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 2500,360Application ReadForward1,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 2500,360Application ReadForward1,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 2500,360Application ReadForward1,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 2500,360Application ReadForward1,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 2500,360Application ReadForward1,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 2500,360Application ReadForward1,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 2500,360Application ReadForward1,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 2500,360Application ReadForward1,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 2500,360Application ReadForward1,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 2500,360Application ReadForward1,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 2500,360Application ReadForward1,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 2500,360Application ReadForward1,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 2500,360Application ReadForward1,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 2500,360Application ReadForward1,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 2500,360Application ReadForward1,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 2500,360Application ReadForward1,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 2500,360Application ReadForward1,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 2500,360Application ReadForward1,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 2500,360Application ReadForward1,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
4407,ERR1427376,ERX1497908,ERS1183210,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#48,SAMEA4012100,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012100|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#48|broker name:ArrayExpress|common name:zebrafish|fsc:NaN|gfp:NaN|individual:2|pi:NaN|plate:7|sample name:E MTAB 4617:LCK 7#48|ssc:NaN|tissue:Testes|well:H6,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#48,LCK 7#48,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Testes:tissue|Experimental Factor: NaN:fsc|Experimental Factor: NaN:ssc|Experimental Factor: NaN:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,2500FApplication ReadForward11RApplication ReadReverse126,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_48_mod.bam LCK_7_48.cram,bam cram,,,E MTAB 4617:LCK 7#48,0:125 1:125,A:84706839;C:81480882;G:75512683;T:89639016;N:40330,125,125,,,84706839,81480882,75512683,89639016,40330,ERX1497908,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.19405,0.19075,0.02782,0.02779,0.9795,0.98013,0.73205,0.73409,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Gonad,Reproductive System
4415,ERR1427368,ERX1497900,ERS1183202,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#40,SAMEA4012092,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012092|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#40|broker name:ArrayExpress|common name:zebrafish|fsc:NaN|gfp:NaN|individual:2|pi:NaN|plate:7|sample name:E MTAB 4617:LCK 7#40|ssc:NaN|tissue:Testes|well:H5,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#40,LCK 7#40,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Testes:tissue|Experimental Factor: NaN:fsc|Experimental Factor: NaN:ssc|Experimental Factor: NaN:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,2500FApplication ReadForward11RApplication ReadReverse126,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_40_mod.bam LCK_7_40.cram,bam cram,,,E MTAB 4617:LCK 7#40,0:125 1:125,A:98690446;C:95653530;G:87621123;T:105368805;N:43346,125,125,,,98690446,95653530,87621123,105368805,43346,ERX1497900,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.20112,0.19727,0.01661,0.01621,0.9797,0.9806,0.44206,0.42908,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Gonad,Reproductive System
4424,ERR1427359,ERX1497891,ERS1183193,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#32,SAMEA4012083,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012083|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#32|broker name:ArrayExpress|common name:zebrafish|fsc:NaN|gfp:NaN|individual:2|pi:NaN|plate:7|sample name:E MTAB 4617:LCK 7#32|ssc:NaN|tissue:Testes|well:H4,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#32,LCK 7#32,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Testes:tissue|Experimental Factor: NaN:fsc|Experimental Factor: NaN:ssc|Experimental Factor: NaN:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,2500FApplication ReadForward11RApplication ReadReverse126,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_32_mod.bam LCK_7_32.cram,bam cram,,,E MTAB 4617:LCK 7#32,0:125 1:125,A:102670073;C:105552903;G:96042262;T:111286167;N:48595,125,125,,,102670073,105552903,96042262,111286167,48595,ERX1497891,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.0367,0.03586,0.00293,0.00297,0.99316,0.99387,0.82316,0.80581,125,125,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Gonad,Reproductive System
