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
50,DRR029944,DRX026962,DRS086502,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,ovulation duirng natural paring,zebrafish ovary isolated from adult fish at ovulation duirng natural paring. [RNAseq],SAMD00025434,,sample name:6 Ovu|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025434,DRX026962,6 Ovu,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025434,,,,351766656.0,9771296.0,DRR029944,0:36,A:79811727;C:85391142;G:90185809;T:96371771;N:6207,36,,,,79811727,85391142,90185809,96371771,6207,DRX026962,DRS086502,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91956,,0.01686,,0.76637,,0.45997,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
52,DRR029942,DRX026960,DRS086500,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo testosterone treatment,zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq  replicate],SAMD00025432,,sample name:4 Tes rep|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025432,DRX026960,4 Tes rep,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025432,,,,366042528.0,10167848.0,DRR029942,0:36,A:84988522;C:88640326;G:93559022;T:98847003;N:7655,36,,,,84988522,88640326,93559022,98847003,7655,DRX026960,DRS086500,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91602,,0.01846,,0.76015,,0.46475,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
53,DRR029941,DRX026959,DRS086499,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo testosterone treatment,zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq],SAMD00025431,,sample name:4 Tes|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025431,DRX026959,4 Tes,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025431,,,,1269835992.0,35273222.0,DRR029941,0:36,A:275250658;C:323605136;G:316729009;T:354204170;N:47019,36,,,,275250658,323605136,316729009,354204170,47019,DRX026959,DRS086499,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91467,,0.02353,,0.75962,,0.46861,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
54,DRR029940,DRX026958,DRS086498,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo diethylstilbestrol DES treatment,zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq  replicate],SAMD00025430,,sample name:3 DES rep|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025430,DRX026958,3 DES rep,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025430,,,,658651536.0,18295876.0,DRR029940,,,,,,,,,,,,DRX026958,DRS086498,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.89964,,0.01785,,0.76451,,0.45872,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
55,DRR029939,DRX026957,DRS086497,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo diethylstilbestrol DES treatment,zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq],SAMD00025429,,sample name:3 DES|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025429,DRX026957,3 DES,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025429,,,,1202024016.0,33389556.0,DRR029939,0:36,A:263319430;C:305852921;G:298798093;T:334008544;N:45028,36,,,,263319430,305852921,298798093,334008544,45028,DRX026957,DRS086497,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.90643,,0.02337,,0.75008,,0.47587,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
56,DRR029938,DRX026956,DRS086496,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo maturation inducing hormone DHP treatment,zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq  replicate],SAMD00025428,,sample name:2 DHP rep|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025428,DRX026956,2 DHP rep,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025428,,,,434243088.0,12062308.0,DRR029938,0:36,A:99859342;C:105890785;G:110526688;T:117957580;N:8693,36,,,,99859342,105890785,110526688,117957580,8693,DRX026956,DRS086496,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91529,,0.02061,,0.7595,,0.45809,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
57,DRR029937,DRX026955,DRS086495,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo maturation inducing hormone DHP treatment,zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq],SAMD00025427,,sample name:2 DHP|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025427,DRX026955,2 DHP,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025427,,,,1463868972.0,40663027.0,DRR029937,0:36,A:316060780;C:369221844;G:372845502;T:405685804;N:55042,36,,,,316060780,369221844,372845502,405685804,55042,DRX026955,DRS086495,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91556,,0.01967,,0.76621,,0.46541,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
58,DRR029936,DRX026954,DRS086494,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo ethanol treatment,zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq  replicate],SAMD00025426,,sample name:1 EtOH rep|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025426,DRX026954,1 EtOH rep,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025426,,,,438020208.0,12167228.0,DRR029936,0:36,A:101672612;C:105602774;G:110120652;T:120615069;N:9101,36,,,,101672612,105602774,110120652,120615069,9101,DRX026954,DRS086494,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.90777,,0.01929,,0.7652,,0.45988,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
59,DRR029935,DRX026953,DRS086493,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo ethanol treatment,zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq],SAMD00025425,,sample name:1 EtOH|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025425,DRX026953,1 EtOH,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025425,,,,1365603372.0,37933427.0,DRR029935,0:36,A:299786286;C:345487829;G:342408447;T:377870789;N:50021,36,,,,299786286,345487829,342408447,377870789,50021,DRX026953,DRS086493,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91103,,0.02142,,0.75402,,0.46574,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
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,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,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,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,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,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,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
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+/+ and Cdkn1a +/  zebrafish. We then established 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.,,,,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,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+/+ and Cdkn1a +/  zebrafish. We then established 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.,,,,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,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+/+ and Cdkn1a +/  zebrafish. We then established 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.,,,,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,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+/+ and Cdkn1a +/  zebrafish. We then established 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.,,,,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,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+/+ and Cdkn1a +/  zebrafish. We then established 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.,,,,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,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+/+ and Cdkn1a +/  zebrafish. We then established 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.,,,,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,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+/+ and Cdkn1a +/  zebrafish. We then established 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.,,,,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,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+/+ and Cdkn1a +/  zebrafish. We then established 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.,,,,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,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+/+ and Cdkn1a +/  zebrafish. We then established 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.,,,,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,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+/+ and Cdkn1a +/  zebrafish. We then established 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.,,,,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,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+/+ and Cdkn1a +/  zebrafish. We then established 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.,,,,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,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+/+ and Cdkn1a +/  zebrafish. We then established 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.,,,,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,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,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,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,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,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,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,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,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,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,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,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,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
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 Gene Expression Analysis.,,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,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 Gene Expression Analysis.,,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,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 Gene Expression Analysis.,,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,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 Gene Expression Analysis.,,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,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 Gene Expression Analysis.,,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,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 Gene Expression Analysis.,,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,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 Gene Expression Analysis.,,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,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 Gene Expression Analysis.,,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,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 Gene Expression Analysis.,,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,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 Gene Expression Analysis.,,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,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 Gene Expression Analysis.,,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,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 Gene Expression Analysis.,,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,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 Gene Expression Analysis.,,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,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 Gene Expression Analysis.,,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,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 Gene Expression Analysis.,,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,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 Gene Expression Analysis.,,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,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,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,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,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,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,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,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,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,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
