rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
50,DRR029944,DRX026962,DRS086502,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,ovulation duirng natural paring,zebrafish ovary isolated from adult fish at ovulation duirng natural paring. [RNAseq],SAMD00025434,,sample name:6 Ovu|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025434,DRX026962,6 Ovu,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025434,,,,351766656.0,9771296.0,DRR029944,0:36,A:79811727;C:85391142;G:90185809;T:96371771;N:6207,36,,,,79811727,85391142,90185809,96371771,6207,DRX026962,DRS086502,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91956,,0.01686,,0.76637,,0.45997,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
52,DRR029942,DRX026960,DRS086500,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo testosterone treatment,zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq  replicate],SAMD00025432,,sample name:4 Tes rep|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025432,DRX026960,4 Tes rep,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025432,,,,366042528.0,10167848.0,DRR029942,0:36,A:84988522;C:88640326;G:93559022;T:98847003;N:7655,36,,,,84988522,88640326,93559022,98847003,7655,DRX026960,DRS086500,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91602,,0.01846,,0.76015,,0.46475,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
53,DRR029941,DRX026959,DRS086499,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo testosterone treatment,zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq],SAMD00025431,,sample name:4 Tes|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025431,DRX026959,4 Tes,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025431,,,,1269835992.0,35273222.0,DRR029941,0:36,A:275250658;C:323605136;G:316729009;T:354204170;N:47019,36,,,,275250658,323605136,316729009,354204170,47019,DRX026959,DRS086499,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91467,,0.02353,,0.75962,,0.46861,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
54,DRR029940,DRX026958,DRS086498,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo diethylstilbestrol DES treatment,zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq  replicate],SAMD00025430,,sample name:3 DES rep|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025430,DRX026958,3 DES rep,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025430,,,,658651536.0,18295876.0,DRR029940,,,,,,,,,,,,DRX026958,DRS086498,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.89964,,0.01785,,0.76451,,0.45872,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
55,DRR029939,DRX026957,DRS086497,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo diethylstilbestrol DES treatment,zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq],SAMD00025429,,sample name:3 DES|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025429,DRX026957,3 DES,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025429,,,,1202024016.0,33389556.0,DRR029939,0:36,A:263319430;C:305852921;G:298798093;T:334008544;N:45028,36,,,,263319430,305852921,298798093,334008544,45028,DRX026957,DRS086497,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.90643,,0.02337,,0.75008,,0.47587,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
56,DRR029938,DRX026956,DRS086496,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo maturation inducing hormone DHP treatment,zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq  replicate],SAMD00025428,,sample name:2 DHP rep|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025428,DRX026956,2 DHP rep,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025428,,,,434243088.0,12062308.0,DRR029938,0:36,A:99859342;C:105890785;G:110526688;T:117957580;N:8693,36,,,,99859342,105890785,110526688,117957580,8693,DRX026956,DRS086496,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91529,,0.02061,,0.7595,,0.45809,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
57,DRR029937,DRX026955,DRS086495,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo maturation inducing hormone DHP treatment,zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq],SAMD00025427,,sample name:2 DHP|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025427,DRX026955,2 DHP,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025427,,,,1463868972.0,40663027.0,DRR029937,0:36,A:316060780;C:369221844;G:372845502;T:405685804;N:55042,36,,,,316060780,369221844,372845502,405685804,55042,DRX026955,DRS086495,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91556,,0.01967,,0.76621,,0.46541,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
58,DRR029936,DRX026954,DRS086494,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo ethanol treatment,zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq  replicate],SAMD00025426,,sample name:1 EtOH rep|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025426,DRX026954,1 EtOH rep,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025426,,,,438020208.0,12167228.0,DRR029936,0:36,A:101672612;C:105602774;G:110120652;T:120615069;N:9101,36,,,,101672612,105602774,110120652,120615069,9101,DRX026954,DRS086494,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.90777,,0.01929,,0.7652,,0.45988,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
59,DRR029935,DRX026953,DRS086493,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,in vivo ethanol treatment,zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq],SAMD00025425,,sample name:1 EtOH|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025425,DRX026953,1 EtOH,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025425,,,,1365603372.0,37933427.0,DRR029935,0:36,A:299786286;C:345487829;G:342408447;T:377870789;N:50021,36,,,,299786286,345487829,342408447,377870789,50021,DRX026953,DRS086493,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91103,,0.02142,,0.75402,,0.46574,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
174,DRR084198,DRX078029,DRS086523,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo testosterone treatment,zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq  replicate2],SAMD00073605,,sample name:TES1 4th|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073605,DRX078029,zebrafish ovary isolated from adult fish in vivo testosterone treatment. [RNAseq  replicate2],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073605,,,,1382763132.0,38410087.0,DRR084198,0:36,A:314367195;C:333340483;G:353519828;T:378654329;N:2881297,36,,,,314367195,333340483,353519828,378654329,2881297,DRX078029,DRS086523,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.90366,,0.02033,,0.77104,,0.46543,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
176,DRR084196,DRX078027,DRS086521,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo ethanol treatment,zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq  replicate2],SAMD00073603,,sample name:Et 4th|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073603,DRX078027,zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq  replicate2],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073603,,,,1456791660.0,40466435.0,DRR084196,0:36,A:336533534;C:355126203;G:368021063;T:394179246;N:2931614,36,,,,336533534,355126203,368021063,394179246,2931614,DRX078027,DRS086521,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.89408,,0.02082,,0.77027,,0.45866,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
177,DRR084195,DRX078026,DRS086520,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,natural paring late sample,zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq  replicate2],SAMD00073602,,sample name:O 4th|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073602,DRX078026,zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq  replicate2],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073602,,,,1627945092.0,45220697.0,DRR084195,0:36,A:381205209;C:392853175;G:410714269;T:439790560;N:3381879,36,,,,381205209,392853175,410714269,439790560,3381879,DRX078026,DRS086520,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.89419,,0.02159,,0.76848,,0.46407,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
