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574 rows where experiment.library_selection = "cDNA" and tissue_curation = "Gonad"

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devstage_curation 8

technology 7

devstage_curation_coarse 6

experiment.platform 3

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Gonad · 574 ✖

experiment.library_strategy 1

experiment.library_selection 1

  • cDNA · 574 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
50 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 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 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 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 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 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 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 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 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 4407 ERR1427376 ERX1497908 ERS1183210 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#48 SAMEA4012100 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012100|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#48|broker name:ArrayExpress|common name:zebrafish|fsc:NaN|gfp:NaN|individual:2|pi:NaN|plate:7|sample name:E MTAB 4617:LCK 7#48|ssc:NaN|tissue:Testes|well:H6                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#48 LCK 7#48 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Testes:tissue|Experimental Factor: NaN:fsc|Experimental Factor: NaN:ssc|Experimental Factor: NaN:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_48_mod.bam LCK_7_48.cram bam cram     E MTAB 4617:LCK 7#48 0:125 1:125 A:84706839;C:81480882;G:75512683;T:89639016;N:40330 125 125     84706839 81480882 75512683 89639016 40330 ERX1497908   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.19405 0.19075 0.02782 0.02779 0.9795 0.98013 0.73205 0.73409 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Gonad Reproductive System
4415 4415 ERR1427368 ERX1497900 ERS1183202 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#40 SAMEA4012092 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012092|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#40|broker name:ArrayExpress|common name:zebrafish|fsc:NaN|gfp:NaN|individual:2|pi:NaN|plate:7|sample name:E MTAB 4617:LCK 7#40|ssc:NaN|tissue:Testes|well:H5                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#40 LCK 7#40 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Testes:tissue|Experimental Factor: NaN:fsc|Experimental Factor: NaN:ssc|Experimental Factor: NaN:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_40_mod.bam LCK_7_40.cram bam cram     E MTAB 4617:LCK 7#40 0:125 1:125 A:98690446;C:95653530;G:87621123;T:105368805;N:43346 125 125     98690446 95653530 87621123 105368805 43346 ERX1497900   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.20112 0.19727 0.01661 0.01621 0.9797 0.9806 0.44206 0.42908 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Gonad Reproductive System
4424 4424 ERR1427359 ERX1497891 ERS1183193 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#32 SAMEA4012083 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012083|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#32|broker name:ArrayExpress|common name:zebrafish|fsc:NaN|gfp:NaN|individual:2|pi:NaN|plate:7|sample name:E MTAB 4617:LCK 7#32|ssc:NaN|tissue:Testes|well:H4                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#32 LCK 7#32 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Testes:tissue|Experimental Factor: NaN:fsc|Experimental Factor: NaN:ssc|Experimental Factor: NaN:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_32_mod.bam LCK_7_32.cram bam cram     E MTAB 4617:LCK 7#32 0:125 1:125 A:102670073;C:105552903;G:96042262;T:111286167;N:48595 125 125     102670073 105552903 96042262 111286167 48595 ERX1497891   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.0367 0.03586 0.00293 0.00297 0.99316 0.99387 0.82316 0.80581 125 125 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Gonad Reproductive System
4433 4433 ERR1427350 ERX1497882 ERS1183184 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#24 SAMEA4012074 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012074|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#24|broker name:ArrayExpress|common name:zebrafish|fsc:NaN|gfp:NaN|individual:2|pi:NaN|plate:7|sample name:E MTAB 4617:LCK 7#24|ssc:NaN|tissue:Testes|well:H3                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#24 LCK 7#24 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Testes:tissue|Experimental Factor: NaN:fsc|Experimental Factor: NaN:ssc|Experimental Factor: NaN:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_24_mod.bam LCK_7_24.cram bam cram     E MTAB 4617:LCK 7#24 0:125 1:125 A:97411995;C:91321821;G:84912221;T:100868660;N:45803 125 125     97411995 91321821 84912221 100868660 45803 ERX1497882   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.25757 0.25144 0.03087 0.02958 0.97642 0.97695 0.71128 0.71145 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Gonad Reproductive System
4442 4442 ERR1427341 ERX1497873 ERS1183175 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#16 SAMEA4012065 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012065|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#16|broker name:ArrayExpress|common name:zebrafish|fsc:NaN|gfp:NaN|individual:2|pi:NaN|plate:7|sample name:E MTAB 4617:LCK 7#16|ssc:NaN|tissue:Testes|well:H2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#16 LCK 7#16 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Testes:tissue|Experimental Factor: NaN:fsc|Experimental Factor: NaN:ssc|Experimental Factor: NaN:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_16_mod.bam LCK_7_16.cram bam cram     E MTAB 4617:LCK 7#16 0:125 1:125 A:81321616;C:79315899;G:72476597;T:85676964;N:38424 125 125     81321616 79315899 72476597 85676964 38424 ERX1497873   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.20776 0.20306 0.02431 0.02397 0.9654 0.96621 0.66321 0.66592 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Gonad Reproductive System
5793 5793 ERR1955208 ERX2020800 ERS1697077 ERP017053 PRJEB15333 Transposon driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution ena-STUDY-EMBL EUROPEAN BIOINFORMATICS INSTITUTE-07-09-2016-10:25:55:499-247 Other In order to better understand the features associated with male germline transcription we profiled the RNA expression in a number of germline cell types. These include spermatogonial stem cells spermatocytes and round spermatids in mouse and spermatocytes in rat. We also profiled the transcription in zebrafish testes. As a consequence it became apparent that transposable elements are driving considerable lncRNA expression in the later stages of spermatogenesis. This is particularly apparent in the case of endogenous retroviruses in rodents. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 05 08     Transcriptional profiling of zebrafish testes for analysis of conserved repeat element associations SAMEA104033184 EMBL EUROPEAN BIOINFORMATICS INSTITUTE ENA FIRST PUBLIC:2017 05 10T17:01:28Z|ENA LAST UPDATE:2017 04 28T10:34:37Z|External Id:SAMEA104033184|INSDC center name:EMBL EUROPEAN BIOINFORMATICS INSTITUTE|INSDC first public:2017 05 10T17:01:28Z|INSDC last update:2017 04 28T10:34:37Z|INSDC status:public|Submitter Id:Zebrafish.Testis 2|common name:zebrafish|sample name:Zebrafish.Testis 2|scientific name:Danio rerio|strain:AB|tissue type:testis                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 16 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP017053 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 05 10|ENA LAST UPDATE:2018 11 16 zebrafish_testis_2.conserved.1.fastq.gz zebrafish_testis_2.conserved.2.fastq.gz fastq fastq 46555372886.0 230472143.0 ena RUN EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 16 0:101 1:101 A:12260062264;C:10888457642;G:11605642683;T:11637267744;N:163942553 101 101     12260062264 10888457642 11605642683 11637267744 163942553 ERX2020800 ERS1697077 ERA904389 EMBL EUROPEAN BIOINFORMATICS INSTITUTE|European Nucleotide Archive EMBL EUROPEAN BIOINFORMATICS INSTITUTE 2 0.93165 0.92785 0.29822 0.32141 0.71386 0.71971 0.66173 0.63843 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2017-01-31 Undetermined Undetermined Gonad Reproductive System