31840,SRR28709004,SRX24276189,SRS21041153,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 wt 3,GSM8212805,,source name:Ovary|tissue:Ovary|age:dpf 61|genotype:wildtype|geo loc name:missing|collection date:missing,dpf61 Ov wt 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:wildtype,GSM8212805,GSM8212805: dpf61 Ov wt 3; Danio rerio; RNA Seq,GSM8212805 r1,GSM8212805,1,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.M17_20230510_103430.L001.1.fastq.gz NS51397.M17_20230510_103430.L001.2.fastq.gz,fastq fastq,16726684646.0,55386373.0,GSM8212805 r1,0:151 1:151,A:4912874254;C:2935821083;G:3844206542;T:5030341800;N:3440967,151,151,,,4912874254,2935821083,3844206542,5030341800,3440967,SRX24276189,SRS21041153,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
31841,SRR28709005,SRX24276188,SRS21041152,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 wt 2,GSM8212804,,source name:Ovary|tissue:Ovary|age:dpf 61|genotype:wildtype|geo loc name:missing|collection date:missing,dpf61 Ov wt 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:wildtype,GSM8212804,GSM8212804: dpf61 Ov wt 2; Danio rerio; RNA Seq,GSM8212804 r1,GSM8212804,1,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.M14_20230510_103430.L001.1.fastq.gz NS51397.M14_20230510_103430.L001.2.fastq.gz,fastq fastq,11600612146.0,38412623.0,GSM8212804 r1,0:151 1:151,A:3087038432;C:2559546168;G:3029729871;T:2921939557;N:2358118,151,151,,,3087038432,2559546168,3029729871,2921939557,2358118,SRX24276188,SRS21041152,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
31842,SRR28709006,SRX24276187,SRS21041151,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 wt 1,GSM8212803,,source name:Ovary|tissue:Ovary|age:dpf 61|genotype:wildtype|geo loc name:missing|collection date:missing,dpf61 Ov wt 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:wildtype,GSM8212803,GSM8212803: dpf61 Ov wt 1; Danio rerio; RNA Seq,GSM8212803 r1,GSM8212803,1,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.M9_20230510_103430.L001.1.fastq.gz NS51397.M9_20230510_103430.L001.2.fastq.gz,fastq fastq,19081987478.0,63185389.0,GSM8212803 r1,0:151 1:151,A:5188307750;C:4048527738;G:4868706940;T:4972575432;N:3869618,151,151,,,5188307750,4048527738,4868706940,4972575432,3869618,SRX24276187,SRS21041151,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
31843,SRR28709007,SRX24276186,SRS21041150,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.,,,,dpf47 Ov mt 3,GSM8212802,,source name:Ovary|tissue:Ovary|age:dpf 47|genotype:mutant|geo loc name:missing|collection date:missing,dpf47 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 47|genotype:mutant,GSM8212802,GSM8212802: dpf47 Ov mt 3; Danio rerio; RNA Seq,GSM8212802 r1,GSM8212802,1,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.C33_20230510_103430.L001.1.fastq.gz NS51397.C33_20230510_103430.L001.2.fastq.gz,fastq fastq,8256087174.0,27338037.0,GSM8212802 r1,0:151 1:151,A:2217123657;C:1857924925;G:2109544983;T:2069850323;N:1643286,151,151,,,2217123657,1857924925,2109544983,2069850323,1643286,SRX24276186,SRS21041150,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
31844,SRR28709008,SRX24276185,SRS21041149,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.,,,,dpf47 Ov mt 2,GSM8212801,,source name:Ovary|tissue:Ovary|age:dpf 47|genotype:mutant|geo loc name:missing|collection date:missing,dpf47 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 47|genotype:mutant,GSM8212801,GSM8212801: dpf47 Ov mt 2; Danio rerio; RNA Seq,GSM8212801 r1,GSM8212801,1,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.C32_20230510_103430.L001.1.fastq.gz NS51397.C32_20230510_103430.L001.2.fastq.gz,fastq fastq,14985320634.0,49620267.0,GSM8212801 r1,0:151 1:151,A:4058920258;C:3245799385;G:3815485722;T:3862070151;N:3045118,151,151,,,4058920258,3245799385,3815485722,3862070151,3045118,SRX24276185,SRS21041149,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
31845,SRR28709009,SRX24276184,SRS21041147,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.,,,,dpf47 Ov mt 1,GSM8212800,,source name:Ovary|tissue:Ovary|age:dpf 47|genotype:mutant|geo loc name:missing|collection date:missing,dpf47 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 47|genotype:mutant,GSM8212800,GSM8212800: dpf47 Ov mt 1; Danio rerio; RNA Seq,GSM8212800 r1,GSM8212800,1,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.C29_20230510_103430.L001.1.fastq.gz NS51397.C29_20230510_103430.L001.2.fastq.gz,fastq fastq,11177741176.0,37012388.0,GSM8212800 r1,0:151 1:151,A:3060199842;C:2374800912;G:2799391711;T:2941063533;N:2285178,151,151,,,3060199842,2374800912,2799391711,2941063533,2285178,SRX24276184,SRS21041147,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
31846,SRR28709010,SRX24276183,SRS21041146,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.,,,,dpf47 Ov wt 3,GSM8212799,,source name:Ovary|tissue:Ovary|age:dpf 47|genotype:wildtype|geo loc name:missing|collection date:missing,dpf47 Ov wt 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 47|genotype:wildtype,GSM8212799,GSM8212799: dpf47 Ov wt 3; Danio rerio; RNA Seq,GSM8212799 r1,GSM8212799,1,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.C21_20230510_103430.L001.1.fastq.gz NS51397.C21_20230510_103430.L001.2.fastq.gz,fastq fastq,13599817718.0,45032509.0,GSM8212799 r1,0:151 1:151,A:3724782410;C:2835413438;G:3575258078;T:3461647906;N:2715886,151,151,,,3724782410,2835413438,3575258078,3461647906,2715886,SRX24276183,SRS21041146,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
31847,SRR28709011,SRX24276182,SRS21041148,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.,,,,dpf47 Ov wt 2,GSM8212798,,source name:Ovary|tissue:Ovary|age:dpf 47|genotype:wildtype|geo loc name:missing|collection date:missing,dpf47 Ov wt 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 47|genotype:wildtype,GSM8212798,GSM8212798: dpf47 Ov wt 2; Danio rerio; RNA Seq,GSM8212798 r1,GSM8212798,1,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.C20_20230510_103430.L001.1.fastq.gz NS51397.C20_20230510_103430.L001.2.fastq.gz,fastq fastq,13632935642.0,45142171.0,GSM8212798 r1,0:151 1:151,A:3708965267;C:2903664830;G:3492295019;T:3525245989;N:2764537,151,151,,,3708965267,2903664830,3492295019,3525245989,2764537,SRX24276182,SRS21041148,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
31848,SRR28709012,SRX24276181,SRS21041145,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.,,,,dpf47 Ov wt 1,GSM8212797,,source name:Ovary|tissue:Ovary|age:dpf 47|genotype:wildtype|geo loc name:missing|collection date:missing,dpf47 Ov wt 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 47|genotype:wildtype,GSM8212797,GSM8212797: dpf47 Ov wt 1; Danio rerio; RNA Seq,GSM8212797 r1,GSM8212797,1,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.C4_20230510_103430.L001.1.fastq.gz NS51397.C4_20230510_103430.L001.2.fastq.gz,fastq fastq,12378485324.0,40988362.0,GSM8212797 r1,0:151 1:151,A:3378421522;C:2638098449;G:3108553273;T:3250895048;N:2517032,151,151,,,3378421522,2638098449,3108553273,3250895048,2517032,SRX24276181,SRS21041145,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
33663,SRR30502664,SRX25926478,SRS22513929,SRP529840,PRJNA1154960,Deletion of ddx4 ovary specific transcript causes downregulation of sycp1 and derepression of DNA transposons in zebrafish ovaries,GSE276129,Transcriptome Analysis,Ddx4 DEAD box helicase 4 is a well established marker gene for early stage germlines and is required for the development of germ cells. Alternative splicing of ddx4 produces a long transcript that is exclusively expressed in zebrafish ovaries. The function of this ovary specific transcript ddx4 L remains unclear. In this study  using the ddx4 L knockout zebrafish model  we found that elimination of ddx4 L results in a decrease in fertilization rate and in the number of mature eggs laid by the female mutants. Transcriptome analysis was performed to identify the underlying changes of gene expression between WT and ddx4 L knockout ovaries. A total of 1134 differentially expressed genes were identified  of which 524 were upregulated and 610 were downregulated. Functional enrichment analysis showed that the terms of negative regulation of fertilization  sperm egg recognition process  and oocyte meiosis might be affected by elimination of ddx4 L. Furthermore  we found that Sycp1  a synaptonemal complex protein involved in meiosis and fertility  was dramatically decreased in the ddx4 L knockout ovaries at both mRNA and protein levels. Moreover  the activities of transposable elements were analyzed based on the RNA seq data. The result showed that elimination of ddx4 L causes the derepression of DNA transposons  a subclass of transposable elements  in zebrafish ovaries. In conclusion  the aforementioned findings indicate that the ovary specific transcript of ddx4 plays an important role in oocyte development and egg quality  possibly by maintaining sycp1 expression and repressing DNA transposons. Our work provide novel insights into the functions and regulatory mechanisms of ddx4 in zebrafish oogenesis. Overall design: Ovaries were dissected from three WT and three ddx4 E4? zebrafish at 6 mpf  respectively. Six total RNA samples were extracted and subjected to RNA sequencing. Differentially expressed genes DEGs and transposable elements TEs between WT and ddx4 E4? zebrafish ovaries were analyzed.,,pubmed:39765722,,ddx4E4Δ ovary rep3,GSM8491761,,source name:Ovary|tissue:Ovary|genotype:ddx4E4{delta}|geo loc name:missing|collection date:missing,ddx4E4Δ ovary rep3,The raw paired end reads were trimmed and quality controlled by SeqPrep https://github.com/jstjohn/SeqPrep and Sickle https://github.com/najoshi/sickle with default parameters. Then clean reads were separately aligned to zebrafish reference genome GRCz11 with orientation mode using HISAT2 http://ccb.jhu.edu/software/hisat2/index.shtml software. The mapped reads of each sample were assembled by StringTie https://ccb.jhu.edu/software/stringtie/index.shtml in a reference based approach. To identify DEGs differential expression genes between the ovaries of WT and ddx4 E4Δ zebrafish  the expression level of each transcript was calculated according to the transcripts per million reads TPM method. RSEM http://deweylab.biostat.wisc.edu/rsem/ was used to quantify gene abundances. Essentially  differential expression analysis was performed using the DESeq2 software. DEGs with |log2FC|>1 and Q value <= 0.05 were considered to be significantly different expressed genes. Functional enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni corrected P value ≤0.05 compared with the whole transcriptome background. Assembly: GRCz11 Supplementary files format and content: read count.txt is a tab delimited text file for read count numbers of each gene in all six samples.,Ovary,,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer’s protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,tissue:Ovary|genotype:ddx4E4{delta},GSM8491761,GSM8491761: ddx4E4Δ ovary rep3; Danio rerio; RNA Seq,GSM8491761 r1,GSM8491761,1,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer's protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP529840,,,D3_R1.fastq.gz D3_R2.fastq.gz,fastq fastq,8532086786.0,28251943.0,GSM8491761 r1,0:151 1:151,A:2175886107;C:2065104971;G:2109654211;T:2181416846;N:24651,151,151,,,2175886107,2065104971,2109654211,2181416846,24651,SRX25926478,SRS22513929,SRA1960397,"Institute of Hydrobiology, Chinese Academy of Sciences","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2024-08-31,Adult,Adult,Gonad,Reproductive System