178,DRR084194,DRX078025,DRS086519,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo maturation inducing hormone DHP treatment,zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq  replicate2],SAMD00073601,,sample name:DHP 4th|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073601,DRX078025,zebrafish ovary isolated from adult fish in vivo maturation inducing hormone DHP treatment. [RNAseq  replicate2],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073601,,,,969680196.0,26935561.0,DRR084194,0:36,A:223558856;C:233793515;G:244712298;T:265549055;N:2066472,36,,,,223558856,233793515,244712298,265549055,2066472,DRX078025,DRS086519,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.90178,,0.02203,,0.76579,,0.46491,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
179,DRR084193,DRX078024,DRS086518,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo diethylstilbestrol DES treatment,zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq  replicate2],SAMD00073600,,sample name:DES 4th|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073600,DRX078024,zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq  replicate2],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073600,,,,825301296.0,22925036.0,DRR084193,0:36,A:189771874;C:198593952;G:209666041;T:225480165;N:1789264,36,,,,189771874,198593952,209666041,225480165,1789264,DRX078024,DRS086518,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.90036,,0.0197,,0.7721,,0.45773,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
180,DRR084192,DRX078023,DRS086517,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,natural paring late sample,zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq  replicate1],SAMD00073599,,sample name:O|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073599,DRX078023,zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq  replicate1],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073599,,,,1474870356.0,40968621.0,DRR084192,0:36,A:334130826;C:361572335;G:369758908;T:409173431;N:234856,36,,,,334130826,361572335,369758908,409173431,234856,DRX078023,DRS086517,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91516,,0.02086,,0.76792,,0.47914,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
182,DRR084190,DRX078021,DRS086515,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo maturation inducing hormone DHP treatment,zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq  replicate1],SAMD00073597,,sample name:DHP|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073597,DRX078021,zebrafish ovary isolated from adult fish in vivo maturation inducing hormone DHP treatment. [RNAseq  replicate1],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073597,,,,1527194556.0,42422071.0,DRR084190,0:36,A:352068936;C:371030475;G:383086948;T:420761508;N:246689,36,,,,352068936,371030475,383086948,420761508,246689,DRX078021,DRS086515,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91815,,0.02248,,0.76209,,0.46867,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
183,DRR084189,DRX078020,DRS086514,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo testosterone treatment,zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq  replicate1],SAMD00073596,,sample name:TES|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073596,DRX078020,zebrafish ovary isolated from adult fish in vivo testosterone treatment. [RNAseq  replicate1],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073596,,,,1403618796.0,38989411.0,DRR084189,0:36,A:321063874;C:342718133;G:352434647;T:387171455;N:230687,36,,,,321063874,342718133,352434647,387171455,230687,DRX078020,DRS086514,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91583,,0.02212,,0.76073,,0.47596,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
184,DRR084188,DRX078019,DRS086513,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo diethylstilbestrol DES treatment,zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq  replicate1],SAMD00073595,,sample name:DES|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073595,DRX078019,zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq  replicate1],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073595,,,,1532053512.0,42557042.0,DRR084188,0:36,A:342701220;C:372650449;G:392432461;T:424025702;N:243680,36,,,,342701220,372650449,392432461,424025702,243680,DRX078019,DRS086513,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91276,,0.01965,,0.77358,,0.46461,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
185,DRR084187,DRX078018,DRS086512,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo ethanol treatment,zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq  replicate1],SAMD00073594,,sample name:EtOH|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073594,DRX078018,zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq  replicate1],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073594,,,,1152032724.0,32000909.0,DRR084187,0:36,A:265166034;C:279617628;G:285136940;T:321928656;N:183466,36,,,,265166034,279617628,285136940,321928656,183466,DRX078018,DRS086512,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.90791,,0.02405,,0.75972,,0.48931,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
29259,SRR27336917,SRX23013778,SRS19977075,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 PaternalKO gonads 31dpf rep2,miR214 PaternalKO gonads 31dpf rep2,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep2|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A11",miR214 PaternalKO gonads 31dpf rep2,miR214 PaternalKO gonads 31dpf rep2,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_PaternalKO_gonads_31dpf_rep2.fastq.gz,fastq,2327996832.0,27714248.0,miR214 PaternalKO gonads 31dpf rep2.fastq.gz,0:84,A:602135965;C:552786494;G:537368428;T:635697339;N:8606,84,,,,602135965,552786494,537368428,635697339,8606,SRX23013778,SRS19977075,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95369,,0.06146,,0.69203,,0.47259,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29260,SRR27336918,SRX23013777,SRS19977074,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 PaternalKO gonads 31dpf rep1,miR214 PaternalKO gonads 31dpf rep1,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep1|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A10",miR214 PaternalKO gonads 31dpf rep1,miR214 PaternalKO gonads 31dpf rep1,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_PaternalKO_gonads_31dpf_rep1.fastq.gz,fastq,2500978452.0,29773553.0,miR214 PaternalKO gonads 31dpf rep1.fastq.gz,0:84,A:646162933;C:593855971;G:578265372;T:682684551;N:9625,84,,,,646162933,593855971,578265372,682684551,9625,SRX23013777,SRS19977074,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95147,,0.05972,,0.69071,,0.47043,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29261,SRR27336919,SRX23013776,SRS19977073,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 maternalHET gonads 31dpf rep4,miR214 maternalHET gonads 31dpf rep4,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep4|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A9",miR214 maternalHET gonads 31dpf rep4,miR214 maternalHET gonads 31dpf rep4,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_maternalHET_gonads_31dpf_rep4.fastq.gz,fastq,2365480908.0,28160487.0,miR214 maternalHET gonads 31dpf rep4.fastq.gz,0:84,A:613121312;C:560582165;G:549338096;T:642429834;N:9501,84,,,,613121312,560582165,549338096,642429834,9501,SRX23013776,SRS19977073,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95304,,0.05342,,0.7108,,0.46822,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29262,SRR27336920,SRX23013775,SRS19977072,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 maternalHET gonads 31dpf rep3,miR214 maternalHET gonads 31dpf