rerio; ssRNA seq GSM7730281 r1 GSM7730281 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_HOM2_1.fastq.gz Ovary_HOM2_2.fastq.gz fastq fastq 3459149000.0 17124500.0 GSM7730281 r1 0:101 1:101 A:876732239;C:796603142;G:882912604;T:902886783;N:14232 101 101     876732239 796603142 882912604 902886783 14232 SRX21467661 SRS18702379 SRA1698764 IMP IMP 2 0.81761 0.79589 0.26282 0.24746 0.70607 0.7039 0.50658 0.49236 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25269 25269 SRR25744344 SRX21467660 SRS18702381 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad eif4e1b 1 GSM7730280   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / |geo loc name:missing|collection date:missing Gonad eif4e1b 1 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / GSM7730280 GSM7730280: Gonad eif4e1b 1; Danio rerio; ssRNA seq GSM7730280 r1 GSM7730280 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_HOM1_1.fastq.gz Ovary_HOM1_2.fastq.gz fastq fastq 2189781202.0 10840501.0 GSM7730280 r1 0:101 1:101 A:537591255;C:525448020;G:568979980;T:557754770;N:7177 101 101     537591255 525448020 568979980 557754770 7177 SRX21467660 SRS18702381 SRA1698764 IMP IMP 2 0.7459 0.74191 0.15778 0.15291 0.65543 0.65841 0.48578 0.48291 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25270 25270 SRR25744345 SRX21467659 SRS18702378 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad WT 3 GSM7730279   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+|geo loc name:missing|collection date:missing Gonad WT 3 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+ GSM7730279 GSM7730279: Gonad WT 3; Danio rerio; ssRNA seq GSM7730279 r1 GSM7730279 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_WT3_1.fastq.gz Ovary_WT3_2.fastq.gz fastq fastq 3674041448.0 18188324.0 GSM7730279 r1 0:101 1:101 A:910831144;C:876967044;G:953299105;T:932928913;N:15242 101 101     910831144 876967044 953299105 932928913 15242 SRX21467659 SRS18702378 SRA1698764 IMP IMP 2 0.89093 0.89038 0.09253 0.09348 0.73892 0.73858 0.47115 0.47218 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25271 25271 SRR25744346 SRX21467658 SRS18702377 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad WT 2 GSM7730278   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+|geo loc name:missing|collection date:missing Gonad WT 2 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+ GSM7730278 GSM7730278: Gonad WT 2; Danio rerio; ssRNA seq GSM7730278 r1 GSM7730278 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_WT2_1.fastq.gz Ovary_WT2_2.fastq.gz fastq fastq 3024886370.0 14974685.0 GSM7730278 r1 0:101 1:101 A:744374909;C:727299396;G:782294774;T:770904797;N:12494 101 101     744374909 727299396 782294774 770904797 12494 SRX21467658 SRS18702377 SRA1698764 IMP IMP 2 0.91806 0.91689 0.06949 0.07178 0.74458 0.74474 0.47548 0.47338 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25272 25272 SRR25744347 SRX21467657 SRS18702376 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad WT 1 GSM7730277   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+|geo loc name:missing|collection date:missing Gonad WT 1 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+ GSM7730277 GSM7730277: Gonad WT 1; Danio rerio; ssRNA seq GSM7730277 r1 GSM7730277 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_WT1_2.fastq.gz Ovary_WT1_1.fastq.gz fastq fastq 3571638356.0 17681378.0 GSM7730277 r1 0:101 1:101 A:876280472;C:856417516;G:935896746;T:903028845;N:14777 101 101     876280472 856417516 935896746 903028845 14777 SRX21467657 SRS18702376 SRA1698764 IMP IMP 2 0.89559 0.89353 0.09223 0.09423 0.73052 0.73012 0.47772 0.47408 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
26542 26542 SRR28370185 SRX23975270 SRS20773688 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         L13 2 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 27|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E27 E27 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     L13-2_1.fq.gz L13-2_2.fq.gz fastq fastq 6912432900.0 23041443.0 L13 2 1.fq.gz 0:150 1:150 A:1784119910;C:1650041348;G:1690584500;T:1787634630;N:52512 150 150     1784119910 1650041348 1690584500 1787634630 52512 SRX23975270 SRS20773688 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26543 26543 SRR28370183 SRX23975269 SRS20773687 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         L13 3 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 29|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E29 E29 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     L13-3_1.fq.gz L13-3_2.fq.gz fastq fastq 6353525700.0 21178419.0 L13 3 1.fq.gz 0:150 1:150 A:1642863679;C:1514378445;G:1549765145;T:1646469683;N:48748 150 150     1642863679 1514378445 1549765145 1646469683 48748 SRX23975269 SRS20773687 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26544 26544 SRR28370186 SRX23975268 SRS20773685 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         L13 4 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 31|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E31 E31 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     L13-4_1.fq.gz L13-4_2.fq.gz fastq fastq 6026853600.0 20089512.0 L13 4 1.fq.gz 0:150 1:150 A:1557631540;C:1437822618;G:1472097382;T:1559255786;N:46274 150 150     1557631540 1437822618 1472097382 1559255786 46274 SRX23975268 SRS20773685 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26545 26545 SRR28370187 SRX23975267 