33664,SRR30502665,SRX25926477,SRS22513928,SRP529840,PRJNA1154960,Deletion of ddx4 ovary specific transcript causes downregulation of sycp1 and derepression of DNA transposons in zebrafish ovaries,GSE276129,Transcriptome Analysis,Ddx4 DEAD box helicase 4 is a well established marker gene for early stage germlines and is required for the development of germ cells. Alternative splicing of ddx4 produces a long transcript that is exclusively expressed in zebrafish ovaries. The function of this ovary specific transcript ddx4 L remains unclear. In this study  using the ddx4 L knockout zebrafish model  we found that elimination of ddx4 L results in a decrease in fertilization rate and in the number of mature eggs laid by the female mutants. Transcriptome analysis was performed to identify the underlying changes of gene expression between WT and ddx4 L knockout ovaries. A total of 1134 differentially expressed genes were identified  of which 524 were upregulated and 610 were downregulated. Functional enrichment analysis showed that the terms of negative regulation of fertilization  sperm egg recognition process  and oocyte meiosis might be affected by elimination of ddx4 L. Furthermore  we found that Sycp1  a synaptonemal complex protein involved in meiosis and fertility  was dramatically decreased in the ddx4 L knockout ovaries at both mRNA and protein levels. Moreover  the activities of transposable elements were analyzed based on the RNA seq data. The result showed that elimination of ddx4 L causes the derepression of DNA transposons  a subclass of transposable elements  in zebrafish ovaries. In conclusion  the aforementioned findings indicate that the ovary specific transcript of ddx4 plays an important role in oocyte development and egg quality  possibly by maintaining sycp1 expression and repressing DNA transposons. Our work provide novel insights into the functions and regulatory mechanisms of ddx4 in zebrafish oogenesis. Overall design: Ovaries were dissected from three WT and three ddx4 E4? zebrafish at 6 mpf  respectively. Six total RNA samples were extracted and subjected to RNA sequencing. Differentially expressed genes DEGs and transposable elements TEs between WT and ddx4 E4? zebrafish ovaries were analyzed.,,pubmed:39765722,,ddx4E4Δ ovary rep2,GSM8491760,,source name:Ovary|tissue:Ovary|genotype:ddx4E4{delta}|geo loc name:missing|collection date:missing,ddx4E4Δ ovary rep2,The raw paired end reads were trimmed and quality controlled by SeqPrep https://github.com/jstjohn/SeqPrep and Sickle https://github.com/najoshi/sickle with default parameters. Then clean reads were separately aligned to zebrafish reference genome GRCz11 with orientation mode using HISAT2 http://ccb.jhu.edu/software/hisat2/index.shtml software. The mapped reads of each sample were assembled by StringTie https://ccb.jhu.edu/software/stringtie/index.shtml in a reference based approach. To identify DEGs differential expression genes between the ovaries of WT and ddx4 E4Δ zebrafish  the expression level of each transcript was calculated according to the transcripts per million reads TPM method. RSEM http://deweylab.biostat.wisc.edu/rsem/ was used to quantify gene abundances. Essentially  differential expression analysis was performed using the DESeq2 software. DEGs with |log2FC|>1 and Q value <= 0.05 were considered to be significantly different expressed genes. Functional enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni corrected P value ≤0.05 compared with the whole transcriptome background. Assembly: GRCz11 Supplementary files format and content: read count.txt is a tab delimited text file for read count numbers of each gene in all six samples.,Ovary,,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer’s protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,tissue:Ovary|genotype:ddx4E4{delta},GSM8491760,GSM8491760: ddx4E4Δ ovary rep2; Danio rerio; RNA Seq,GSM8491760 r1,GSM8491760,1,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer's protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP529840,,,D2_R1.fastq.gz D2_R2.fastq.gz,fastq fastq,8420834516.0,27883558.0,GSM8491760 r1,0:151 1:151,A:2130607193;C:2053627459;G:2099203008;T:2137372997;N:23859,151,151,,,2130607193,2053627459,2099203008,2137372997,23859,SRX25926477,SRS22513928,SRA1960397,"Institute of Hydrobiology, Chinese Academy of Sciences","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2024-08-31,Adult,Adult,Gonad,Reproductive System
33665,SRR30502666,SRX25926476,SRS22513927,SRP529840,PRJNA1154960,Deletion of ddx4 ovary specific transcript causes downregulation of sycp1 and derepression of DNA transposons in zebrafish ovaries,GSE276129,Transcriptome Analysis,Ddx4 DEAD box helicase 4 is a well established marker gene for early stage germlines and is required for the development of germ cells. Alternative splicing of ddx4 produces a long transcript that is exclusively expressed in zebrafish ovaries. The function of this ovary specific transcript ddx4 L remains unclear. In this study  using the ddx4 L knockout zebrafish model  we found that elimination of ddx4 L results in a decrease in fertilization rate and in the number of mature eggs laid by the female mutants. Transcriptome analysis was performed to identify the underlying changes of gene expression between WT and ddx4 L knockout ovaries. A total of 1134 differentially expressed genes were identified  of which 524 were upregulated and 610 were downregulated. Functional enrichment analysis showed that the terms of negative regulation of fertilization  sperm egg recognition process  and oocyte meiosis might be affected by elimination of ddx4 L. Furthermore  we found that Sycp1  a synaptonemal complex protein involved in meiosis and fertility  was dramatically decreased in the ddx4 L knockout ovaries at both mRNA and protein levels. Moreover  the activities of transposable elements were analyzed based on the RNA seq data. The result showed that elimination of ddx4 L causes the derepression of DNA transposons  a subclass of transposable elements  in zebrafish ovaries. In conclusion  the aforementioned findings indicate that the ovary specific transcript of ddx4 plays an important role in oocyte development and egg quality  possibly by maintaining sycp1 expression and repressing DNA transposons. Our work provide novel insights into the functions and regulatory mechanisms of ddx4 in zebrafish oogenesis. Overall design: Ovaries were dissected from three WT and three ddx4 E4? zebrafish at 6 mpf  respectively. Six total RNA samples were extracted and subjected to RNA sequencing. Differentially expressed genes DEGs and transposable elements TEs between WT and ddx4 E4? zebrafish ovaries were analyzed.,,pubmed:39765722,,ddx4E4Δ ovary rep1,GSM8491759,,source name:Ovary|tissue:Ovary|genotype:ddx4E4{delta}|geo loc name:missing|collection date:missing,ddx4E4Δ ovary rep1,The raw paired end reads were trimmed and quality controlled by SeqPrep https://github.com/jstjohn/SeqPrep and Sickle https://github.com/najoshi/sickle with default parameters. Then clean reads were separately aligned to zebrafish reference genome GRCz11 with orientation mode using HISAT2 http://ccb.jhu.edu/software/hisat2/index.shtml software. The mapped reads of each sample were assembled by StringTie https://ccb.jhu.edu/software/stringtie/index.shtml in a reference based approach. To identify DEGs differential expression genes between the ovaries of WT and ddx4 E4Δ zebrafish  the expression level of each transcript was calculated according to the transcripts per million reads TPM method. RSEM http://deweylab.biostat.wisc.edu/rsem/ was used to quantify gene abundances. Essentially  differential expression analysis was performed using the DESeq2 software. DEGs with |log2FC|>1 and Q value <= 0.05 were considered to be significantly different expressed genes. Functional enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni corrected P value ≤0.05 compared with the whole transcriptome background. Assembly: GRCz11 Supplementary files format and content: read count.txt is a tab delimited text file for read count numbers of each gene in all six samples.,Ovary,,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer’s protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,tissue:Ovary|genotype:ddx4E4{delta},GSM8491759,GSM8491759: ddx4E4Δ ovary rep1; Danio rerio; RNA Seq,GSM8491759 r1,GSM8491759,1,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer's protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP529840,,,D1_R1.fastq.gz D1_R2.fastq.gz,fastq fastq,8478573292.0,28074746.0,GSM8491759 r1,0:151 1:151,A:2141904837;C:2071392554;G:2116256871;T:2148995183;N:23847,151,151,,,2141904837,2071392554,2116256871,2148995183,23847,SRX25926476,SRS22513927,SRA1960397,"Institute of Hydrobiology, Chinese Academy of Sciences","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2024-08-31,Adult,Adult,Gonad,Reproductive System
33666,SRR30502667,SRX25926475,SRS22513926,SRP529840,PRJNA1154960,Deletion of ddx4 ovary specific transcript causes downregulation of sycp1 and derepression of DNA transposons in zebrafish ovaries,GSE276129,Transcriptome Analysis,Ddx4 DEAD box helicase 4 is a well established marker gene for early stage germlines and is required for the development of germ cells. Alternative splicing of ddx4 produces a long transcript that is exclusively expressed in zebrafish ovaries. The function of this ovary specific transcript ddx4 L remains unclear. In this study  using the ddx4 L knockout zebrafish model  we found that elimination of ddx4 L results in a decrease in fertilization rate and in the number of mature eggs laid by the female mutants. Transcriptome analysis was performed to identify the underlying changes of gene expression between WT and ddx4 L knockout ovaries. A total of 1134 differentially expressed genes were identified  of which 524 were upregulated and 610 were downregulated. Functional enrichment analysis showed that the terms of negative regulation of fertilization  sperm egg recognition process  and oocyte meiosis might be affected by elimination of ddx4 L. Furthermore  we found that Sycp1  a synaptonemal complex protein involved in meiosis and fertility  was dramatically decreased in the ddx4 L knockout ovaries at both mRNA and protein levels. Moreover  the activities of transposable elements were analyzed based on the RNA seq data. The result showed that elimination of ddx4 L causes the derepression of DNA transposons  a subclass of transposable elements  in zebrafish ovaries. In conclusion  the aforementioned findings indicate that the ovary specific transcript of ddx4 plays an important