rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
50,DRR029944,DRX026962,DRS086502,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,ovulation duirng natural paring,zebrafish ovary isolated from adult fish at ovulation duirng natural paring. [RNAseq],SAMD00025434,,sample name:6 Ovu|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025434,DRX026962,6 Ovu,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025434,,,,351766656.0,9771296.0,DRR029944,0:36,A:79811727;C:85391142;G:90185809;T:96371771;N:6207,36,,,,79811727,85391142,90185809,96371771,6207,DRX026962,DRS086502,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91956,,0.01686,,0.76637,,0.45997,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
52,DRR029942,DRX026960,DRS086500,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo testosterone treatment,zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq  replicate],SAMD00025432,,sample name:4 Tes rep|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025432,DRX026960,4 Tes rep,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025432,,,,366042528.0,10167848.0,DRR029942,0:36,A:84988522;C:88640326;G:93559022;T:98847003;N:7655,36,,,,84988522,88640326,93559022,98847003,7655,DRX026960,DRS086500,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91602,,0.01846,,0.76015,,0.46475,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
53,DRR029941,DRX026959,DRS086499,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo testosterone treatment,zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq],SAMD00025431,,sample name:4 Tes|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025431,DRX026959,4 Tes,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025431,,,,1269835992.0,35273222.0,DRR029941,0:36,A:275250658;C:323605136;G:316729009;T:354204170;N:47019,36,,,,275250658,323605136,316729009,354204170,47019,DRX026959,DRS086499,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91467,,0.02353,,0.75962,,0.46861,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
54,DRR029940,DRX026958,DRS086498,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo diethylstilbestrol DES treatment,zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq  replicate],SAMD00025430,,sample name:3 DES rep|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025430,DRX026958,3 DES rep,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025430,,,,658651536.0,18295876.0,DRR029940,,,,,,,,,,,,DRX026958,DRS086498,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.89964,,0.01785,,0.76451,,0.45872,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
55,DRR029939,DRX026957,DRS086497,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo diethylstilbestrol DES treatment,zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq],SAMD00025429,,sample name:3 DES|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025429,DRX026957,3 DES,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025429,,,,1202024016.0,33389556.0,DRR029939,0:36,A:263319430;C:305852921;G:298798093;T:334008544;N:45028,36,,,,263319430,305852921,298798093,334008544,45028,DRX026957,DRS086497,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.90643,,0.02337,,0.75008,,0.47587,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
56,DRR029938,DRX026956,DRS086496,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo maturation inducing hormone DHP treatment,zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq  replicate],SAMD00025428,,sample name:2 DHP rep|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025428,DRX026956,2 DHP rep,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025428,,,,434243088.0,12062308.0,DRR029938,0:36,A:99859342;C:105890785;G:110526688;T:117957580;N:8693,36,,,,99859342,105890785,110526688,117957580,8693,DRX026956,DRS086496,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91529,,0.02061,,0.7595,,0.45809,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
57,DRR029937,DRX026955,DRS086495,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo maturation inducing hormone DHP treatment,zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq],SAMD00025427,,sample name:2 DHP|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025427,DRX026955,2 DHP,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025427,,,,1463868972.0,40663027.0,DRR029937,0:36,A:316060780;C:369221844;G:372845502;T:405685804;N:55042,36,,,,316060780,369221844,372845502,405685804,55042,DRX026955,DRS086495,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91556,,0.01967,,0.76621,,0.46541,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
58,DRR029936,DRX026954,DRS086494,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo ethanol treatment,zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq  replicate],SAMD00025426,,sample name:1 EtOH rep|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025426,DRX026954,1 EtOH rep,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025426,,,,438020208.0,12167228.0,DRR029936,0:36,A:101672612;C:105602774;G:110120652;T:120615069;N:9101,36,,,,101672612,105602774,110120652,120615069,9101,DRX026954,DRS086494,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.90777,,0.01929,,0.7652,,0.45988,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
59,DRR029935,DRX026953,DRS086493,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo ethanol treatment,zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq],SAMD00025425,,sample name:1 EtOH|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025425,DRX026953,1 EtOH,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025425,,,,1365603372.0,37933427.0,DRR029935,0:36,A:299786286;C:345487829;G:342408447;T:377870789;N:50021,36,,,,299786286,345487829,342408447,377870789,50021,DRX026953,DRS086493,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91103,,0.02142,,0.75402,,0.46574,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
174,DRR084198,DRX078029,DRS086523,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo testosterone treatment,zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq  replicate2],SAMD00073605,,sample name:TES1 4th|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073605,DRX078029,zebrafish ovary isolated from adult fish in vivo testosterone treatment. [RNAseq  replicate2],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,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>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073605,,,,1382763132.0,38410087.0,DRR084198,0:36,A:314367195;C:333340483;G:353519828;T:378654329;N:2881297,36,,,,314367195,333340483,353519828,378654329,2881297,DRX078029,DRS086523,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.90366,,0.02033,,0.77104,,0.46543,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
176,DRR084196,DRX078027,DRS086521,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo ethanol treatment,zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq  replicate2],SAMD00073603,,sample name:Et 4th|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073603,DRX078027,zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq  replicate2],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,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>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073603,,,,1456791660.0,40466435.0,DRR084196,0:36,A:336533534;C:355126203;G:368021063;T:394179246;N:2931614,36,,,,336533534,355126203,368021063,394179246,2931614,DRX078027,DRS086521,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.89408,,0.02082,,0.77027,,0.45866,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
177,DRR084195,DRX078026,DRS086520,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,natural paring late sample,zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq  replicate2],SAMD00073602,,sample name:O 4th|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073602,DRX078026,zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq  replicate2],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,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>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073602,,,,1627945092.0,45220697.0,DRR084195,0:36,A:381205209;C:392853175;G:410714269;T:439790560;N:3381879,36,,,,381205209,392853175,410714269,439790560,3381879,DRX078026,DRS086520,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.89419,,0.02159,,0.76848,,0.46407,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
178,DRR084194,DRX078025,DRS086519,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo maturation inducing hormone DHP treatment,zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq  replicate2],SAMD00073601,,sample name:DHP 4th|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073601,DRX078025,zebrafish ovary isolated from adult fish in vivo maturation inducing hormone DHP treatment. [RNAseq  replicate2],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,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>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073601,,,,969680196.0,26935561.0,DRR084194,0:36,A:223558856;C:233793515;G:244712298;T:265549055;N:2066472,36,,,,223558856,233793515,244712298,265549055,2066472,DRX078025,DRS086519,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.90178,,0.02203,,0.76579,,0.46491,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
179,DRR084193,DRX078024,DRS086518,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo diethylstilbestrol DES treatment,zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq  replicate2],SAMD00073600,,sample name:DES 4th|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073600,DRX078024,zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq  replicate2],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,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>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073600,,,,825301296.0,22925036.0,DRR084193,0:36,A:189771874;C:198593952;G:209666041;T:225480165;N:1789264,36,,,,189771874,198593952,209666041,225480165,1789264,DRX078024,DRS086518,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.90036,,0.0197,,0.7721,,0.45773,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