4433,ERR1427350,ERX1497882,ERS1183184,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#24,SAMEA4012074,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012074|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#24|broker name:ArrayExpress|common name:zebrafish|fsc:NaN|gfp:NaN|individual:2|pi:NaN|plate:7|sample name:E MTAB 4617:LCK 7#24|ssc:NaN|tissue:Testes|well:H3,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#24,LCK 7#24,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Testes:tissue|Experimental Factor: NaN:fsc|Experimental Factor: NaN:ssc|Experimental Factor: NaN:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,2500FApplication ReadForward11RApplication ReadReverse126,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_24_mod.bam LCK_7_24.cram,bam cram,,,E MTAB 4617:LCK 7#24,0:125 1:125,A:97411995;C:91321821;G:84912221;T:100868660;N:45803,125,125,,,97411995,91321821,84912221,100868660,45803,ERX1497882,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.25757,0.25144,0.03087,0.02958,0.97642,0.97695,0.71128,0.71145,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Gonad,Reproductive System
4442,ERR1427341,ERX1497873,ERS1183175,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#16,SAMEA4012065,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012065|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#16|broker name:ArrayExpress|common name:zebrafish|fsc:NaN|gfp:NaN|individual:2|pi:NaN|plate:7|sample name:E MTAB 4617:LCK 7#16|ssc:NaN|tissue:Testes|well:H2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#16,LCK 7#16,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Testes:tissue|Experimental Factor: NaN:fsc|Experimental Factor: NaN:ssc|Experimental Factor: NaN:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,2500FApplication ReadForward11RApplication ReadReverse126,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_16_mod.bam LCK_7_16.cram,bam cram,,,E MTAB 4617:LCK 7#16,0:125 1:125,A:81321616;C:79315899;G:72476597;T:85676964;N:38424,125,125,,,81321616,79315899,72476597,85676964,38424,ERX1497873,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.20776,0.20306,0.02431,0.02397,0.9654,0.96621,0.66321,0.66592,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Gonad,Reproductive System
5793,ERR1955208,ERX2020800,ERS1697077,ERP017053,PRJEB15333,Transposon driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution,ena-STUDY-EMBL EUROPEAN BIOINFORMATICS INSTITUTE-07-09-2016-10:25:55:499-247,Other,In order to better understand the features associated with male germline transcription we profiled the RNA expression in a number of germline cell types. These include spermatogonial stem cells spermatocytes and round spermatids in mouse and spermatocytes in rat. We also profiled the transcription in zebrafish testes. As a consequence it became apparent that transposable elements are driving considerable lncRNA expression in the later stages of spermatogenesis. This is particularly apparent in the case of endogenous retroviruses in rodents.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 05 08,,,Transcriptional profiling of zebrafish testes for analysis of conserved repeat element associations,SAMEA104033184,EMBL EUROPEAN BIOINFORMATICS INSTITUTE,ENA FIRST PUBLIC:2017 05 10T17:01:28Z|ENA LAST UPDATE:2017 04 28T10:34:37Z|External Id:SAMEA104033184|INSDC center name:EMBL EUROPEAN BIOINFORMATICS INSTITUTE|INSDC first public:2017 05 10T17:01:28Z|INSDC last update:2017 04 28T10:34:37Z|INSDC status:public|Submitter Id:Zebrafish.Testis 2|common name:zebrafish|sample name:Zebrafish.Testis 2|scientific name:Danio rerio|strain:AB|tissue type:testis,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 16,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP017053,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 05 10|ENA LAST UPDATE:2018 11 16,zebrafish_testis_2.conserved.1.fastq.gz zebrafish_testis_2.conserved.2.fastq.gz,fastq fastq,46555372886.0,230472143.0,ena RUN EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 16,0:101 1:101,A:12260062264;C:10888457642;G:11605642683;T:11637267744;N:163942553,101,101,,,12260062264,10888457642,11605642683,11637267744,163942553,ERX2020800,ERS1697077,ERA904389,EMBL EUROPEAN BIOINFORMATICS INSTITUTE|European Nucleotide Archive,EMBL EUROPEAN BIOINFORMATICS INSTITUTE,2,0.93165,0.92785,0.29822,0.32141,0.71386,0.71971,0.66173,0.63843,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2017-01-31,Undetermined,Undetermined,Gonad,Reproductive System