role in oocyte development and egg quality  possibly by maintaining sycp1 expression and repressing DNA transposons. Our work provide novel insights into the functions and regulatory mechanisms of ddx4 in zebrafish oogenesis. Overall design: Ovaries were dissected from three WT and three ddx4 E4? zebrafish at 6 mpf  respectively. Six total RNA samples were extracted and subjected to RNA sequencing. Differentially expressed genes DEGs and transposable elements TEs between WT and ddx4 E4? zebrafish ovaries were analyzed.,,pubmed:39765722,,WT ovary rep3,GSM8491758,,source name:Ovary|tissue:Ovary|genotype:WT|geo loc name:missing|collection date:missing,WT ovary rep3,The raw paired end reads were trimmed and quality controlled by SeqPrep https://github.com/jstjohn/SeqPrep and Sickle https://github.com/najoshi/sickle with default parameters. Then clean reads were separately aligned to zebrafish reference genome GRCz11 with orientation mode using HISAT2 http://ccb.jhu.edu/software/hisat2/index.shtml software. The mapped reads of each sample were assembled by StringTie https://ccb.jhu.edu/software/stringtie/index.shtml in a reference based approach. To identify DEGs differential expression genes between the ovaries of WT and ddx4 E4Δ zebrafish  the expression level of each transcript was calculated according to the transcripts per million reads TPM method. RSEM http://deweylab.biostat.wisc.edu/rsem/ was used to quantify gene abundances. Essentially  differential expression analysis was performed using the DESeq2 software. DEGs with |log2FC|>1 and Q value <= 0.05 were considered to be significantly different expressed genes. Functional enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni corrected P value ≤0.05 compared with the whole transcriptome background. Assembly: GRCz11 Supplementary files format and content: read count.txt is a tab delimited text file for read count numbers of each gene in all six samples.,Ovary,,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer’s protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,tissue:Ovary|genotype:WT,GSM8491758,GSM8491758: WT ovary rep3; Danio rerio; RNA Seq,GSM8491758 r1,GSM8491758,1,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer's protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP529840,,,W3_R1.fastq.gz W3_R2.fastq.gz,fastq fastq,9507568228.0,31482014.0,GSM8491758 r1,0:151 1:151,A:2403365632;C:2318225719;G:2368354059;T:2417595791;N:27027,151,151,,,2403365632,2318225719,2368354059,2417595791,27027,SRX25926475,SRS22513926,SRA1960397,"Institute of Hydrobiology, Chinese Academy of Sciences","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2024-08-31,Adult,Adult,Gonad,Reproductive System
33667,SRR30502668,SRX25926474,SRS22513925,SRP529840,PRJNA1154960,Deletion of ddx4 ovary specific transcript causes downregulation of sycp1 and derepression of DNA transposons in zebrafish ovaries,GSE276129,Transcriptome Analysis,Ddx4 DEAD box helicase 4 is a well established marker gene for early stage germlines and is required for the development of germ cells. Alternative splicing of ddx4 produces a long transcript that is exclusively expressed in zebrafish ovaries. The function of this ovary specific transcript ddx4 L remains unclear. In this study  using the ddx4 L knockout zebrafish model  we found that elimination of ddx4 L results in a decrease in fertilization rate and in the number of mature eggs laid by the female mutants. Transcriptome analysis was performed to identify the underlying changes of gene expression between WT and ddx4 L knockout ovaries. A total of 1134 differentially expressed genes were identified  of which 524 were upregulated and 610 were downregulated. Functional enrichment analysis showed that the terms of negative regulation of fertilization  sperm egg recognition process  and oocyte meiosis might be affected by elimination of ddx4 L. Furthermore  we found that Sycp1  a synaptonemal complex protein involved in meiosis and fertility  was dramatically decreased in the ddx4 L knockout ovaries at both mRNA and protein levels. Moreover  the activities of transposable elements were analyzed based on the RNA seq data. The result showed that elimination of ddx4 L causes the derepression of DNA transposons  a subclass of transposable elements  in zebrafish ovaries. In conclusion  the aforementioned findings indicate that the ovary specific transcript of ddx4 plays an important role in oocyte development and egg quality  possibly by maintaining sycp1 expression and repressing DNA transposons. Our work provide novel insights into the functions and regulatory mechanisms of ddx4 in zebrafish oogenesis. Overall design: Ovaries were dissected from three WT and three ddx4 E4? zebrafish at 6 mpf  respectively. Six total RNA samples were extracted and subjected to RNA sequencing. Differentially expressed genes DEGs and transposable elements TEs between WT and ddx4 E4? zebrafish ovaries were analyzed.,,pubmed:39765722,,WT ovary rep2,GSM8491757,,source name:Ovary|tissue:Ovary|genotype:WT|geo loc name:missing|collection date:missing,WT ovary rep2,The raw paired end reads were trimmed and quality controlled by SeqPrep https://github.com/jstjohn/SeqPrep and Sickle https://github.com/najoshi/sickle with default parameters. Then clean reads were separately aligned to zebrafish reference genome GRCz11 with orientation mode using HISAT2 http://ccb.jhu.edu/software/hisat2/index.shtml software. The mapped reads of each sample were assembled by StringTie https://ccb.jhu.edu/software/stringtie/index.shtml in a reference based approach. To identify DEGs differential expression genes between the ovaries of WT and ddx4 E4Δ zebrafish  the expression level of each transcript was calculated according to the transcripts per million reads TPM method. RSEM http://deweylab.biostat.wisc.edu/rsem/ was used to quantify gene abundances. Essentially  differential expression analysis was performed using the DESeq2 software. DEGs with |log2FC|>1 and Q value <= 0.05 were considered to be significantly different expressed genes. Functional enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni corrected P value ≤0.05 compared with the whole transcriptome background. Assembly: GRCz11 Supplementary files format and content: read count.txt is a tab delimited text file for read count numbers of each gene in all six samples.,Ovary,,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer’s protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,tissue:Ovary|genotype:WT,GSM8491757,GSM8491757: WT ovary rep2; Danio rerio; RNA Seq,GSM8491757 r1,GSM8491757,1,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer's protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP529840,,,W2_R1.fastq.gz W2_R2.fastq.gz,fastq fastq,8515265084.0,28196242.0,GSM8491757 r1,0:151 1:151,A:2152677268;C:2074877248;G:2122308956;T:2165377885;N:23727,151,151,,,2152677268,2074877248,2122308956,2165377885,23727,SRX25926474,SRS22513925,SRA1960397,"Institute of Hydrobiology, Chinese Academy of Sciences","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2024-08-31,Adult,Adult,Gonad,Reproductive System
33668,SRR30502669,SRX25926473,SRS22513924,SRP529840,PRJNA1154960,Deletion of ddx4 ovary specific transcript causes downregulation of sycp1 and derepression of DNA transposons in zebrafish ovaries,GSE276129,Transcriptome Analysis,Ddx4 DEAD box helicase 4 is a well established marker gene for early stage germlines and is required for the development of germ cells. Alternative splicing of ddx4 produces a long transcript that is exclusively expressed in zebrafish ovaries. The function of this ovary specific transcript ddx4 L remains unclear. In this study  using the ddx4 L knockout zebrafish model  we found that elimination of ddx4 L results in a decrease in fertilization rate and in the number of mature eggs laid by the female mutants. Transcriptome analysis was performed to identify the underlying changes of gene expression between WT and ddx4 L knockout ovaries. A total of 1134 differentially expressed genes were identified  of which 524 were upregulated and 610 were downregulated. Functional enrichment analysis showed that the terms of negative regulation of fertilization  sperm egg recognition process  and oocyte meiosis might be affected by elimination of ddx4 L. Furthermore  we found that Sycp1  a synaptonemal complex protein involved in meiosis and fertility  was dramatically decreased in the ddx4 L knockout ovaries at both mRNA and protein levels. Moreover  the activities of transposable elements were analyzed based on the RNA seq data. The result showed that elimination of ddx4 L causes the derepression of DNA transposons  a subclass of transposable elements  in zebrafish ovaries. In conclusion  the aforementioned findings indicate that the ovary specific transcript of ddx4 plays an important role in oocyte development and egg quality  possibly by maintaining sycp1 expression and repressing DNA transposons. Our work provide novel insights into the functions and regulatory mechanisms of ddx4 in zebrafish oogenesis. Overall design: Ovaries were dissected from three WT and three ddx4 E4? zebrafish at 6 mpf  respectively. Six total RNA samples were extracted and subjected to RNA sequencing. Differentially expressed genes DEGs and transposable elements TEs between WT and ddx4 E4? zebrafish ovaries were analyzed.,,pubmed:39765722,,WT ovary rep1,GSM8491756,,source name:Ovary|tissue:Ovary|genotype:WT|geo loc name:missing|collection date:missing,WT ovary rep1,The raw paired end reads were trimmed and quality controlled by SeqPrep https://github.com/jstjohn/SeqPrep and Sickle https://github.com/najoshi/sickle with default parameters. Then clean reads were separately aligned to zebrafish reference genome GRCz11 with orientation mode using HISAT2 http://ccb.jhu.edu/software/hisat2/index.shtml software. The mapped reads of each sample were assembled by StringTie https://ccb.jhu.edu/software/stringtie/index.shtml in a reference based approach. To identify DEGs differential expression genes between the ovaries of WT and ddx4 E4Δ zebrafish  the expression level of each transcript was calculated according to the transcripts per million reads TPM method. RSEM http://deweylab.biostat.wisc.edu/rsem/ was used to quantify gene abundances. Essentially  differential expression analysis was performed using the DESeq2 software. DEGs with |log2FC|>1 and Q value <= 0.05 were considered to be significantly different expressed genes. Functional enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni corrected P value ≤0.05 compared with the whole transcriptome background. Assembly: GRCz11 Supplementary files format and content: read count.txt is a tab delimited text file for read count numbers of each gene in all six samples.,Ovary,,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer’s protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,tissue:Ovary|genotype:WT,GSM8491756,GSM8491756: WT ovary rep1; Danio rerio; RNA Seq,GSM8491756 r1,GSM8491756,1,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer's protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP529840,,,W1_R1.fastq.gz W1_R2.fastq.gz,fastq fastq,8347159200.0,27639600.0,GSM8491756 r1,0:151 1:151,A:2109928092;C:2033967699;G:2079802211;T:2123438464;N:22734,151,151,,,2109928092,2033967699,2079802211,2123438464,22734,SRX25926473,SRS22513924,SRA1960397,"Institute of Hydrobiology, Chinese Academy of Sciences","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2024-08-31,Adult,Adult,Gonad,Reproductive System