SRS20773686 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         H27 3 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 5|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E5 E5 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     H27-3_1.fq.gz H27-3_2.fq.gz fastq fastq 6437512500.0 21458375.0 H27 3 1.fq.gz 0:150 1:150 A:1664818485;C:1534913781;G:1570911516;T:1666819538;N:49180 150 150     1664818485 1534913781 1570911516 1666819538 49180 SRX23975267 SRS20773686 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26546 26546 SRR28370188 SRX23975266 SRS20773684 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         H27 4 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 7|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E7 E7 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     H27-4_1.fq.gz H27-4_2.fq.gz fastq fastq 6583604100.0 21945347.0 H27 4 1.fq.gz 0:150 1:150 A:1701207657;C:1570727535;G:1607990863;T:1703626924;N:51121 150 150     1701207657 1570727535 1607990863 1703626924 51121 SRX23975266 SRS20773684 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26547 26547 SRR28370189 SRX23975265 SRS20773683 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         M20 1 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 9|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E9 E9 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     M20-1_1.fq.gz M20-1_2.fq.gz fastq fastq 7048815900.0 23496053.0 M20 1 1.fq.gz 0:150 1:150 A:1818915133;C:1681912688;G:1724222526;T:1823711995;N:53558 150 150     1818915133 1681912688 1724222526 1823711995 53558 SRX23975265 SRS20773683 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26548 26548 SRR28370190 SRX23975264 SRS20773682 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         M22 2 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 19|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E19 E19 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     M22-2_1.fq.gz M22-2_2.fq.gz fastq fastq 6844400100.0 22814667.0 M22 2 1.fq.gz 0:150 1:150 A:1770073015;C:1631597148;G:1666105661;T:1776572883;N:51393 150 150     1770073015 1631597148 1666105661 1776572883 51393 SRX23975264 SRS20773682 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26549 26549 SRR28370191 SRX23975263 SRS20773681 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         H27 2 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 3|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E3 E3 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     H27-2_1.fq.gz H27-2_2.fq.gz fastq fastq 6803741100.0 22679137.0 H27 2 1.fq.gz 0:150 1:150 A:1759471720;C:1621328873;G:1660379342;T:1762509905;N:51260 150 150     1759471720 1621328873 1660379342 1762509905 51260 SRX23975263 SRS20773681 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26550 26550 SRR28370184 SRX23975262 SRS20773680 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         M22 3 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 21|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E21 E21 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     M22-3_1.fq.gz M22-3_2.fq.gz fastq fastq 6312346800.0 21041156.0 M22 3 1.fq.gz 0:150 1:150 A:1638152183;C:1500304435;G:1533591340;T:1640250617;N:48225 150 150     1638152183 1500304435 1533591340 1640250617 48225 SRX23975262 SRS20773680 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26551 26551 SRR28370192 SRX23975261 SRS20773679 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         M22 4 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 23|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E23 E23 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     M22-4_1.fq.gz M22-4_2.fq.gz fastq fastq 7163095500.0 23876985.0 M22 4 1.fq.gz 0:150 1:150 A:1851012240;C:1707016293;G:1748790263;T:1856222899;N:53805 150 150     1851012240 1707016293 1748790263 1856222899 53805 SRX23975261 SRS20773679 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26552 26552 SRR28370193 SRX23975260 SRS20773678 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         L13 1 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 25|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E25 E25 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     L13-1_1.fq.gz L13-1_2.fq.gz fastq fastq 6191424300.0 20638081.0 L13 1 1.fq.gz 0:150 1:150 A:1605753886;C:1471890545;G:1506901769;T:1606830995;N:47105 150 150     1605753886 1471890545 1506901769 1606830995 47105 SRX23975260 SRS20773678 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26553 26553 SRR28370194 SRX23975259 SRS20773677 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         M22 1 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 17|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E17 E17 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     M22-1_1.fq.gz M22-1_2.fq.gz fastq fastq 6102383400.0 20341278.0 M22 1 1.fq.gz 0:150 1:150 A:1577012976;C:1455984420;G:1487747979;T:1581590987;N:47038 150 150     1577012976 1455984420 1487747979 1581590987 47038 SRX23975259 SRS20773677 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26554 26554 SRR28370195 SRX23975258 SRS20773676 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         M20 4 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 15|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E15 E15 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     