5794,ERR1955207,ERX2020799,ERS1697076,ERP017053,PRJEB15333,Transposon driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution,ena-STUDY-EMBL EUROPEAN BIOINFORMATICS INSTITUTE-07-09-2016-10:25:55:499-247,Other,In order to better understand the features associated with male germline transcription we profiled the RNA expression in a number of germline cell types. These include spermatogonial stem cells spermatocytes and round spermatids in mouse and spermatocytes in rat. We also profiled the transcription in zebrafish testes. As a consequence it became apparent that transposable elements are driving considerable lncRNA expression in the later stages of spermatogenesis. This is particularly apparent in the case of endogenous retroviruses in rodents.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 05 08,,,Transcriptional profiling of zebrafish testes for analysis of conserved repeat element associations,SAMEA104033183,EMBL EUROPEAN BIOINFORMATICS INSTITUTE,ENA FIRST PUBLIC:2017 05 10T17:01:28Z|ENA LAST UPDATE:2017 04 28T10:34:37Z|External Id:SAMEA104033183|INSDC center name:EMBL EUROPEAN BIOINFORMATICS INSTITUTE|INSDC first public:2017 05 10T17:01:28Z|INSDC last update:2017 04 28T10:34:37Z|INSDC status:public|Submitter Id:Zebrafish.Testis 1|common name:zebrafish|sample name:Zebrafish.Testis 1|scientific name:Danio rerio|strain:AB|tissue type:testis,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 15,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP017053,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 05 10|ENA LAST UPDATE:2018 11 16,zebrafish_testis_1.conserved.1.fastq.gz zebrafish_testis_1.conserved.2.fastq.gz,fastq fastq,41056086708.0,203247954.0,ena RUN EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 15,0:101 1:101,A:10675591750;C:9672762387;G:10139834713;T:10380949257;N:186948601,101,101,,,10675591750,9672762387,10139834713,10380949257,186948601,ERX2020799,ERS1697076,ERA904389,EMBL EUROPEAN BIOINFORMATICS INSTITUTE|European Nucleotide Archive,EMBL EUROPEAN BIOINFORMATICS INSTITUTE,2,0.92308,0.9157,0.30221,0.31293,0.68276,0.68836,0.56114,0.5857,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2017-01-31,Undetermined,Undetermined,Gonad,Reproductive System
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 4000,2000FApplication ReadForward11RApplication ReadReverse101,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 4000,2000FApplication ReadForward11RApplication ReadReverse101,ERP112513,Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danionine species,ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05,FCHNW2WBBXX_L6_HKZEBodsEAAERAAPEI-208_1.fq.gz FCHNW2WBBXX_L6_HKZEBodsEAAERAAPEI-208_2.fq.gz,fastq fastq,3574419200.0,17872096.0,E MTAB 7476:FCHNW2WBBXX L6 HKZEBodsEAAERAAPEI 208 ,0:100 1:100,A:927454175;C:863033369;G:844910972;T:938253904;N:766780,100,100,,,927454175,863033369,844910972,938253904,766780,ERX2986065,ERS2955653,ERA1674470,"University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive","University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive",2,0.93851,0.93973,0.02799,0.02809,0.72701,0.72914,0.48827,0.48841,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2018-12-05,Adult,Adult,Gonad,Reproductive System
24582,SRR25462250,SRX21195051,SRS18453977,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/ zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG HE 8mpf 3,GSM7669027,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing,PG HE 8mpf 3,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ ,GSM7669027,GSM7669027: PG HE 8mpf 3; Danio rerio; RNA Seq,GSM7669027 r1,GSM7669027,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,HE_PG_8mpf_3_S11_L003_R1_001.fastq.gz HE_PG_8mpf_3_S11_L003_R2_001.fastq.gz,fastq fastq,7161373434.0,60309247.0,GSM7669027 r1,0:59.39 1:59.35,A:1783731260;C:1744025029;G:1733970346;T:1880173306;N:19473493,59,59,,,1783731260,1744025029,1733970346,1880173306,19473493,SRX21195051,SRS18453977,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94187,0.94592,0.01475,0.01464,0.77447,0.77498,0.45855,0.4635,60,60,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Adult,Adult,Gonad,Reproductive System