5794 5794 ERR1955207 ERX2020799 ERS1697076 ERP017053 PRJEB15333 Transposon driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution ena-STUDY-EMBL EUROPEAN BIOINFORMATICS INSTITUTE-07-09-2016-10:25:55:499-247 Other In order to better understand the features associated with male germline transcription we profiled the RNA expression in a number of germline cell types. These include spermatogonial stem cells spermatocytes and round spermatids in mouse and spermatocytes in rat. We also profiled the transcription in zebrafish testes. As a consequence it became apparent that transposable elements are driving considerable lncRNA expression in the later stages of spermatogenesis. This is particularly apparent in the case of endogenous retroviruses in rodents. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 05 08     Transcriptional profiling of zebrafish testes for analysis of conserved repeat element associations SAMEA104033183 EMBL EUROPEAN BIOINFORMATICS INSTITUTE ENA FIRST PUBLIC:2017 05 10T17:01:28Z|ENA LAST UPDATE:2017 04 28T10:34:37Z|External Id:SAMEA104033183|INSDC center name:EMBL EUROPEAN BIOINFORMATICS INSTITUTE|INSDC first public:2017 05 10T17:01:28Z|INSDC last update:2017 04 28T10:34:37Z|INSDC status:public|Submitter Id:Zebrafish.Testis 1|common name:zebrafish|sample name:Zebrafish.Testis 1|scientific name:Danio rerio|strain:AB|tissue type:testis                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 15 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP017053 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 05 10|ENA LAST UPDATE:2018 11 16 zebrafish_testis_1.conserved.1.fastq.gz zebrafish_testis_1.conserved.2.fastq.gz fastq fastq 41056086708.0 203247954.0 ena RUN EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 15 0:101 1:101 A:10675591750;C:9672762387;G:10139834713;T:10380949257;N:186948601 101 101     10675591750 9672762387 10139834713 10380949257 186948601 ERX2020799 ERS1697076 ERA904389 EMBL EUROPEAN BIOINFORMATICS INSTITUTE|European Nucleotide Archive EMBL EUROPEAN BIOINFORMATICS INSTITUTE 2 0.92308 0.9157 0.30221 0.31293 0.68276 0.68836 0.56114 0.5857 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2017-01-31 Undetermined Undetermined Gonad Reproductive System
24582 24582 SRR25462250 SRX21195051 SRS18453977 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG HE 8mpf 3 GSM7669027   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing PG HE 8mpf 3 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ GSM7669027 GSM7669027: PG HE 8mpf 3; Danio rerio; RNA Seq GSM7669027 r1 GSM7669027 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     HE_PG_8mpf_3_S11_L003_R1_001.fastq.gz HE_PG_8mpf_3_S11_L003_R2_001.fastq.gz fastq fastq 7161373434.0 60309247.0 GSM7669027 r1 0:59.39 1:59.35 A:1783731260;C:1744025029;G:1733970346;T:1880173306;N:19473493 59 59     1783731260 1744025029 1733970346 1880173306 19473493 SRX21195051 SRS18453977     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.94187 0.94592 0.01475 0.01464 0.77447 0.77498 0.45855 0.4635 60 60 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Adult Adult Gonad Reproductive System
24583 24583 SRR25462251 SRX21195050 SRS18453976 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG HE 8mpf 2 GSM7669026   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing PG HE 8mpf 2 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ GSM7669026 GSM7669026: PG HE 8mpf 2; Danio rerio; RNA Seq GSM7669026 r1 GSM7669026 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     HE_PG_8mpf_2_S7_L003_R1_001.fastq.gz HE_PG_8mpf_2_S7_L003_R2_001.fastq.gz fastq fastq 3176994053.0 26828357.0 GSM7669026 r1 0:59.22 1:59.20 A:793619267;C:767135191;G:764404567;T:830643823;N:21191205 59 59     793619267 767135191 764404567 830643823 21191205 SRX21195050 SRS18453976     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.93822 0.94226 0.01596 0.0161 0.77684 0.77772 0.47008 0.46904 59 60 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Adult Adult Gonad Reproductive System
24584 24584 SRR25462252 SRX21195049 SRS18453975 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG HE 8mpf 1 GSM7669025   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing PG HE 8mpf 1 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ GSM7669025 GSM7669025: PG HE 8mpf 1; Danio rerio; RNA Seq GSM7669025 r1 GSM7669025 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     HE_PG_8mpf_1_S6_L003_R1_001.fastq.gz HE_PG_8mpf_1_S6_L003_R2_001.fastq.gz fastq fastq 4587580737.0 38590260.0 GSM7669025 r1 0:59.45 1:59.43 A:1149031944;C:1121086335;G:1106925902;T:1203970839;N:6565717 59 59     1149031944 1121086335 1106925902 1203970839 6565717 SRX21195049 SRS18453975     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.94032 0.9437 0.01481 0.01462 0.77682 0.77774 0.45843 0.4699 58 60 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Adult Adult Gonad Reproductive System
24585 24585 SRR25462253 SRX21195048 SRS18453974 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG WT 8mpf 3 GSM7669024   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing PG WT 8mpf 3 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+ GSM7669024 GSM7669024: PG WT 8mpf 3; Danio rerio; RNA Seq GSM7669024 r1 GSM7669024 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     WT_PG_8mpf_3_S8_L003_R2_001.fastq.gz WT_PG_8mpf_3_S8_L003_R1_001.fastq.gz fastq fastq 3920821867.0 33089226.0 GSM7669024 r1 0:59.26 1:59.23 A:977738236;C:951999354;G:944769809;T:1023828622;N:22485846 59 59     977738236 951999354 944769809 1023828622 22485846 SRX21195048 SRS18453974     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.94193 0.94555 0.01657 0.01646 0.76784 0.76919 0.47238 0.47016 60 60 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Adult Adult Gonad Reproductive System
24586 24586 SRR25462254 SRX21195047 SRS18453973 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG WT 8mpf 2 GSM7669023   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing PG WT 8mpf 2 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+ GSM7669023 GSM7669023: PG WT 8mpf 2; Danio rerio; RNA Seq GSM7669023 r1 GSM7669023 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     WT_PG_8mpf_2_S10_L003_R2_001.fastq.gz WT_PG_8mpf_2_S10_L003_R1_001.fastq.gz fastq fastq 4917868553.0 41430484.0 GSM7669023 r1 0:59.37 1:59.33 A:1231173294;C:1195692797;G:1182545852;T:1292018757;N:16437853 59 59     1231173294 1195692797 1182545852 1292018757 16437853 SRX21195047 SRS18453973     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.94048 0.94432 0.0178 0.0178 0.75645 0.7569 0.46332 0.46812 59 57 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Adult Adult Gonad Reproductive System
24587 24587 SRR25462255 SRX21195046 SRS18453972 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG WT 8mpf 1 GSM7669022   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing PG WT 8mpf 1 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+ GSM7669022 GSM7669022: PG WT 8mpf 1; Danio rerio; RNA Seq GSM7669022 r1 GSM7669022 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     WT_PG_8mpf_1_S9_L003_R1_001.fastq.gz WT_PG_8mpf_1_S9_L003_R2_001.fastq.gz fastq fastq 3375380667.0 28408784.0 GSM7669022 r1 0:59.42 1:59.40 A:842316103;C:825987175;G:818715765;T:881225528;N:7136096 59 59     842316103 825987175 818715765 881225528 7136096 SRX21195046 SRS18453972     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.94039 0.9444 0.0162 0.01617 0.7697 0.76986 0.47132 0.46938 60 60 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Adult Adult Gonad Reproductive System
24588 24588 SRR25462256 SRX21195045 SRS18453971 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG HE 50dpf 3 GSM7669021   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing PG HE 50dpf 3 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ GSM7669021 GSM7669021: PG HE 50dpf 3; Danio rerio; RNA Seq GSM7669021 r1 GSM7669021 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     PG_HE_3_S26_L003_R1_001.fastq.gz PG_HE_3_S26_L003_R2_001.fastq.gz fastq fastq 4520051001.0 22984712.0 GSM7669021 r1 0:98.32 1:98.33 A:1134815259;C:1102592573;G:1104475707;T:1160918938;N:17248524 98 98     1134815259 1102592573 1104475707 1160918938 17248524 SRX21195045 SRS18453971     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.93438 0.93937 0.01237 0.01252 0.78208 0.78192 0.48454 0.49474 99 99 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Juvenile Juvenile Gonad Reproductive System
24589 24589 SRR25462257 SRX21195044 SRS18453970 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG HE 50dpf 2 GSM7669020   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing PG HE 50dpf 2 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ GSM7669020 GSM7669020: PG HE 50dpf 2; Danio rerio; RNA Seq GSM7669020 r1 GSM7669020 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     PG_HE_2_S25_L003_R2_001.fastq.gz PG_HE_2_S25_L003_R1_001.fastq.gz fastq fastq 3915471868.0 19847479.0 GSM7669020 r1 0:98.64 1:98.64 A:982714666;C:957212118;G:961590362;T:1003408448;N:10546274 98 98     982714666 957212118 961590362 1003408448 10546274 SRX21195044 SRS18453970     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.93184 0.93552 0.01275 0.01275 0.78356 0.7835 0.49472 0.48841 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Juvenile Juvenile Gonad Reproductive System
24590 24590 SRR25462258 SRX21195043 SRS18453969 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG HE 50dpf 1 GSM7669019   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing PG HE 50dpf 1 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ GSM7669019 GSM7669019: PG HE 50dpf 1; Danio rerio; RNA Seq GSM7669019 r1 GSM7669019 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     PG_HE_1_S24_L003_R1_001.fastq.gz PG_HE_1_S24_L003_R2_001.fastq.gz fastq fastq 4764998144.0 24264412.0 GSM7669019 r1 0:98.18 1:98.20 A:1194676445;C:1161648051;G:1165061360;T:1221860864;N:21751424 98 98     1194676445 1161648051 1165061360 1221860864 21751424 SRX21195043 SRS18453969     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.91864 0.92247 0.01213 0.01245 0.7949 0.79584 0.50422 0.50318 100 98 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Juvenile Juvenile Gonad Reproductive System