rep3,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep3|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A8",miR214 maternalHET gonads 31dpf rep3,miR214 maternalHET gonads 31dpf rep3,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_maternalHET_gonads_31dpf_rep3.fastq.gz,fastq,2537794644.0,30211841.0,miR214 maternalHET gonads 31dpf rep3.fastq.gz,0:84,A:658687178;C:600742464;G:585643169;T:692712057;N:9776,84,,,,658687178,600742464,585643169,692712057,9776,SRX23013775,SRS19977072,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95177,,0.06701,,0.68195,,0.47393,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29263,SRR27336921,SRX23013774,SRS19977071,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 maternalHET gonads 31dpf rep2,miR214 maternalHET gonads 31dpf rep2,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep2|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A7",miR214 maternalHET gonads 31dpf rep2,miR214 maternalHET gonads 31dpf rep2,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_maternalHET_gonads_31dpf_rep2.fastq.gz,fastq,2417384424.0,28778386.0,miR214 maternalHET gonads 31dpf rep2.fastq.gz,0:84,A:625935186;C:574179061;G:560498085;T:656762980;N:9112,84,,,,625935186,574179061,560498085,656762980,9112,SRX23013774,SRS19977071,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95259,,0.05852,,0.6981,,0.47435,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29264,SRR27336922,SRX23013773,SRS19977070,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 maternalHET gonads 31dpf rep1,miR214 maternalHET gonads 31dpf rep1,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep1|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A6",miR214 maternalHET gonads 31dpf rep1,miR214 maternalHET gonads 31dpf rep1,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_maternalHET_gonads_31dpf_rep1.fastq.gz,fastq,2330886180.0,27748645.0,miR214 maternalHET gonads 31dpf rep1.fastq.gz,0:84,A:601589571;C:554105326;G:542789267;T:632393158;N:8858,84,,,,601589571,554105326,542789267,632393158,8858,SRX23013773,SRS19977070,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95338,,0.05239,,0.71366,,0.47291,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29265,SRR27336923,SRX23013772,SRS19977069,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 maternalKO gonads 31dpf rep4,miR214 maternalKO gonads 31dpf rep4,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalKO|biological replicate:rep4|number of gonads:8 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A5",miR214 maternalKO gonads 31dpf rep4,miR214 maternalKO gonads 31dpf rep4,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_maternalKO_gonads_31dpf_rep4.fastq.gz,fastq,2340233784.0,27859926.0,miR214 maternalKO gonads 31dpf rep4.fastq.gz,0:84,A:606735187;C:553647808;G:539865459;T:639976430;N:8900,84,,,,606735187,553647808,539865459,639976430,8900,SRX23013772,SRS19977069,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95406,,0.06415,,0.68225,,0.47695,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29266,SRR27336924,SRX23013771,SRS19977068,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 maternalKO gonads 31dpf rep3,miR214 maternalKO gonads 31dpf rep3,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalKO|biological replicate:rep3|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A4",miR214 maternalKO gonads 31dpf rep3,miR214 maternalKO gonads 31dpf rep3,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_maternalKO_gonads_31dpf_rep3.fastq.gz,fastq,2058505512.0,24506018.0,miR214 maternalKO gonads 31dpf rep3.fastq.gz,0:84,A:537425814;C:485664494;G:471526682;T:563881213;N:7309,84,,,,537425814,485664494,471526682,563881213,7309,SRX23013771,SRS19977068,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95296,,0.06728,,0.69266,,0.47627,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29267,SRR27336925,SRX23013770,SRS19977067,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 PaternalHET gonads 31dpf rep4,miR214 PaternalHET gonads 31dpf rep4,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep4|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A17",miR214 PaternalHET gonads 31dpf rep4,miR214 PaternalHET gonads 31dpf rep4,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_PaternalHET_gonads_31dpf_rep4.fastq.gz,fastq,3001613328.0,35733492.0,miR214 PaternalHET gonads 31dpf rep4.fastq.gz,0:84,A:778860501;C:711155422;G:688784969;T:822801157;N:11279,84,,,,778860501,711155422,688784969,822801157,11279,SRX23013770,SRS19977067,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95361,,0.05653,,0.7051,,0.48382,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29268,SRR27336926,SRX23013769,SRS19977066,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 PaternalHET gonads 31dpf rep3,miR214 PaternalHET gonads 31dpf rep3,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep3|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A16",miR214 PaternalHET gonads 31dpf rep3,miR214 PaternalHET gonads 31dpf rep3,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_PaternalHET_gonads_31dpf_rep3.fastq.gz,fastq,3053630664.0,36352746.0,miR214 PaternalHET gonads 31dpf rep3.fastq.gz,0:84,A:785219727;C:726431662;G:713454025;T:828513556;N:11694,84,,,,785219727,726431662,713454025,828513556,11694,SRX23013769,SRS19977066,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95309,,0.04588,,0.71997,,0.46447,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29269,SRR27336927,SRX23013768,SRS19977065,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 PaternalHET gonads 31dpf rep2,miR214 PaternalHET gonads 31dpf rep2,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep2|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A15",miR214 PaternalHET gonads 31dpf rep2,miR214 PaternalHET gonads 31dpf rep2,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_PaternalHET_gonads_31dpf_rep2.fastq.gz,fastq,3063695208.0,36472562.0,miR214 PaternalHET gonads 31dpf rep2.fastq.gz,0:84,A:784924646;C:728941687;G:720847462;T:828969510;N:11903,84,,,,784924646,728941687,720847462,828969510,11903,SRX23013768,SRS19977065,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95413,,0.04739,,0.71936,,0.4704,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29270,SRR27336928,SRX23013767,SRS19977064,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 PaternalHET gonads 31dpf rep1,miR214 PaternalHET gonads 31dpf rep1,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep1|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A14",miR214 PaternalHET gonads 31dpf rep1,miR214 PaternalHET gonads 31dpf rep1,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_PaternalHET_gonads_31dpf_rep1.fastq.gz,fastq,2699154024.0,32132786.0,miR214 PaternalHET gonads 31dpf rep1.fastq.gz,0:84,A:694174797;C:642049572;G:627991562;T:734927762;N:10331,84,,,,694174797,642049572,627991562,734927762,10331,SRX23013767,SRS19977064,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95518,,0.05525,,0.70285,,0.47695,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29271,SRR27336929,SRX23013766,SRS19977063,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 PaternalKO gonads 31dpf rep4,miR214 PaternalKO gonads 31dpf rep4,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep4|number of gonads:8 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A13",miR214 PaternalKO gonads 31dpf rep4,miR214 PaternalKO gonads 31dpf rep4,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_PaternalKO_gonads_31dpf_rep4.fastq.gz,fastq,2514248016.0,29931524.0,miR214 PaternalKO gonads 31dpf rep4.fastq.gz,0:84,A:648908956;C:598837726;G:580002743;T:686488678;N:9913,84,,,,648908956,598837726,580002743,686488678,9913,SRX23013766,SRS19977063,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.94978,,0.06951,,0.67896,,0.47686,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29272,SRR27336930,SRX23013765,SRS19977062,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 PaternalKO gonads 31dpf rep3,miR214 