M20-4_1.fq.gz M20-4_2.fq.gz fastq fastq 6636566100.0 22121887.0 M20 4 1.fq.gz 0:150 1:150 A:1715667953;C:1580553403;G:1620418612;T:1719875870;N:50262 150 150     1715667953 1580553403 1620418612 1719875870 50262 SRX23975258 SRS20773676 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26555 26555 SRR28370196 SRX23975257 SRS20773675 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         M20 3 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 13|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E13 E13 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     M20-3_1.fq.gz M20-3_2.fq.gz fastq fastq 6761256900.0 22537523.0 M20 3 1.fq.gz 0:150 1:150 A:1758917520;C:1603264927;G:1642146940;T:1756875822;N:51691 150 150     1758917520 1603264927 1642146940 1756875822 51691 SRX23975257 SRS20773675 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26556 26556 SRR28370197 SRX23975256 SRS20773674 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         M20 2 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 11|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E11 E11 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     M20-2_1.fq.gz M20-2_2.fq.gz fastq fastq 6746623800.0 22488746.0 M20 2 1.fq.gz 0:150 1:150 A:1744481110;C:1606775717;G:1646048497;T:1749267538;N:50938 150 150     1744481110 1606775717 1646048497 1749267538 50938 SRX23975256 SRS20773674 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26557 26557 SRR28370198 SRX23975255 SRS20773673 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         H27 1 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 1|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E1 E1 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     H27-1_1.fq.gz H27-1_2.fq.gz fastq fastq 6713598900.0 22378663.0 H27 1 1.fq.gz 0:150 1:150 A:1734915716;C:1602520747;G:1639382442;T:1736729508;N:50487 150 150     1734915716 1602520747 1639382442 1736729508 50487 SRX23975255 SRS20773673 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
28800 28800 SRR26744390 SRX22443207 SRS19460925 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       TL1 AWG21KI956   strain:AB wild type|age:4 mpf|collection date:2021 10 20|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 RNAseq of zebrafish LM LM normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     TL1_2.clean.fq.gz TL1_1.clean.fq.gz fastq fastq 5699083800.0 18996946.0 TL1 1.clean.fq.gz 0:150 1:150 A:1551237534;C:1296027828;G:1322262120;T:1529547653;N:8665 150 150     1551237534 1296027828 1322262120 1529547653 8665 SRX22443207 SRS19460925 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92378 0.91959 0.10498 0.1026 0.6299 0.64319 0.49163 0.48651 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28801 28801 SRR26744391 SRX22443206 SRS19460924 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       OL3 AWG21KN131   strain:AB wild type|age:4 mpf|collection date:2021 10 19|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 RNAseq of zebrafish LF3 LF3 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     OL3_2.clean.fq.gz OL3_1.clean.fq.gz fastq fastq 6314250900.0 21047503.0 OL3 1.clean.fq.gz 0:150 1:150 A:1645668992;C:1501216557;G:1526087917;T:1641268461;N:8973 150 150     1645668992 1501216557 1526087917 1641268461 8973 SRX22443206 SRS19460924 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92555 0.92469 0.01845 0.01818 0.75146 0.75298 0.4697 0.47119 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28802 28802 SRR26744392 SRX22443205 SRS19460920 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       OL2 AWG21KN130   strain:AB wild type|age:4 mpf|collection date:2021 10 18|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 RNAseq of zebrafish LF2 LF2 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     OL2_1.clean.fq.gz OL2_2.clean.fq.gz fastq fastq 5723391300.0 19077971.0 OL2 1.clean.fq.gz 0:150 1:150 A:1493997463;C:1358589750;G:1376156813;T:1494638946;N:8328 150 150     1493997463 1358589750 1376156813 1494638946 8328 SRX22443205 SRS19460920 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92147 0.92251 0.0187 0.01891 0.75077 0.75156 0.46983 0.46864 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28803 28803 SRR26744393 SRX22443204 SRS19460923 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       OL1 AWG21KI955   strain:AB wild type|age:4 mpf|collection date:2021 10 17|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 RNAseq of zebrafish LF LF normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     OL1_1.clean.fq.gz OL1_2.clean.fq.gz fastq fastq 5769588600.0 19231962.0 OL1 1.clean.fq.gz 0:150 1:150 A:1506564191;C:1368903119;G:1393174106;T:1500937757;N:9427 150 150     1506564191 1368903119 1393174106 1500937757 9427 SRX22443204 SRS19460923 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92622 0.92542 0.01753 0.01714 0.75694 0.7596 0.47038 0.46862 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28804 28804 SRR26744394 SRX22443203 SRS19460921 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       TC3 AWG21KN129   strain:AB wild type|age:4 mpf|collection date:2021 10 16|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 RNAseq of zebrafish CM3 CM3 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     TC3_2.clean.fq.gz TC3_1.clean.fq.gz fastq fastq 5849082900.0 19496943.0 TC3 1.clean.fq.gz 0:150 1:150 A:1588589470;C:1336193891;G:1355933296;T:1568357820;N:8423 