34094,SRR31050909,SRX26435351,SRS22952031,SRP539687,PRJNA1175381,Short term polystyrene nanoplastic exposure alters zebrafish male and female germline and reproductive outcomes  unveiling pollutant impacted molecular pathways,GSE279916,Transcriptome Analysis,Nanoplastics pollution is a rising environmental concern whose impacts on biodiversity and human health are far from being understood. This is particularly salient in aquatic ecosystems  where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end  zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that  in males  nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction  resulting in viable spermatozoa but with reduced motility. Moreover  in females we observed an alteration in oocyte stages frequencies during oogenesis  possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure  meiosis and DNA double strand break formation and repair progression  and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall  our results demonstrate that acute exposure to NPs can compromise reproductive fitness  underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples,,pubmed:39556913,,Zebrafish  Testicle  Plastic  Replicate 3  Animal 3,GSM8583344,,source name:testicles|tissue:testicles|cell line:germline|genotype:WT|treatment:Plastic|geo loc name:missing|collection date:missing,Zebrafish  Testicle  Plastic  Replicate 3  Animal 3,Anaconda The sequencing quality was checked before performing the assembly. STAR bioconda was used for the assembly smartools bioconda was used to generate the intermediate files Sam and Bam Counts were obtained from the bam intermediate file Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample,testicles,Half of the fish were exposed to polystyrene nanoplastics each 24 hours added in the water during 96 hours accute exposure. The rest were used as controls  so no plastics were added in the water.,Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment,Adult zebrafish were maintained at the animal house under standard conditions,tissue:testicles|cell line:germline|genotype:WT|treatment:Plastic,GSM8583344,GSM8583344: Zebrafish  Testicle  Plastic  Replicate 3  Animal 3; Danio rerio; RNA Seq,GSM8583344 r1,GSM8583344,1,Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP539687,,,M6_C2_R3_A3_EKRN230074904-1A_HWT7HDSX7_L3_1.fq M6_C2_R3_A3_EKRN230074904-1A_HWT7HDSX7_L3_2.fq,fastq fastq,24813339000.0,82711130.0,GSM8583344 r1,,,,,,,,,,,,SRX26435351,SRS22952031,SRA1994234,UAB (Universidad Autónoma de Barcelona),UAB (Universidad Autónoma de Barcelona),,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Spain,2024-10-20,Adult,Adult,Gonad,Reproductive System
34095,SRR31050910,SRX26435350,SRS22952030,SRP539687,PRJNA1175381,Short term polystyrene nanoplastic exposure alters zebrafish male and female germline and reproductive outcomes  unveiling pollutant impacted molecular pathways,GSE279916,Transcriptome Analysis,Nanoplastics pollution is a rising environmental concern whose impacts on biodiversity and human health are far from being understood. This is particularly salient in aquatic ecosystems  where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end  zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that  in males  nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction  resulting in viable spermatozoa but with reduced motility. Moreover  in females we observed an alteration in oocyte stages frequencies during oogenesis  possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure  meiosis and DNA double strand break formation and repair progression  and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall  our results demonstrate that acute exposure to NPs can compromise reproductive fitness  underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples,,pubmed:39556913,,Zebrafish  Testicle  Plastic  Replicate 3  Animal 1,GSM8583343,,source name:testicles|tissue:testicles|cell line:germline|genotype:WT|treatment:Plastic|geo loc name:missing|collection date:missing,Zebrafish  Testicle  Plastic  Replicate 3  Animal 1,Anaconda The sequencing quality was checked before performing the assembly. STAR bioconda was used for the assembly smartools bioconda was used to generate the intermediate files Sam and Bam Counts were obtained from the bam intermediate file Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample,testicles,Half of the fish were exposed to polystyrene nanoplastics each 24 hours added in the water during 96 hours accute exposure. The rest were used as controls  so no plastics were added in the water.,Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment,Adult zebrafish were maintained at the animal house under standard conditions,tissue:testicles|cell line:germline|genotype:WT|treatment:Plastic,GSM8583343,GSM8583343: Zebrafish  Testicle  Plastic  Replicate 3  Animal 1; Danio rerio; RNA Seq,GSM8583343 r1,GSM8583343,1,Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP539687,,,M6_C2_R3_A1_EKRN230074902-1A_HWT7HDSX7_L3_1.fq M6_C2_R3_A1_EKRN230074902-1A_HWT7HDSX7_L3_2.fq,fastq fastq,21334650000.0,71115500.0,GSM8583343 r1,,,,,,,,,,,,SRX26435350,SRS22952030,SRA1994234,UAB (Universidad Autónoma de Barcelona),UAB (Universidad Autónoma de Barcelona),,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Spain,2024-10-20,Adult,Adult,Gonad,Reproductive System
34096,SRR31050911,SRX26435349,SRS22952029,SRP539687,PRJNA1175381,Short term polystyrene nanoplastic exposure alters zebrafish male and female germline and reproductive outcomes  unveiling pollutant impacted molecular pathways,GSE279916,Transcriptome Analysis,Nanoplastics pollution is a rising environmental concern whose impacts on biodiversity and human health are far from being understood. This is particularly salient in aquatic ecosystems  where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end  zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that  in males  nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction  resulting in viable spermatozoa but with reduced motility. Moreover  in females we observed an alteration in oocyte stages frequencies during oogenesis  possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure  meiosis and DNA double strand break formation and repair progression  and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall  our results demonstrate that acute exposure to NPs can compromise reproductive fitness  underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples,,pubmed:39556913,,Zebrafish  Testicle  Plastic  Replicate 2  Animal 2,GSM8583342,,source name:testicles|tissue:testicles|cell line:germline|genotype:WT|treatment:Plastic|geo loc name:missing|collection date:missing,Zebrafish  Testicle  Plastic  Replicate 2  Animal 2,Anaconda The sequencing quality was checked before performing the assembly. STAR bioconda was used for the assembly smartools bioconda was used to generate the intermediate files Sam and Bam Counts were obtained from the bam intermediate file Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample,testicles,Half of the fish were exposed to polystyrene nanoplastics each 24 hours added in the water during 96 hours accute exposure. The rest were used as controls  so no plastics were added in the water.,Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment,Adult zebrafish were maintained at the animal house under standard conditions,tissue:testicles|cell line:germline|genotype:WT|treatment:Plastic,GSM8583342,GSM8583342: Zebrafish  Testicle  Plastic  Replicate 2  Animal 2; Danio rerio; RNA Seq,GSM8583342 r1,GSM8583342,1,Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP539687,,,M6_C2_R2_A2_EKRN230074901-1A_HWT7HDSX7_L2_1.fq M6_C2_R2_A2_EKRN230074901-1A_HWT7HDSX7_L2_2.fq,fastq fastq,23956812900.0,79856043.0,GSM8583342 r1,,,,,,,,,,,,SRX26435349,SRS22952029,SRA1994234,UAB (Universidad Autónoma de Barcelona),UAB (Universidad Autónoma de Barcelona),,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Spain,2024-10-20,Adult,Adult,Gonad,Reproductive System
34097,SRR31050912,SRX26435348,SRS22952028,SRP539687,PRJNA1175381,Short term polystyrene nanoplastic exposure alters zebrafish male and female germline and reproductive outcomes  unveiling pollutant impacted molecular pathways,GSE279916,Transcriptome Analysis,Nanoplastics pollution is a rising environmental concern whose impacts on biodiversity and human health are far from being understood. This is particularly salient in aquatic ecosystems  where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end  zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that  in males  nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction  resulting in viable spermatozoa but with reduced motility. Moreover  in females we observed an alteration in oocyte stages frequencies during oogenesis  possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure  meiosis and DNA double strand break formation and repair progression  and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall  our results demonstrate that acute exposure to NPs can compromise reproductive fitness  underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples,,pubmed:39556913,,Zebrafish  Testicle  Control  Replicate 3  Animal 1,GSM8583341,,source name:testicles|tissue:testicles|cell line:germline|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing,Zebrafish  Testicle  Control  Replicate 3  Animal 1,Anaconda The sequencing quality was checked before performing the assembly. STAR bioconda was used for the assembly smartools bioconda was used to generate the intermediate files Sam and Bam Counts were obtained from the bam intermediate file Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample,testicles,Half of the fish were exposed to polystyrene nanoplastics each 24 hours added in the water during 96 hours accute exposure. The rest were used as controls  so no plastics were added in the water.,Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment,Adult zebrafish were maintained at the animal house under standard conditions,tissue:testicles|cell line:germline|genotype:WT|treatment:Control,GSM8583341,GSM8583341: Zebrafish  Testicle  Control  Replicate 3  Animal 1; Danio rerio; RNA Seq,GSM8583341 r1,GSM8583341,1,Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP539687,,,M6_C1_R3_A1_EKRN230074898-1A_HWT7HDSX7_L2_1.fq M6_C1_R3_A1_EKRN230074898-1A_HWT7HDSX7_L2_2.fq,fastq fastq,17143802100.0,57146007.0,GSM8583341 r1,0:150 1:150,A:4588084574;C:4015807096;G:4039433882;T:4500279277;N:197271,150,150,,,4588084574,4015807096,4039433882,4500279277,197271,SRX26435348,SRS22952028,SRA1994234,UAB (Universidad Autónoma de Barcelona),UAB (Universidad Autónoma de Barcelona),,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Spain,2024-10-20,Adult,Adult,Gonad,Reproductive System