PaternalKO gonads 31dpf rep3,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep3|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A12",miR214 PaternalKO gonads 31dpf rep3,miR214 PaternalKO gonads 31dpf rep3,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_PaternalKO_gonads_31dpf_rep3.fastq.gz,fastq,2499529200.0,29756300.0,miR214 PaternalKO gonads 31dpf rep3.fastq.gz,0:84,A:642490769;C:597403823;G:580565141;T:679060154;N:9313,84,,,,642490769,597403823,580565141,679060154,9313,SRX23013765,SRS19977062,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95284,,0.05602,,0.70289,,0.47154,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29273,SRR27336931,SRX23013764,SRS19977061,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 maternalKO gonads 31dpf rep2,miR214 maternalKO gonads 31dpf rep2,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalKO|biological replicate:rep2|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A3",miR214 maternalKO gonads 31dpf rep2,miR214 maternalKO gonads 31dpf rep2,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_maternalKO_gonads_31dpf_rep2.fastq.gz,fastq,2529742404.0,30115981.0,miR214 maternalKO gonads 31dpf rep2.fastq.gz,0:84,A:652091166;C:600932059;G:589100617;T:687608862;N:9700,84,,,,652091166,600932059,589100617,687608862,9700,SRX23013764,SRS19977061,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95498,,0.05524,,0.70366,,0.47319,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29274,SRR27336932,SRX23013763,SRS19977060,SRP479907,PRJNA1056454,miR214 regulates sex determination through gsdf in zebrafish,PRJNA1056454,Other,Sex determination is a variable and complex mechanism  yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it  we can provide a piece of the puzzle  which once again highlights the complexity and flexibility of sex determination.,,,CrisprCas9 generated using 2 sgRNAs  >F3  crossed toTgvasa:eGFP,miR214 maternalKO gonads 31dpf rep1,miR214 maternalKO gonads 31dpf rep1,,strain:mz 06de  tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalKO|biological replicate:rep1|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal,,,,,,,,,"= xlfn.CONCAT""mrna sequencing of zebrafish: "" A2",miR214 maternalKO gonads 31dpf rep1,miR214 maternalKO gonads 31dpf rep1,NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev  E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles  Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC  SR for 1 x 84 cycles plus 7 cycles for the index read.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP479907,,,miR214_maternalKO_gonads_31dpf_rep1.fastq.gz,fastq,2310878136.0,27510454.0,miR214 maternalKO gonads 31dpf rep1.fastq.gz,0:84,A:598541924;C:547875391;G:533137786;T:631314274;N:8761,84,,,,598541924,547875391,533137786,631314274,8761,SRX23013763,SRS19977060,SRA1775014,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.95279,,0.06446,,0.68757,,0.4758,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2023-12-24,Larval,Larval,Gonad,Reproductive System
29720,SRR27485665,SRX23156884,SRS20107305,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary R3,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: ovary  rep4,EV06008,EV06008,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV06008.R1.fastq.gz,fastq,585955025.0,7769646.0,EV06008.R1.fastq.gz,0:75.42,A:167210227;C:106735220;G:128095616;T:183896888;N:17074,75,,,,167210227,106735220,128095616,183896888,17074,SRX23156884,SRS20107305,SRA1783314,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.85544,,0.05096,,0.78441,,0.53007,,76,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-11,Adult,Adult,Gonad,Reproductive System
29731,SRR27485676,SRX23156873,SRS20107294,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: ovary  rep4,EV06001,EV06001,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV06001.R1.fastq.gz,fastq,685280356.0,9098789.0,EV06001.R1.fastq.gz,0:75.32,A:194596366;C:122550539;G:153504013;T:214558450;N:70988,75,,,,194596366,122550539,153504013,214558450,70988,SRX23156873,SRS20107294,SRA1783314,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.8304,,0.04498,,0.80166,,0.5028,,74,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-11,Adult,Adult,Gonad,Reproductive System
29738,SRR27477298,SRX23148649,SRS20099367,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|replicate:4|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: ovary  rep4,EV09001,EV09001,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV09001.R1.fastq.gz,fastq,456295310.0,6058854.0,EV09001.R1.fastq.gz,0:75.31,A:135579999;C:83364677;G:101608151;T:135700843;N:41640,75,,,,135579999,83364677,101608151,135700843,41640,SRX23148649,SRS20099367,SRA1782413,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.85088,,0.05876,,0.7791,,0.50948,,75,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-10,Adult,Adult,Gonad,Reproductive System
30755,SRR28348921,SRX23954975,SRS20755396,SRP495323,PRJNA1088158,Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.,GSE261646,Transcriptome Analysis,The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp  stage III oocytes germinal vesicle in central position at 4–7 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.,,pubmed:39302832,,Zebrafish Oocyte  Stage IV  rep2,GSM8147872,,source name:Oocyte|tissue:Oocyte|developmental stage:Stage IV|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing,Zebrafish Oocyte  Stage IV  rep2,Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates,Oocyte,,Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.,,tissue:Oocyte|developmental stage:Stage IV|genotype:AB  TF and TLF,GSM8147872,GSM8147872: Zebrafish Oocyte  Stage IV  rep2; Danio rerio; RNA Seq,GSM8147872 r1,GSM8147872,1,Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP495323,,,Z_oocyte_stage_4_2_Pa.fastq,fastq,2456514332.0,32322557.0,GSM8147872 r1,0:76,A:588246161;C:609187233;G:593122683;T:665837765;N:120490,76,,,,588246161,609187233,593122683,665837765,120490,SRX23954975,SRS20755396,SRA1824599,"Computational Biology, Stowers Institute for Medical Research","Computational Biology, Stowers Institute for Medical Research",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2024-03-14,Multi-stage,Embryo,Oocyte,Reproductive System
30756,SRR28348922,SRX23954974,SRS20755395,SRP495323,PRJNA1088158,Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.,GSE261646,Transcriptome Analysis,The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp  stage III oocytes germinal vesicle in central position at 4–7 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.,,pubmed:39302832,,Zebrafish Oocyte  Stage IV  rep1,GSM8147871,,source name:Oocyte|tissue:Oocyte|developmental stage:Stage IV|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing,Zebrafish Oocyte  Stage IV  rep1,Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates,Oocyte,,Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.,,tissue:Oocyte|developmental stage:Stage IV|genotype:AB  TF and TLF,GSM8147871,GSM8147871: Zebrafish Oocyte  Stage IV  rep1; Danio rerio; RNA Seq,GSM8147871 r1,GSM8147871,1,Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP495323,,,Z_oocyte_stage_4_1_Pa.fastq,fastq,2650784696.0,34878746.0,GSM8147871 r1,0:76,A:649971632;C:640667370;G:632570967;T:727447552;N:127175,76,,,,649971632,640667370,632570967,727447552,127175,SRX23954974,SRS20755395,SRA1824599,"Computational Biology, Stowers Institute for Medical Research","Computational Biology, Stowers Institute for Medical Research",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2024-03-14,Multi-stage,Embryo,Oocyte,Reproductive System