24591 24591 SRR25462259 SRX21195042 SRS18453968 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG WT 50dpf 3 GSM7669018   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing PG WT 50dpf 3 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+ GSM7669018 GSM7669018: PG WT 50dpf 3; Danio rerio; RNA Seq GSM7669018 r1 GSM7669018 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     PG_WT_3_S23_L003_R1_001.fastq.gz PG_WT_3_S23_L003_R2_001.fastq.gz fastq fastq 6204452412.0 31480139.0 GSM7669018 r1 0:98.55 1:98.54 A:1567898375;C:1505755791;G:1512895523;T:1599284546;N:18618177 98 98     1567898375 1505755791 1512895523 1599284546 18618177 SRX21195042 SRS18453968     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.9312 0.93599 0.01692 0.01686 0.76426 0.76439 0.46519 0.47751 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Juvenile Juvenile Gonad Reproductive System
24592 24592 SRR25462260 SRX21195041 SRS18453967 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG WT 50dpf 2 GSM7669017   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing PG WT 50dpf 2 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+ GSM7669017 GSM7669017: PG WT 50dpf 2; Danio rerio; RNA Seq GSM7669017 r1 GSM7669017 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     PG_WT_2_S22_L003_R1_001.fastq.gz PG_WT_2_S22_L003_R2_001.fastq.gz fastq fastq 3907759829.0 19906505.0 GSM7669017 r1 0:98.15 1:98.15 A:991973983;C:940499355;G:946342572;T:1011476708;N:17467211 98 98     991973983 940499355 946342572 1011476708 17467211 SRX21195041 SRS18453967     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.91435 0.9186 0.02035 0.02032 0.764 0.76321 0.48743 0.48644 97 99 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Juvenile Juvenile Gonad Reproductive System
24593 24593 SRR25462261 SRX21195040 SRS18453966 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG WT 50dpf 1 GSM7669016   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing PG WT 50dpf 1 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+ GSM7669016 GSM7669016: PG WT 50dpf 1; Danio rerio; RNA Seq GSM7669016 r1 GSM7669016 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     PG_WT_1_S21_L003_R2_001.fastq.gz PG_WT_1_S21_L003_R1_001.fastq.gz fastq fastq 7395136401.0 37752582.0 GSM7669016 r1 0:97.94 1:97.94 A:1865709287;C:1789949400;G:1796311820;T:1908470411;N:34695483 97 97     1865709287 1789949400 1796311820 1908470411 34695483 SRX21195040 SRS18453966     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.9216 0.92737 0.01817 0.01802 0.76601 0.76593 0.48894 0.4975 100 99 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Juvenile Juvenile Gonad Reproductive System
24594 24594 SRR25462243 SRX21195038 SRS18453964 SRP452269 PRJNA1000446 Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish GSE239623 Transcriptome Analysis Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.       PV M3 GSM7669033   source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing PV M3 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / GSM7669033 GSM7669033: PV M3; Danio rerio; RNA Seq GSM7669033 r1 GSM7669033 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452269     PV_M3_R1.fastq.gz PV_M3_R2.fastq.gz fastq fastq 4644457090.0 23465750.0 GSM7669033 r1 0:98.98 1:98.94 A:1196567358;C:1114203322;G:1109379777;T:1223156356;N:1150277 98 98     1196567358 1114203322 1109379777 1223156356 1150277 SRX21195038 SRS18453964     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.94849 0.95248 0.02727 0.02708 0.73602 0.73718 0.48396 0.4855 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Undetermined Embryo Gonad Reproductive System
24595 24595 SRR25462244 SRX21195037 SRS18453963 SRP452269 PRJNA1000446 Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish GSE239623 Transcriptome Analysis Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.       PV M2 GSM7669032   source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing PV M2 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / GSM7669032 GSM7669032: PV M2; Danio rerio; RNA Seq GSM7669032 r1 GSM7669032 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452269     PV_M2_R1.fastq.gz PV_M2_R2.fastq.gz fastq fastq 2464506276.0 12449948.0 GSM7669032 r1 0:98.99 1:98.96 A:632587002;C:593372099;G:591579950;T:646214108;N:753117 98 98     632587002 593372099 591579950 646214108 753117 SRX21195037 SRS18453963     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.94889 0.9522 0.02585 0.02585 0.73669 0.73841 0.48398 0.48486 100 99 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Undetermined Embryo Gonad Reproductive System
24596 24596 SRR25462245 SRX21195036 SRS18453962 SRP452269 PRJNA1000446 Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish GSE239623 Transcriptome Analysis Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.       PV M1 GSM7669031   source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing PV M1 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / GSM7669031 GSM7669031: PV M1; Danio rerio; RNA Seq GSM7669031 r1 GSM7669031 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452269     PV_M1_R1.fastq.gz PV_M1_R2.fastq.gz fastq fastq 3634173229.0 18461903.0 GSM7669031 r1 0:98.44 1:98.41 A:930322973;C:875929476;G:875710056;T:948595199;N:3615525 98 98     930322973 875929476 875710056 948595199 3615525 SRX21195036 SRS18453962     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.94787 0.95134 0.02457 0.02445 0.73762 0.73843 0.48244 0.48069 100 98 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Undetermined Embryo Gonad Reproductive System
24597 24597 SRR25462246 SRX21195035 SRS18453961 SRP452269 PRJNA1000446 Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish GSE239623 Transcriptome Analysis Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.       PV WT3 GSM7669030   source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing PV WT3 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+ GSM7669030 GSM7669030: PV WT3; Danio rerio; RNA Seq GSM7669030 r1 GSM7669030 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452269     PV_WT3_R2.fastq PV_WT3_R1.fastq fastq fastq 2965772270.0 14976621.0 GSM7669030 r1 0:99.03 1:98.99 A:759343389;C:716154246;G:713466520;T:775995980;N:812135 99 98     759343389 716154246 713466520 775995980 812135 SRX21195035 SRS18453961     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.95027 0.95485 0.02356 0.02292 0.74422 0.74554 0.47974 0.48267 100 98 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Undetermined Embryo Gonad Reproductive System
24598 24598 SRR25462247 SRX21195034 SRS18453960 SRP452269 PRJNA1000446 Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish GSE239623 Transcriptome Analysis Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.       PV WT2 GSM7669029   source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing PV WT2 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+ GSM7669029 GSM7669029: PV WT2; Danio rerio; RNA Seq GSM7669029 r1 GSM7669029 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452269     PV_WT2_R2.fastq PV_WT2_R1.fastq fastq fastq 2021387268.0 10195384.0 GSM7669029 r1 0:99.15 1:99.12 A:517788644;C:487363563;G:485168383;T:530550229;N:516449 99 99     517788644 487363563 485168383 530550229 516449 SRX21195034 SRS18453960     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.95113 0.9544 0.02394 0.02364 0.74168 0.74363 0.47881 0.47499 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Undetermined Embryo Gonad Reproductive System
24599 24599 SRR25462248 SRX21195033 SRS18453959 SRP452269 PRJNA1000446 Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish GSE239623 Transcriptome Analysis Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.       PV WT1 GSM7669028   source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing PV WT1 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+ GSM7669028 GSM7669028: PV WT1; Danio rerio; RNA Seq GSM7669028 r1 GSM7669028 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452269     PV_WT1_R1.fastq PV_WT1_R2.fastq fastq fastq 3244660111.0 16481925.0 GSM7669028 r1 0:98.44 1:98.42 A:831426044;C:781489498;G:779991004;T:848549246;N:3204319 98 98     831426044 781489498 779991004 848549246 3204319 SRX21195033 SRS18453959     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.94779 0.95185 0.02328 0.02298 0.74294 0.74391 0.48052 0.47966 95 95 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Undetermined Embryo Gonad Reproductive System