34098,SRR31050913,SRX26435347,SRS22952027,SRP539687,PRJNA1175381,Short term polystyrene nanoplastic exposure alters zebrafish male and female germline and reproductive outcomes  unveiling pollutant impacted molecular pathways,GSE279916,Transcriptome Analysis,Nanoplastics pollution is a rising environmental concern whose impacts on biodiversity and human health are far from being understood. This is particularly salient in aquatic ecosystems  where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end  zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that  in males  nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction  resulting in viable spermatozoa but with reduced motility. Moreover  in females we observed an alteration in oocyte stages frequencies during oogenesis  possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure  meiosis and DNA double strand break formation and repair progression  and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall  our results demonstrate that acute exposure to NPs can compromise reproductive fitness  underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples,,pubmed:39556913,,Zebrafish  Testicle  Control  Replicate 2  Animal 2,GSM8583340,,source name:testicles|tissue:testicles|cell line:germline|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing,Zebrafish  Testicle  Control  Replicate 2  Animal 2,Anaconda The sequencing quality was checked before performing the assembly. STAR bioconda was used for the assembly smartools bioconda was used to generate the intermediate files Sam and Bam Counts were obtained from the bam intermediate file Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample,testicles,Half of the fish were exposed to polystyrene nanoplastics each 24 hours added in the water during 96 hours accute exposure. The rest were used as controls  so no plastics were added in the water.,Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment,Adult zebrafish were maintained at the animal house under standard conditions,tissue:testicles|cell line:germline|genotype:WT|treatment:Control,GSM8583340,GSM8583340: Zebrafish  Testicle  Control  Replicate 2  Animal 2; Danio rerio; RNA Seq,GSM8583340 r1,GSM8583340,1,Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP539687,,,M6_C1_R2_A2_1.fq M6_C1_R2_A2_2.fq,fastq fastq,17289440100.0,57631467.0,GSM8583340 r1,,,,,,,,,,,,SRX26435347,SRS22952027,SRA1994234,UAB (Universidad Autónoma de Barcelona),UAB (Universidad Autónoma de Barcelona),,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Spain,2024-10-20,Adult,Adult,Gonad,Reproductive System
34099,SRR31050914,SRX26435346,SRS22952026,SRP539687,PRJNA1175381,Short term polystyrene nanoplastic exposure alters zebrafish male and female germline and reproductive outcomes  unveiling pollutant impacted molecular pathways,GSE279916,Transcriptome Analysis,Nanoplastics pollution is a rising environmental concern whose impacts on biodiversity and human health are far from being understood. This is particularly salient in aquatic ecosystems  where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end  zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that  in males  nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction  resulting in viable spermatozoa but with reduced motility. Moreover  in females we observed an alteration in oocyte stages frequencies during oogenesis  possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure  meiosis and DNA double strand break formation and repair progression  and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall  our results demonstrate that acute exposure to NPs can compromise reproductive fitness  underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples,,pubmed:39556913,,Zebrafish  Testicle  Control  Replicate 1  Animal 2,GSM8583339,,source name:testicles|tissue:testicles|cell line:germline|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing,Zebrafish  Testicle  Control  Replicate 1  Animal 2,Anaconda The sequencing quality was checked before performing the assembly. STAR bioconda was used for the assembly smartools bioconda was used to generate the intermediate files Sam and Bam Counts were obtained from the bam intermediate file Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample,testicles,Half of the fish were exposed to polystyrene nanoplastics each 24 hours added in the water during 96 hours accute exposure. The rest were used as controls  so no plastics were added in the water.,Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment,Adult zebrafish were maintained at the animal house under standard conditions,tissue:testicles|cell line:germline|genotype:WT|treatment:Control,GSM8583339,GSM8583339: Zebrafish  Testicle  Control  Replicate 1  Animal 2; Danio rerio; RNA Seq,GSM8583339 r1,GSM8583339,1,Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP539687,,,M6_C1_R1_A2_EKRN230074896-1A_HWT7HDSX7_L2_1.fq M6_C1_R1_A2_EKRN230074896-1A_HWT7HDSX7_L2_2.fq,fastq fastq,19275937200.0,64253124.0,GSM8583339 r1,0:150 1:150,A:5148413409;C:4525316389;G:4541110001;T:5060873310;N:224091,150,150,,,5148413409,4525316389,4541110001,5060873310,224091,SRX26435346,SRS22952026,SRA1994234,UAB (Universidad Autónoma de Barcelona),UAB (Universidad Autónoma de Barcelona),,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Spain,2024-10-20,Adult,Adult,Gonad,Reproductive System
34965,SRR32588722,SRX27895229,SRS24266229,SRP568323,PRJNA1232602,Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains,PRJNA1232602,Other,In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.,,,,Iso Seq RNA from Danio rerio,C2 F2 M T,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from testis,C2 F2 M T,C2 F2 M T,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m84270_240911_150713_s1.skera.flnc.fastq.gz,fastq,103111938047.0,50624762.0,m84270 240911 150713 s1.skera.flnc.fastq.gz,0:2036.79,A:30106378730;C:21760983790;G:23176083069;T:28068492458;N:0,2036,,,,30106378730,21760983790,23176083069,28068492458,0,SRX27895229,SRS24266229,SRA2089085,National Human Genome Research Institute|Translational and Functional Genomics Branch,National Human Genome Research Institute National Human Genome Research Institute,,,,,,,,,,,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2025-03-06,Adult,Adult,Gonad,Reproductive System
34974,SRR32588731,SRX27895220,SRS24266226,SRP568323,PRJNA1232602,Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains,PRJNA1232602,Other,In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.,,,,Iso Seq RNA from Danio rerio,C2 F2 F O32,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from ovary,C2 F2 F O32,C2 F2 F O32,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m64467e_240815_161552.hifi_reads.flnc.fastq.gz,fastq,12555748052.0,3350326.0,m64467e 240815 161552.hifi reads.flnc.fastq.gz,0:3747.62,A:3457885256;C:2882310858;G:2971165409;T:3244386529;N:0,3747,,,,3457885256,2882310858,2971165409,3244386529,0,SRX27895220,SRS24266226,SRA2089085,National Human Genome Research Institute|Translational and Functional Genomics Branch,National Human Genome Research Institute National Human Genome Research Institute,,,,,,,,,,,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2025-03-06,Adult,Adult,Gonad,Reproductive System
34975,SRR32588732,SRX27895219,SRS24266221,SRP568323,PRJNA1232602,Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains,PRJNA1232602,Other,In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.,,,,Iso Seq RNA from Danio rerio,C2 F2 F O31,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:Ovary|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from ovary,C2 F2 F O31,C2 F2 F O31,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m84270_240911_210533_s4.skera.flnc.fastq.gz,fastq,91708771607.0,33888263.0,m84270 240911 210533 s4.skera.flnc.fastq.gz,0:2706.21,A:25318206966;C:20635348405;G:21357313254;T:24397902982;N:0,2706,,,,25318206966,20635348405,21357313254,24397902982,0,SRX27895219,SRS24266221,SRA2089085,National Human Genome Research Institute|Translational and Functional Genomics Branch,National Human Genome Research Institute National Human Genome Research Institute,,,,,,,,,,,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2025-03-06,Adult,Adult,Gonad,Reproductive System
36288,SRR363982,SRX105295,SRS270138,SRP009275,PRJNA148581,Hen1 analysis in zebrafish,GSE33582,Transcriptome Analysis,small RNA libraries from wild type and Hen1 mutant testes were made with either polyA tailing VASAGFPHen1minus/plus or adapter ligation Hen1Testis and WTTestis and sequenced on an Illumina GAII platform. Overall design: RNA was isolated from total testis tissue of both Hen1 wildtype and Hen1 mutant animals. post size selection from gel  the small RNA libraries wre made.,,pubmed:20859253,,hen1 mutant polyA,GSM830244,,source name:testis|strain:TL|genotype/variation:Hen1 mutant|tissue:testis|small rna library prep method:polyA tailing,hen1 mutant polyA,three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome Zv8,testis,,Small RNAs in the size range of 19 31 bases were excised from a denaturing gel. RNA was polyA tailed using polyA polymerase followed by ligation of a RNA adaptor to the five prime phosphate of the small RNAs. First strand cDNA synthesis was performed using an oligodT linker primer and M MLV RNase H  reverse transcriptase. post amplification the cDNA was sent for sequencing on an Illumina/Solexa platform.,,strain:TL|genotype/variation:Hen1 mutant|tissue:testis|small rna library prep method:polyA tailing,GSM830244,GSM830244: hen1 mutant polyA,GSM830244: hen1 mutant polyA,GSM830244: hen1 mutant polyA,1,,GEO Accession:GSM830244,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>44</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP009275,,read name barcode proc directive:ignore,VASAGFPHEN1minusMALE.fastq,fastq,267208964.0,6072931.0,GSM830244 1,0:44,A:143478691;C:30051676;G:33682677;T:59883224;N:112696,44,,,,143478691,30051676,33682677,59883224,112696,SRX105295,SRS270138,SRA047996,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.01616,,0.01033,,0.99381,,0.76337,,44,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,Netherlands,2011-11-09,Undetermined,Undetermined,Gonad,Reproductive System
36361,SRR489488,SRX143565,SRS310286,SRP012376,PRJNA160143,Extensive alternative polyadenylation during zebrafish development,GSE37453,Transcriptome Analysis,The post transcriptional fate of messenger RNAs mRNAs is largely dictated by their three prime' untranslated regions three prime'UTRs  which are defined by cleavage and polyadenylation CPA of pre mRNAs. We used polyA position profiling by sequencing 3P Seq to map polyA sites at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P Seq reads substantially increased and improved existing three prime'UTR annotations  resulting in confidently identified three prime'UTRs for more than 78.79% of the annotated protein coding genes in zebrafish. Most zebrafish genes undergo alternative CPA with more than a thousand genes using different dominant three prime'UTRs at different stages. three prime'UTRs tend to be shortest in the ovaries and longest in the brain. Isoforms with some of the shortest three prime'UTRs are highly expressed in the ovary yet absent in the maternally contributed RNAs of the embryo  perhaps because their three prime'UTRs are too short to accommodate a uridine rich motif required for stability of the maternal mRNA. At two hpf  thousands of unique polyA sites appear at locations lacking a typical polyadenylation signal  which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into the identities  formation  and evolution of zebrafish three prime'UTRs provide a resource for studying gene regulation during vertebrate development. Overall design: 3P Seq was used to map the three prime' ends of protein coding genes in the zebrafish genome,,pubmed:22722342,,3P Seq Testis,GSM919971,,source name:male adults|genotype/variation:wild type|tissue:testis|development stage:adult,3P Seq Testis,For 3P Seq: Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. The BED file is as in Jan et al. GSE24924 For 3P PE Seq: In each read pair  read #1 captured the three prime end of the polyA tail in the antisense orientation  and read #2 captured a portion of the three prime region of the transcript  and occasionally  the beginning of the polyA tail  in the sense orientation. Read #2 began with an adapter of 26 bases. Reads with more than 10 mismatches to the adapter were discarded and the first 26 bases were removed before further processing.  