24583,SRR25462251,SRX21195050,SRS18453976,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/ zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG HE 8mpf 2,GSM7669026,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing,PG HE 8mpf 2,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ ,GSM7669026,GSM7669026: PG HE 8mpf 2; Danio rerio; RNA Seq,GSM7669026 r1,GSM7669026,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,HE_PG_8mpf_2_S7_L003_R1_001.fastq.gz HE_PG_8mpf_2_S7_L003_R2_001.fastq.gz,fastq fastq,3176994053.0,26828357.0,GSM7669026 r1,0:59.22 1:59.20,A:793619267;C:767135191;G:764404567;T:830643823;N:21191205,59,59,,,793619267,767135191,764404567,830643823,21191205,SRX21195050,SRS18453976,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.93822,0.94226,0.01596,0.0161,0.77684,0.77772,0.47008,0.46904,59,60,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Adult,Adult,Gonad,Reproductive System
24584,SRR25462252,SRX21195049,SRS18453975,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/ zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG HE 8mpf 1,GSM7669025,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing,PG HE 8mpf 1,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ ,GSM7669025,GSM7669025: PG HE 8mpf 1; Danio rerio; RNA Seq,GSM7669025 r1,GSM7669025,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,HE_PG_8mpf_1_S6_L003_R1_001.fastq.gz HE_PG_8mpf_1_S6_L003_R2_001.fastq.gz,fastq fastq,4587580737.0,38590260.0,GSM7669025 r1,0:59.45 1:59.43,A:1149031944;C:1121086335;G:1106925902;T:1203970839;N:6565717,59,59,,,1149031944,1121086335,1106925902,1203970839,6565717,SRX21195049,SRS18453975,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94032,0.9437,0.01481,0.01462,0.77682,0.77774,0.45843,0.4699,58,60,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Adult,Adult,Gonad,Reproductive System
24585,SRR25462253,SRX21195048,SRS18453974,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/ zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG WT 8mpf 3,GSM7669024,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing,PG WT 8mpf 3,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+,GSM7669024,GSM7669024: PG WT 8mpf 3; Danio rerio; RNA Seq,GSM7669024 r1,GSM7669024,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,WT_PG_8mpf_3_S8_L003_R2_001.fastq.gz WT_PG_8mpf_3_S8_L003_R1_001.fastq.gz,fastq fastq,3920821867.0,33089226.0,GSM7669024 r1,0:59.26 1:59.23,A:977738236;C:951999354;G:944769809;T:1023828622;N:22485846,59,59,,,977738236,951999354,944769809,1023828622,22485846,SRX21195048,SRS18453974,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94193,0.94555,0.01657,0.01646,0.76784,0.76919,0.47238,0.47016,60,60,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Adult,Adult,Gonad,Reproductive System
24586,SRR25462254,SRX21195047,SRS18453973,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/ zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG WT 8mpf 2,GSM7669023,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing,PG WT 8mpf 2,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+,GSM7669023,GSM7669023: PG WT 8mpf 2; Danio rerio; RNA Seq,GSM7669023 r1,GSM7669023,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,WT_PG_8mpf_2_S10_L003_R2_001.fastq.gz WT_PG_8mpf_2_S10_L003_R1_001.fastq.gz,fastq fastq,4917868553.0,41430484.0,GSM7669023 r1,0:59.37 1:59.33,A:1231173294;C:1195692797;G:1182545852;T:1292018757;N:16437853,59,59,,,1231173294,1195692797,1182545852,1292018757,16437853,SRX21195047,SRS18453973,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94048,0.94432,0.0178,0.0178,0.75645,0.7569,0.46332,0.46812,59,57,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Adult,Adult,Gonad,Reproductive System
24587,SRR25462255,SRX21195046,SRS18453972,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/ zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG WT 8mpf 1,GSM7669022,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing,PG WT 8mpf 1,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+,GSM7669022,GSM7669022: PG WT 8mpf 1; Danio rerio; RNA Seq,GSM7669022 r1,GSM7669022,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,WT_PG_8mpf_1_S9_L003_R1_001.fastq.gz WT_PG_8mpf_1_S9_L003_R2_001.fastq.gz,fastq fastq,3375380667.0,28408784.0,GSM7669022 r1,0:59.42 1:59.40,A:842316103;C:825987175;G:818715765;T:881225528;N:7136096,59,59,,,842316103,825987175,818715765,881225528,7136096,SRX21195046,SRS18453972,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94039,0.9444,0.0162,0.01617,0.7697,0.76986,0.47132,0.46938,60,60,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Adult,Adult,Gonad,Reproductive System
24588,SRR25462256,SRX21195045,SRS18453971,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/ zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG HE 50dpf 3,GSM7669021,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing,PG HE 50dpf 3,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ ,GSM7669021,GSM7669021: PG HE 50dpf 3; Danio rerio; RNA Seq,GSM7669021 r1,GSM7669021,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_HE_3_S26_L003_R1_001.fastq.gz PG_HE_3_S26_L003_R2_001.fastq.gz,fastq fastq,4520051001.0,22984712.0,GSM7669021 r1,0:98.32 1:98.33,A:1134815259;C:1102592573;G:1104475707;T:1160918938;N:17248524,98,98,,,1134815259,1102592573,1104475707,1160918938,17248524,SRX21195045,SRS18453971,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.93438,0.93937,0.01237,0.01252,0.78208,0.78192,0.48454,0.49474,99,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