30757,SRR28348923,SRX23954973,SRS20755394,SRP495323,PRJNA1088158,Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.,GSE261646,Transcriptome Analysis,The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp  stage III oocytes germinal vesicle in central position at 4–7 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.,,pubmed:39302832,,Zebrafish Oocyte  Stage III  rep2,GSM8147870,,source name:Oocyte|tissue:Oocyte|developmental stage:Stage III|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing,Zebrafish Oocyte  Stage III  rep2,Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates,Oocyte,,Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.,,tissue:Oocyte|developmental stage:Stage III|genotype:AB  TF and TLF,GSM8147870,GSM8147870: Zebrafish Oocyte  Stage III  rep2; Danio rerio; RNA Seq,GSM8147870 r1,GSM8147870,1,Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP495323,,,Z_oocyte_stage_3_2_Pa.fastq,fastq,2809957956.0,36973131.0,GSM8147870 r1,0:76,A:679041537;C:690924547;G:702857353;T:736996218;N:138301,76,,,,679041537,690924547,702857353,736996218,138301,SRX23954973,SRS20755394,SRA1824599,"Computational Biology, Stowers Institute for Medical Research","Computational Biology, Stowers Institute for Medical Research",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2024-03-14,Multi-stage,Embryo,Oocyte,Reproductive System
30758,SRR28348924,SRX23954972,SRS20755393,SRP495323,PRJNA1088158,Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.,GSE261646,Transcriptome Analysis,The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp  stage III oocytes germinal vesicle in central position at 4–7 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.,,pubmed:39302832,,Zebrafish Oocyte  Stage III  rep1,GSM8147869,,source name:Oocyte|tissue:Oocyte|developmental stage:Stage III|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing,Zebrafish Oocyte  Stage III  rep1,Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates,Oocyte,,Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.,,tissue:Oocyte|developmental stage:Stage III|genotype:AB  TF and TLF,GSM8147869,GSM8147869: Zebrafish Oocyte  Stage III  rep1; Danio rerio; RNA Seq,GSM8147869 r1,GSM8147869,1,Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP495323,,,Z_oocyte_stage_3_1_Pa.fastq,fastq,2828372376.0,37215426.0,GSM8147869 r1,0:76,A:701751055;C:680571938;G:664212213;T:781698241;N:138929,76,,,,701751055,680571938,664212213,781698241,138929,SRX23954972,SRS20755393,SRA1824599,"Computational Biology, Stowers Institute for Medical Research","Computational Biology, Stowers Institute for Medical Research",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2024-03-14,Multi-stage,Embryo,Oocyte,Reproductive System
30759,SRR28348925,SRX23954971,SRS20755392,SRP495323,PRJNA1088158,Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.,GSE261646,Transcriptome Analysis,The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp  stage III oocytes germinal vesicle in central position at 4–7 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.,,pubmed:39302832,,Zebrafish Oocyte  Stage II  rep2,GSM8147868,,source name:Oocyte|tissue:Oocyte|developmental stage:Stage II|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing,Zebrafish Oocyte  Stage II  rep2,Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates,Oocyte,,Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.,,tissue:Oocyte|developmental stage:Stage II|genotype:AB  TF and TLF,GSM8147868,GSM8147868: Zebrafish Oocyte  Stage II  rep2; Danio rerio; RNA Seq,GSM8147868 r1,GSM8147868,1,Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP495323,,,Z_oocyte_stage_2_2_Pa.fastq,fastq,2837652432.0,37337532.0,GSM8147868 r1,0:76,A:698931608;C:681467909;G:683751172;T:773364392;N:137351,76,,,,698931608,681467909,683751172,773364392,137351,SRX23954971,SRS20755392,SRA1824599,"Computational Biology, Stowers Institute for Medical Research","Computational Biology, Stowers Institute for Medical Research",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2024-03-14,Multi-stage,Embryo,Oocyte,Reproductive System
30760,SRR28348926,SRX23954970,SRS20755391,SRP495323,PRJNA1088158,Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.,GSE261646,Transcriptome Analysis,The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp  stage III oocytes germinal vesicle in central position at 4–7 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.,,pubmed:39302832,,Zebrafish Oocyte  Stage II  rep1,GSM8147867,,source name:Oocyte|tissue:Oocyte|developmental stage:Stage II|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing,Zebrafish Oocyte  Stage II  rep1,Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates,Oocyte,,Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.,,tissue:Oocyte|developmental stage:Stage II|genotype:AB  TF and TLF,GSM8147867,GSM8147867: Zebrafish Oocyte  Stage II  rep1; Danio rerio; RNA Seq,GSM8147867 r1,GSM8147867,1,Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP495323,,,Z_oocyte_stage_2_1_Pa.fastq,fastq,3360126820.0,44212195.0,GSM8147867 r1,0:76,A:829333798;C:802089215;G:804982077;T:923557236;N:164494,76,,,,829333798,802089215,804982077,923557236,164494,SRX23954970,SRS20755391,SRA1824599,"Computational Biology, Stowers Institute for Medical Research","Computational Biology, Stowers Institute for Medical Research",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2024-03-14,Multi-stage,Embryo,Oocyte,Reproductive System
30761,SRR28348927,SRX23954969,SRS20755390,SRP495323,PRJNA1088158,Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.,GSE261646,Transcriptome Analysis,The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp  stage III oocytes germinal vesicle in central position at 4–7 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.,,pubmed:39302832,,Zebrafish Oocyte  Stage I  rep2,GSM8147866,,source name:Oocyte|tissue:Oocyte|developmental stage:Stage I|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing,Zebrafish Oocyte  Stage I  rep2,Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates,Oocyte,,Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.,,tissue:Oocyte|developmental stage:Stage I|genotype:AB  TF and TLF,GSM8147866,GSM8147866: Zebrafish Oocyte  Stage I  rep2; Danio rerio; RNA Seq,GSM8147866 r1,GSM8147866,1,Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP495323,,,Z_oocyte_stage_1_2_Pa.fastq,fastq,2739674220.0,36048345.0,GSM8147866 r1,0:76,A:653441701;C:681445567;G:663740568;T:740918288;N:128096,76,,,,653441701,681445567,663740568,740918288,128096,SRX23954969,SRS20755390,SRA1824599,"Computational Biology, Stowers Institute for Medical Research","Computational Biology, Stowers Institute for Medical Research",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2024-03-14,Multi-stage,Embryo,Oocyte,Reproductive System
30762,SRR28348928,SRX23954968,SRS20755389,SRP495323,PRJNA1088158,Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.,GSE261646,Transcriptome Analysis,The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp  stage III oocytes germinal vesicle in central position at 4–7 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.,,pubmed:39302832,,Zebrafish Oocyte  Stage I  rep1,GSM8147865,,source name:Oocyte|tissue:Oocyte|developmental stage:Stage I|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing,Zebrafish Oocyte  Stage I  rep1,Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates,Oocyte,,Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.,,tissue:Oocyte|developmental stage:Stage I|genotype:AB  TF and TLF,GSM8147865,GSM8147865: Zebrafish Oocyte  Stage I  rep1; Danio rerio; RNA Seq,GSM8147865 r1,GSM8147865,1,Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP495323,,,Z_oocyte_stage_1_1_Pa.fastq,fastq,3348831852.0,44063577.0,GSM8147865 r1,0:76,A:815134657;C:817210346;G:809175239;T:907149915;N:161695,76,,,,815134657,817210346,809175239,907149915,161695,SRX23954968,SRS20755389,SRA1824599,"Computational Biology, Stowers Institute for Medical Research","Computational Biology, Stowers Institute for Medical Research",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2024-03-14,Multi-stage,Embryo,Oocyte,Reproductive System