180,DRR084192,DRX078023,DRS086517,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,natural paring late sample,zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq  replicate1],SAMD00073599,,sample name:O|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073599,DRX078023,zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq  replicate1],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,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>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073599,,,,1474870356.0,40968621.0,DRR084192,0:36,A:334130826;C:361572335;G:369758908;T:409173431;N:234856,36,,,,334130826,361572335,369758908,409173431,234856,DRX078023,DRS086517,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91516,,0.02086,,0.76792,,0.47914,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
182,DRR084190,DRX078021,DRS086515,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo maturation inducing hormone DHP treatment,zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq  replicate1],SAMD00073597,,sample name:DHP|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073597,DRX078021,zebrafish ovary isolated from adult fish in vivo maturation inducing hormone DHP treatment. [RNAseq  replicate1],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,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>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073597,,,,1527194556.0,42422071.0,DRR084190,0:36,A:352068936;C:371030475;G:383086948;T:420761508;N:246689,36,,,,352068936,371030475,383086948,420761508,246689,DRX078021,DRS086515,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91815,,0.02248,,0.76209,,0.46867,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
183,DRR084189,DRX078020,DRS086514,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo testosterone treatment,zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq  replicate1],SAMD00073596,,sample name:TES|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073596,DRX078020,zebrafish ovary isolated from adult fish in vivo testosterone treatment. [RNAseq  replicate1],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,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>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073596,,,,1403618796.0,38989411.0,DRR084189,0:36,A:321063874;C:342718133;G:352434647;T:387171455;N:230687,36,,,,321063874,342718133,352434647,387171455,230687,DRX078020,DRS086514,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91583,,0.02212,,0.76073,,0.47596,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
184,DRR084188,DRX078019,DRS086513,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo diethylstilbestrol DES treatment,zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq  replicate1],SAMD00073595,,sample name:DES|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073595,DRX078019,zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq  replicate1],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,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>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073595,,,,1532053512.0,42557042.0,DRR084188,0:36,A:342701220;C:372650449;G:392432461;T:424025702;N:243680,36,,,,342701220,372650449,392432461,424025702,243680,DRX078019,DRS086513,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91276,,0.01965,,0.77358,,0.46461,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
185,DRR084187,DRX078018,DRS086512,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo ethanol treatment,zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq  replicate1],SAMD00073594,,sample name:EtOH|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073594,DRX078018,zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq  replicate1],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,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>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073594,,,,1152032724.0,32000909.0,DRR084187,0:36,A:265166034;C:279617628;G:285136940;T:321928656;N:183466,36,,,,265166034,279617628,285136940,321928656,183466,DRX078018,DRS086512,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.90791,,0.02405,,0.75972,,0.48931,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
5793,ERR1955208,ERX2020800,ERS1697077,ERP017053,PRJEB15333,Transposon driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution,ena-STUDY-EMBL EUROPEAN BIOINFORMATICS INSTITUTE-07-09-2016-10:25:55:499-247,Other,In order to better understand the features associated with male germline transcription we profiled the RNA expression in a number of germline cell types. These include spermatogonial stem cells  spermatocytes and round spermatids in mouse and spermatocytes in rat. We also profiled the transcription in zebrafish testes. As a consequence it became apparent that transposable elements are driving considerable lncRNA expression in the later stages of spermatogenesis. This is particularly apparent in the case of endogenous retroviruses in rodents.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 05 08,,,Transcriptional profiling of zebrafish testes for analysis of conserved repeat element associations,SAMEA104033184,EMBL EUROPEAN BIOINFORMATICS INSTITUTE,ENA FIRST PUBLIC:2017 05 10T17:01:28Z|ENA LAST UPDATE:2017 04 28T10:34:37Z|External Id:SAMEA104033184|INSDC center name:EMBL EUROPEAN BIOINFORMATICS INSTITUTE|INSDC first public:2017 05 10T17:01:28Z|INSDC last update:2017 04 28T10:34:37Z|INSDC status:public|Submitter Id:Zebrafish.Testis 2|common name:zebrafish|sample name:Zebrafish.Testis 2|scientific name:Danio rerio|strain:AB|tissue type:testis,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 16,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP017053,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 05 10|ENA LAST UPDATE:2018 11 16,zebrafish_testis_2.conserved.1.fastq.gz zebrafish_testis_2.conserved.2.fastq.gz,fastq fastq,46555372886.0,230472143.0,ena RUN EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 16,0:101 1:101,A:12260062264;C:10888457642;G:11605642683;T:11637267744;N:163942553,101,101,,,12260062264,10888457642,11605642683,11637267744,163942553,ERX2020800,ERS1697077,ERA904389,EMBL EUROPEAN BIOINFORMATICS INSTITUTE|European Nucleotide Archive,EMBL EUROPEAN BIOINFORMATICS INSTITUTE,2,0.93165,0.92785,0.29822,0.32141,0.71386,0.71971,0.66173,0.63843,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2017-01-31,Undetermined,Undetermined,Gonad,Reproductive System
5794,ERR1955207,ERX2020799,ERS1697076,ERP017053,PRJEB15333,Transposon driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution,ena-STUDY-EMBL EUROPEAN BIOINFORMATICS INSTITUTE-07-09-2016-10:25:55:499-247,Other,In order to better understand the features associated with male germline transcription we profiled the RNA expression in a number of germline cell types. These include spermatogonial stem cells  spermatocytes and round spermatids in mouse and spermatocytes in rat. We also profiled the transcription in zebrafish testes. As a consequence it became apparent that transposable elements are driving considerable lncRNA expression in the later stages of spermatogenesis. This is particularly apparent in the case of endogenous retroviruses in rodents.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 05 08,,,Transcriptional profiling of zebrafish testes for analysis of conserved repeat element associations,SAMEA104033183,EMBL EUROPEAN BIOINFORMATICS INSTITUTE,ENA FIRST PUBLIC:2017 05 10T17:01:28Z|ENA LAST UPDATE:2017 04 28T10:34:37Z|External Id:SAMEA104033183|INSDC center name:EMBL EUROPEAN BIOINFORMATICS INSTITUTE|INSDC first public:2017 05 10T17:01:28Z|INSDC last update:2017 04 28T10:34:37Z|INSDC status:public|Submitter Id:Zebrafish.Testis 1|common name:zebrafish|sample name:Zebrafish.Testis 1|scientific name:Danio rerio|strain:AB|tissue type:testis,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 15,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP017053,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 05 10|ENA LAST UPDATE:2018 11 16,zebrafish_testis_1.conserved.1.fastq.gz zebrafish_testis_1.conserved.2.fastq.gz,fastq fastq,41056086708.0,203247954.0,ena RUN EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 15,0:101 1:101,A:10675591750;C:9672762387;G:10139834713;T:10380949257;N:186948601,101,101,,,10675591750,9672762387,10139834713,10380949257,186948601,ERX2020799,ERS1697076,ERA904389,EMBL EUROPEAN BIOINFORMATICS INSTITUTE|European Nucleotide Archive,EMBL EUROPEAN BIOINFORMATICS INSTITUTE,2,0.92308,0.9157,0.30221,0.31293,0.68276,0.68836,0.56114,0.5857,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2017-01-31,Undetermined,Undetermined,Gonad,Reproductive System
7949,ERR015566,ERX005931,ERS000090,ERP000263,PRJEB2208,Zebrafish gene three prime end pull down for genome annotation,E-MTAB-308,Transcriptome Analysis,,,,,ZF ovary sample1,SAMEA708832,Wellcome Sanger Institute,Alias:ZF ovary sample1|Description:RNA extracted from adult zebrafish ovary|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:24:37Z|INSDC status:public|SRA accession:ERS000090|Sample Name:ERS000090|Sex:female|Strain:Tuebingen|Title:Danio rerio,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Zebrafish gene 3 prime end pull down for genome annotation,E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish ovary dpf three prime pull down paired end 250 to 300 bp insert,Zebrafish adult ovary mRNA three prime end,Zebrafish gene three prime end pull down for genome annotation,20 ug of total RNA was fragmented using RNA Fragmentation Reagent Ambion for 5 minutes at 70 C and ethanol precipitated with glycogen and LiCl.   RNA was annealed to the oligo stBPM1polyT22 biotin GGCCAGTCCTGGAGTTTTTTTTTTTTTTTTTTTTTTVN and bound to streptavidin  magnetic beads.   post washing by pull down on a magnet  the bound RNA was reverse transcribed with SuperScript II Invitrogen and a second strand synthesised with DNA polymerase I Promega and RNase H NEB.   post further washing  the double strand cDNA was released from the beads with BpmI NEB.   The cDNA was recovered with the QIAgen PCR Purification Kit and made into a standard Illumina library following the manufacturer's protocol with a fragment size of 250 to 300 bp.,Experimental Factor: DEVELOPMENTAL STAGE:adult|Experimental Factor: ORGANISM PART:ovary|Experimental Factor: SEX:female,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000263,Illumina Genome Analyzer II paired end sequencing; Zebrafish gene three prime end pull down for genome annotation,ENA FIRST PUBLIC:2010 08 19|ENA LAST UPDATE:2018 11 16,3444_6.srf,srf,1150193272.0,7567061.0,E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish ovary dpf three prime pull down paired end 250 to 300 bp insert,0:76 1:76,A:280621121;C:291623460;G:285422205;T:273609496;N:18916990,76,76,,,280621121,291623460,285422205,273609496,18916990,ERX005931,ERS000090,ERA010603,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.96663,0.96605,0.0126,0.01249,0.82272,0.82548,0.45602,0.45286,76,76,B,B,biological fallback assumption,illumina,early_illumina,3prime,other,unknown,bulk,unknown,unknown,,United Kingdom,2010-02-26,Adult,Adult,Gonad,Reproductive System