24589,SRR25462257,SRX21195044,SRS18453970,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/ zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG HE 50dpf 2,GSM7669020,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing,PG HE 50dpf 2,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ ,GSM7669020,GSM7669020: PG HE 50dpf 2; Danio rerio; RNA Seq,GSM7669020 r1,GSM7669020,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_HE_2_S25_L003_R2_001.fastq.gz PG_HE_2_S25_L003_R1_001.fastq.gz,fastq fastq,3915471868.0,19847479.0,GSM7669020 r1,0:98.64 1:98.64,A:982714666;C:957212118;G:961590362;T:1003408448;N:10546274,98,98,,,982714666,957212118,961590362,1003408448,10546274,SRX21195044,SRS18453970,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.93184,0.93552,0.01275,0.01275,0.78356,0.7835,0.49472,0.48841,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
24590,SRR25462258,SRX21195043,SRS18453969,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/ zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG HE 50dpf 1,GSM7669019,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing,PG HE 50dpf 1,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ ,GSM7669019,GSM7669019: PG HE 50dpf 1; Danio rerio; RNA Seq,GSM7669019 r1,GSM7669019,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_HE_1_S24_L003_R1_001.fastq.gz PG_HE_1_S24_L003_R2_001.fastq.gz,fastq fastq,4764998144.0,24264412.0,GSM7669019 r1,0:98.18 1:98.20,A:1194676445;C:1161648051;G:1165061360;T:1221860864;N:21751424,98,98,,,1194676445,1161648051,1165061360,1221860864,21751424,SRX21195043,SRS18453969,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.91864,0.92247,0.01213,0.01245,0.7949,0.79584,0.50422,0.50318,100,98,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
24591,SRR25462259,SRX21195042,SRS18453968,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/ zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG WT 50dpf 3,GSM7669018,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing,PG WT 50dpf 3,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+,GSM7669018,GSM7669018: PG WT 50dpf 3; Danio rerio; RNA Seq,GSM7669018 r1,GSM7669018,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_WT_3_S23_L003_R1_001.fastq.gz PG_WT_3_S23_L003_R2_001.fastq.gz,fastq fastq,6204452412.0,31480139.0,GSM7669018 r1,0:98.55 1:98.54,A:1567898375;C:1505755791;G:1512895523;T:1599284546;N:18618177,98,98,,,1567898375,1505755791,1512895523,1599284546,18618177,SRX21195042,SRS18453968,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.9312,0.93599,0.01692,0.01686,0.76426,0.76439,0.46519,0.47751,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
24592,SRR25462260,SRX21195041,SRS18453967,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/ zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG WT 50dpf 2,GSM7669017,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing,PG WT 50dpf 2,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+,GSM7669017,GSM7669017: PG WT 50dpf 2; Danio rerio; RNA Seq,GSM7669017 r1,GSM7669017,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_WT_2_S22_L003_R1_001.fastq.gz PG_WT_2_S22_L003_R2_001.fastq.gz,fastq fastq,3907759829.0,19906505.0,GSM7669017 r1,0:98.15 1:98.15,A:991973983;C:940499355;G:946342572;T:1011476708;N:17467211,98,98,,,991973983,940499355,946342572,1011476708,17467211,SRX21195041,SRS18453967,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.91435,0.9186,0.02035,0.02032,0.764,0.76321,0.48743,0.48644,97,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
24593,SRR25462261,SRX21195040,SRS18453966,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/ zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG WT 50dpf 1,GSM7669016,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing,PG WT 50dpf 1,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+,GSM7669016,GSM7669016: PG WT 50dpf 1; Danio rerio; RNA Seq,GSM7669016 r1,GSM7669016,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_WT_1_S21_L003_R2_001.fastq.gz PG_WT_1_S21_L003_R1_001.fastq.gz,fastq fastq,7395136401.0,37752582.0,GSM7669016 r1,0:97.94 1:97.94,A:1865709287;C:1789949400;G:1796311820;T:1908470411;N:34695483,97,97,,,1865709287,1789949400,1796311820,1908470411,34695483,SRX21195040,SRS18453966,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.9216,0.92737,0.01817,0.01802,0.76601,0.76593,0.48894,0.4975,100,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