150 150     1588589470 1336193891 1355933296 1568357820 8423 SRX22443203 SRS19460921 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.9259 0.92501 0.09579 0.09483 0.62501 0.6266 0.49341 0.49677 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28805 28805 SRR26744395 SRX22443202 SRS19460922 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       TC2 AWG21KN128   strain:AB wild type|age:4 mpf|collection date:2021 10 15|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 RNAseq of zebrafish CM2 CM2 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     TC2_2.clean.fq.gz TC2_1.clean.fq.gz fastq fastq 6060182100.0 20200607.0 TC2 1.clean.fq.gz 0:150 1:150 A:1640267244;C:1389270827;G:1407872392;T:1622763112;N:8525 150 150     1640267244 1389270827 1407872392 1622763112 8525 SRX22443202 SRS19460922 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92414 0.9235 0.0895 0.08929 0.62528 0.62682 0.48981 0.48954 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28806 28806 SRR26744396 SRX22443201 SRS19460918 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       TC1 AWG21KI954   strain:AB wild type|age:4 mpf|collection date:2021 10 14|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 RNAseq of zebrafish CM CM normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     TC1_1.clean.fq.gz TC1_2.clean.fq.gz fastq fastq 5990926200.0 19969754.0 TC1 1.clean.fq.gz 0:150 1:150 A:1624594580;C:1370442060;G:1389854623;T:1606025586;N:9351 150 150     1624594580 1370442060 1389854623 1606025586 9351 SRX22443201 SRS19460918 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92373 0.92279 0.09865 0.09887 0.62568 0.62889 0.49516 0.49165 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28807 28807 SRR26744397 SRX22443200 SRS19460914 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       OC3 AWG21KN127   strain:AB wild type|age:4 mpf|collection date:2021 10 13|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 RNAseq of zebrafish CF3 CF3 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     OC3_1.clean.fq.gz OC3_2.clean.fq.gz fastq fastq 6016914600.0 20056382.0 OC3 1.clean.fq.gz 0:150 1:150 A:1568359804;C:1431107464;G:1450792678;T:1566645836;N:8818 150 150     1568359804 1431107464 1450792678 1566645836 8818 SRX22443200 SRS19460914 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92534 0.92528 0.01718 0.017 0.75201 0.753 0.47491 0.48041 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28808 28808 SRR26744398 SRX22443199 SRS19460915 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       TL3 AWG21KN137   strain:AB wild type|age:4 mpf|collection date:2021 10 28|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 RNAseq of zebrafish HM3 HM3 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     TH3_1.clean.fq.gz TH3_2.clean.fq.gz fastq fastq 5656023900.0 18853413.0 TH3 1.clean.fq.gz 0:150 1:150 A:1543170407;C:1285816998;G:1307460034;T:1519567327;N:9134 150 150     1543170407 1285816998 1307460034 1519567327 9134 SRX22443199 SRS19460915 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92316 0.92166 0.10167 0.10105 0.61546 0.61712 0.482 0.4844 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28809 28809 SRR26744399 SRX22443198 SRS19460919 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       TL2 AWG21KN136   strain:AB wild type|age:4 mpf|collection date:2021 10 27|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 RNAseq of zebrafish HM2 HM2 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     TH2_2.clean.fq.gz TH2_1.clean.fq.gz fastq fastq 6625748400.0 22085828.0 TH2 1.clean.fq.gz 0:150 1:150 A:1808454203;C:1505432915;G:1526482662;T:1785369099;N:9521 150 150     1808454203 1505432915 1526482662 1785369099 9521 SRX22443198 SRS19460919 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92273 0.92286 0.09974 0.09973 0.62043 0.62203 0.48636 0.48603 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28810 28810 SRR26744400 SRX22443197 SRS19460917 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       TL1 AWG21KI958   strain:AB wild type|age:4 mpf|collection date:2021 10 26|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 RNAseq of zebrafish HM HM normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     TH1_1.clean.fq.gz TH1_2.clean.fq.gz fastq fastq 6588309600.0 21961032.0 TH1 1.clean.fq.gz 0:150 1:150 A:1793735270;C:1500551703;G:1518029671;T:1775983548;N:9408 150 150     1793735270 1500551703 1518029671 1775983548 9408 SRX22443197 SRS19460917 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92046 0.91969 0.10181 0.10206 0.61505 0.61477 0.48395 0.48957 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28811 28811 SRR26744401 SRX22443196 SRS19460916 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       OL3 AWG21KN135   strain:AB wild type|age:4 mpf|collection date:2021 10 25|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 RNAseq of zebrafish HF3 HF3 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     OH3_1.clean.fq.gz OH3_2.clean.fq.gz fastq fastq 5690890500.0 18969635.0 OH3 1.clean.fq.gz 0:150 1:150 A:1485585756;C:1351021989;G:1373539521;T:1480733791;N:9443 150 150     1485585756 1351021989 1373539521 1480733791 9443 SRX22443196 SRS19460916 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92616 0.9273 0.01843 0.01865 0.74793 0.74925 0.4724 0.47202 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28812 28812 SRR26744402 SRX22443195 SRS19460912 