A read pair was considered informative only if read #1 began with Ts and read #2 contained 2–39 terminal As. post leading Ts and terminal As were removed from reads #1 and #2  respectively  they were mapped to the genome using Bowtie  allowing for up to two mismatches and requiring a unique mapping position in the zebrafish genome. The length of the tail encoded in read #2 was defined as the maximum number of trailing As allowing for up to one mismatch. Only cases in which this number was larger than the number of As encoded in the genome at the predicted cleavage position by at least 2 bases were carried forward. Cleavage and polyadenylation position was defined as the last non A base in read #2. The length of the polyA tail at that position was estimated using the corresponding read #1  and defined as the maximal i for which >90% of the bases in the first i bases of read #1 were Ts. This criterion was used to allow for some sequencing errors expected when sequencing long homopolymers. Genome build: danRer7 Supplementary files format and content: The .bed files contain the positions where 3P Seq reads were mapped  and the name of each track is the number of reads mapping to that position. Supplementary files format and content: The bigWig .bw files contain a summary of the number of reads whose three prime ends mapped to each position in the genome. Supplementary files format and content: For the paired end sequencing for mapping polyA tail lengths  the text files contain the following columns : chromosome  position  strand  number of polyA length reads  followed by the individual measurements lower bounds on polyA tail length,male adults,Ovaries and testes were obtained as described  in Gupta and Mullins 2010.,3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html,Zebrafish embryos or adults grown under standard condition,genotype/variation:wild type|tissue:testis|developmental stage:adult,GSM919971,GSM919971: 3P Seq Testis; Danio rerio; RNA Seq,GSM919971 1,GSM919971: 3P Seq Testis,1,,GEO Accession:GSM919971,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP012376,,,3P_Seq_Testis.fastq,fastq,633839040.0,17606640.0,GSM919971 r1,0:36,A:250493743;C:111846021;G:97558731;T:173764035;N:176510,36,,,,250493743,111846021,97558731,173764035,176510,SRX143565,SRS310286,SRA051955,GEO,Whitehead Institute for Biomedical Research,1,0.56499,,0.1059,,0.72468,,0.46158,,36,,B,,usable mapping rate,illumina,early_illumina,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2012-04-20,Adult,Adult,Gonad,Reproductive System
36362,SRR489487,SRX143564,SRS310285,SRP012376,PRJNA160143,Extensive alternative polyadenylation during zebrafish development,GSE37453,Transcriptome Analysis,The post transcriptional fate of messenger RNAs mRNAs is largely dictated by their three prime' untranslated regions three prime'UTRs  which are defined by cleavage and polyadenylation CPA of pre mRNAs. We used polyA position profiling by sequencing 3P Seq to map polyA sites at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P Seq reads substantially increased and improved existing three prime'UTR annotations  resulting in confidently identified three prime'UTRs for more than 78.79% of the annotated protein coding genes in zebrafish. Most zebrafish genes undergo alternative CPA with more than a thousand genes using different dominant three prime'UTRs at different stages. three prime'UTRs tend to be shortest in the ovaries and longest in the brain. Isoforms with some of the shortest three prime'UTRs are highly expressed in the ovary yet absent in the maternally contributed RNAs of the embryo  perhaps because their three prime'UTRs are too short to accommodate a uridine rich motif required for stability of the maternal mRNA. At two hpf  thousands of unique polyA sites appear at locations lacking a typical polyadenylation signal  which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into the identities  formation  and evolution of zebrafish three prime'UTRs provide a resource for studying gene regulation during vertebrate development. Overall design: 3P Seq was used to map the three prime' ends of protein coding genes in the zebrafish genome,,pubmed:22722342,,3P Seq Ovary,GSM919970,,source name:female adults|genotype/variation:wild type|tissue:ovary|development stage:adult,3P Seq Ovary,For 3P Seq: Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. The BED file is as in Jan et al. GSE24924 For 3P PE Seq: In each read pair  read #1 captured the three prime end of the polyA tail in the antisense orientation  and read #2 captured a portion of the three prime region of the transcript  and occasionally  the beginning of the polyA tail  in the sense orientation. Read #2 began with an adapter of 26 bases. Reads with more than 10 mismatches to the adapter were discarded and the first 26 bases were removed before further processing.  A read pair was considered informative only if read #1 began with Ts and read #2 contained 2–39 terminal As. post leading Ts and terminal As were removed from reads #1 and #2  respectively  they were mapped to the genome using Bowtie  allowing for up to two mismatches and requiring a unique mapping position in the zebrafish genome. The length of the tail encoded in read #2 was defined as the maximum number of trailing As allowing for up to one mismatch. Only cases in which this number was larger than the number of As encoded in the genome at the predicted cleavage position by at least 2 bases were carried forward. Cleavage and polyadenylation position was defined as the last non A base in read #2. The length of the polyA tail at that position was estimated using the corresponding read #1  and defined as the maximal i for which >90% of the bases in the first i bases of read #1 were Ts. This criterion was used to allow for some sequencing errors expected when sequencing long homopolymers. Genome build: danRer7 Supplementary files format and content: The .bed files contain the positions where 3P Seq reads were mapped  and the name of each track is the number of reads mapping to that position. Supplementary files format and content: The bigWig .bw files contain a summary of the number of reads whose three prime ends mapped to each position in the genome. Supplementary files format and content: For the paired end sequencing for mapping polyA tail lengths  the text files contain the following columns : chromosome  position  strand  number of polyA length reads  followed by the individual measurements lower bounds on polyA tail length,female adults,Ovaries and testes were obtained as described  in Gupta and Mullins 2010.,3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html,Zebrafish embryos or adults grown under standard condition,genotype/variation:wild type|tissue:ovary|developmental stage:adult,GSM919970,GSM919970: 3P Seq Ovary; Danio rerio; RNA Seq,GSM919970 1,GSM919970: 3P Seq Ovary,1,,GEO Accession:GSM919970,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP012376,,,3P_Seq_Ovary.fastq,fastq,644470380.0,17901955.0,GSM919970 r1,0:36,A:263871252;C:97757369;G:94972134;T:187683515;N:186110,36,,,,263871252,97757369,94972134,187683515,186110,SRX143564,SRS310285,SRA051955,GEO,Whitehead Institute for Biomedical Research,1,0.51356,,0.04868,,0.821,,0.48788,,36,,B,,usable mapping rate,illumina,early_illumina,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2012-04-20,Adult,Adult,Gonad,Reproductive System
38055,SRR1524249,SRX661014,SRS665988,SRP044781,PRJNA255848,Danio rerio Transcriptome,PRJNA255848,Transcriptome Analysis,Transcriptome analysis of 12 zebrafish tissues,parent bioproject:PRJNA255979,pubmed:27189481,Zebrafish testis,Zebrafish testis,F Dr 10,,strain:AB|age:5 month|biomaterial provider:INRA|sex:male|tissue:Testis|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish testis,F Dr 10,F Dr 10,Total RNA was qualified using an Agilent BioAnalyzer and 1 µg was used for polyA selection and library construction with Illumina's TruSeq stranded total RNA sample preparation kit according to the manufacturer's instructions TruSeq stranded total RNA SamplePrep Guide RevC,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP044781,,,F_Dr_10_CAGATC_L003_R2.fastq.gz F_Dr_10_CAGATC_L003_R1.fastq.gz,fastq fastq,11979537200.0,59897686.0,F Dr 10 files,0:100 1:100,A:3163301263;C:2775393678;G:2795402967;T:3125382350;N:120056942,100,100,,,3163301263,2775393678,2795402967,3125382350,120056942,SRX661014,SRS665988,SRA176464,INRA|Fish Physiology and Genomics,INRA PhyloFish,2,0.86011,0.88922,0.11073,0.11591,0.67359,0.67596,0.4986,0.50073,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,France,2014-07-25,Adult,Adult,Gonad,Reproductive System
38056,SRR1524248,SRX661013,SRS665989,SRP044781,PRJNA255848,Danio rerio Transcriptome,PRJNA255848,Transcriptome Analysis,Transcriptome analysis of 12 zebrafish tissues,parent bioproject:PRJNA255979,pubmed:27189481,Zebrafish ovary,Zebrafish ovary,F Dr 1,,strain:AB|age:5 month|biomaterial provider:INRA|sex:female|tissue:Ovary|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish ovary,F Dr 1,F Dr 1,Total RNA was qualified using an Agilent BioAnalyzer and 1 µg was used for polyA selection and library construction with Illumina's TruSeq stranded total RNA sample preparation kit according to the manufacturer's instructions TruSeq stranded total RNA SamplePrep Guide RevC,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP044781,,,F_Dr_1_ATCACG_L008_R2.fastq.gz F_Dr_1_ATCACG_L008_R1.fastq.gz,fastq fastq,4405297200.0,22026486.0,F Dr 1 files,0:100 1:100,A:1143385640;C:1055537748;G:1050116650;T:1145226897;N:11030265,100,100,,,1143385640,1055537748,1050116650,1145226897,11030265,SRX661013,SRS665989,SRA176464,INRA|Fish Physiology and Genomics,INRA PhyloFish,2,0.9327,0.93326,0.01849,0.01893,0.76773,0.77029,0.47583,0.47445,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,France,2015-07-24,Adult,Adult,Gonad,Reproductive System
39859,SRR2177445,SRX1161440,SRS1042403,SRP062685,PRJNA293388,Danio rerio Transcriptome or Gene expression,PRJNA293388,Other,Differential Expression between testis and ovary in two months of fish,,,Differential Expression between testis and ovary in two months of fish,,T,,isolate:Danio rerio testis|age:2 months|sex:male|tissue:testis|biomaterial provider:Department of Biology and Biotechnology|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio transcriptome sequencing,T,1,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062685,,,T_R1.fastq.gz T_R2.fastq.gz,fastq fastq,7616200600.0,38081003.0,T,0:100 1:100,A:2018574469;C:1797807061;G:1758967564;T:2040674119;N:177387,100,100,,,2018574469,1797807061,1758967564,2040674119,177387,SRX1161440,SRS1042403,SRA290385,Shanghai Ocean University|Department of Biology and Biotechnology,Shanghai Ocean University,2,0.946,0.93541,0.0936,0.09298,0.62929,0.63343,0.49102,0.48875,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2016-08-01,Juvenile,Juvenile,Gonad,Reproductive System