9357,ERR2983451,ERX2986067,ERS2955655,ERP112513,PRJEB30097,RNA Seq of Danionine species,E-MTAB-7476,Transcriptome Analysis,Tissues specific transcriptomes of Danio rerio  Danio albolineatus and Danio aesculapii Brain  Liver and Gonads.,ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05,,Protocols: Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers.,R2wG,SAMEA5147910,"University of Hamburg, Institute of Zoology, Molecular Animal Physiology",ENA FIRST PUBLIC:2018 12 05T17:02:27Z|ENA LAST UPDATE:2018 12 05T10:01:48Z|External Id:SAMEA5147910|INSDC center name:University of Hamburg  Institute of Zoology  Molecular Animal Physiology|INSDC first public:2018 12 05T17:02:27Z|INSDC last update:2018 12 05T10:01:48Z|INSDC status:public|Submitter Id:E MTAB 7476:R2wG|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|individual:2|organism part:gonad|sample name:E MTAB 7476:R2wG|scientific name:Danio rerio|sex:female|strain:tu,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danio9 species,E MTAB 7476:R2wG p,R2wG p,RNA Seq of Danionine species,Organs were sampled and snap frozen in liquid nitrogen   RNA was extracted using Trizol and standard silica membrane protocol  Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers.,Experimental Factor: organism:Danio rerio|Experimental Factor: organism part:gonad,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP112513,Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danionine species,ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05,FCHNW2WBBXX_L6_HKZEBodsEAAFRAAPEI-209_1.fq.gz FCHNW2WBBXX_L6_HKZEBodsEAAFRAAPEI-209_2.fq.gz,fastq fastq,4276100600.0,21380503.0,E MTAB 7476:FCHNW2WBBXX L6 HKZEBodsEAAFRAAPEI 209 ,0:100 1:100,A:1108098396;C:1033423434;G:1019885778;T:1113782383;N:910609,100,100,,,1108098396,1033423434,1019885778,1113782383,910609,ERX2986067,ERS2955655,ERA1674470,"University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive","University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive",2,0.9444,0.94495,0.02624,0.02606,0.74959,0.7512,0.48453,0.48539,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2018-12-05,Adult,Adult,Gonad,Reproductive System
9359,ERR2983449,ERX2986065,ERS2955653,ERP112513,PRJEB30097,RNA Seq of Danionine species,E-MTAB-7476,Transcriptome Analysis,Tissues specific transcriptomes of Danio rerio  Danio albolineatus and Danio aesculapii Brain  Liver and Gonads.,ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05,,Protocols: Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers.,R1wG,SAMEA5147908,"University of Hamburg, Institute of Zoology, Molecular Animal Physiology",ENA FIRST PUBLIC:2018 12 05T17:02:27Z|ENA LAST UPDATE:2018 12 05T10:01:48Z|External Id:SAMEA5147908|INSDC center name:University of Hamburg  Institute of Zoology  Molecular Animal Physiology|INSDC first public:2018 12 05T17:02:27Z|INSDC last update:2018 12 05T10:01:48Z|INSDC status:public|Submitter Id:E MTAB 7476:R1wG|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|individual:1|organism part:gonad|sample name:E MTAB 7476:R1wG|scientific name:Danio rerio|sex:female|strain:tu,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danio9 species,E MTAB 7476:R1wG p,R1wG p,RNA Seq of Danionine species,Organs were sampled and snap frozen in liquid nitrogen   RNA was extracted using Trizol and standard silica membrane protocol  Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers.,Experimental Factor: organism:Danio rerio|Experimental Factor: organism part:gonad,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP112513,Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danionine species,ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05,FCHNW2WBBXX_L6_HKZEBodsEAAERAAPEI-208_1.fq.gz FCHNW2WBBXX_L6_HKZEBodsEAAERAAPEI-208_2.fq.gz,fastq fastq,3574419200.0,17872096.0,E MTAB 7476:FCHNW2WBBXX L6 HKZEBodsEAAERAAPEI 208 ,0:100 1:100,A:927454175;C:863033369;G:844910972;T:938253904;N:766780,100,100,,,927454175,863033369,844910972,938253904,766780,ERX2986065,ERS2955653,ERA1674470,"University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive","University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive",2,0.93851,0.93973,0.02799,0.02809,0.72701,0.72914,0.48827,0.48841,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2018-12-05,Adult,Adult,Gonad,Reproductive System
25267,SRR25744342,SRX21467662,SRS18702380,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish  we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad eif4e1b 3,GSM7730282,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b  / |geo loc name:missing|collection date:missing,Gonad eif4e1b 3,RNA seq reads were trimmed using trim galore v0.5.0  and reads mapping to abundant sequences Dr mitochondrial chromosome  SILVA Dr ribosomal RNA  phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts  subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b  / ,GSM7730282,GSM7730282: Gonad eif4e1b 3; Danio rerio; ssRNA seq,GSM7730282 r1,GSM7730282,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_HOM3_1.fastq.gz Ovary_HOM3_2.fastq.gz,fastq fastq,2170738056.0,10746228.0,GSM7730282 r1,0:101 1:101,A:531993767;C:520631008;G:565772072;T:552334154;N:7055,101,101,,,531993767,520631008,565772072,552334154,7055,SRX21467662,SRS18702380,SRA1698764,IMP,IMP,2,0.77665,0.7702,0.14988,0.14284,0.66716,0.66957,0.49991,0.47425,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
25268,SRR25744343,SRX21467661,SRS18702379,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish  we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad eif4e1b 2,GSM7730281,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b  / |geo loc name:missing|collection date:missing,Gonad eif4e1b 2,RNA seq reads were trimmed using trim galore v0.5.0  and reads mapping to abundant sequences Dr mitochondrial chromosome  SILVA Dr ribosomal RNA  phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts  subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b  / ,GSM7730281,GSM7730281: Gonad eif4e1b 2; Danio rerio; ssRNA seq,GSM7730281 r1,GSM7730281,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_HOM2_1.fastq.gz Ovary_HOM2_2.fastq.gz,fastq fastq,3459149000.0,17124500.0,GSM7730281 r1,0:101 1:101,A:876732239;C:796603142;G:882912604;T:902886783;N:14232,101,101,,,876732239,796603142,882912604,902886783,14232,SRX21467661,SRS18702379,SRA1698764,IMP,IMP,2,0.81761,0.79589,0.26282,0.24746,0.70607,0.7039,0.50658,0.49236,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
25269,SRR25744344,SRX21467660,SRS18702381,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish  we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad eif4e1b 1,GSM7730280,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b  / |geo loc name:missing|collection date:missing,Gonad eif4e1b 1,RNA seq reads were trimmed using trim galore v0.5.0  and reads mapping to abundant sequences Dr mitochondrial chromosome  SILVA Dr ribosomal RNA  phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts  subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b  / ,GSM7730280,GSM7730280: Gonad eif4e1b 1; Danio rerio; ssRNA seq,GSM7730280 r1,GSM7730280,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_HOM1_1.fastq.gz Ovary_HOM1_2.fastq.gz,fastq fastq,2189781202.0,10840501.0,GSM7730280 r1,0:101 1:101,A:537591255;C:525448020;G:568979980;T:557754770;N:7177,101,101,,,537591255,525448020,568979980,557754770,7177,SRX21467660,SRS18702381,SRA1698764,IMP,IMP,2,0.7459,0.74191,0.15778,0.15291,0.65543,0.65841,0.48578,0.48291,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
25270,SRR25744345,SRX21467659,SRS18702378,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish  we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad WT 3,GSM7730279,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b +/+|geo loc name:missing|collection date:missing,Gonad WT 3,RNA seq reads were trimmed using trim galore v0.5.0  and reads mapping to abundant sequences Dr mitochondrial chromosome  SILVA Dr ribosomal RNA  phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts  subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b +/+,GSM7730279,GSM7730279: Gonad WT 3; Danio rerio; ssRNA seq,GSM7730279 r1,GSM7730279,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_WT3_1.fastq.gz Ovary_WT3_2.fastq.gz,fastq fastq,3674041448.0,18188324.0,GSM7730279 r1,0:101 1:101,A:910831144;C:876967044;G:953299105;T:932928913;N:15242,101,101,,,910831144,876967044,953299105,932928913,15242,SRX21467659,SRS18702378,SRA1698764,IMP,IMP,2,0.89093,0.89038,0.09253,0.09348,0.73892,0.73858,0.47115,0.47218,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
25271,SRR25744346,SRX21467658,SRS18702377,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish  we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad WT 2,GSM7730278,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b +/+|geo loc name:missing|collection date:missing,Gonad WT 2,RNA seq reads were trimmed using trim galore v0.5.0  and reads mapping to abundant sequences Dr mitochondrial chromosome  SILVA Dr ribosomal RNA  phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts  subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b +/+,GSM7730278,GSM7730278: Gonad WT 2; Danio rerio; ssRNA seq,GSM7730278 r1,GSM7730278,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_WT2_1.fastq.gz Ovary_WT2_2.fastq.gz,fastq fastq,3024886370.0,14974685.0,GSM7730278 r1,0:101 1:101,A:744374909;C:727299396;G:782294774;T:770904797;N:12494,101,101,,,744374909,727299396,782294774,770904797,12494,SRX21467658,SRS18702377,SRA1698764,IMP,IMP,2,0.91806,0.91689,0.06949,0.07178,0.74458,0.74474,0.47548,0.47338,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
25272,SRR25744347,SRX21467657,SRS18702376,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish  we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad WT 1,GSM7730277,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b +/+|geo loc name:missing|collection date:missing,Gonad WT 1,RNA seq reads were trimmed using trim galore v0.5.0  and reads mapping to abundant sequences Dr mitochondrial chromosome  SILVA Dr ribosomal RNA  phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts  subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b +/+,GSM7730277,GSM7730277: Gonad WT 1; Danio rerio; ssRNA seq,GSM7730277 r1,GSM7730277,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_WT1_2.fastq.gz Ovary_WT1_1.fastq.gz,fastq fastq,3571638356.0,17681378.0,GSM7730277 r1,0:101 1:101,A:876280472;C:856417516;G:935896746;T:903028845;N:14777,101,101,,,876280472,856417516,935896746,903028845,14777,SRX21467657,SRS18702376,SRA1698764,IMP,IMP,2,0.89559,0.89353,0.09223,0.09423,0.73052,0.73012,0.47772,0.47408,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