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       OL2 AWG21KN134   strain:AB wild type|age:4 mpf|collection date:2021 10 24|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 RNAseq of zebrafish HF2 HF2 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     OH2_2.clean.fq.gz OH2_1.clean.fq.gz fastq fastq 6047756700.0 20159189.0 OH2 1.clean.fq.gz 0:150 1:150 A:1577825068;C:1435108510;G:1458998347;T:1575814993;N:9782 150 150     1577825068 1435108510 1458998347 1575814993 9782 SRX22443195 SRS19460912 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.9233 0.92363 0.01923 0.01923 0.74474 0.74686 0.46918 0.46911 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28813 28813 SRR26744403 SRX22443194 SRS19460913 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       OL1 AWG21KI957   strain:AB wild type|age:4 mpf|collection date:2021 10 23|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 RNAseq of zebrafish HF HF normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     OH1_1.clean.fq.gz OH1_2.clean.fq.gz fastq fastq 5756713800.0 19189046.0 OH1 1.clean.fq.gz 0:150 1:150 A:1501851096;C:1366577079;G:1382910165;T:1505367292;N:8168 150 150     1501851096 1366577079 1382910165 1505367292 8168 SRX22443194 SRS19460913 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92555 0.92628 0.0184 0.01828 0.74968 0.7512 0.47643 0.4776 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28814 28814 SRR26744404 SRX22443193 SRS19460908 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       TL3 AWG21KN133   strain:AB wild type|age:4 mpf|collection date:2021 10 22|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 RNAseq of zebrafish LM3 LM3 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     TL3_1.clean.fq.gz TL3_2.clean.fq.gz fastq fastq 5675551800.0 18918506.0 TL3 1.clean.fq.gz 0:150 1:150 A:1544159251;C:1294658828;G:1308831043;T:1527894467;N:8211 150 150     1544159251 1294658828 1308831043 1527894467 8211 SRX22443193 SRS19460908 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92069 0.92047 0.10371 0.10354 0.62741 0.62954 0.48923 0.48839 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28815 28815 SRR26744405 SRX22443192 SRS19460909 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       TL2 AWG21KN132   strain:AB wild type|age:4 mpf|collection date:2021 10 21|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 RNAseq of zebrafish LM2 LM2 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     TL2_1.clean.fq.gz TL2_2.clean.fq.gz fastq fastq 5834343300.0 19447811.0 TL2 1.clean.fq.gz 0:150 1:150 A:1583809689;C:1333511774;G:1345919597;T:1571093925;N:8315 150 150     1583809689 1333511774 1345919597 1571093925 8315 SRX22443192 SRS19460909 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.91878 0.92054 0.10134 0.10105 0.62708 0.62759 0.48763 0.48708 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28816 28816 SRR26744406 SRX22443191 SRS19460911 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       OC2 AWG21KN126   strain:AB wild type|age:4 mpf|collection date:2021 10 12|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 RNAseq of zebrafish CF2 CF2 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     OC2_2.clean.fq.gz OC2_1.clean.fq.gz fastq fastq 6462335700.0 21541119.0 OC2 1.clean.fq.gz 0:150 1:150 A:1684794140;C:1535771967;G:1553892063;T:1687868172;N:9358 150 150     1684794140 1535771967 1553892063 1687868172 9358 SRX22443191 SRS19460911 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92236 0.92263 0.01803 0.01777 0.74945 0.75081 0.47372 0.47191 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28817 28817 SRR26744407 SRX22443190 SRS19460907 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       OC1 AWG21KI953   strain:AB wild type|age:4 mpf|collection date:2021 10 11|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 RNAseq of zebrafish CF CF normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     OC1_1.clean.fq.gz OC1_2.clean.fq.gz fastq fastq 5719061700.0 19063539.0 OC1 1.clean.fq.gz 0:150 1:150 A:1489404392;C:1360123113;G:1386373369;T:1483151708;N:9118 150 150     1489404392 1360123113 1386373369 1483151708 9118 SRX22443190 SRS19460907 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92595 0.92513 0.0166 0.0163 0.75187 0.75503 0.47431 0.47637 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
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
29188 29188 SRR8176753 SRX4996870 SRS4031878 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 30dpf ZZ Gonad Single Cell RNA Seq Nadia 30dpf ZZ Gonad Single Cell RNA Seq   strain:Nadia|age:30 dpf provider:John H. Postlethwait University of Oregon|genotype:ZZ|BioSampleModel:Model organism or animal                 scRNA Seq of Danio rerio: Nadia 30dpf ZZ gonad Nadia 30dpf ZZ gonad Nadia 30dpf 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     23587173438.0 167284918.0 1 I1 001.fastq.gz 0:8 1:133 A:6732844252;C:4934497997;G:5685086026;T:6219863789;N:14881374 8 133     6732844252 4934497997 5685086026 6219863789 14881374 SRX4996870 SRS4031878 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 Juvenile Juvenile Gonad Reproductive System