39860,SRR2177444,SRX1161439,SRS1042402,SRP062685,PRJNA293388,Danio rerio Transcriptome or Gene expression,PRJNA293388,Other,Differential Expression between testis and ovary in two months of fish,,,Differential Expression between testis and ovary in two months of fish,,O,,isolate:Danio rerio ovary|age:2 months|sex:female|tissue:ovary|biomaterial provider:Department of Biology and Biotechnology|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio transcriptome sequencing,O,1,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062685,,,O_R1.fastq.gz O_R2.fastq.gz,fastq fastq,6602802000.0,33014010.0,O,0:100 1:100,A:1705654028;C:1598182709;G:1559109823;T:1739704779;N:150661,100,100,,,1705654028,1598182709,1559109823,1739704779,150661,SRX1161439,SRS1042402,SRA290385,Shanghai Ocean University|Department of Biology and Biotechnology,Shanghai Ocean University,2,0.94263,0.93359,0.02018,0.02017,0.74842,0.75087,0.47643,0.47578,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2016-08-01,Juvenile,Juvenile,Gonad,Reproductive System
39861,SRR2177451,SRX1161443,SRS1042406,SRP062686,PRJNA293487,Danio rerio Digital Gene Expression Sequencing,PRJNA293487,Other,Differential expression between WT and CD82a from Morpholino treated embyro of Danio rerio,,,Differential expression between WT and CD82a Morpholino treated embyro of Danio rerio,,control,,isolate:Danio rerio embyro|dev stage:embyro|sex:missing|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Digital Gene Expression Sequencing,control,1,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062686,,,control_R1.fastq.gz control_R2.fastq.gz,fastq fastq,1381289200.0,6906446.0,control,0:100 1:100,A:362182510;C:331106787;G:327770778;T:360198909;N:30216,100,100,,,362182510,331106787,327770778,360198909,30216,SRX1161443,SRS1042406,SRA290388,Shanghai Ocean University|Department of Biology and Biotechnology,Shanghai Ocean University,2,0.95634,0.95016,0.06922,0.06922,0.7013,0.70368,0.46985,0.47013,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2016-08-21,Undetermined,Embryo,Gonad,Reproductive System
39862,SRR2177447,SRX1161442,SRS1042404,SRP062686,PRJNA293487,Danio rerio Digital Gene Expression Sequencing,PRJNA293487,Other,Differential expression between WT and CD82a from Morpholino treated embyro of Danio rerio,,,Differential expression between WT and CD82a Morpholino treated embyro of Danio rerio,,ATG,,isolate:Danio rerio embyro|dev stage:embyro|sex:missing|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Digital Gene Expression Sequencing,ATG,1,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062686,,,ATG_R1.fastq.gz ATG_R2.fastq.gz,fastq fastq,1278088000.0,6390440.0,ATG,0:100 1:100,A:335532626;C:305947212;G:302508524;T:334072046;N:27592,100,100,,,335532626,305947212,302508524,334072046,27592,SRX1161442,SRS1042404,SRA290388,Shanghai Ocean University|Department of Biology and Biotechnology,Shanghai Ocean University,2,0.95535,0.94653,0.07264,0.07271,0.70402,0.7082,0.46712,0.46962,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2016-08-21,Undetermined,Embryo,Gonad,Reproductive System
39938,SRR2541826,SRX1297648,SRS1095788,SRP064360,PRJNA297460,Female Reproductive Impacts of Dietary Methylmercury in Yellow Perch Perca flavescens and Zebrafish Danio rerio,GSE73615,Transcriptome Analysis,This study sought to evaluate the effects of dietary MeHg exposure on adult female yellow perch Perca flavescens and zebrafish Danio rerio reproduction by relating controlled exposures with subsequent reproductive effects. Yellow perch were used in the study for their socioeconomic and ecological importance within the Great Lakes basin  and the use of zebrafish allowed for a detailed analysis of the molecular effects of MeHg. MeHg exposures at environmentally relevant levels were done in zebrafish for a full life cycle  mimicking a realistic exposure scenario  and in adult yellow perch for twenty weeks  capturing early seasonal ovarian development. In zebrafish  several genes involved in reproductive processes were shown to be dysregulated by RNA seq and QPCR  but no significant phenotypic or physiological changes were observed with ovarian staging  fecundity  or embryo mortality. Yellow perch did not appear to be affected by MeHg  either at a molecular level  as assessed by QPCR of eight genes in the pituitary  liver  and ovary tissue  or a physiological level  as seen with ovarian somatic index  circulating estradiol  and ovarian staging. Lack of impact in yellow perch limits the usefulness of zebrafish as a model and suggests that the reproductive sensitivity to environmentally relevant levels of MeHg differs between yellow perch and zebrafish. Overall design: 12 samples of total RNA isolated from adult zebrafish ovaries were analyzed. Each exposure group 1  3  and 10 ppm MeHg had three replicates  as did the vehicle control. Each sample was comprised of pooled total RNA of up to 6 individual fish.,,pubmed:29272799,,zfish 10ppm R3,GSM1899557,,source name:ovary|tissue:ovary|strain:EK|mehg exposure:10 ppm,zfish 10ppm R3,Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9  UCSC using TopHat The alignment output from TopHat was converted into a transcriptome using Cufflinks v. 2.2.1  and alignment data was confirmed using RNAseQC against the Zv9 reference transcriptome of zebrafish Sample specific transcriptomes were assembled using Cufflinks with the Zv9 transcriptome as a reference to correct fragment biases by better identifying the start/end point of each exon Transcriptomes from each sample were merged into an ovary specific transcriptome using Cuffmerge Differential expression was conducted with Cuffdiff using pooled dispersion  geometric normalization  and the merged ovary transcriptome. Genome build: UCSC Zv9 Supplementary files format and content: Cuffdiff outputs FPKM files  which show expression values. Included in ovary.zip,ovary,Ovaries were flash frozen in RNA later and placed on dry ice immediately post dissection until proper storage at  80C.,High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc.  San Diego  CA  USA. Samples were run with 12 samples per lane  with 100 base pair  paired end reads.,Adult EK female zebrafish were exposed to MeHg 0  1  3  or 10 ppm with ethanol as the vehicle for an entire life cycle  starting with maternal exposure. Fish were exposed until euthanized.,tissue:ovary|strain:EK|mehg exposure:10 ppm,GSM1899557,GSM1899557: zfish 10ppm R3; Danio rerio; RNA Seq,GSM1899557,,1,High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc.  San Diego  CA  USA. Samples were run with 12 samples per lane  with 100 base pair  paired end reads.,GEO Accession:GSM1899557,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP064360,,,run448.R3-10ppm_AGTTCC_L003_R1.fastq.gz run448.R3-10ppm_AGTTCC_L003_R2.fastq.gz,fastq fastq,1525386436.0,7551418.0,GSM1899557 r1,0:101 1:101,A:413205816;C:348712240;G:344513814;T:414908557;N:4046009,101,101,,,413205816,348712240,344513814,414908557,4046009,SRX1297648,SRS1095788,SRA302185,GEO,"School of Freshwater Sciences, University of Wisconsin-Milwaukee",2,0.92358,0.92408,0.02862,0.02882,0.73898,0.74014,0.46916,0.46537,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2015-09-30,Adult,Adult,Gonad,Reproductive System
39939,SRR2541825,SRX1297647,SRS1095789,SRP064360,PRJNA297460,Female Reproductive Impacts of Dietary Methylmercury in Yellow Perch Perca flavescens and Zebrafish Danio rerio,GSE73615,Transcriptome Analysis,This study sought to evaluate the effects of dietary MeHg exposure on adult female yellow perch Perca flavescens and zebrafish Danio rerio reproduction by relating controlled exposures with subsequent reproductive effects. Yellow perch were used in the study for their socioeconomic and ecological importance within the Great Lakes basin  and the use of zebrafish allowed for a detailed analysis of the molecular effects of MeHg. MeHg exposures at environmentally relevant levels were done in zebrafish for a full life cycle  mimicking a realistic exposure scenario  and in adult yellow perch for twenty weeks  capturing early seasonal ovarian development. In zebrafish  several genes involved in reproductive processes were shown to be dysregulated by RNA seq and QPCR  but no significant phenotypic or physiological changes were observed with ovarian staging  fecundity  or embryo mortality. Yellow perch did not appear to be affected by MeHg  either at a molecular level  as assessed by QPCR of eight genes in the pituitary  liver  and ovary tissue  or a physiological level  as seen with ovarian somatic index  circulating estradiol  and ovarian staging. Lack of impact in yellow perch limits the usefulness of zebrafish as a model and suggests that the reproductive sensitivity to environmentally relevant levels of MeHg differs between yellow perch and zebrafish. Overall design: 12 samples of total RNA isolated from adult zebrafish ovaries were analyzed. Each exposure group 1  3  and 10 ppm MeHg had three replicates  as did the vehicle control. Each sample was comprised of pooled total RNA of up to 6 individual fish.,,pubmed:29272799,,zfish 10ppm R2,GSM1899556,,source name:ovary|tissue:ovary|strain:EK|mehg exposure:10 ppm,zfish 10ppm R2,Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9  UCSC using TopHat The alignment output from TopHat was converted into a transcriptome using Cufflinks v. 2.2.1  and alignment data was confirmed using RNAseQC against the Zv9 reference transcriptome of zebrafish Sample specific transcriptomes were assembled using Cufflinks with the Zv9 transcriptome as a reference to correct fragment biases by better identifying the start/end point of each exon Transcriptomes from each sample were merged into an ovary specific transcriptome using Cuffmerge Differential expression was conducted with Cuffdiff using pooled dispersion  geometric normalization  and the merged ovary transcriptome. Genome build: UCSC Zv9 Supplementary files format and content: Cuffdiff outputs FPKM files  which show expression values. Included in ovary.zip,ovary,Ovaries were flash frozen in RNA later and placed on dry ice immediately post dissection until proper storage at  80C.,High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc.  San Diego  CA  USA. Samples were run with 12 samples per lane  with 100 base pair  paired end reads.,Adult EK female zebrafish were exposed to MeHg 0  1  3  or 10 ppm with ethanol as the vehicle for an entire life cycle  starting with maternal exposure. Fish were exposed until euthanized.,tissue:ovary|strain:EK|mehg exposure:10 ppm,GSM1899556,GSM1899556: zfish 10ppm R2; Danio rerio; RNA Seq,GSM1899556,,1,High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc.  San Diego  CA  USA. Samples were run with 12 samples per lane  with 100 base pair  paired end reads.,GEO Accession:GSM1899556,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP064360,,,run448.R2-10ppm_TAGCTT_L003_R2.fastq.gz run448.R2-10ppm_TAGCTT_L003_R1.fastq.gz,fastq fastq,2061452016.0,10205208.0,GSM1899556 r1,0:101 1:101,A:557864095;C:473236506;G:465541615;T:559336990;N:5472810,101,101,,,557864095,473236506,465541615,559336990,5472810,SRX1297647,SRS1095789,SRA302185,GEO,"School of Freshwater Sciences, University of Wisconsin-Milwaukee",2,0.91738,0.91678,0.02538,0.0255,0.74454,0.74546,0.45899,0.4623,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2015-09-30,Adult,Adult,Gonad,Reproductive System