25267 25267 SRR25744342 SRX21467662 SRS18702380 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad eif4e1b 3 GSM7730282   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / |geo loc name:missing|collection date:missing Gonad eif4e1b 3 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / GSM7730282 GSM7730282: Gonad eif4e1b 3; Danio rerio; ssRNA seq GSM7730282 r1 GSM7730282 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_HOM3_1.fastq.gz Ovary_HOM3_2.fastq.gz fastq fastq 2170738056.0 10746228.0 GSM7730282 r1 0:101 1:101 A:531993767;C:520631008;G:565772072;T:552334154;N:7055 101 101     531993767 520631008 565772072 552334154 7055 SRX21467662 SRS18702380 SRA1698764 IMP IMP 2 0.77665 0.7702 0.14988 0.14284 0.66716 0.66957 0.49991 0.47425 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25268 25268 SRR25744343 SRX21467661 SRS18702379 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad eif4e1b 2 GSM7730281   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / |geo loc name:missing|collection date:missing Gonad eif4e1b 2 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / GSM7730281 GSM7730281: Gonad eif4e1b 2; Danio rerio; ssRNA seq GSM7730281 r1 GSM7730281 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_HOM2_1.fastq.gz Ovary_HOM2_2.fastq.gz fastq fastq 3459149000.0 17124500.0 GSM7730281 r1 0:101 1:101 A:876732239;C:796603142;G:882912604;T:902886783;N:14232 101 101     876732239 796603142 882912604 902886783 14232 SRX21467661 SRS18702379 SRA1698764 IMP IMP 2 0.81761 0.79589 0.26282 0.24746 0.70607 0.7039 0.50658 0.49236 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25269 25269 SRR25744344 SRX21467660 SRS18702381 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad eif4e1b 1 GSM7730280   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / |geo loc name:missing|collection date:missing Gonad eif4e1b 1 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / GSM7730280 GSM7730280: Gonad eif4e1b 1; Danio rerio; ssRNA seq GSM7730280 r1 GSM7730280 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_HOM1_1.fastq.gz Ovary_HOM1_2.fastq.gz fastq fastq 2189781202.0 10840501.0 GSM7730280 r1 0:101 1:101 A:537591255;C:525448020;G:568979980;T:557754770;N:7177 101 101     537591255 525448020 568979980 557754770 7177 SRX21467660 SRS18702381 SRA1698764 IMP IMP 2 0.7459 0.74191 0.15778 0.15291 0.65543 0.65841 0.48578 0.48291 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25270 25270 SRR25744345 SRX21467659 SRS18702378 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad WT 3 GSM7730279   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+|geo loc name:missing|collection date:missing Gonad WT 3 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+ GSM7730279 GSM7730279: Gonad WT 3; Danio rerio; ssRNA seq GSM7730279 r1 GSM7730279 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_WT3_1.fastq.gz Ovary_WT3_2.fastq.gz fastq fastq 3674041448.0 18188324.0 GSM7730279 r1 0:101 1:101 A:910831144;C:876967044;G:953299105;T:932928913;N:15242 101 101     910831144 876967044 953299105 932928913 15242 SRX21467659 SRS18702378 SRA1698764 IMP IMP 2 0.89093 0.89038 0.09253 0.09348 0.73892 0.73858 0.47115 0.47218 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25271 25271 SRR25744346 SRX21467658 SRS18702377 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad WT 2 GSM7730278   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+|geo loc name:missing|collection date:missing Gonad WT 2 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+ GSM7730278 GSM7730278: Gonad WT 2; Danio rerio; ssRNA seq GSM7730278 r1 GSM7730278 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_WT2_1.fastq.gz Ovary_WT2_2.fastq.gz fastq fastq 3024886370.0 14974685.0 GSM7730278 r1 0:101 1:101 A:744374909;C:727299396;G:782294774;T:770904797;N:12494 101 101     744374909 727299396 782294774 770904797 12494 SRX21467658 SRS18702377 SRA1698764 IMP IMP 2 0.91806 0.91689 0.06949 0.07178 0.74458 0.74474 0.47548 0.47338 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25272 25272 SRR25744347 SRX21467657 SRS18702376 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad WT 1 GSM7730277   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+|geo loc name:missing|collection date:missing Gonad WT 1 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+ GSM7730277 GSM7730277: Gonad WT 1; Danio rerio; ssRNA seq GSM7730277 r1 GSM7730277 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_WT1_2.fastq.gz Ovary_WT1_1.fastq.gz fastq fastq 3571638356.0 17681378.0 GSM7730277 r1 0:101 1:101 A:876280472;C:856417516;G:935896746;T:903028845;N:14777 101 101     876280472 856417516 935896746 903028845 14777 SRX21467657 SRS18702376 SRA1698764 IMP IMP 2 0.89559 0.89353 0.09223 0.09423 0.73052 0.73012 0.47772 0.47408 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
30556 30556 SRR27836071 SRX23499420 SRS20351177 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   Rbpms2 mApple crosslinked SR3 GSM8059038   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing Rbpms2 mApple crosslinked SR3 Basespace illumina platform was used and reads were mapped using tophate2 aligner. Estimation of reference genes and transcript was done using cufflinks and reads were mapped to the genome GRCz10. Reads were aligned with the TopHat Alignment App. GRCz10 CSV file that compiled includes tracking ids gene loci and FPKMs for each samples CSV files include tracking and gene id gene short name tss id locus and FPKM for each sample Gonad   RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589   tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype GSM8059038 GSM8059038: Rbpms2 mApple crosslinked SR3; Danio rerio; RNA Seq GSM8059038 r1 GSM8059038 1 RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485     SR-3_S4_L001_R1_001.fastq.gz SR-3_S4_L001_R2_001.fastq.gz fastq fastq 588252864.0 3949222.0 GSM8059038 r1 0:74.42 1:74.53 A:116383167;C:176622592;G:176850622;T:118306997;N:89486 74 74     116383167 176622592 176850622 118306997 89486 SRX23499420 SRS20351177 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2024-02-01 Undetermined Undetermined Gonad Reproductive System
30557 30557 SRR27836072 SRX23499419 SRS20351178 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   Rbpms2 mApple uncrosslinked SR2 GSM8059037   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing Rbpms2 mApple uncrosslinked SR2 Basespace illumina platform was used and reads were mapped using tophate2 aligner. Estimation of reference genes and transcript was done using cufflinks and reads were mapped to the genome GRCz10. Reads were aligned with the TopHat Alignment App. GRCz10 CSV file that compiled includes tracking ids gene loci and FPKMs for each samples CSV files include tracking and gene id gene short name tss id locus and FPKM for each sample Gonad   RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589   tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype GSM8059037 GSM8059037: Rbpms2 mApple uncrosslinked SR2; Danio rerio; RNA Seq GSM8059037 r1 GSM8059037 1 RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485     SR-2_S3_L001_R1_001.fastq.gz SR-2_S3_L001_R2_001.fastq.gz fastq fastq 547329260.0 3670350.0 GSM8059037 r1 0:74.51 1:74.61 A:109193152;C:163365002;G:162344228;T:112378069;N:48809 74 74     109193152 163365002 162344228 112378069 48809 SRX23499419 SRS20351178 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2024-02-01 Undetermined Undetermined Gonad Reproductive System
30558 30558 SRR27836073 SRX23499418 SRS20351176 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   mApple control crosslinked SR8 GSM8059036   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing mApple control crosslinked SR8 Basespace illumina platform was used and reads were mapped using tophate2 aligner. Estimation of reference genes and transcript was done using cufflinks and reads were mapped to the genome GRCz10. Reads were aligned with the TopHat Alignment App. GRCz10 CSV file that compiled includes tracking ids gene loci and FPKMs for each samples CSV files include tracking and gene id gene short name tss id locus and FPKM for each sample Gonad   RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589   tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype GSM8059036 GSM8059036: mApple control crosslinked SR8; Danio rerio; RNA Seq GSM8059036 r1 GSM8059036 1 RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485     SR-8_S6_L001_R1_001.fastq.gz SR-8_S6_L001_R2_001.fastq.gz fastq fastq 474378287.0 3180744.0 GSM8059036 r1 0:74.52 1:74.62 A:90310344;C:145884340;G:146185172;T:91942086;N:56345 74 74     90310344 145884340 146185172 91942086 56345 SRX23499418 SRS20351176 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2024-02-01 Undetermined Undetermined Gonad Reproductive System
30559 30559 SRR27836074 SRX23499417 SRS20351175 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   mApple control uncrosslinked SR6 GSM8059035   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing mApple control uncrosslinked SR6 Basespace illumina platform was used and reads were mapped using tophate2 aligner. Estimation of reference genes and transcript was done using cufflinks and reads were mapped to the genome GRCz10. Reads were aligned with the TopHat Alignment App. GRCz10 CSV file that compiled includes tracking ids gene loci and FPKMs for each samples CSV files include tracking and gene id gene short name tss id locus and FPKM for each sample Gonad   RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589   tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype GSM8059035 GSM8059035: mApple control uncrosslinked SR6; Danio rerio; RNA Seq GSM8059035 r1 GSM8059035 1 RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485     SR-6_S5_L001_R1_001.fastq.gz SR-6_S5_L001_R2_001.fastq.gz fastq fastq 1667210566.0 11187841.0 GSM8059035 r1 0:74.46 1:74.56 A:348153529;C:480420209;G:474792496;T:363567978;N:276354 74 74     348153529 480420209 474792496 363567978 276354 SRX23499417 SRS20351175 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2024-02-01 Undetermined Undetermined Gonad Reproductive System