26542,SRR28370185,SRX23975270,SRS20773688,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,L13 2 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 27|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E27,E27,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,L13-2_1.fq.gz L13-2_2.fq.gz,fastq fastq,6912432900.0,23041443.0,L13 2 1.fq.gz,0:150 1:150,A:1784119910;C:1650041348;G:1690584500;T:1787634630;N:52512,150,150,,,1784119910,1650041348,1690584500,1787634630,52512,SRX23975270,SRS20773688,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26543,SRR28370183,SRX23975269,SRS20773687,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,L13 3 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 29|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E29,E29,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,L13-3_1.fq.gz L13-3_2.fq.gz,fastq fastq,6353525700.0,21178419.0,L13 3 1.fq.gz,0:150 1:150,A:1642863679;C:1514378445;G:1549765145;T:1646469683;N:48748,150,150,,,1642863679,1514378445,1549765145,1646469683,48748,SRX23975269,SRS20773687,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26544,SRR28370186,SRX23975268,SRS20773685,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,L13 4 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 31|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E31,E31,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,L13-4_1.fq.gz L13-4_2.fq.gz,fastq fastq,6026853600.0,20089512.0,L13 4 1.fq.gz,0:150 1:150,A:1557631540;C:1437822618;G:1472097382;T:1559255786;N:46274,150,150,,,1557631540,1437822618,1472097382,1559255786,46274,SRX23975268,SRS20773685,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26545,SRR28370187,SRX23975267,SRS20773686,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,H27 3 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 5|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E5,E5,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,H27-3_1.fq.gz H27-3_2.fq.gz,fastq fastq,6437512500.0,21458375.0,H27 3 1.fq.gz,0:150 1:150,A:1664818485;C:1534913781;G:1570911516;T:1666819538;N:49180,150,150,,,1664818485,1534913781,1570911516,1666819538,49180,SRX23975267,SRS20773686,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26546,SRR28370188,SRX23975266,SRS20773684,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,H27 4 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 7|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E7,E7,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,H27-4_1.fq.gz H27-4_2.fq.gz,fastq fastq,6583604100.0,21945347.0,H27 4 1.fq.gz,0:150 1:150,A:1701207657;C:1570727535;G:1607990863;T:1703626924;N:51121,150,150,,,1701207657,1570727535,1607990863,1703626924,51121,SRX23975266,SRS20773684,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26547,SRR28370189,SRX23975265,SRS20773683,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,M20 1 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 9|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E9,E9,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,M20-1_1.fq.gz M20-1_2.fq.gz,fastq fastq,7048815900.0,23496053.0,M20 1 1.fq.gz,0:150 1:150,A:1818915133;C:1681912688;G:1724222526;T:1823711995;N:53558,150,150,,,1818915133,1681912688,1724222526,1823711995,53558,SRX23975265,SRS20773683,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26548,SRR28370190,SRX23975264,SRS20773682,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,M22 2 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 19|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E19,E19,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,M22-2_1.fq.gz M22-2_2.fq.gz,fastq fastq,6844400100.0,22814667.0,M22 2 1.fq.gz,0:150 1:150,A:1770073015;C:1631597148;G:1666105661;T:1776572883;N:51393,150,150,,,1770073015,1631597148,1666105661,1776572883,51393,SRX23975264,SRS20773682,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26549,SRR28370191,SRX23975263,SRS20773681,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,H27 2 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E3,E3,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,H27-2_1.fq.gz H27-2_2.fq.gz,fastq fastq,6803741100.0,22679137.0,H27 2 1.fq.gz,0:150 1:150,A:1759471720;C:1621328873;G:1660379342;T:1762509905;N:51260,150,150,,,1759471720,1621328873,1660379342,1762509905,51260,SRX23975263,SRS20773681,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26550,SRR28370184,SRX23975262,SRS20773680,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,M22 3 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 21|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E21,E21,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,M22-3_1.fq.gz M22-3_2.fq.gz,fastq fastq,6312346800.0,21041156.0,M22 3 1.fq.gz,0:150 1:150,A:1638152183;C:1500304435;G:1533591340;T:1640250617;N:48225,150,150,,,1638152183,1500304435,1533591340,1640250617,48225,SRX23975262,SRS20773680,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26551,SRR28370192,SRX23975261,SRS20773679,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,M22 4 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 23|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E23,E23,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,M22-4_1.fq.gz M22-4_2.fq.gz,fastq fastq,7163095500.0,23876985.0,M22 4 1.fq.gz,0:150 1:150,A:1851012240;C:1707016293;G:1748790263;T:1856222899;N:53805,150,150,,,1851012240,1707016293,1748790263,1856222899,53805,SRX23975261,SRS20773679,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26552,SRR28370193,SRX23975260,SRS20773678,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,L13 1 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 25|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E25,E25,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,L13-1_1.fq.gz L13-1_2.fq.gz,fastq fastq,6191424300.0,20638081.0,L13 1 1.fq.gz,0:150 1:150,A:1605753886;C:1471890545;G:1506901769;T:1606830995;N:47105,150,150,,,1605753886,1471890545,1506901769,1606830995,47105,SRX23975260,SRS20773678,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26553,SRR28370194,SRX23975259,SRS20773677,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,M22 1 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 17|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E17,E17,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,M22-1_1.fq.gz M22-1_2.fq.gz,fastq fastq,6102383400.0,20341278.0,M22 1 1.fq.gz,0:150 1:150,A:1577012976;C:1455984420;G:1487747979;T:1581590987;N:47038,150,150,,,1577012976,1455984420,1487747979,1581590987,47038,SRX23975259,SRS20773677,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26554,SRR28370195,SRX23975258,SRS20773676,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,M20 4 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 15|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E15,E15,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,M20-4_1.fq.gz M20-4_2.fq.gz,fastq fastq,6636566100.0,22121887.0,M20 4 1.fq.gz,0:150 1:150,A:1715667953;C:1580553403;G:1620418612;T:1719875870;N:50262,150,150,,,1715667953,1580553403,1620418612,1719875870,50262,SRX23975258,SRS20773676,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26555,SRR28370196,SRX23975257,SRS20773675,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,M20 3 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 13|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E13,E13,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,M20-3_1.fq.gz M20-3_2.fq.gz,fastq fastq,6761256900.0,22537523.0,M20 3 1.fq.gz,0:150 1:150,A:1758917520;C:1603264927;G:1642146940;T:1756875822;N:51691,150,150,,,1758917520,1603264927,1642146940,1756875822,51691,SRX23975257,SRS20773675,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26556,SRR28370197,SRX23975256,SRS20773674,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,M20 2 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 11|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E11,E11,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,M20-2_1.fq.gz M20-2_2.fq.gz,fastq fastq,6746623800.0,22488746.0,M20 2 1.fq.gz,0:150 1:150,A:1744481110;C:1606775717;G:1646048497;T:1749267538;N:50938,150,150,,,1744481110,1606775717,1646048497,1749267538,50938,SRX23975256,SRS20773674,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26557,SRR28370198,SRX23975255,SRS20773673,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,H27 1 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E1,E1,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,H27-1_1.fq.gz H27-1_2.fq.gz,fastq fastq,6713598900.0,22378663.0,H27 1 1.fq.gz,0:150 1:150,A:1734915716;C:1602520747;G:1639382442;T:1736729508;N:50487,150,150,,,1734915716,1602520747,1639382442,1736729508,50487,SRX23975255,SRS20773673,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