34965,SRR32588722,SRX27895229,SRS24266229,SRP568323,PRJNA1232602,Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains,PRJNA1232602,Other,In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.,,,,Iso Seq RNA from Danio rerio,C2 F2 M T,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from testis,C2 F2 M T,C2 F2 M T,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m84270_240911_150713_s1.skera.flnc.fastq.gz,fastq,103111938047.0,50624762.0,m84270 240911 150713 s1.skera.flnc.fastq.gz,0:2036.79,A:30106378730;C:21760983790;G:23176083069;T:28068492458;N:0,2036,,,,30106378730,21760983790,23176083069,28068492458,0,SRX27895229,SRS24266229,SRA2089085,National Human Genome Research Institute|Translational and Functional Genomics Branch,National Human Genome Research Institute National Human Genome Research Institute,,,,,,,,,,,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2025-03-06,Adult,Adult,Gonad,Reproductive System
34974,SRR32588731,SRX27895220,SRS24266226,SRP568323,PRJNA1232602,Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains,PRJNA1232602,Other,In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.,,,,Iso Seq RNA from Danio rerio,C2 F2 F O32,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from ovary,C2 F2 F O32,C2 F2 F O32,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m64467e_240815_161552.hifi_reads.flnc.fastq.gz,fastq,12555748052.0,3350326.0,m64467e 240815 161552.hifi reads.flnc.fastq.gz,0:3747.62,A:3457885256;C:2882310858;G:2971165409;T:3244386529;N:0,3747,,,,3457885256,2882310858,2971165409,3244386529,0,SRX27895220,SRS24266226,SRA2089085,National Human Genome Research Institute|Translational and Functional Genomics Branch,National Human Genome Research Institute National Human Genome Research Institute,,,,,,,,,,,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2025-03-06,Adult,Adult,Gonad,Reproductive System
34975,SRR32588732,SRX27895219,SRS24266221,SRP568323,PRJNA1232602,Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains,PRJNA1232602,Other,In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.,,,,Iso Seq RNA from Danio rerio,C2 F2 F O31,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:Ovary|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from ovary,C2 F2 F O31,C2 F2 F O31,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m84270_240911_210533_s4.skera.flnc.fastq.gz,fastq,91708771607.0,33888263.0,m84270 240911 210533 s4.skera.flnc.fastq.gz,0:2706.21,A:25318206966;C:20635348405;G:21357313254;T:24397902982;N:0,2706,,,,25318206966,20635348405,21357313254,24397902982,0,SRX27895219,SRS24266221,SRA2089085,National Human Genome Research Institute|Translational and Functional Genomics Branch,National Human Genome Research Institute National Human Genome Research Institute,,,,,,,,,,,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2025-03-06,Adult,Adult,Gonad,Reproductive System
36260,SRR062657,SRX025025,SRS085804,SRP003165,PRJNA127881,High throughput sequencing of mRNA from oocyte  1 cell  16/32 cells  128/256 cells  3.5hpf and 5.3hpf zebrafish embryos Wild type; AB line,GSE22830,Transcriptome Analysis,mRNA seq based approach to determine the transcriptome dynamics during early development To study the mechanisms regulating this developmental event in zebrafish  we applied RNA deep sequencing technology and generated comprehensive transcriptome profiles of 6 developmental stages from oocyte to early gastrulation. We determined the expression levels of maternal and zygotic transcripts and clustered them based on expression pattern. We identified a large number of novel transcribed regions in un annotated regions of the genome  as well as splice variants with an estimated frequency of 40 75% during early zebrafish embryogenesis. Our data constitute a useful resource for developmental studies  gene discovery  and genome annotation. Overall design: RNA was extracted from pooled embryos of desired stages and one RNA seq library was generated for each sample.  Totally 6 stages were selected: Maternal  1cell  16/32 cells  128/256 cells  3.5hpf and 5.3hpf,,pubmed:21555364;pubmed:24586560;pubmed:23676078,,Maternal,GSM564427,,tissue:Unfertilized egg|background:AB; wild type|developmental stage:unfertilized eggs,Maternal,ABI pipeline BioScope v1.0.1 Data analysis: The SOLiD generated RNA Seq reads was in 50bp length and an initial filtering process was taken to remove any non desirable contamination sequences  such as rRNA  tRNA  and repeats etc. A seed and extension mapping approach was developed to map the 50bp reads into reference genome zv7 and also into the respective zv7 refGene annotation separately. During mapping of the reads to the refGene annotation  a splice junction database fasta file is generated to which the reads are mapped to. This database contains known and putative junction sequences  created by taking 46bp from the joining ends of adjacent and non adjacent exons for each gene and putting them together  simulating the genomic sequences of known and putative junctions respectively. The first 25bp of the 50bp read was used as the seed for alignment for each read. When an alignment cannot be found using these 25bp seed  the seed window is shifted and the next 25bp seed is taken from the 21st to the 45th base of the read. An extension step follows when the seed is able to map  and a score generated for each extended base to determine best alignment. A merging step is performed on the genome mapping and splice junction mapping to determine a set of alignments for each read  from which a unique alignment is found based on the score generated for these alignments. Mapping parameters:  Mapping was done using Applied Biosystems’ SOLiD BioScope alignment for whole transcriptome analysis pipeline.  Two mismatches were allowed in the 25bp color space seed sequence with extension alignment performed to find the full mapping location.  A score is computed for each mapping location and any location that scored <22 were filtered. Generation of gff and bedgraph files: GFF files were produced by parsing the output BAM format and extracted for unique alignments with score >22. The bedgraph files are then produced with the resulting gff file.,Unfertilized egg,Embryos were frozen at the desired developmental stages and RNAs was extracted for sequencing.,mRNA seq was performed by Mission Biotech Taiwan. SOLiD sequencing libraries were prepared using the Whole Transcriptome Library Preparation for SOLiD™ Sequencing kit ABI according to manufacturer’s instructions. About 200 280 µg of total RNAs were used as starting materials  which were subjected to polyA selection using Applied Biosystems PolyA Purist Kit AM1916  fragmentation  and library construction using distinct adapters for each library SOLiD Barcoding. From each library  equal volumes were pooled together and sequenced in SOLiD3 ABI platform generating 50bp tags.,Zebrafish embryos AB background collected just post fertilization  were reared and harvested at  desired time points.   Unfertilized oocytes were collected by squeezing the abdomen of spawning females. Harvested embryos were snap frozen in liquid nitrogen and stored in −80°C. Total RNA was extracted from whole embryos using Trizol Invitrogen according to manufacturer’s instructions. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. Integrity of RNA samples were determined using Agilent RNA 6000 Nano chip and size separated using Agilent 2100 Bioanalyzer. Total RNA obtained per 100 embryos at each developmental stage was calculated for data normalization purposes.,background:AB; wild type|developmental stage:unfertilized eggs,GSM564427,GSM564427: Maternal,GSM564427: Maternal,GSM564427: Maternal,1,,GEO Accession:GSM564427,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP003165,,,,,1566199300.0,31323986.0,GSM564427 1,0:50,,50,,,,,,,,,SRX025025,SRS085804,SRA022850,GEO,"Computational and Systems Biology, Genome Institute of Singapore",1,0.72688,,0.05657,,0.876,,0.51223,,50,,B,,usable mapping rate,legacy,early,full_length,poly_a,unknown,bulk,unknown,unknown,,Singapore,2010-07-08,Zygote,Embryo,Oocyte,Reproductive System