30560 30560 SRR27836075 SRX23499416 SRS20351174 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 mutant 4 21 dpf GSM8059034   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing rbpms2 mutant 4 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM GSM8059034 GSM8059034: rbpms2 mutant 4 21 dpf; Danio rerio; RNA Seq GSM8059034 r1 GSM8059034 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-DM_4_S8_L001_R1_001.fastq.gz rbpms2-d21-DM_4_S8_L001_R2_001.fastq.gz fastq fastq 2533252722.0 24835811.0 GSM8059034 r1 0:51 1:51 A:767895104;C:496128064;G:502250517;T:766951391;N:27646 51 51     767895104 496128064 502250517 766951391 27646 SRX23499416 SRS20351174 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
30561 30561 SRR27836076 SRX23499416 SRS20351174 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 mutant 4 21 dpf GSM8059034   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing rbpms2 mutant 4 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM GSM8059034 GSM8059034: rbpms2 mutant 4 21 dpf; Danio rerio; RNA Seq GSM8059034 r1 GSM8059034 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-DM_4_S8_L002_R1_001.fastq.gz rbpms2-d21-DM_4_S8_L002_R2_001.fastq.gz fastq fastq 2500214514.0 24511907.0 GSM8059034 r2 0:51 1:51 A:757980090;C:489633622;G:495839519;T:756737989;N:23294 51 51     757980090 489633622 495839519 756737989 23294 SRX23499416 SRS20351174 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
30562 30562 SRR27836077 SRX23499415 SRS20351173 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 mutant 3 21 dpf GSM8059033   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing rbpms2 mutant 3 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM GSM8059033 GSM8059033: rbpms2 mutant 3 21 dpf; Danio rerio; RNA Seq GSM8059033 r1 GSM8059033 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-DM_3_S7_L001_R1_001.fastq.gz rbpms2-d21-DM_3_S7_L001_R2_001.fastq.gz fastq fastq 2383569354.0 23368327.0 GSM8059033 r1 0:51 1:51 A:705650487;C:468856307;G:473479720;T:735556568;N:26272 51 51     705650487 468856307 473479720 735556568 26272 SRX23499415 SRS20351173 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
30563 30563 SRR27836078 SRX23499415 SRS20351173 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 mutant 3 21 dpf GSM8059033   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing rbpms2 mutant 3 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM GSM8059033 GSM8059033: rbpms2 mutant 3 21 dpf; Danio rerio; RNA Seq GSM8059033 r1 GSM8059033 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-DM_3_S7_L002_R1_001.fastq.gz rbpms2-d21-DM_3_S7_L002_R2_001.fastq.gz fastq fastq 2324856114.0 22792707.0 GSM8059033 r2 0:51 1:51 A:688232198;C:457346277;G:462034541;T:717221485;N:21613 51 51     688232198 457346277 462034541 717221485 21613 SRX23499415 SRS20351173 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
30564 30564 SRR27836079 SRX23499414 SRS20351172 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 mutant 1 21 dpf GSM8059032   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing rbpms2 mutant 1 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM GSM8059032 GSM8059032: rbpms2 mutant 1 21 dpf; Danio rerio; RNA Seq GSM8059032 r1 GSM8059032 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-DM_1_S5_L001_R1_001.fastq.gz rbpms2-d21-DM_1_S5_L001_R2_001.fastq.gz fastq fastq 2412458100.0 23651550.0 GSM8059032 r1 0:51 1:51 A:726246267;C:465733066;G:465377798;T:755071663;N:29306 51 51     726246267 465733066 465377798 755071663 29306 SRX23499414 SRS20351172 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
30565 30565 SRR27836080 SRX23499414 SRS20351172 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 mutant 1 21 dpf GSM8059032   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing rbpms2 mutant 1 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM GSM8059032 GSM8059032: rbpms2 mutant 1 21 dpf; Danio rerio; RNA Seq GSM8059032 r1 GSM8059032 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-DM_1_S5_L002_R1_001.fastq.gz rbpms2-d21-DM_1_S5_L002_R2_001.fastq.gz fastq fastq 2363898144.0 23175472.0 GSM8059032 r2 0:51 1:51 A:711756208;C:456236364;G:456088591;T:739792903;N:24078 51 51     711756208 456236364 456088591 739792903 24078 SRX23499414 SRS20351172 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
30566 30566 SRR27836081 SRX23499413 SRS20351171 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 wildtype 3 21 dpf GSM8059031   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing rbpms2 wildtype 3 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype GSM8059031 GSM8059031: rbpms2 wildtype 3 21 dpf; Danio rerio; RNA Seq GSM8059031 r1 GSM8059031 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-WT_3_S3_L001_R1_001.fastq.gz rbpms2-d21-WT_3_S3_L001_R2_001.fastq.gz fastq fastq 2048418162.0 20082531.0 GSM8059031 r1 0:51 1:51 A:612611264;C:409068349;G:413909657;T:612805097;N:23795 51 51     612611264 409068349 413909657 612805097 23795 SRX23499413 SRS20351171 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
30567 30567 SRR27836082 SRX23499413 SRS20351171 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 wildtype 3 21 dpf GSM8059031   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing rbpms2 wildtype 3 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype GSM8059031 GSM8059031: rbpms2 wildtype 3 21 dpf; Danio rerio; RNA Seq GSM8059031 r1 GSM8059031 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-WT_3_S3_L002_R1_001.fastq.gz rbpms2-d21-WT_3_S3_L002_R2_001.fastq.gz fastq fastq 2018915070.0 19793285.0 GSM8059031 r2 0:51 1:51 A:603776465;C:403221066;G:408169193;T:603728354;N:19992 51 51     603776465 403221066 408169193 603728354 19992 SRX23499413 SRS20351171 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
30568 30568 SRR27836083 SRX23499412 SRS20351179 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 wildtype 2 21 dpf GSM8059030   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing rbpms2 wildtype 2 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype GSM8059030 GSM8059030: rbpms2 wildtype 2 21 dpf; Danio rerio; RNA Seq GSM8059030 r1 GSM8059030 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-WT_2_S2_L001_R1_001.fastq.gz rbpms2-d21-WT_2_S2_L001_R2_001.fastq.gz fastq fastq 1927777866.0 18899783.0 GSM8059030 r1 0:51 1:51 A:589122616;C:372230241;G:374787285;T:591617780;N:19944 51 51     589122616 372230241 374787285 591617780 19944 SRX23499412 SRS20351179 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
30569 30569 SRR27836084 SRX23499412 SRS20351179 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 wildtype 2 21 dpf GSM8059030   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing rbpms2 wildtype 2 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype GSM8059030 GSM8059030: rbpms2 wildtype 2 21 dpf; Danio rerio; RNA Seq GSM8059030 r1 GSM8059030 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-WT_2_S2_L002_R1_001.fastq.gz rbpms2-d21-WT_2_S2_L002_R2_001.fastq.gz fastq fastq 1901436570.0 18641535.0 GSM8059030 r2 0:51 1:51 A:581077435;C:367152917;G:369822980;T:583366137;N:17101 51 51     581077435 367152917 369822980 583366137 17101 SRX23499412 SRS20351179 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
30570 30570 SRR27836085 SRX23499411 SRS20351170 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 wildtype 1 21 dpf GSM8059029   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing rbpms2 wildtype 1 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype GSM8059029 GSM8059029: rbpms2 wildtype 1 21 dpf; Danio rerio; RNA Seq GSM8059029 r1 GSM8059029 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-WT_1_S1_L001_R1_001.fastq.gz rbpms2-d21-WT_1_S1_L001_R2_001.fastq.gz fastq fastq 1878693222.0 18418561.0 GSM8059029 r1 0:51 1:51 A:581058368;C:356028122;G:360378733;T:581204723;N:23276 51 51     581058368 356028122 360378733 581204723 23276 SRX23499411 SRS20351170 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
30571 30571 SRR27836086 SRX23499411 SRS20351170 SRP487485 PRJNA1072072 Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios GSE254850 Transcriptome Analysis Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…   pubmed:38898112   rbpms2 wildtype 1 21 dpf GSM8059029   source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing rbpms2 wildtype 1 21 dpf Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample Gonad   RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype GSM8059029 GSM8059029: rbpms2 wildtype 1 21 dpf; Danio rerio; RNA Seq GSM8059029 r1 GSM8059029 1 RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487485   loader:fastq load.py rbpms2-d21-WT_1_S1_L002_R1_001.fastq.gz rbpms2-d21-WT_1_S1_L002_R2_001.fastq.gz fastq fastq 1861916160.0 18254080.0 GSM8059029 r2 0:51 1:51 A:575859972;C:352771580;G:357641601;T:575624138;N:18869 51 51     575859972 352771580 357641601 575624138 18869 SRX23499411 SRS20351170 SRA1796363 Marlow, CDRB, Icahn School of Medicine Mount Sinai Marlow, CDRB, Icahn School of Medicine Mount Sinai                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2024-02-01 Larval Larval Gonad Reproductive System