29189 29189 SRR8176754 SRX4996869 SRS4031877 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 30dpf ZW Gonad Single Cell RNA Seq Nadia 30dpf ZW Gonad Single Cell RNA Seq   strain:Nadia|age:30 dpf provider:John H. Postlethwait University of Oregon|genotype:ZW|BioSampleModel:Model organism or animal                 scRNA Seq of Danio rerio: Nadia 30dpf ZW gonad Nadia 30dpf ZW gonad Nadia 30dpf 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     43358808480.0 307509280.0 2 I1 001.fastq.gz 0:8 1:133 A:12290612367;C:8880655083;G:10261318751;T:11898771792;N:27450487 8 133     12290612367 8880655083 10261318751 11898771792 27450487 SRX4996869 SRS4031877 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 Juvenile Juvenile 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
29746 29746 SRR27467679 SRX23139227 SRS20090270 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary BS R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary BS rep2 EV02003 EV02003 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA NextSeq 500   SRP482074     EV02003.R1.fastq.gz EV02003.R2.fastq.gz fastq fastq 1031891720.0 3416860.0 EV02003.R1.fastq.gz 0:151 1:151 A:264464363;C:153440613;G:408557241;T:205367487;N:62016 151 151     264464363 153440613 408557241 205367487 62016 SRX23139227 SRS20090270 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 2 0.0 0.00019 0.0 0.00015 1.0 0.99993   1.0 151 151 T T mates < 9% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Adult Adult Gonad Reproductive System
29755 29755 SRR27467688 SRX23139218 SRS20090261 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary DM R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary DM rep2 EV02002 EV02002 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA NextSeq 500   SRP482074     EV02002.R1.fastq.gz EV02002.R2.fastq.gz fastq fastq 861320308.0 2852054.0 EV02002.R1.fastq.gz 0:151 1:151 A:205625519;C:162178974;G:334206312;T:159256900;N:52603 151 151     205625519 162178974 334206312 159256900 52603 SRX23139218 SRS20090261 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 2 2e-05 0.00049 0.0 0.00027 1.0 0.99947   0.44444 151 151 T T mates < 9% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Adult Adult Gonad Reproductive System
29756 29756 SRR27467689 SRX23139217 SRS20090260 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary mock R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary mock rep2 EV02001 EV02001 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA NextSeq 500   SRP482074     EV02001.R1.fastq.gz EV02001.R2.fastq.gz fastq fastq 520371066.0 1723083.0 EV02001.R1.fastq.gz 0:151 1:151 A:116107273;C:90896560;G:218652568;T:94682244;N:32421 151 151     116107273 90896560 218652568 94682244 32421 SRX23139217 SRS20090260 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 2 2e-05 0.00086 0.0 0.00078 0.99995 0.99981 0.0 0.61538 151 151 T T mates < 9% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Adult Adult Gonad Reproductive System
30556 30556 SRR27836071 SRX23499420 SRS20351177 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 mApple crosslinked SR3 GSM8059038   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing Rbpms2 mApple crosslinked SR3 Basespace illumina platform was used and reads were mapped using tophate2 aligner. Estimation of reference genes and transcript was done using cufflinks and reads were mapped to the genome GRCz10. Reads were aligned with the TopHat Alignment App. GRCz10 CSV file that compiled includes tracking ids gene loci and FPKMs for each samples CSV files include tracking and gene id gene short name tss id locus and FPKM for each sample Gonad   RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589   tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype GSM8059038 GSM8059038: Rbpms2 mApple crosslinked SR3; Danio rerio; RNA Seq GSM8059038 r1 GSM8059038 1 RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485     SR-3_S4_L001_R1_001.fastq.gz SR-3_S4_L001_R2_001.fastq.gz fastq fastq 588252864.0 3949222.0 GSM8059038 r1 0:74.42 1:74.53 A:116383167;C:176622592;G:176850622;T:118306997;N:89486 74 74     116383167 176622592 176850622 118306997 89486 SRX23499420 SRS20351177 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 trueseq bulk bulk bulk   United States 2024-02-01 Undetermined Undetermined Gonad Reproductive System
30557 30557 SRR27836072 SRX23499419 SRS20351178 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 mApple uncrosslinked SR2 GSM8059037   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing Rbpms2 mApple uncrosslinked SR2 Basespace illumina platform was used and reads were mapped using tophate2 aligner. Estimation of reference genes and transcript was done using cufflinks and reads were mapped to the genome GRCz10. Reads were aligned with the TopHat Alignment App. GRCz10 CSV file that compiled includes tracking ids gene loci and FPKMs for each samples CSV files include tracking and gene id gene short name tss id locus and FPKM for each sample Gonad   RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589   tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype GSM8059037 GSM8059037: Rbpms2 mApple uncrosslinked SR2; Danio rerio; RNA Seq GSM8059037 r1 GSM8059037 1 RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485     SR-2_S3_L001_R1_001.fastq.gz SR-2_S3_L001_R2_001.fastq.gz fastq fastq 547329260.0 3670350.0 GSM8059037 r1 0:74.51 1:74.61 A:109193152;C:163365002;G:162344228;T:112378069;N:48809 74 74     109193152 163365002 162344228 112378069 48809 SRX23499419 SRS20351178 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 trueseq bulk bulk bulk   United States 2024-02-01 Undetermined Undetermined Gonad Reproductive System