28800,SRR26744390,SRX22443207,SRS19460925,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,TL1,AWG21KI956,,strain:AB wild type|age:4 mpf|collection date:2021 10 20|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,LM,LM,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,TL1_2.clean.fq.gz TL1_1.clean.fq.gz,fastq fastq,5699083800.0,18996946.0,TL1 1.clean.fq.gz,0:150 1:150,A:1551237534;C:1296027828;G:1322262120;T:1529547653;N:8665,150,150,,,1551237534,1296027828,1322262120,1529547653,8665,SRX22443207,SRS19460925,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92378,0.91959,0.10498,0.1026,0.6299,0.64319,0.49163,0.48651,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28801,SRR26744391,SRX22443206,SRS19460924,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,OL3,AWG21KN131,,strain:AB wild type|age:4 mpf|collection date:2021 10 19|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,LF3,LF3,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,OL3_2.clean.fq.gz OL3_1.clean.fq.gz,fastq fastq,6314250900.0,21047503.0,OL3 1.clean.fq.gz,0:150 1:150,A:1645668992;C:1501216557;G:1526087917;T:1641268461;N:8973,150,150,,,1645668992,1501216557,1526087917,1641268461,8973,SRX22443206,SRS19460924,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92555,0.92469,0.01845,0.01818,0.75146,0.75298,0.4697,0.47119,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28802,SRR26744392,SRX22443205,SRS19460920,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,OL2,AWG21KN130,,strain:AB wild type|age:4 mpf|collection date:2021 10 18|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,LF2,LF2,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,OL2_1.clean.fq.gz OL2_2.clean.fq.gz,fastq fastq,5723391300.0,19077971.0,OL2 1.clean.fq.gz,0:150 1:150,A:1493997463;C:1358589750;G:1376156813;T:1494638946;N:8328,150,150,,,1493997463,1358589750,1376156813,1494638946,8328,SRX22443205,SRS19460920,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92147,0.92251,0.0187,0.01891,0.75077,0.75156,0.46983,0.46864,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28803,SRR26744393,SRX22443204,SRS19460923,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,OL1,AWG21KI955,,strain:AB wild type|age:4 mpf|collection date:2021 10 17|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,LF,LF,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,OL1_1.clean.fq.gz OL1_2.clean.fq.gz,fastq fastq,5769588600.0,19231962.0,OL1 1.clean.fq.gz,0:150 1:150,A:1506564191;C:1368903119;G:1393174106;T:1500937757;N:9427,150,150,,,1506564191,1368903119,1393174106,1500937757,9427,SRX22443204,SRS19460923,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92622,0.92542,0.01753,0.01714,0.75694,0.7596,0.47038,0.46862,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28804,SRR26744394,SRX22443203,SRS19460921,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,TC3,AWG21KN129,,strain:AB wild type|age:4 mpf|collection date:2021 10 16|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,CM3,CM3,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,TC3_2.clean.fq.gz TC3_1.clean.fq.gz,fastq fastq,5849082900.0,19496943.0,TC3 1.clean.fq.gz,0:150 1:150,A:1588589470;C:1336193891;G:1355933296;T:1568357820;N:8423,150,150,,,1588589470,1336193891,1355933296,1568357820,8423,SRX22443203,SRS19460921,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.9259,0.92501,0.09579,0.09483,0.62501,0.6266,0.49341,0.49677,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28805,SRR26744395,SRX22443202,SRS19460922,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,TC2,AWG21KN128,,strain:AB wild type|age:4 mpf|collection date:2021 10 15|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,CM2,CM2,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,TC2_2.clean.fq.gz TC2_1.clean.fq.gz,fastq fastq,6060182100.0,20200607.0,TC2 1.clean.fq.gz,0:150 1:150,A:1640267244;C:1389270827;G:1407872392;T:1622763112;N:8525,150,150,,,1640267244,1389270827,1407872392,1622763112,8525,SRX22443202,SRS19460922,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92414,0.9235,0.0895,0.08929,0.62528,0.62682,0.48981,0.48954,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28806,SRR26744396,SRX22443201,SRS19460918,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,TC1,AWG21KI954,,strain:AB wild type|age:4 mpf|collection date:2021 10 14|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,CM,CM,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,TC1_1.clean.fq.gz TC1_2.clean.fq.gz,fastq fastq,5990926200.0,19969754.0,TC1 1.clean.fq.gz,0:150 1:150,A:1624594580;C:1370442060;G:1389854623;T:1606025586;N:9351,150,150,,,1624594580,1370442060,1389854623,1606025586,9351,SRX22443201,SRS19460918,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92373,0.92279,0.09865,0.09887,0.62568,0.62889,0.49516,0.49165,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28807,SRR26744397,SRX22443200,SRS19460914,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,OC3,AWG21KN127,,strain:AB wild type|age:4 mpf|collection date:2021 10 13|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,CF3,CF3,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,OC3_1.clean.fq.gz OC3_2.clean.fq.gz,fastq fastq,6016914600.0,20056382.0,OC3 1.clean.fq.gz,0:150 1:150,A:1568359804;C:1431107464;G:1450792678;T:1566645836;N:8818,150,150,,,1568359804,1431107464,1450792678,1566645836,8818,SRX22443200,SRS19460914,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92534,0.92528,0.01718,0.017,0.75201,0.753,0.47491,0.48041,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28808,SRR26744398,SRX22443199,SRS19460915,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,TL3,AWG21KN137,,strain:AB wild type|age:4 mpf|collection date:2021 10 28|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,HM3,HM3,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,TH3_1.clean.fq.gz TH3_2.clean.fq.gz,fastq fastq,5656023900.0,18853413.0,TH3 1.clean.fq.gz,0:150 1:150,A:1543170407;C:1285816998;G:1307460034;T:1519567327;N:9134,150,150,,,1543170407,1285816998,1307460034,1519567327,9134,SRX22443199,SRS19460915,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92316,0.92166,0.10167,0.10105,0.61546,0.61712,0.482,0.4844,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28809,SRR26744399,SRX22443198,SRS19460919,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,TL2,AWG21KN136,,strain:AB wild type|age:4 mpf|collection date:2021 10 27|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,HM2,HM2,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,TH2_2.clean.fq.gz TH2_1.clean.fq.gz,fastq fastq,6625748400.0,22085828.0,TH2 1.clean.fq.gz,0:150 1:150,A:1808454203;C:1505432915;G:1526482662;T:1785369099;N:9521,150,150,,,1808454203,1505432915,1526482662,1785369099,9521,SRX22443198,SRS19460919,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92273,0.92286,0.09974,0.09973,0.62043,0.62203,0.48636,0.48603,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28810,SRR26744400,SRX22443197,SRS19460917,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,TL1,AWG21KI958,,strain:AB wild type|age:4 mpf|collection date:2021 10 26|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,HM,HM,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,TH1_1.clean.fq.gz TH1_2.clean.fq.gz,fastq fastq,6588309600.0,21961032.0,TH1 1.clean.fq.gz,0:150 1:150,A:1793735270;C:1500551703;G:1518029671;T:1775983548;N:9408,150,150,,,1793735270,1500551703,1518029671,1775983548,9408,SRX22443197,SRS19460917,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92046,0.91969,0.10181,0.10206,0.61505,0.61477,0.48395,0.48957,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28811,SRR26744401,SRX22443196,SRS19460916,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,OL3,AWG21KN135,,strain:AB wild type|age:4 mpf|collection date:2021 10 25|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,HF3,HF3,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,OH3_1.clean.fq.gz OH3_2.clean.fq.gz,fastq fastq,5690890500.0,18969635.0,OH3 1.clean.fq.gz,0:150 1:150,A:1485585756;C:1351021989;G:1373539521;T:1480733791;N:9443,150,150,,,1485585756,1351021989,1373539521,1480733791,9443,SRX22443196,SRS19460916,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92616,0.9273,0.01843,0.01865,0.74793,0.74925,0.4724,0.47202,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28812,SRR26744402,SRX22443195,SRS19460912,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,OL2,AWG21KN134,,strain:AB wild type|age:4 mpf|collection date:2021 10 24|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,HF2,HF2,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,OH2_2.clean.fq.gz OH2_1.clean.fq.gz,fastq fastq,6047756700.0,20159189.0,OH2 1.clean.fq.gz,0:150 1:150,A:1577825068;C:1435108510;G:1458998347;T:1575814993;N:9782,150,150,,,1577825068,1435108510,1458998347,1575814993,9782,SRX22443195,SRS19460912,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.9233,0.92363,0.01923,0.01923,0.74474,0.74686,0.46918,0.46911,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28813,SRR26744403,SRX22443194,SRS19460913,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,OL1,AWG21KI957,,strain:AB wild type|age:4 mpf|collection date:2021 10 23|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,HF,HF,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,OH1_1.clean.fq.gz OH1_2.clean.fq.gz,fastq fastq,5756713800.0,19189046.0,OH1 1.clean.fq.gz,0:150 1:150,A:1501851096;C:1366577079;G:1382910165;T:1505367292;N:8168,150,150,,,1501851096,1366577079,1382910165,1505367292,8168,SRX22443194,SRS19460913,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92555,0.92628,0.0184,0.01828,0.74968,0.7512,0.47643,0.4776,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28814,SRR26744404,SRX22443193,SRS19460908,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,TL3,AWG21KN133,,strain:AB wild type|age:4 mpf|collection date:2021 10 22|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,LM3,LM3,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,TL3_1.clean.fq.gz TL3_2.clean.fq.gz,fastq fastq,5675551800.0,18918506.0,TL3 1.clean.fq.gz,0:150 1:150,A:1544159251;C:1294658828;G:1308831043;T:1527894467;N:8211,150,150,,,1544159251,1294658828,1308831043,1527894467,8211,SRX22443193,SRS19460908,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92069,0.92047,0.10371,0.10354,0.62741,0.62954,0.48923,0.48839,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28815,SRR26744405,SRX22443192,SRS19460909,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,TL2,AWG21KN132,,strain:AB wild type|age:4 mpf|collection date:2021 10 21|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,LM2,LM2,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,TL2_1.clean.fq.gz TL2_2.clean.fq.gz,fastq fastq,5834343300.0,19447811.0,TL2 1.clean.fq.gz,0:150 1:150,A:1583809689;C:1333511774;G:1345919597;T:1571093925;N:8315,150,150,,,1583809689,1333511774,1345919597,1571093925,8315,SRX22443192,SRS19460909,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.91878,0.92054,0.10134,0.10105,0.62708,0.62759,0.48763,0.48708,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28816,SRR26744406,SRX22443191,SRS19460911,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,OC2,AWG21KN126,,strain:AB wild type|age:4 mpf|collection date:2021 10 12|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,CF2,CF2,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,OC2_2.clean.fq.gz OC2_1.clean.fq.gz,fastq fastq,6462335700.0,21541119.0,OC2 1.clean.fq.gz,0:150 1:150,A:1684794140;C:1535771967;G:1553892063;T:1687868172;N:9358,150,150,,,1684794140,1535771967,1553892063,1687868172,9358,SRX22443191,SRS19460911,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92236,0.92263,0.01803,0.01777,0.74945,0.75081,0.47372,0.47191,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28817,SRR26744407,SRX22443190,SRS19460907,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,OC1,AWG21KI953,,strain:AB wild type|age:4 mpf|collection date:2021 10 11|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,CF,CF,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,OC1_1.clean.fq.gz OC1_2.clean.fq.gz,fastq fastq,5719061700.0,19063539.0,OC1 1.clean.fq.gz,0:150 1:150,A:1489404392;C:1360123113;G:1386373369;T:1483151708;N:9118,150,150,,,1489404392,1360123113,1386373369,1483151708,9118,SRX22443190,SRS19460907,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92595,0.92513,0.0166,0.0163,0.75187,0.75503,0.47431,0.47637,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