31721 31721 SRR28537217 SRX24137319 SRS20921922 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         ko3   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:ko biological replicate 3|BioSampleModel:Model organism or animal                 ko3 ko3 ko3 ko ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     ko3_1.fq.gz ko3_2.fq.gz fastq fastq 8310654000.0 27702180.0 ko3 1.fq.gz 0:150 1:150 A:2164758632;C:1964255570;G:1984514973;T:2197073890;N:50935 150 150     2164758632 1964255570 1984514973 2197073890 50935 SRX24137319 SRS20921922     Shenzhen Second People's Hospital 2 0.9472 0.94617 0.02506 0.02527 0.74286 0.74535 0.45316 0.45662 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
31722 31722 SRR28537218 SRX24137318 SRS20921924 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         ko2   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:ko biological replicate 2|BioSampleModel:Model organism or animal                 ko2 ko2 ko2 ko ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     ko2_1.fq.gz ko2_2.fq.gz fastq fastq 8095711800.0 26985706.0 ko2 1.fq.gz 0:150 1:150 A:2117986563;C:1909094084;G:1931885806;T:2136732639;N:12708 150 150     2117986563 1909094084 1931885806 2136732639 12708 SRX24137318 SRS20921924     Shenzhen Second People's Hospital 2 0.9483 0.94443 0.02385 0.02347 0.74266 0.74686 0.45568 0.45676 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
31723 31723 SRR28537219 SRX24137317 SRS20921925 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         ko1   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:ko biological replicate 1|BioSampleModel:Model organism or animal                 ko1 ko1 ko1 ko ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     ko1_1.fq.gz ko1_2.fq.gz fastq fastq 9904629000.0 33015430.0 ko1 1.fq.gz 0:150 1:150 A:2565332092;C:2354153391;G:2380645312;T:2604437822;N:60383 150 150     2565332092 2354153391 2380645312 2604437822 60383 SRX24137317 SRS20921925     Shenzhen Second People's Hospital 2 0.94565 0.94416 0.01943 0.01956 0.7559 0.75739 0.456 0.45903 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
31724 31724 SRR28537220 SRX24137316 SRS20921923 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         wt3   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:wt biological replicate 3|BioSampleModel:Model organism or animal                 wt3 wt3 wt3 wt ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     wt3_1.fq.gz wt3_2.fq.gz fastq fastq 10079485500.0 33598285.0 wt3 1.fq.gz 0:150 1:150 A:2607822943;C:2396994959;G:2427407078;T:2647197813;N:62707 150 150     2607822943 2396994959 2427407078 2647197813 62707 SRX24137316 SRS20921923     Shenzhen Second People's Hospital 2 0.94735 0.94594 0.01733 0.01743 0.75635 0.75712 0.44042 0.46348 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
31725 31725 SRR28537221 SRX24137315 SRS20921920 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         wt2   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:wt biological replicate 2|BioSampleModel:Model organism or animal                 wt2 wt2 wt2 wt ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     wt2_2.fq.gz wt2_1.fq.gz fastq fastq 8980086900.0 29933623.0 wt2 1.fq.gz 0:150 1:150 A:2333474507;C:2131182397;G:2149144543;T:2366230132;N:55321 150 150     2333474507 2131182397 2149144543 2366230132 55321 SRX24137315 SRS20921920     Shenzhen Second People's Hospital 2 0.94182 0.94004 0.0187 0.01854 0.75077 0.75132 0.46271 0.46384 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
31726 31726 SRR28537222 SRX24137314 SRS20921921 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         wt1   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:wt biological replicate 1|BioSampleModel:Model organism or animal                 wt1 wt1 wt1 wt ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     wt1_1.fq.gz wt1_2.fq.gz fastq fastq 5436554400.0 18121848.0 wt1 1.fq.gz 0:150 1:150 A:1418897733;C:1287256771;G:1297629578;T:1432736726;N:33592 150 150     1418897733 1287256771 1297629578 1432736726 33592 SRX24137314 SRS20921921     Shenzhen Second People's Hospital 2 0.9407 0.94657 0.02199 0.02152 0.74655 0.74679 0.47086 0.47165 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
31837 31837 SRR28709001 SRX24276192 SRS21041156 SRP502090 PRJNA1101048 Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish GSE264143 Transcriptome Analysis Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.       dpf61 Ov mt 3 GSM8212808   source name:Ovary|tissue:Ovary|age:dpf 61|genotype:mutant|geo loc name:missing|collection date:missing dpf61 Ov mt 3 Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample. Ovary   Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples. WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food. tissue:Ovary|age:dpf 61|genotype:mutant GSM8212808 GSM8212808: dpf61 Ov mt 3; Danio rerio; RNA Seq GSM8212808 r1 GSM8212808 1 Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP502090   loader:fastq load.py NS51397.M43_20230510_103430.L001.1.fastq.gz NS51397.M43_20230510_103430.L001.2.fastq.gz fastq fastq 9024444634.0 29882267.0 GSM8212808 r1 0:151 1:151 A:2471288260;C:1931225512;G:2256742565;T:2363378475;N:1809822 151 151     2471288260 1931225512 2256742565 2363378475 1809822 SRX24276192 SRS21041156 SRA1847037 Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences                       B B biological fallback assumption illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-04-16 Juvenile Juvenile Gonad Reproductive System
31838 31838 SRR28709002 SRX24276191 SRS21041154 SRP502090 PRJNA1101048 Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish GSE264143 Transcriptome Analysis Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.       dpf61 Ov mt 2 GSM8212807   source name:Ovary|tissue:Ovary|age:dpf 61|genotype:mutant|geo loc name:missing|collection date:missing dpf61 Ov mt 2 Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample. Ovary   Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples. WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food. tissue:Ovary|age:dpf 61|genotype:mutant GSM8212807 GSM8212807: dpf61 Ov mt 2; Danio rerio; RNA Seq GSM8212807 r1 GSM8212807 1 Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP502090   loader:fastq load.py NS51397.M41_20230510_103430.L001.1.fastq.gz NS51397.M41_20230510_103430.L001.2.fastq.gz fastq fastq 13553131538.0 44877919.0 GSM8212807 r1 0:151 1:151 A:3707129145;C:2878818514;G:3433054125;T:3531357698;N:2772056 151 151     3707129145 2878818514 3433054125 3531357698 2772056 SRX24276191 SRS21041154 SRA1847037 Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences                       B B biological fallback assumption illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-04-16 Juvenile Juvenile Gonad Reproductive System
31839 31839 SRR28709003 SRX24276190 SRS21041155 SRP502090 PRJNA1101048 Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish GSE264143 Transcriptome Analysis Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.       dpf61 Ov mt 1 GSM8212806   source name:Ovary|tissue:Ovary|age:dpf 61|genotype:mutant|geo loc name:missing|collection date:missing dpf61 Ov mt 1 Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample. Ovary   Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples. WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food. tissue:Ovary|age:dpf 61|genotype:mutant GSM8212806 GSM8212806: dpf61 Ov mt 1; Danio rerio; RNA Seq GSM8212806 r1 GSM8212806 1 Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP502090   loader:fastq load.py NS51397.M32_20230510_103430.L001.1.fastq.gz NS51397.M32_20230510_103430.L001.2.fastq.gz fastq fastq 11752803234.0 38916567.0 GSM8212806 r1 0:151 1:151 A:3199511211;C:2525248103;G:2947698766;T:3077964367;N:2380787 151 151     3199511211 2525248103 2947698766 3077964367 2380787 SRX24276190 SRS21041155 SRA1847037 Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences                       B B biological fallback assumption illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-04-16 Juvenile Juvenile Gonad Reproductive System
31840 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 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 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 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 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 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 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 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 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