30558 30558 SRR27836073 SRX23499418 SRS20351176 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   mApple control crosslinked SR8 GSM8059036   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing mApple control crosslinked SR8 Basespace illumina platform was used and reads were mapped using tophate2 aligner. Estimation of reference genes and transcript was done using cufflinks and reads were mapped to the genome GRCz10. Reads were aligned with the TopHat Alignment App. GRCz10 CSV file that compiled includes tracking ids gene loci and FPKMs for each samples CSV files include tracking and gene id gene short name tss id locus and FPKM for each sample Gonad   RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589   tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype GSM8059036 GSM8059036: mApple control crosslinked SR8; Danio rerio; RNA Seq GSM8059036 r1 GSM8059036 1 RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485     SR-8_S6_L001_R1_001.fastq.gz SR-8_S6_L001_R2_001.fastq.gz fastq fastq 474378287.0 3180744.0 GSM8059036 r1 0:74.52 1:74.62 A:90310344;C:145884340;G:146185172;T:91942086;N:56345 74 74     90310344 145884340 146185172 91942086 56345 SRX23499418 SRS20351176 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 trueseq bulk bulk bulk   United States 2024-02-01 Undetermined Undetermined Gonad Reproductive System
30559 30559 SRR27836074 SRX23499417 SRS20351175 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   mApple control uncrosslinked SR6 GSM8059035   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing mApple control uncrosslinked SR6 Basespace illumina platform was used and reads were mapped using tophate2 aligner. Estimation of reference genes and transcript was done using cufflinks and reads were mapped to the genome GRCz10. Reads were aligned with the TopHat Alignment App. GRCz10 CSV file that compiled includes tracking ids gene loci and FPKMs for each samples CSV files include tracking and gene id gene short name tss id locus and FPKM for each sample Gonad   RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589   tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype GSM8059035 GSM8059035: mApple control uncrosslinked SR6; Danio rerio; RNA Seq GSM8059035 r1 GSM8059035 1 RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485     SR-6_S5_L001_R1_001.fastq.gz SR-6_S5_L001_R2_001.fastq.gz fastq fastq 1667210566.0 11187841.0 GSM8059035 r1 0:74.46 1:74.56 A:348153529;C:480420209;G:474792496;T:363567978;N:276354 74 74     348153529 480420209 474792496 363567978 276354 SRX23499417 SRS20351175 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 trueseq bulk bulk bulk   United States 2024-02-01 Undetermined Undetermined 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
31721 31721 SRR28537217 SRX24137319 SRS20921922 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         ko3   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:ko biological replicate 3|BioSampleModel:Model organism or animal                 ko3 ko3 ko3 ko ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     ko3_1.fq.gz ko3_2.fq.gz fastq fastq 8310654000.0 27702180.0 ko3 1.fq.gz 0:150 1:150 A:2164758632;C:1964255570;G:1984514973;T:2197073890;N:50935 150 150     2164758632 1964255570 1984514973 2197073890 50935 SRX24137319 SRS20921922     Shenzhen Second People's Hospital 2 0.9472 0.94617 0.02506 0.02527 0.74286 0.74535 0.45316 0.45662 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
31722 31722 SRR28537218 SRX24137318 SRS20921924 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         ko2   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:ko biological replicate 2|BioSampleModel:Model organism or animal                 ko2 ko2 ko2 ko ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     ko2_1.fq.gz ko2_2.fq.gz fastq fastq 8095711800.0 26985706.0 ko2 1.fq.gz 0:150 1:150 A:2117986563;C:1909094084;G:1931885806;T:2136732639;N:12708 150 150     2117986563 1909094084 1931885806 2136732639 12708 SRX24137318 SRS20921924     Shenzhen Second People's Hospital 2 0.9483 0.94443 0.02385 0.02347 0.74266 0.74686 0.45568 0.45676 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
31723 31723 SRR28537219 SRX24137317 SRS20921925 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         ko1   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:ko biological replicate 1|BioSampleModel:Model organism or animal                 ko1 ko1 ko1 ko ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     ko1_1.fq.gz ko1_2.fq.gz fastq fastq 9904629000.0 33015430.0 ko1 1.fq.gz 0:150 1:150 A:2565332092;C:2354153391;G:2380645312;T:2604437822;N:60383 150 150     2565332092 2354153391 2380645312 2604437822 60383 SRX24137317 SRS20921925     Shenzhen Second People's Hospital 2 0.94565 0.94416 0.01943 0.01956 0.7559 0.75739 0.456 0.45903 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
31724 31724 SRR28537220 SRX24137316 SRS20921923 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         wt3   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:wt biological replicate 3|BioSampleModel:Model organism or animal                 wt3 wt3 wt3 wt ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     wt3_1.fq.gz wt3_2.fq.gz fastq fastq 10079485500.0 33598285.0 wt3 1.fq.gz 0:150 1:150 A:2607822943;C:2396994959;G:2427407078;T:2647197813;N:62707 150 150     2607822943 2396994959 2427407078 2647197813 62707 SRX24137316 SRS20921923     Shenzhen Second People's Hospital 2 0.94735 0.94594 0.01733 0.01743 0.75635 0.75712 0.44042 0.46348 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