36273,SRR298566,SRX079844,SRS212650,SRP007331,PRJNA141525,Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.,GSE29418,Transcriptome Analysis,RNA libraries from immunoprecipitates of Tdrd1  Ziwi and Zili  total testis RNA  total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.,,pubmed:21743441,,WTTESTIS,GSM727523,,tissue:adult testis extract|strain:TL,WTTESTIS,three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9.,adult testis extract,,Tissue was homogenized in trizol and total RNA was isolated. RNAs ranging from 18 35 nucleotides were size selected from gel. For cDNA synthesis  the RNA molecules in the immunoprecipitated fraction were first poly A tailed using polyApolymerase followed by ligation of synthetic RNA adapter to the five prime phosphate. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H  reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.,,strain:TL,GSM727523,GSM727523: WTTESTIS,GSM727523: WTTESTIS,GSM727523: WTTESTIS,1,,GEO Accession:GSM727523,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP007331,,read name barcode proc directive:ignore,WTTESTIS.fastq,fastq,732997980.0,20361055.0,GSM727523 1,0:36,,36,,,,,,,,,SRX079844,SRS212650,SRA039167,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.08155,,0.07176,,0.97851,,0.52359,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2011-05-20,Adult,Adult,Gonad,Reproductive System
36274,SRR298565,SRX079843,SRS212649,SRP007331,PRJNA141525,Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.,GSE29418,Transcriptome Analysis,RNA libraries from immunoprecipitates of Tdrd1  Ziwi and Zili  total testis RNA  total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.,,pubmed:21743441,,WT3WK,GSM727522,,tissue:3 wpf whole gonads|strain:TL,WT3WK,three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9.,3 wpf whole gonads,,Tissue was homogenized in trizol and total RNA was isolated. RNAs ranging from 18 35 nucleotides were size selected from gel. For cDNA synthesis  the RNA molecules in the immunoprecipitated fraction were first poly A tailed using polyApolymerase followed by ligation of synthetic RNA adapter to the five prime phosphate. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H  reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.,,strain:TL,GSM727522,GSM727522: WT3WK,GSM727522: WT3WK,GSM727522: WT3WK,1,,GEO Accession:GSM727522,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP007331,,read name barcode proc directive:ignore,WT3WK.fastq,fastq,365473116.0,10152031.0,GSM727522 1,0:36,,36,,,,,,,,,SRX079843,SRS212649,SRA039167,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.09055,,0.0603,,0.97798,,0.44571,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2011-05-20,Larval,Larval,Gonad,Reproductive System
36275,SRR298564,SRX079842,SRS212648,SRP007331,PRJNA141525,Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.,GSE29418,Transcriptome Analysis,RNA libraries from immunoprecipitates of Tdrd1  Ziwi and Zili  total testis RNA  total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.,,pubmed:21743441,,TDRD1WK3,GSM727521,,tissue:3 wpf tdrd1 mutant gonads|strain:TL,TDRD1WK3,three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9.,3 wpf tdrd1 mutant gonads,,Tissue was homogenized in trizol and total RNA was isolated. RNAs ranging from 18 35 nucleotides were size selected from gel. For cDNA synthesis  the RNA molecules in the immunoprecipitated fraction were first poly A tailed using polyApolymerase followed by ligation of synthetic RNA adapter to the five prime phosphate. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H  reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.,,strain:TL,GSM727521,GSM727521: TDRD1WK3,GSM727521: TDRD1WK3,GSM727521: TDRD1WK3,1,,GEO Accession:GSM727521,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP007331,,read name barcode proc directive:ignore,TDRD1WK3.fastq,fastq,369931536.0,10275876.0,GSM727521 1,0:36,,36,,,,,,,,,SRX079842,SRS212648,SRA039167,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.08303,,0.04674,,0.97938,,0.35673,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2011-05-20,Larval,Larval,Gonad,Reproductive System
36285,SRR363985,SRX105298,SRS270141,SRP009275,PRJNA148581,Hen1 analysis in zebrafish,GSE33582,Transcriptome Analysis,small RNA libraries from wild type and Hen1 mutant testes were made with either polyA tailing VASAGFPHen1minus/plus or adapter ligation Hen1Testis and WTTestis and sequenced on an Illumina GAII platform. Overall design: RNA was isolated from total testis tissue of both Hen1 wildtype and Hen1 mutant animals. post size selection from gel  the small RNA libraries wre made.,,pubmed:20859253,,wildtype ligation,GSM830247,,source name:testis|strain:TL|genotype/variation:Hen1 wildtype|tissue:testis|small rna library prep method:adapter ligation,wildtype ligation,three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome Zv8,testis,,Small RNAs in the size range of 19 31 bases were excised from a denaturing gel. Adaptors were ligated to the five prime and three prime ends of the isolated RNA  and the product was converted to cDNA using a primer on the three prime adaptor. post 15 cycles PCR amplification of the library the product was gel purified and sequenced on a Solexa platform.,,strain:TL|genotype/variation:Hen1 wildtype|tissue:testis|small rna library prep method:adapter ligation,GSM830247,GSM830247: wildtype ligation,GSM830247: wildtype ligation,GSM830247: wildtype ligation,1,,GEO Accession:GSM830247,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>46</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP009275,,read name barcode proc directive:ignore,WTTESTIS.fastq,fastq,395791130.0,8604155.0,GSM830247 1,0:46,A:79045664;C:90489917;G:99082007;T:127024229;N:149313,46,,,,79045664,90489917,99082007,127024229,149313,SRX105298,SRS270141,SRA047996,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.00021,,0.00015,,0.99989,,0.0,,46,,T,,under 1.2% mapping rate,illumina,early_illumina,5prime,poly_a,unknown,bulk,unknown,unknown,,Netherlands,2011-11-09,Undetermined,Undetermined,Gonad,Reproductive System
36286,SRR363984,SRX105297,SRS270140,SRP009275,PRJNA148581,Hen1 analysis in zebrafish,GSE33582,Transcriptome Analysis,small RNA libraries from wild type and Hen1 mutant testes were made with either polyA tailing VASAGFPHen1minus/plus or adapter ligation Hen1Testis and WTTestis and sequenced on an Illumina GAII platform. Overall design: RNA was isolated from total testis tissue of both Hen1 wildtype and Hen1 mutant animals. post size selection from gel  the small RNA libraries wre made.,,pubmed:20859253,,hen1 mutant ligation,GSM830246,,source name:testis|strain:TL|genotype/variation:Hen1 mutant|tissue:testis|small rna library prep method:adapter ligation,hen1 mutant ligation,three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome Zv8,testis,,Small RNAs in the size range of 19 31 bases were excised from a denaturing gel. Adaptors were ligated to the five prime and three prime ends of the isolated RNA  and the product was converted to cDNA using a primer on the three prime adaptor. post 15 cycles PCR amplification of the library the product was gel purified and sequenced on a Solexa platform.,,strain:TL|genotype/variation:Hen1 mutant|tissue:testis|small rna library prep method:adapter ligation,GSM830246,GSM830246: hen1 mutant ligation,GSM830246: hen1 mutant ligation,GSM830246: hen1 mutant ligation,1,,GEO Accession:GSM830246,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>46</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP009275,,read name barcode proc directive:ignore,HEN1TESTIS.fastq,fastq,440876374.0,9584269.0,GSM830246 1,0:46,A:91693980;C:99515953;G:105634029;T:143841954;N:190458,46,,,,91693980,99515953,105634029,143841954,190458,SRX105297,SRS270140,SRA047996,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.00039,,0.00033,,0.99995,,0.0,,46,,T,,under 1.2% mapping rate,illumina,early_illumina,5prime,poly_a,unknown,bulk,unknown,unknown,,Netherlands,2011-11-09,Undetermined,Undetermined,Gonad,Reproductive System