33631 33631 SRR30329352 SRX25789588 SRS22421035 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo27 fish4 rep2 GSM8475571   source name:Testis|tissue:Testis|age:27 month|geo loc name:missing|collection date:missing mo27 fish4 rep2 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:27 month GSM8475571 GSM8475571: mo27 fish4 rep2; Danio rerio; RNA Seq GSM8475571 r1 GSM8475571 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 23822X4_20240226_LH00227_0052_A22HJWLLT3_S8_L003_I1_001.fastq.gz 23822X4_20240226_LH00227_0052_A22HJWLLT3_S8_L003_I2_001.fastq.gz 23822X4_20240226_LH00227_0052_A22HJWLLT3_S8_L003_R1_001.fastq.gz 23822X4_20240226_LH00227_0052_A22HJWLLT3_S8_L003_R2_001.fastq.gz fastq fastq fastq fastq 62332746910.0 328067089.0 GSM8475571 r1 0:6 1:6 2:28 3:150 A:14114753316;C:10050790836;G:11058814166;T:13983250670;N:2454362 6 6 28 150 14114753316 10050790836 11058814166 13983250670 2454362 SRX25789588 SRS22421035 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.854   0.31359   0.74659   0.69085   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33632 33632 SRR30329353 SRX25789587 SRS22421034 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo27 fish4 rep1 GSM8475570   source name:Testis|tissue:Testis|age:27 month|geo loc name:missing|collection date:missing mo27 fish4 rep1 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:27 month GSM8475570 GSM8475570: mo27 fish4 rep1; Danio rerio; RNA Seq GSM8475570 r1 GSM8475570 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 23822X3_20240226_LH00227_0052_A22HJWLLT3_S7_L003_I1_001.fastq.gz 23822X3_20240226_LH00227_0052_A22HJWLLT3_S7_L003_I2_001.fastq.gz 23822X3_20240226_LH00227_0052_A22HJWLLT3_S7_L003_R1_001.fastq.gz 23822X3_20240226_LH00227_0052_A22HJWLLT3_S7_L003_R2_001.fastq.gz fastq fastq fastq fastq 68435798090.0 360188411.0 GSM8475570 r1 0:6 1:6 2:28 3:150 A:15473213482;C:11152077954;G:12263658125;T:15136431378;N:2880711 6 6 28 150 15473213482 11152077954 12263658125 15136431378 2880711 SRX25789587 SRS22421034 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.85213   0.30845   0.7543   0.68115   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33633 33633 SRR30329354 SRX25789586 SRS22421033 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo27 fish3 rep2 GSM8475569   source name:Testis|tissue:Testis|age:27 month|geo loc name:missing|collection date:missing mo27 fish3 rep2 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:27 month GSM8475569 GSM8475569: mo27 fish3 rep2; Danio rerio; RNA Seq GSM8475569 r1 GSM8475569 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 23822X2_20240226_LH00227_0052_A22HJWLLT3_S6_L003_R2_001.fastq.gz 23822X2_20240226_LH00227_0052_A22HJWLLT3_S6_L003_R1_001.fastq.gz 23822X2_20240226_LH00227_0052_A22HJWLLT3_S6_L003_I2_001.fastq.gz 23822X2_20240226_LH00227_0052_A22HJWLLT3_S6_L003_I1_001.fastq.gz fastq fastq fastq fastq 47201245520.0 248427608.0 GSM8475569 r1 0:6 1:6 2:28 3:150 A:10398745837;C:7966730578;G:8916412008;T:9980276803;N:1975974 6 6 28 150 10398745837 7966730578 8916412008 9980276803 1975974 SRX25789586 SRS22421033 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.87941   0.25226   0.76045   0.55073   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33634 33634 SRR30329357 SRX25789585 SRS22421029 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo27 fish3 rep1 GSM8475568   source name:Testis|tissue:Testis|age:27 month|geo loc name:missing|collection date:missing mo27 fish3 rep1 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:27 month GSM8475568 GSM8475568: mo27 fish3 rep1; Danio rerio; RNA Seq GSM8475568 r1 GSM8475568 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 23822X1_20240226_LH00227_0052_A22HJWLLT3_S5_L003_R2_001.fastq.gz 23822X1_20240226_LH00227_0052_A22HJWLLT3_S5_L003_R1_001.fastq.gz 23822X1_20240226_LH00227_0052_A22HJWLLT3_S5_L003_I2_001.fastq.gz 23822X1_20240226_LH00227_0052_A22HJWLLT3_S5_L003_I1_001.fastq.gz fastq fastq fastq fastq 50530978990.0 265952521.0 GSM8475568 r1 0:6 1:6 2:28 3:150 A:10826041411;C:8852230501;G:9916508585;T:10296022501;N:2075152 6 6 28 150 10826041411 8852230501 9916508585 10296022501 2075152 SRX25789585 SRS22421029 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.89468   0.23873   0.76688   0.66783   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33635 33635 SRR30329355 SRX25789584 SRS22421032 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo27 fish2 rep1 GSM8475567   source name:Testis|tissue:Testis|age:27 month|geo loc name:missing|collection date:missing mo27 fish2 rep1 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:27 month GSM8475567 GSM8475567: mo27 fish2 rep1; Danio rerio; RNA Seq GSM8475567 r1 GSM8475567 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 19226X4_211001_A00421_0374_BHMGTFDSX2_S4_L004_I1_001.fastq.gz 19226X4_211001_A00421_0374_BHMGTFDSX2_S4_L004_I2_001.fastq.gz 19226X4_211001_A00421_0374_BHMGTFDSX2_S4_L004_R1_001.fastq.gz 19226X4_211001_A00421_0374_BHMGTFDSX2_S4_L004_R2_001.fastq.gz fastq fastq fastq fastq 61159613328.0 308886936.0 GSM8475567 r1 0:10 1:10 2:28 3:150 A:13534358992;C:9743134047;G:11041233192;T:12013610107;N:704062 10 10 28 150 13534358992 9743134047 11041233192 12013610107 704062 SRX25789584 SRS22421032 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.89529   0.10879   0.74671   0.53003   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33636 33636 SRR30329356 SRX25789583 SRS22421031 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo27 fish1 rep1 GSM8475566   source name:Testis|tissue:Testis|age:27 month|geo loc name:missing|collection date:missing mo27 fish1 rep1 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:27 month GSM8475566 GSM8475566: mo27 fish1 rep1; Danio rerio; RNA Seq GSM8475566 r1 GSM8475566 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 19226X3_211001_A00421_0374_BHMGTFDSX2_S3_L004_R2_001.fastq.gz 19226X3_211001_A00421_0374_BHMGTFDSX2_S3_L004_R1_001.fastq.gz 19226X3_211001_A00421_0374_BHMGTFDSX2_S3_L004_I2_001.fastq.gz 19226X3_211001_A00421_0374_BHMGTFDSX2_S3_L004_I1_001.fastq.gz fastq fastq fastq fastq 81122109948.0 409707626.0 GSM8475566 r1 0:10 1:10 2:28 3:150 A:18515219377;C:12708263135;G:14580444363;T:15651262388;N:954637 10 10 28 150 18515219377 12708263135 14580444363 15651262388 954637 SRX25789583 SRS22421031 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.88948   0.1044   0.77571   0.55175   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33637 33637 SRR30329358 SRX25789582 SRS22421030 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo22 fish1 rep2 GSM8475565   source name:Testis|tissue:Testis|age:22 month|geo loc name:missing|collection date:missing mo22 fish1 rep2 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:22 month GSM8475565 GSM8475565: mo22 fish1 rep2; Danio rerio; RNA Seq GSM8475565 r1 GSM8475565 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 18827X3_210414_A00421_0315_BH225KDSX2_S3_L004_I1_001.fastq.gz 18827X3_210414_A00421_0315_BH225KDSX2_S3_L004_I2_001.fastq.gz 18827X3_210414_A00421_0315_BH225KDSX2_S3_L004_R1_001.fastq.gz 18827X3_210414_A00421_0315_BH225KDSX2_S3_L004_R2_001.fastq.gz fastq fastq fastq fastq 71619246666.0 361713367.0 GSM8475565 r1 0:10 1:10 2:28 3:150 A:16269086558;C:11392726801;G:12707460817;T:13887610399;N:120475 10 10 28 150 16269086558 11392726801 12707460817 13887610399 120475 SRX25789582 SRS22421030 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.91983   0.15397   0.72354   0.51746   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33638 33638 SRR30329359 SRX25789581 SRS22421026 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo22 fish1 rep1 GSM8475564   source name:Testis|tissue:Testis|age:22 month|geo loc name:missing|collection date:missing mo22 fish1 rep1 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:22 month GSM8475564 GSM8475564: mo22 fish1 rep1; Danio rerio; RNA Seq GSM8475564 r1 GSM8475564 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 18827X1_210414_A00421_0315_BH225KDSX2_S1_L004_R2_001.fastq.gz 18827X1_210414_A00421_0315_BH225KDSX2_S1_L004_R1_001.fastq.gz 18827X1_210414_A00421_0315_BH225KDSX2_S1_L004_I2_001.fastq.gz 18827X1_210414_A00421_0315_BH225KDSX2_S1_L004_I1_001.fastq.gz fastq fastq fastq fastq 75353487858.0 380573171.0 GSM8475564 r1 0:10 1:10 2:28 3:150 A:17277856526;C:11721380902;G:13064732269;T:15021876455;N:129498 10 10 28 150 17277856526 11721380902 13064732269 15021876455 129498 SRX25789581 SRS22421026 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.91525   0.16024   0.71526   0.51211   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33639 33639 SRR30329362 SRX25789580 SRS22421025 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo20 fish1 rep2 GSM8475563   source name:Testis|tissue:Testis|age:20 month|geo loc name:missing|collection date:missing mo20 fish1 rep2 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:20 month GSM8475563 GSM8475563: mo20 fish1 rep2; Danio rerio; RNA Seq GSM8475563 r1 GSM8475563 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 18827X4_210414_A00421_0315_BH225KDSX2_S4_L004_I1_001.fastq.gz 18827X4_210414_A00421_0315_BH225KDSX2_S4_L004_I2_001.fastq.gz 18827X4_210414_A00421_0315_BH225KDSX2_S4_L004_R1_001.fastq.gz 18827X4_210414_A00421_0315_BH225KDSX2_S4_L004_R2_001.fastq.gz fastq fastq fastq fastq 66564197766.0 336182817.0 GSM8475563 r1 0:10 1:10 2:28 3:150 A:15385982034;C:10396224096;G:11708098438;T:12937004162;N:113820 10 10 28 150 15385982034 10396224096 11708098438 12937004162 113820 SRX25789580 SRS22421025 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.90394   0.15438   0.73888   0.52949   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33640 33640 SRR30329360 SRX25789579 SRS22421023 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo20 fish1 rep1 GSM8475562   source name:Testis|tissue:Testis|age:20 month|geo loc name:missing|collection date:missing mo20 fish1 rep1 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:20 month GSM8475562 GSM8475562: mo20 fish1 rep1; Danio rerio; RNA Seq GSM8475562 r1 GSM8475562 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 