31725 31725 SRR28537221 SRX24137315 SRS20921920 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         wt2   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:wt biological replicate 2|BioSampleModel:Model organism or animal                 wt2 wt2 wt2 wt ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     wt2_2.fq.gz wt2_1.fq.gz fastq fastq 8980086900.0 29933623.0 wt2 1.fq.gz 0:150 1:150 A:2333474507;C:2131182397;G:2149144543;T:2366230132;N:55321 150 150     2333474507 2131182397 2149144543 2366230132 55321 SRX24137315 SRS20921920     Shenzhen Second People's Hospital 2 0.94182 0.94004 0.0187 0.01854 0.75077 0.75132 0.46271 0.46384 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
31726 31726 SRR28537222 SRX24137314 SRS20921921 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         wt1   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:wt biological replicate 1|BioSampleModel:Model organism or animal                 wt1 wt1 wt1 wt ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     wt1_1.fq.gz wt1_2.fq.gz fastq fastq 5436554400.0 18121848.0 wt1 1.fq.gz 0:150 1:150 A:1418897733;C:1287256771;G:1297629578;T:1432736726;N:33592 150 150     1418897733 1287256771 1297629578 1432736726 33592 SRX24137314 SRS20921921     Shenzhen Second People's Hospital 2 0.9407 0.94657 0.02199 0.02152 0.74655 0.74679 0.47086 0.47165 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
31837 31837 SRR28709001 SRX24276192 SRS21041156 SRP502090 PRJNA1101048 Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish GSE264143 Transcriptome Analysis Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.       dpf61 Ov mt 3 GSM8212808   source name:Ovary|tissue:Ovary|age:dpf 61|genotype:mutant|geo loc name:missing|collection date:missing dpf61 Ov mt 3 Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample. Ovary   Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples. WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food. tissue:Ovary|age:dpf 61|genotype:mutant GSM8212808 GSM8212808: dpf61 Ov mt 3; Danio rerio; RNA Seq GSM8212808 r1 GSM8212808 1 Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP502090   loader:fastq load.py NS51397.M43_20230510_103430.L001.1.fastq.gz NS51397.M43_20230510_103430.L001.2.fastq.gz fastq fastq 9024444634.0 29882267.0 GSM8212808 r1 0:151 1:151 A:2471288260;C:1931225512;G:2256742565;T:2363378475;N:1809822 151 151     2471288260 1931225512 2256742565 2363378475 1809822 SRX24276192 SRS21041156 SRA1847037 Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences                       B B biological fallback assumption illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-04-16 Juvenile Juvenile Gonad Reproductive System
31838 31838 SRR28709002 SRX24276191 SRS21041154 SRP502090 PRJNA1101048 Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish GSE264143 Transcriptome Analysis Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.       dpf61 Ov mt 2 GSM8212807   source name:Ovary|tissue:Ovary|age:dpf 61|genotype:mutant|geo loc name:missing|collection date:missing dpf61 Ov mt 2 Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample. Ovary   Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples. WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food. tissue:Ovary|age:dpf 61|genotype:mutant GSM8212807 GSM8212807: dpf61 Ov mt 2; Danio rerio; RNA Seq GSM8212807 r1 GSM8212807 1 Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP502090   loader:fastq load.py NS51397.M41_20230510_103430.L001.1.fastq.gz NS51397.M41_20230510_103430.L001.2.fastq.gz fastq fastq 13553131538.0 44877919.0 GSM8212807 r1 0:151 1:151 A:3707129145;C:2878818514;G:3433054125;T:3531357698;N:2772056 151 151     3707129145 2878818514 3433054125 3531357698 2772056 SRX24276191 SRS21041154 SRA1847037 Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences                       B B biological fallback assumption illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-04-16 Juvenile Juvenile Gonad Reproductive System
31839 31839 SRR28709003 SRX24276190 SRS21041155 SRP502090 PRJNA1101048 Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish GSE264143 Transcriptome Analysis Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.       dpf61 Ov mt 1 GSM8212806   source name:Ovary|tissue:Ovary|age:dpf 61|genotype:mutant|geo loc name:missing|collection date:missing dpf61 Ov mt 1 Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample. Ovary   Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples. WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food. tissue:Ovary|age:dpf 61|genotype:mutant GSM8212806 GSM8212806: dpf61 Ov mt 1; Danio rerio; RNA Seq GSM8212806 r1 GSM8212806 1 Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP502090   loader:fastq load.py NS51397.M32_20230510_103430.L001.1.fastq.gz NS51397.M32_20230510_103430.L001.2.fastq.gz fastq fastq 11752803234.0 38916567.0 GSM8212806 r1 0:151 1:151 A:3199511211;C:2525248103;G:2947698766;T:3077964367;N:2380787 151 151     3199511211 2525248103 2947698766 3077964367 2380787 SRX24276190 SRS21041155 SRA1847037 Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences                       B B biological fallback assumption illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-04-16 Juvenile Juvenile 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");;