24594,SRR25462243,SRX21195038,SRS18453964,SRP452269,PRJNA1000446,Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish,GSE239623,Transcriptome Analysis,Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PV M3,GSM7669033,,source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing,PV M3,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / ,GSM7669033,GSM7669033: PV M3; Danio rerio; RNA Seq,GSM7669033 r1,GSM7669033,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452269,,,PV_M3_R1.fastq.gz PV_M3_R2.fastq.gz,fastq fastq,4644457090.0,23465750.0,GSM7669033 r1,0:98.98 1:98.94,A:1196567358;C:1114203322;G:1109379777;T:1223156356;N:1150277,98,98,,,1196567358,1114203322,1109379777,1223156356,1150277,SRX21195038,SRS18453964,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94849,0.95248,0.02727,0.02708,0.73602,0.73718,0.48396,0.4855,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Undetermined,Embryo,Gonad,Reproductive System
24595,SRR25462244,SRX21195037,SRS18453963,SRP452269,PRJNA1000446,Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish,GSE239623,Transcriptome Analysis,Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PV M2,GSM7669032,,source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing,PV M2,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / ,GSM7669032,GSM7669032: PV M2; Danio rerio; RNA Seq,GSM7669032 r1,GSM7669032,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452269,,,PV_M2_R1.fastq.gz PV_M2_R2.fastq.gz,fastq fastq,2464506276.0,12449948.0,GSM7669032 r1,0:98.99 1:98.96,A:632587002;C:593372099;G:591579950;T:646214108;N:753117,98,98,,,632587002,593372099,591579950,646214108,753117,SRX21195037,SRS18453963,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94889,0.9522,0.02585,0.02585,0.73669,0.73841,0.48398,0.48486,100,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Undetermined,Embryo,Gonad,Reproductive System
24596,SRR25462245,SRX21195036,SRS18453962,SRP452269,PRJNA1000446,Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish,GSE239623,Transcriptome Analysis,Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PV M1,GSM7669031,,source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing,PV M1,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / ,GSM7669031,GSM7669031: PV M1; Danio rerio; RNA Seq,GSM7669031 r1,GSM7669031,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452269,,,PV_M1_R1.fastq.gz PV_M1_R2.fastq.gz,fastq fastq,3634173229.0,18461903.0,GSM7669031 r1,0:98.44 1:98.41,A:930322973;C:875929476;G:875710056;T:948595199;N:3615525,98,98,,,930322973,875929476,875710056,948595199,3615525,SRX21195036,SRS18453962,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94787,0.95134,0.02457,0.02445,0.73762,0.73843,0.48244,0.48069,100,98,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Undetermined,Embryo,Gonad,Reproductive System
24597,SRR25462246,SRX21195035,SRS18453961,SRP452269,PRJNA1000446,Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish,GSE239623,Transcriptome Analysis,Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PV WT3,GSM7669030,,source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing,PV WT3,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+,GSM7669030,GSM7669030: PV WT3; Danio rerio; RNA Seq,GSM7669030 r1,GSM7669030,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452269,,,PV_WT3_R2.fastq PV_WT3_R1.fastq,fastq fastq,2965772270.0,14976621.0,GSM7669030 r1,0:99.03 1:98.99,A:759343389;C:716154246;G:713466520;T:775995980;N:812135,99,98,,,759343389,716154246,713466520,775995980,812135,SRX21195035,SRS18453961,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.95027,0.95485,0.02356,0.02292,0.74422,0.74554,0.47974,0.48267,100,98,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Undetermined,Embryo,Gonad,Reproductive System
24598,SRR25462247,SRX21195034,SRS18453960,SRP452269,PRJNA1000446,Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish,GSE239623,Transcriptome Analysis,Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PV WT2,GSM7669029,,source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing,PV WT2,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+,GSM7669029,GSM7669029: PV WT2; Danio rerio; RNA Seq,GSM7669029 r1,GSM7669029,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452269,,,PV_WT2_R2.fastq PV_WT2_R1.fastq,fastq fastq,2021387268.0,10195384.0,GSM7669029 r1,0:99.15 1:99.12,A:517788644;C:487363563;G:485168383;T:530550229;N:516449,99,99,,,517788644,487363563,485168383,530550229,516449,SRX21195034,SRS18453960,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.95113,0.9544,0.02394,0.02364,0.74168,0.74363,0.47881,0.47499,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Undetermined,Embryo,Gonad,Reproductive System