18827X2_210414_A00421_0315_BH225KDSX2_S2_L004_R2_001.fastq.gz 18827X2_210414_A00421_0315_BH225KDSX2_S2_L004_R1_001.fastq.gz 18827X2_210414_A00421_0315_BH225KDSX2_S2_L004_I2_001.fastq.gz 18827X2_210414_A00421_0315_BH225KDSX2_S2_L004_I1_001.fastq.gz fastq fastq fastq fastq 76196757582.0 384832109.0 GSM8475562 r1 0:10 1:10 2:28 3:150 A:17603147649;C:11925253793;G:13442889985;T:14753395348;N:129575 10 10 28 150 17603147649 11925253793 13442889985 14753395348 129575 SRX25789579 SRS22421023 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.90462   0.14351   0.74513   0.52838   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33641 33641 SRR30329361 SRX25789578 SRS22421027 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo12 fish2 rep1 GSM8475561   source name:Testis|tissue:Testis|age:12 month|geo loc name:missing|collection date:missing mo12 fish2 rep1 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:12 month GSM8475561 GSM8475561: mo12 fish2 rep1; Danio rerio; RNA Seq GSM8475561 r1 GSM8475561 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 15756X4_S4_L001_I1_001.fastq.gz 15756X4_S4_L001_R1_001.fastq.gz 15756X4_S4_L001_R2_001.fastq.gz fastq fastq fastq 29487024682.0 220052423.0 GSM8475561 r1 0:8 1:26 2:100 A:6603266449;C:4452149795;G:4932656681;T:6015543518;N:1625857 8 26 100   6603266449 4452149795 4932656681 6015543518 1625857 SRX25789578 SRS22421027 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.923   0.08981   0.74446   0.49211   100   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33642 33642 SRR30329363 SRX25789577 SRS22421019 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo12 fish1 rep1 GSM8475560   source name:Testis|tissue:Testis|age:12 month|geo loc name:missing|collection date:missing mo12 fish1 rep1 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:12 month GSM8475560 GSM8475560: mo12 fish1 rep1; Danio rerio; RNA Seq GSM8475560 r1 GSM8475560 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 15756X3_S3_L001_R2_001.fastq.gz 15756X3_S3_L001_R1_001.fastq.gz 15756X3_S3_L001_I1_001.fastq.gz fastq fastq fastq 24877403778.0 185652267.0 GSM8475560 r1 0:8 1:26 2:100 A:5596266137;C:3743379083;G:4132198708;T:5092012085;N:1370687 8 26 100   5596266137 3743379083 4132198708 5092012085 1370687 SRX25789577 SRS22421019 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.92275   0.09038   0.74572   0.48557   100   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33643 33643 SRR30329364 SRX25789576 SRS22421017 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo5 fish2 rep3 GSM8475559   source name:Testis|tissue:Testis|age:5 month|geo loc name:missing|collection date:missing mo5 fish2 rep3 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:5 month GSM8475559 GSM8475559: mo5 fish2 rep3; Danio rerio; RNA Seq GSM8475559 r1 GSM8475559 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 19779X6_220608_A00421_0445_BHVGF7DSX3_S7_L003_R2_001.fastq.gz 19779X6_220608_A00421_0445_BHVGF7DSX3_S7_L003_R1_001.fastq.gz 19779X6_220608_A00421_0445_BHVGF7DSX3_S7_L003_I2_001.fastq.gz 19779X6_220608_A00421_0445_BHVGF7DSX3_S7_L003_I1_001.fastq.gz fastq fastq fastq fastq 68519376288.0 346057456.0 GSM8475559 r1 0:10 1:10 2:28 3:150 A:15372037903;C:10806459023;G:12028186552;T:13701892692;N:42230 10 10 28 150 15372037903 10806459023 12028186552 13701892692 42230 SRX25789576 SRS22421017 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.93821   0.18284   0.70709   0.49769   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33644 33644 SRR30329367 SRX25789575 SRS22421028 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo5 fish2 rep2 GSM8475558   source name:Testis|tissue:Testis|age:5 month|geo loc name:missing|collection date:missing mo5 fish2 rep2 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:5 month GSM8475558 GSM8475558: mo5 fish2 rep2; Danio rerio; RNA Seq GSM8475558 r1 GSM8475558 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 19779X5_220608_A00421_0445_BHVGF7DSX3_S6_L003_I1_001.fastq.gz 19779X5_220608_A00421_0445_BHVGF7DSX3_S6_L003_I2_001.fastq.gz 19779X5_220608_A00421_0445_BHVGF7DSX3_S6_L003_R1_001.fastq.gz 19779X5_220608_A00421_0445_BHVGF7DSX3_S6_L003_R2_001.fastq.gz fastq fastq fastq fastq 67592651346.0 341377027.0 GSM8475558 r1 0:10 1:10 2:28 3:150 A:15408420726;C:10264745865;G:11496692817;T:14036653315;N:41327 10 10 28 150 15408420726 10264745865 11496692817 14036653315 41327 SRX25789575 SRS22421028 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.93225   0.20483   0.70475   0.49687   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33645 33645 SRR30329365 SRX25789574 SRS22421024 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo5 fish2 rep1 GSM8475557   source name:Testis|tissue:Testis|age:5 month|geo loc name:missing|collection date:missing mo5 fish2 rep1 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:5 month GSM8475557 GSM8475557: mo5 fish2 rep1; Danio rerio; RNA Seq GSM8475557 r1 GSM8475557 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 19779X4_220608_A00421_0445_BHVGF7DSX3_S5_L003_I1_001.fastq.gz 19779X4_220608_A00421_0445_BHVGF7DSX3_S5_L003_I2_001.fastq.gz 19779X4_220608_A00421_0445_BHVGF7DSX3_S5_L003_R1_001.fastq.gz 19779X4_220608_A00421_0445_BHVGF7DSX3_S5_L003_R2_001.fastq.gz fastq fastq fastq fastq 82593431316.0 417138542.0 GSM8475557 r1 0:10 1:10 2:28 3:150 A:18738302033;C:12676748417;G:14156436045;T:16999244279;N:50526 10 10 28 150 18738302033 12676748417 14156436045 16999244279 50526 SRX25789574 SRS22421024 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.93364   0.20357   0.70307   0.4898   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33646 33646 SRR30329366 SRX25789573 SRS22421016 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo5 fish1 rep3 GSM8475556   source name:Testis|tissue:Testis|age:5 month|geo loc name:missing|collection date:missing mo5 fish1 rep3 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:5 month GSM8475556 GSM8475556: mo5 fish1 rep3; Danio rerio; RNA Seq GSM8475556 r1 GSM8475556 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 19779X3_220608_A00421_0445_BHVGF7DSX3_S4_L003_R2_001.fastq.gz 19779X3_220608_A00421_0445_BHVGF7DSX3_S4_L003_R1_001.fastq.gz 19779X3_220608_A00421_0445_BHVGF7DSX3_S4_L003_I2_001.fastq.gz 19779X3_220608_A00421_0445_BHVGF7DSX3_S4_L003_I1_001.fastq.gz fastq fastq fastq fastq 73957673592.0 373523604.0 GSM8475556 r1 0:10 1:10 2:28 3:150 A:16641674848;C:11574088141;G:12922095601;T:14890636198;N:45812 10 10 28 150 16641674848 11574088141 12922095601 14890636198 45812 SRX25789573 SRS22421016 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.92791   0.20924   0.70427   0.51976   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33647 33647 SRR30329368 SRX25789572 SRS22421014 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo5 fish1 rep2 GSM8475555   source name:Testis|tissue:Testis|age:5 month|geo loc name:missing|collection date:missing mo5 fish1 rep2 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:5 month GSM8475555 GSM8475555: mo5 fish1 rep2; Danio rerio; RNA Seq GSM8475555 r1 GSM8475555 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 19779X2_220608_A00421_0445_BHVGF7DSX3_S3_L003_R2_001.fastq.gz 19779X2_220608_A00421_0445_BHVGF7DSX3_S3_L003_R1_001.fastq.gz 19779X2_220608_A00421_0445_BHVGF7DSX3_S3_L003_I2_001.fastq.gz 19779X2_220608_A00421_0445_BHVGF7DSX3_S3_L003_I1_001.fastq.gz fastq fastq fastq fastq 81431066970.0 411268015.0 GSM8475555 r1 0:10 1:10 2:28 3:150 A:18341504843;C:12608734527;G:14017359094;T:16722553528;N:50258 10 10 28 150 18341504843 12608734527 14017359094 16722553528 50258 SRX25789572 SRS22421014 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.93012   0.2152   0.70007   0.51331   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33648 33648 SRR30329369 SRX25789571 SRS22421015 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo5 fish1 rep1 GSM8475554   source name:Testis|tissue:Testis|age:5 month|geo loc name:missing|collection date:missing mo5 fish1 rep1 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:5 month GSM8475554 GSM8475554: mo5 fish1 rep1; Danio rerio; RNA Seq GSM8475554 r1 GSM8475554 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 19779X1_220608_A00421_0445_BHVGF7DSX3_S2_L003_R2_001.fastq.gz 19779X1_220608_A00421_0445_BHVGF7DSX3_S2_L003_R1_001.fastq.gz 19779X1_220608_A00421_0445_BHVGF7DSX3_S2_L003_I2_001.fastq.gz 19779X1_220608_A00421_0445_BHVGF7DSX3_S2_L003_I1_001.fastq.gz fastq fastq fastq fastq 76667132916.0 387207742.0 GSM8475554 r1 0:10 1:10 2:28 3:150 A:17411509978;C:12112655410;G:13713621582;T:14843326531;N:47799 10 10 28 150 17411509978 12112655410 13713621582 14843326531 47799 SRX25789571 SRS22421015 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.92205   0.21455   0.69952   0.51581   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33663 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 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 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 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 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 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 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 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

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