29259,SRR27336917,SRX23013778,SRS19977075,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 PaternalKO gonads 31dpf rep2,miR214 PaternalKO gonads 31dpf rep2,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep2|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A11",miR214 PaternalKO gonads 31dpf rep2,miR214 PaternalKO gonads 31dpf rep2,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_PaternalKO_gonads_31dpf_rep2.fastq.gz,fastq,2327996832.0,27714248.0,miR214 PaternalKO gonads 31dpf rep2.fastq.gz,0:84,A:602135965;C:552786494;G:537368428;T:635697339;N:8606,84,,,,602135965,552786494,537368428,635697339,8606,SRX23013778,SRS19977075,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95369,,0.06146,,0.69203,,0.47259,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29260,SRR27336918,SRX23013777,SRS19977074,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 PaternalKO gonads 31dpf rep1,miR214 PaternalKO gonads 31dpf rep1,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep1|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A10",miR214 PaternalKO gonads 31dpf rep1,miR214 PaternalKO gonads 31dpf rep1,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_PaternalKO_gonads_31dpf_rep1.fastq.gz,fastq,2500978452.0,29773553.0,miR214 PaternalKO gonads 31dpf rep1.fastq.gz,0:84,A:646162933;C:593855971;G:578265372;T:682684551;N:9625,84,,,,646162933,593855971,578265372,682684551,9625,SRX23013777,SRS19977074,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95147,,0.05972,,0.69071,,0.47043,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29261,SRR27336919,SRX23013776,SRS19977073,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 maternalHET gonads 31dpf rep4,miR214 maternalHET gonads 31dpf rep4,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep4|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A9",miR214 maternalHET gonads 31dpf rep4,miR214 maternalHET gonads 31dpf rep4,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_maternalHET_gonads_31dpf_rep4.fastq.gz,fastq,2365480908.0,28160487.0,miR214 maternalHET gonads 31dpf rep4.fastq.gz,0:84,A:613121312;C:560582165;G:549338096;T:642429834;N:9501,84,,,,613121312,560582165,549338096,642429834,9501,SRX23013776,SRS19977073,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95304,,0.05342,,0.7108,,0.46822,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29262,SRR27336920,SRX23013775,SRS19977072,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 maternalHET gonads 31dpf rep3,miR214 maternalHET gonads 31dpf rep3,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep3|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A8",miR214 maternalHET gonads 31dpf rep3,miR214 maternalHET gonads 31dpf rep3,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_maternalHET_gonads_31dpf_rep3.fastq.gz,fastq,2537794644.0,30211841.0,miR214 maternalHET gonads 31dpf rep3.fastq.gz,0:84,A:658687178;C:600742464;G:585643169;T:692712057;N:9776,84,,,,658687178,600742464,585643169,692712057,9776,SRX23013775,SRS19977072,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95177,,0.06701,,0.68195,,0.47393,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29263,SRR27336921,SRX23013774,SRS19977071,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 maternalHET gonads 31dpf rep2,miR214 maternalHET gonads 31dpf rep2,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep2|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A7",miR214 maternalHET gonads 31dpf rep2,miR214 maternalHET gonads 31dpf rep2,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_maternalHET_gonads_31dpf_rep2.fastq.gz,fastq,2417384424.0,28778386.0,miR214 maternalHET gonads 31dpf rep2.fastq.gz,0:84,A:625935186;C:574179061;G:560498085;T:656762980;N:9112,84,,,,625935186,574179061,560498085,656762980,9112,SRX23013774,SRS19977071,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95259,,0.05852,,0.6981,,0.47435,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29264,SRR27336922,SRX23013773,SRS19977070,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 maternalHET gonads 31dpf rep1,miR214 maternalHET gonads 31dpf rep1,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep1|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A6",miR214 maternalHET gonads 31dpf rep1,miR214 maternalHET gonads 31dpf rep1,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_maternalHET_gonads_31dpf_rep1.fastq.gz,fastq,2330886180.0,27748645.0,miR214 maternalHET gonads 31dpf rep1.fastq.gz,0:84,A:601589571;C:554105326;G:542789267;T:632393158;N:8858,84,,,,601589571,554105326,542789267,632393158,8858,SRX23013773,SRS19977070,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95338,,0.05239,,0.71366,,0.47291,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29265,SRR27336923,SRX23013772,SRS19977069,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 maternalKO gonads 31dpf rep4,miR214 maternalKO gonads 31dpf rep4,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalKO|biological replicate:rep4|number of gonads:8 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A5",miR214 maternalKO gonads 31dpf rep4,miR214 maternalKO gonads 31dpf rep4,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_maternalKO_gonads_31dpf_rep4.fastq.gz,fastq,2340233784.0,27859926.0,miR214 maternalKO gonads 31dpf rep4.fastq.gz,0:84,A:606735187;C:553647808;G:539865459;T:639976430;N:8900,84,,,,606735187,553647808,539865459,639976430,8900,SRX23013772,SRS19977069,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95406,,0.06415,,0.68225,,0.47695,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29266,SRR27336924,SRX23013771,SRS19977068,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 maternalKO gonads 31dpf rep3,miR214 maternalKO gonads 31dpf rep3,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalKO|biological replicate:rep3|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A4",miR214 maternalKO gonads 31dpf rep3,miR214 maternalKO gonads 31dpf rep3,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_maternalKO_gonads_31dpf_rep3.fastq.gz,fastq,2058505512.0,24506018.0,miR214 maternalKO gonads 31dpf rep3.fastq.gz,0:84,A:537425814;C:485664494;G:471526682;T:563881213;N:7309,84,,,,537425814,485664494,471526682,563881213,7309,SRX23013771,SRS19977068,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95296,,0.06728,,0.69266,,0.47627,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29267,SRR27336925,SRX23013770,SRS19977067,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 PaternalHET gonads 31dpf rep4,miR214 PaternalHET gonads 31dpf rep4,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep4|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A17",miR214 PaternalHET gonads 31dpf rep4,miR214 PaternalHET gonads 31dpf rep4,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_PaternalHET_gonads_31dpf_rep4.fastq.gz,fastq,3001613328.0,35733492.0,miR214 PaternalHET gonads 31dpf rep4.fastq.gz,0:84,A:778860501;C:711155422;G:688784969;T:822801157;N:11279,84,,,,778860501,711155422,688784969,822801157,11279,SRX23013770,SRS19977067,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95361,,0.05653,,0.7051,,0.48382,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29268,SRR27336926,SRX23013769,SRS19977066,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 PaternalHET gonads 31dpf rep3,miR214 PaternalHET gonads 31dpf rep3,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep3|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A16",miR214 PaternalHET gonads 31dpf rep3,miR214 PaternalHET gonads 31dpf rep3,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_PaternalHET_gonads_31dpf_rep3.fastq.gz,fastq,3053630664.0,36352746.0,miR214 PaternalHET gonads 31dpf rep3.fastq.gz,0:84,A:785219727;C:726431662;G:713454025;T:828513556;N:11694,84,,,,785219727,726431662,713454025,828513556,11694,SRX23013769,SRS19977066,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95309,,0.04588,,0.71997,,0.46447,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29269,SRR27336927,SRX23013768,SRS19977065,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 PaternalHET gonads 31dpf rep2,miR214 PaternalHET gonads 31dpf rep2,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep2|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A15",miR214 PaternalHET gonads 31dpf rep2,miR214 PaternalHET gonads 31dpf rep2,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_PaternalHET_gonads_31dpf_rep2.fastq.gz,fastq,3063695208.0,36472562.0,miR214 PaternalHET gonads 31dpf rep2.fastq.gz,0:84,A:784924646;C:728941687;G:720847462;T:828969510;N:11903,84,,,,784924646,728941687,720847462,828969510,11903,SRX23013768,SRS19977065,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95413,,0.04739,,0.71936,,0.4704,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29270,SRR27336928,SRX23013767,SRS19977064,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 PaternalHET gonads 31dpf rep1,miR214 PaternalHET gonads 31dpf rep1,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep1|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A14",miR214 PaternalHET gonads 31dpf rep1,miR214 PaternalHET gonads 31dpf rep1,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_PaternalHET_gonads_31dpf_rep1.fastq.gz,fastq,2699154024.0,32132786.0,miR214 PaternalHET gonads 31dpf rep1.fastq.gz,0:84,A:694174797;C:642049572;G:627991562;T:734927762;N:10331,84,,,,694174797,642049572,627991562,734927762,10331,SRX23013767,SRS19977064,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95518,,0.05525,,0.70285,,0.47695,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29271,SRR27336929,SRX23013766,SRS19977063,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 PaternalKO gonads 31dpf rep4,miR214 PaternalKO gonads 31dpf rep4,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep4|number of gonads:8 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A13",miR214 PaternalKO gonads 31dpf rep4,miR214 PaternalKO gonads 