24599,SRR25462248,SRX21195033,SRS18453959,SRP452269,PRJNA1000446,Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish,GSE239623,Transcriptome Analysis,Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PV WT1,GSM7669028,,source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing,PV WT1,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+,GSM7669028,GSM7669028: PV WT1; Danio rerio; RNA Seq,GSM7669028 r1,GSM7669028,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452269,,,PV_WT1_R1.fastq PV_WT1_R2.fastq,fastq fastq,3244660111.0,16481925.0,GSM7669028 r1,0:98.44 1:98.42,A:831426044;C:781489498;G:779991004;T:848549246;N:3204319,98,98,,,831426044,781489498,779991004,848549246,3204319,SRX21195033,SRS18453959,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94779,0.95185,0.02328,0.02298,0.74294,0.74391,0.48052,0.47966,95,95,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Undetermined,Embryo,Gonad,Reproductive System
25267,SRR25744342,SRX21467662,SRS18702380,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad eif4e1b 3,GSM7730282,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / |geo loc name:missing|collection date:missing,Gonad eif4e1b 3,RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / ,GSM7730282,GSM7730282: Gonad eif4e1b 3; Danio rerio; ssRNA seq,GSM7730282 r1,GSM7730282,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_HOM3_1.fastq.gz Ovary_HOM3_2.fastq.gz,fastq fastq,2170738056.0,10746228.0,GSM7730282 r1,0:101 1:101,A:531993767;C:520631008;G:565772072;T:552334154;N:7055,101,101,,,531993767,520631008,565772072,552334154,7055,SRX21467662,SRS18702380,SRA1698764,IMP,IMP,2,0.77665,0.7702,0.14988,0.14284,0.66716,0.66957,0.49991,0.47425,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
25268,SRR25744343,SRX21467661,SRS18702379,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad eif4e1b 2,GSM7730281,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / |geo loc name:missing|collection date:missing,Gonad eif4e1b 2,RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / ,GSM7730281,GSM7730281: Gonad eif4e1b 2; Danio rerio; ssRNA seq,GSM7730281 r1,GSM7730281,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_HOM2_1.fastq.gz Ovary_HOM2_2.fastq.gz,fastq fastq,3459149000.0,17124500.0,GSM7730281 r1,0:101 1:101,A:876732239;C:796603142;G:882912604;T:902886783;N:14232,101,101,,,876732239,796603142,882912604,902886783,14232,SRX21467661,SRS18702379,SRA1698764,IMP,IMP,2,0.81761,0.79589,0.26282,0.24746,0.70607,0.7039,0.50658,0.49236,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
25269,SRR25744344,SRX21467660,SRS18702381,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad eif4e1b 1,GSM7730280,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / |geo loc name:missing|collection date:missing,Gonad eif4e1b 1,RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / ,GSM7730280,GSM7730280: Gonad eif4e1b 1; Danio rerio; ssRNA seq,GSM7730280 r1,GSM7730280,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_HOM1_1.fastq.gz Ovary_HOM1_2.fastq.gz,fastq fastq,2189781202.0,10840501.0,GSM7730280 r1,0:101 1:101,A:537591255;C:525448020;G:568979980;T:557754770;N:7177,101,101,,,537591255,525448020,568979980,557754770,7177,SRX21467660,SRS18702381,SRA1698764,IMP,IMP,2,0.7459,0.74191,0.15778,0.15291,0.65543,0.65841,0.48578,0.48291,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
25270,SRR25744345,SRX21467659,SRS18702378,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad WT 3,GSM7730279,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+|geo loc name:missing|collection date:missing,Gonad WT 3,RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+,GSM7730279,GSM7730279: Gonad WT 3; Danio rerio; ssRNA seq,GSM7730279 r1,GSM7730279,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_WT3_1.fastq.gz Ovary_WT3_2.fastq.gz,fastq fastq,3674041448.0,18188324.0,GSM7730279 r1,0:101 1:101,A:910831144;C:876967044;G:953299105;T:932928913;N:15242,101,101,,,910831144,876967044,953299105,932928913,15242,SRX21467659,SRS18702378,SRA1698764,IMP,IMP,2,0.89093,0.89038,0.09253,0.09348,0.73892,0.73858,0.47115,0.47218,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
25271,SRR25744346,SRX21467658,SRS18702377,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad WT 2,GSM7730278,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+|geo loc name:missing|collection date:missing,Gonad WT 2,RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+,GSM7730278,GSM7730278: Gonad WT 2; Danio rerio; ssRNA seq,GSM7730278 r1,GSM7730278,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_WT2_1.fastq.gz Ovary_WT2_2.fastq.gz,fastq fastq,3024886370.0,14974685.0,GSM7730278 r1,0:101 1:101,A:744374909;C:727299396;G:782294774;T:770904797;N:12494,101,101,,,744374909,727299396,782294774,770904797,12494,SRX21467658,SRS18702377,SRA1698764,IMP,IMP,2,0.91806,0.91689,0.06949,0.07178,0.74458,0.74474,0.47548,0.47338,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