31dpf rep4,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_PaternalKO_gonads_31dpf_rep4.fastq.gz,fastq,2514248016.0,29931524.0,miR214 PaternalKO gonads 31dpf rep4.fastq.gz,0:84,A:648908956;C:598837726;G:580002743;T:686488678;N:9913,84,,,,648908956,598837726,580002743,686488678,9913,SRX23013766,SRS19977063,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.94978,,0.06951,,0.67896,,0.47686,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29272,SRR27336930,SRX23013765,SRS19977062,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 PaternalKO gonads 31dpf rep3,miR214 PaternalKO gonads 31dpf rep3,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep3|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A12",miR214 PaternalKO gonads 31dpf rep3,miR214 PaternalKO gonads 31dpf rep3,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_PaternalKO_gonads_31dpf_rep3.fastq.gz,fastq,2499529200.0,29756300.0,miR214 PaternalKO gonads 31dpf rep3.fastq.gz,0:84,A:642490769;C:597403823;G:580565141;T:679060154;N:9313,84,,,,642490769,597403823,580565141,679060154,9313,SRX23013765,SRS19977062,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95284,,0.05602,,0.70289,,0.47154,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29273,SRR27336931,SRX23013764,SRS19977061,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 maternalKO gonads 31dpf rep2,miR214 maternalKO gonads 31dpf rep2,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalKO|biological replicate:rep2|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A3",miR214 maternalKO gonads 31dpf rep2,miR214 maternalKO gonads 31dpf rep2,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_maternalKO_gonads_31dpf_rep2.fastq.gz,fastq,2529742404.0,30115981.0,miR214 maternalKO gonads 31dpf rep2.fastq.gz,0:84,A:652091166;C:600932059;G:589100617;T:687608862;N:9700,84,,,,652091166,600932059,589100617,687608862,9700,SRX23013764,SRS19977061,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95498,,0.05524,,0.70366,,0.47319,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29274,SRR27336932,SRX23013763,SRS19977060,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 maternalKO gonads 31dpf rep1,miR214 maternalKO gonads 31dpf rep1,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalKO|biological replicate:rep1|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A2",miR214 maternalKO gonads 31dpf rep1,miR214 maternalKO gonads 31dpf rep1,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_maternalKO_gonads_31dpf_rep1.fastq.gz,fastq,2310878136.0,27510454.0,miR214 maternalKO gonads 31dpf rep1.fastq.gz,0:84,A:598541924;C:547875391;G:533137786;T:631314274;N:8761,84,,,,598541924,547875391,533137786,631314274,8761,SRX23013763,SRS19977060,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95279,,0.06446,,0.68757,,0.4758,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29720,SRR27485665,SRX23156884,SRS20107305,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary R3,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: ovary  rep4,EV06008,EV06008,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV06008.R1.fastq.gz,fastq,585955025.0,7769646.0,EV06008.R1.fastq.gz,0:75.42,A:167210227;C:106735220;G:128095616;T:183896888;N:17074,75,,,,167210227,106735220,128095616,183896888,17074,SRX23156884,SRS20107305,SRA1783314,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.85544,,0.05096,,0.78441,,0.53007,,76,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-11,Adult,Adult,Gonad,Reproductive System
29731,SRR27485676,SRX23156873,SRS20107294,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: ovary  rep4,EV06001,EV06001,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV06001.R1.fastq.gz,fastq,685280356.0,9098789.0,EV06001.R1.fastq.gz,0:75.32,A:194596366;C:122550539;G:153504013;T:214558450;N:70988,75,,,,194596366,122550539,153504013,214558450,70988,SRX23156873,SRS20107294,SRA1783314,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.8304,,0.04498,,0.80166,,0.5028,,74,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-11,Adult,Adult,Gonad,Reproductive System
29738,SRR27477298,SRX23148649,SRS20099367,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|replicate:4|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: ovary  rep4,EV09001,EV09001,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV09001.R1.fastq.gz,fastq,456295310.0,6058854.0,EV09001.R1.fastq.gz,0:75.31,A:135579999;C:83364677;G:101608151;T:135700843;N:41640,75,,,,135579999,83364677,101608151,135700843,41640,SRX23148649,SRS20099367,SRA1782413,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.85088,,0.05876,,0.7791,,0.50948,,75,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-10,Adult,Adult,Gonad,Reproductive System
29746,SRR27467679,SRX23139227,SRS20090270,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary BS R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: ovary  BS  rep2,EV02003,EV02003,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,NextSeq 500,,SRP482074,,,EV02003.R1.fastq.gz EV02003.R2.fastq.gz,fastq fastq,1031891720.0,3416860.0,EV02003.R1.fastq.gz,0:151 1:151,A:264464363;C:153440613;G:408557241;T:205367487;N:62016,151,151,,,264464363,153440613,408557241,205367487,62016,SRX23139227,SRS20090270,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,2,0.0,0.00019,0.0,0.00015,1.0,0.99993,,1.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Adult,Adult,Gonad,Reproductive System
29755,SRR27467688,SRX23139218,SRS20090261,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary DM R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: ovary  DM  rep2,EV02002,EV02002,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,NextSeq 500,,SRP482074,,,EV02002.R1.fastq.gz EV02002.R2.fastq.gz,fastq fastq,861320308.0,2852054.0,EV02002.R1.fastq.gz,0:151 1:151,A:205625519;C:162178974;G:334206312;T:159256900;N:52603,151,151,,,205625519,162178974,334206312,159256900,52603,SRX23139218,SRS20090261,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,2,2e-05,0.00049,0.0,0.00027,1.0,0.99947,,0.44444,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Adult,Adult,Gonad,Reproductive System
29756,SRR27467689,SRX23139217,SRS20090260,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary mock R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: ovary  mock  rep2,EV02001,EV02001,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,NextSeq 500,,SRP482074,,,EV02001.R1.fastq.gz EV02001.R2.fastq.gz,fastq fastq,520371066.0,1723083.0,EV02001.R1.fastq.gz,0:151 1:151,A:116107273;C:90896560;G:218652568;T:94682244;N:32421,151,151,,,116107273,90896560,218652568,94682244,32421,SRX23139217,SRS20090260,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,2,2e-05,0.00086,0.0,0.00078,0.99995,0.99981,0.0,0.61538,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Adult,Adult,Gonad,Reproductive System
29765,SRR27437485,SRX23109812,SRS20064566,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary BS R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: ovary  BS  rep3,EV04017,EV04017,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV04017.R1.fastq.gz,fastq,576584540.0,4118461.0,EV04017.R1.fastq.gz,0:140,A:149516980;C:91163801;G:169046762;T:166831111;N:25886,140,,,,149516980,91163801,169046762,166831111,25886,SRX23109812,SRS20064566,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.0,,0.0,,1.0,,,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Adult,Adult,Gonad,Reproductive System
29776,SRR27437496,SRX23109801,SRS20064555,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary DM R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: ovary  DM  rep3,EV04016,EV04016,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV04016.R1.fastq.gz,fastq,635752880.0,4541092.0,EV04016.R1.fastq.gz,0:140,A:160072248;C:143996869;G:189137330;T:142516059;N:30374,140,,,,160072248,143996869,189137330,142516059,30374,SRX23109801,SRS20064555,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,1e-05,,0.0,,0.99997,,1.0,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Adult,Adult,Gonad,Reproductive System
29777,SRR27437497,SRX23109800,SRS20064554,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary mock R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: ovary  mock  rep3,EV04015,EV04015,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV04015.R1.fastq.gz,fastq,489700680.0,3497862.0,EV04015.R1.fastq.gz,0:140,A:126641754;C:126582886;G:130564204;T:105889815;N:22021,140,,,,126641754,126582886,130564204,105889815,22021,SRX23109800,SRS20064554,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,6e-05,,0.0,,0.99983,,0.55555,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Adult,Adult,Gonad,Reproductive System
29786,SRR27435871,SRX23108225,SRS20063062,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary BS R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: ovary  BS  rep4,EV08003,EV08003,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08003.R1.fastq.gz,fastq,571689580.0,4083497.0,EV08003.R1.fastq.gz,0:140,A:141414131;C:88722455;G:138790445;T:202723075;N:39474,140,,,,141414131,88722455,138790445,202723075,39474,SRX23108225,SRS20063062,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,3e-05,,0.0,,0.99991,,0.75,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Adult,Adult,Gonad,Reproductive System
29797,SRR27435882,SRX23108214,SRS20063050,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary DM R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: ovary  DM  rep4,EV08002,EV08002,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08002.R1.fastq.gz,fastq,668593800.0,4775670.0,EV08002.R1.fastq.gz,0:140,A:164584224;C:175789134;G:175538168;T:152637106;N:45168,140,,,,164584224,175789134,175538168,152637106,45168,SRX23108214,SRS20063050,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.00525,,2e-05,,0.99192,,0.63501,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Adult,Adult,Gonad,Reproductive System
29798,SRR27435883,SRX23108213,SRS20063051,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary mock R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: ovary  mock  rep4,EV08001,EV08001,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08001.R1.fastq.gz,fastq,753247460.0,5380339.0,EV08001.R1.fastq.gz,0:140,A:183862675;C:196453674;G:197604061;T:175275086;N:51964,140,,,,183862675,196453674,197604061,175275086,51964,SRX23108213,SRS20063051,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.00754,,4e-05,,0.98957,,0.51048,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Adult,Adult,Gonad,Reproductive System
31721,SRR28537217,SRX24137319,SRS20921922,SRP499426,PRJNA1095659,lsm14b ko zebrafish RNA seq,PRJNA1095659,Other,Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation  however  the specific translational regulatory mechanisms remain unclear. Here  our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR  which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes  which ensures that the mRNA synthesized and stored during the growth stage of oocytes  is necessary for the normal growth and development of oocytes.,,,,,ko3,,strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:ko biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,ko3,ko3,ko3,ko ovary,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP499426,,,ko3_1.fq.gz ko3_2.fq.gz,fastq fastq,8310654000.0,27702180.0,ko3 1.fq.gz,0:150 1:150,A:2164758632;C:1964255570;G:1984514973;T:2197073890;N:50935,150,150,,,2164758632,1964255570,1984514973,2197073890,50935,SRX24137319,SRS20921922,,,Shenzhen Second People's Hospital,2,0.9472,0.94617,0.02506,0.02527,0.74286,0.74535,0.45316,0.45662,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-04-03,Adult,Adult,Gonad,Reproductive System
31722,SRR28537218,SRX24137318,SRS20921924,SRP499426,PRJNA1095659,lsm14b ko zebrafish RNA seq,PRJNA1095659,Other,Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation  however  the specific translational regulatory mechanisms remain unclear. Here  our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR  which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes  which ensures that the mRNA synthesized and stored during the growth stage of oocytes  is necessary for the normal growth and development of oocytes.,,,,,ko2,,strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:ko biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,ko2,ko2,ko2,ko ovary,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP499426,,,ko2_1.fq.gz ko2_2.fq.gz,fastq fastq,8095711800.0,26985706.0,ko2 1.fq.gz,0:150 1:150,A:2117986563;C:1909094084;G:1931885806;T:2136732639;N:12708,150,150,,,2117986563,1909094084,1931885806,2136732639,12708,SRX24137318,SRS20921924,,,Shenzhen Second People's Hospital,2,0.9483,0.94443,0.02385,0.02347,0.74266,0.74686,0.45568,0.45676,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-04-03,Adult,Adult,Gonad,Reproductive System
31723,SRR28537219,SRX24137317,SRS20921925,SRP499426,PRJNA1095659,lsm14b ko zebrafish RNA seq,PRJNA1095659,Other,Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation  however  the specific translational regulatory mechanisms remain unclear. Here  our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR  which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes  which ensures that the mRNA synthesized and stored during the growth stage of oocytes  is necessary for the normal growth and development of oocytes.,,,,,ko1,,strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:ko biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,ko1,ko1,ko1,ko ovary,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP499426,,,ko1_1.fq.gz ko1_2.fq.gz,fastq fastq,9904629000.0,33015430.0,ko1 1.fq.gz,0:150 1:150,A:2565332092;C:2354153391;G:2380645312;T:2604437822;N:60383,150,150,,,2565332092,2354153391,2380645312,2604437822,60383,SRX24137317,SRS20921925,,,Shenzhen Second People's Hospital,2,0.94565,0.94416,0.01943,0.01956,0.7559,0.75739,0.456,0.45903,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-04-03,Adult,Adult,Gonad,Reproductive System
31724,SRR28537220,SRX24137316,SRS20921923,SRP499426,PRJNA1095659,lsm14b ko zebrafish RNA seq,PRJNA1095659,Other,Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation  however  the specific translational regulatory mechanisms remain unclear. Here  our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR  which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes  which ensures that the mRNA synthesized and stored during the growth stage of oocytes  is necessary for the normal growth and development of oocytes.,,,,,wt3,,strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:wt biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,wt3,wt3,wt3,wt ovary,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP499426,,,wt3_1.fq.gz wt3_2.fq.gz,fastq fastq,10079485500.0,33598285.0,wt3 1.fq.gz,0:150 1:150,A:2607822943;C:2396994959;G:2427407078;T:2647197813;N:62707,150,150,,,2607822943,2396994959,2427407078,2647197813,62707,SRX24137316,SRS20921923,,,Shenzhen Second People's Hospital,2,0.94735,0.94594,0.01733,0.01743,0.75635,0.75712,0.44042,0.46348,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-04-03,Adult,Adult,Gonad,Reproductive System
31725,SRR28537221,SRX24137315,SRS20921920,SRP499426,PRJNA1095659,lsm14b ko zebrafish RNA seq,PRJNA1095659,Other,Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation  however  the specific translational regulatory mechanisms remain unclear. Here  our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR  which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes  which ensures that the mRNA synthesized and stored during the growth stage of oocytes  is necessary for the normal growth and development of oocytes.,,,,,wt2,,strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:wt biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,wt2,wt2,wt2,wt ovary,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP499426,,,wt2_2.fq.gz wt2_1.fq.gz,fastq fastq,8980086900.0,29933623.0,wt2 1.fq.gz,0:150 1:150,A:2333474507;C:2131182397;G:2149144543;T:2366230132;N:55321,150,150,,,2333474507,2131182397,2149144543,2366230132,55321,SRX24137315,SRS20921920,,,Shenzhen Second People's Hospital,2,0.94182,0.94004,0.0187,0.01854,0.75077,0.75132,0.46271,0.46384,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-04-03,Adult,Adult,Gonad,Reproductive System
31726,SRR28537222,SRX24137314,SRS20921921,SRP499426,PRJNA1095659,lsm14b ko zebrafish RNA seq,PRJNA1095659,Other,Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation  however  the specific translational regulatory mechanisms remain unclear. Here  our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR  which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes  which ensures that the mRNA synthesized and stored during the growth stage of oocytes  is necessary for the normal growth and development of oocytes.,,,,,wt1,,strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:wt biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,wt1,wt1,wt1,wt ovary,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP499426,,,wt1_1.fq.gz wt1_2.fq.gz,fastq fastq,5436554400.0,18121848.0,wt1 1.fq.gz,0:150 1:150,A:1418897733;C:1287256771;G:1297629578;T:1432736726;N:33592,150,150,,,1418897733,1287256771,1297629578,1432736726,33592,SRX24137314,SRS20921921,,,Shenzhen Second People's Hospital,2,0.9407,0.94657,0.02199,0.02152,0.74655,0.74679,0.47086,0.47165,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-04-03,Adult,Adult,Gonad,Reproductive System
31837,SRR28709001,SRX24276192,SRS21041156,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs  member 9  an extracellular matrix ECM metalloprotease  participates in primordial germ cell PGC migration and necessary for female fertility. In this study  we found that adamts9 knockout KO led to reduced body size  and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however  primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation  significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO  and arrested development at Stage IB follicles in mid  or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq  we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together  our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish  and loss of adamts9 in zebrafish leads to ovarian follicle arrest  female infertility  and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence  we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf61 Ov mt 3,GSM8212808,,source name:Ovary|tissue:Ovary|age:dpf 61|genotype:mutant|geo loc name:missing|collection date:missing,dpf61 Ov mt 3,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod  lights on at 8:30am  lights off at 10:30pm; at water temperature of 28.5°C  pH of approximately 7.2  and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 61|genotype:mutant,GSM8212808,GSM8212808: dpf61 Ov mt 3; Danio rerio; RNA Seq,GSM8212808 r1,GSM8212808,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.M43_20230510_103430.L001.1.fastq.gz NS51397.M43_20230510_103430.L001.2.fastq.gz,fastq fastq,9024444634.0,29882267.0,GSM8212808 r1,0:151 1:151,A:2471288260;C:1931225512;G:2256742565;T:2363378475;N:1809822,151,151,,,2471288260,1931225512,2256742565,2363378475,1809822,SRX24276192,SRS21041156,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31838,SRR28709002,SRX24276191,SRS21041154,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs  member 9  an extracellular matrix ECM metalloprotease  participates in primordial germ cell PGC migration and necessary for female fertility. In this study  we found that adamts9 knockout KO led to reduced body size  and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however  primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation  significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO  and arrested development at Stage IB follicles in mid  or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq  we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together  our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish  and loss of adamts9 in zebrafish leads to ovarian follicle arrest  female infertility  and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence  we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf61 Ov mt 2,GSM8212807,,source name:Ovary|tissue:Ovary|age:dpf 61|genotype:mutant|geo loc name:missing|collection date:missing,dpf61 Ov mt 2,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod  lights on at 8:30am  lights off at 10:30pm; at water temperature of 28.5°C  pH of approximately 7.2  and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 61|genotype:mutant,GSM8212807,GSM8212807: dpf61 Ov mt 2; Danio rerio; RNA Seq,GSM8212807 r1,GSM8212807,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.M41_20230510_103430.L001.1.fastq.gz NS51397.M41_20230510_103430.L001.2.fastq.gz,fastq fastq,13553131538.0,44877919.0,GSM8212807 r1,0:151 1:151,A:3707129145;C:2878818514;G:3433054125;T:3531357698;N:2772056,151,151,,,3707129145,2878818514,3433054125,3531357698,2772056,SRX24276191,SRS21041154,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System