25272,SRR25744347,SRX21467657,SRS18702376,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad WT 1,GSM7730277,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+|geo loc name:missing|collection date:missing,Gonad WT 1,RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+,GSM7730277,GSM7730277: Gonad WT 1; Danio rerio; ssRNA seq,GSM7730277 r1,GSM7730277,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_WT1_2.fastq.gz Ovary_WT1_1.fastq.gz,fastq fastq,3571638356.0,17681378.0,GSM7730277 r1,0:101 1:101,A:876280472;C:856417516;G:935896746;T:903028845;N:14777,101,101,,,876280472,856417516,935896746,903028845,14777,SRX21467657,SRS18702376,SRA1698764,IMP,IMP,2,0.89559,0.89353,0.09223,0.09423,0.73052,0.73012,0.47772,0.47408,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
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
29187,SRR8176747,SRX4996876,SRS4031879,SRP480945,PRJNA1055160,Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain,PRJNA1055160,Other,We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf,,pubmed:38529407,,Nadia 19dpf ZZ Gonad Single Cell RNA Seq,Nadia 19dpf ZZ Gonad Single Cell RNA Seq,,strain:Nadia|age:19 dpf provider:John H. Postlethwait University of Oregon|genotype:ZZ|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: Nadia 19dpf ZZ gonad,Nadia 19dpf ZZ gonad,Nadia 19dpf ZZ gonad,A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP480945,,loader:fastq load.py,,,15090036999.0,107021539.0,zz 19NAmale I1 001.fastq.gz,0:8 1:133,A:4154103253;C:3402890354;G:3765557416;T:3755723849;N:11762127,8,133,,,4154103253,3402890354,3765557416,3755723849,11762127,SRX4996876,SRS4031879,SRA807619,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2018-11-08,Larval,Larval,Gonad,Reproductive System
29188,SRR8176753,SRX4996870,SRS4031878,SRP480945,PRJNA1055160,Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain,PRJNA1055160,Other,We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf,,pubmed:38529407,,Nadia 30dpf ZZ Gonad Single Cell RNA Seq,Nadia 30dpf ZZ Gonad Single Cell RNA Seq,,strain:Nadia|age:30 dpf provider:John H. Postlethwait University of Oregon|genotype:ZZ|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: Nadia 30dpf ZZ gonad,Nadia 30dpf ZZ gonad,Nadia 30dpf ZZ gonad,A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP480945,,loader:fastq load.py,,,23587173438.0,167284918.0,1 I1 001.fastq.gz,0:8 1:133,A:6732844252;C:4934497997;G:5685086026;T:6219863789;N:14881374,8,133,,,6732844252,4934497997,5685086026,6219863789,14881374,SRX4996870,SRS4031878,SRA807619,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2018-11-08,Juvenile,Juvenile,Gonad,Reproductive System
29189,SRR8176754,SRX4996869,SRS4031877,SRP480945,PRJNA1055160,Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain,PRJNA1055160,Other,We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf,,pubmed:38529407,,Nadia 30dpf ZW Gonad Single Cell RNA Seq,Nadia 30dpf ZW Gonad Single Cell RNA Seq,,strain:Nadia|age:30 dpf provider:John H. Postlethwait University of Oregon|genotype:ZW|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: Nadia 30dpf ZW gonad,Nadia 30dpf ZW gonad,Nadia 30dpf ZW gonad,A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP480945,,loader:fastq load.py,,,43358808480.0,307509280.0,2 I1 001.fastq.gz,0:8 1:133,A:12290612367;C:8880655083;G:10261318751;T:11898771792;N:27450487,8,133,,,12290612367,8880655083,10261318751,11898771792,27450487,SRX4996869,SRS4031877,SRA807619,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2018-11-08,Juvenile,Juvenile,Gonad,Reproductive System
29190,SRR8176756,SRX4996867,SRS4031876,SRP480945,PRJNA1055160,Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain,PRJNA1055160,Other,We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf,,pubmed:38529407,,Nadia 19dpf ZW Gonad Single Cell RNA Seq,Nadia 19dpf ZW Gonad Single Cell RNA Seq,,strain:Nadia|age:19 dpf provider:John H. Postlethwait University of Oregon|genotype:ZW|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: Nadia 19dpf ZW gonad,Nadia 19dpf ZW gonad,Nadia 19dpf ZW gonad,A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP480945,,loader:fastq load.py,,,17141425554.0,121570394.0,zw 19NAfem I1 001.fastq.gz,0:8 1:133,A:4656207219;C:3824531650;G:4322736498;T:4324676442;N:13273745,8,133,,,4656207219,3824531650,4322736498,4324676442,13273745,SRX4996867,SRS4031876,SRA807619,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2018-11-08,Larval,Larval,Gonad,Reproductive System
29259,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