36287,SRR363983,SRX105296,SRS270139,SRP009275,PRJNA148581,Hen1 analysis in zebrafish,GSE33582,Transcriptome Analysis,small RNA libraries from wild type and Hen1 mutant testes were made with either polyA tailing VASAGFPHen1minus/plus or adapter ligation Hen1Testis and WTTestis and sequenced on an Illumina GAII platform. Overall design: RNA was isolated from total testis tissue of both Hen1 wildtype and Hen1 mutant animals. post size selection from gel  the small RNA libraries wre made.,,pubmed:20859253,,wildtype polyA,GSM830245,,source name:testis|strain:TL|genotype/variation:Hen1 wildtype|tissue:testis|small rna library prep method:polyA tailing,wildtype polyA,three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome Zv8,testis,,Small RNAs in the size range of 19 31 bases were excised from a denaturing gel. RNA was polyA tailed using polyA polymerase followed by ligation of a RNA adaptor to the five prime phosphate of the small RNAs. First strand cDNA synthesis was performed using an oligodT linker primer and M MLV RNase H  reverse transcriptase. post amplification the cDNA was sent for sequencing on an Illumina/Solexa platform.,,strain:TL|genotype/variation:Hen1 wildtype|tissue:testis|small rna library prep method:polyA tailing,GSM830245,GSM830245: wildtype polyA,GSM830245: wildtype polyA,GSM830245: wildtype polyA,1,,GEO Accession:GSM830245,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>44</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP009275,,read name barcode proc directive:ignore,VASAGFPHEN1plusMALE.fastq,fastq,167344144.0,3803276.0,GSM830245 1,0:44,A:87935982;C:21182538;G:19081938;T:34474815;N:4668871,44,,,,87935982,21182538,19081938,34474815,4668871,SRX105296,SRS270139,SRA047996,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.06642,,0.05042,,0.99226,,0.38346,,44,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,Netherlands,2011-11-09,Undetermined,Undetermined,Gonad,Reproductive System
36288,SRR363982,SRX105295,SRS270138,SRP009275,PRJNA148581,Hen1 analysis in zebrafish,GSE33582,Transcriptome Analysis,small RNA libraries from wild type and Hen1 mutant testes were made with either polyA tailing VASAGFPHen1minus/plus or adapter ligation Hen1Testis and WTTestis and sequenced on an Illumina GAII platform. Overall design: RNA was isolated from total testis tissue of both Hen1 wildtype and Hen1 mutant animals. post size selection from gel  the small RNA libraries wre made.,,pubmed:20859253,,hen1 mutant polyA,GSM830244,,source name:testis|strain:TL|genotype/variation:Hen1 mutant|tissue:testis|small rna library prep method:polyA tailing,hen1 mutant polyA,three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome Zv8,testis,,Small RNAs in the size range of 19 31 bases were excised from a denaturing gel. RNA was polyA tailed using polyA polymerase followed by ligation of a RNA adaptor to the five prime phosphate of the small RNAs. First strand cDNA synthesis was performed using an oligodT linker primer and M MLV RNase H  reverse transcriptase. post amplification the cDNA was sent for sequencing on an Illumina/Solexa platform.,,strain:TL|genotype/variation:Hen1 mutant|tissue:testis|small rna library prep method:polyA tailing,GSM830244,GSM830244: hen1 mutant polyA,GSM830244: hen1 mutant polyA,GSM830244: hen1 mutant polyA,1,,GEO Accession:GSM830244,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>44</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP009275,,read name barcode proc directive:ignore,VASAGFPHEN1minusMALE.fastq,fastq,267208964.0,6072931.0,GSM830244 1,0:44,A:143478691;C:30051676;G:33682677;T:59883224;N:112696,44,,,,143478691,30051676,33682677,59883224,112696,SRX105295,SRS270138,SRA047996,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.01616,,0.01033,,0.99381,,0.76337,,44,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,Netherlands,2011-11-09,Undetermined,Undetermined,Gonad,Reproductive System
36361,SRR489488,SRX143565,SRS310286,SRP012376,PRJNA160143,Extensive alternative polyadenylation during zebrafish development,GSE37453,Transcriptome Analysis,The post transcriptional fate of messenger RNAs mRNAs is largely dictated by their three prime' untranslated regions three prime'UTRs  which are defined by cleavage and polyadenylation CPA of pre mRNAs. We used polyA position profiling by sequencing 3P Seq to map polyA sites at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P Seq reads substantially increased and improved existing three prime'UTR annotations  resulting in confidently identified three prime'UTRs for more than 78.79% of the annotated protein coding genes in zebrafish. Most zebrafish genes undergo alternative CPA with more than a thousand genes using different dominant three prime'UTRs at different stages. three prime'UTRs tend to be shortest in the ovaries and longest in the brain. Isoforms with some of the shortest three prime'UTRs are highly expressed in the ovary yet absent in the maternally contributed RNAs of the embryo  perhaps because their three prime'UTRs are too short to accommodate a uridine rich motif required for stability of the maternal mRNA. At two hpf  thousands of unique polyA sites appear at locations lacking a typical polyadenylation signal  which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into the identities  formation  and evolution of zebrafish three prime'UTRs provide a resource for studying gene regulation during vertebrate development. Overall design: 3P Seq was used to map the three prime' ends of protein coding genes in the zebrafish genome,,pubmed:22722342,,3P Seq Testis,GSM919971,,source name:male adults|genotype/variation:wild type|tissue:testis|development stage:adult,3P Seq Testis,For 3P Seq: Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. The BED file is as in Jan et al. GSE24924 For 3P PE Seq: In each read pair  read #1 captured the three prime end of the polyA tail in the antisense orientation  and read #2 captured a portion of the three prime region of the transcript  and occasionally  the beginning of the polyA tail  in the sense orientation. Read #2 began with an adapter of 26 bases. Reads with more than 10 mismatches to the adapter were discarded and the first 26 bases were removed before further processing.  A read pair was considered informative only if read #1 began with Ts and read #2 contained 2–39 terminal As. post leading Ts and terminal As were removed from reads #1 and #2  respectively  they were mapped to the genome using Bowtie  allowing for up to two mismatches and requiring a unique mapping position in the zebrafish genome. The length of the tail encoded in read #2 was defined as the maximum number of trailing As allowing for up to one mismatch. Only cases in which this number was larger than the number of As encoded in the genome at the predicted cleavage position by at least 2 bases were carried forward. Cleavage and polyadenylation position was defined as the last non A base in read #2. The length of the polyA tail at that position was estimated using the corresponding read #1  and defined as the maximal i for which >90% of the bases in the first i bases of read #1 were Ts. This criterion was used to allow for some sequencing errors expected when sequencing long homopolymers. Genome build: danRer7 Supplementary files format and content: The .bed files contain the positions where 3P Seq reads were mapped  and the name of each track is the number of reads mapping to that position. Supplementary files format and content: The bigWig .bw files contain a summary of the number of reads whose three prime ends mapped to each position in the genome. Supplementary files format and content: For the paired end sequencing for mapping polyA tail lengths  the text files contain the following columns : chromosome  position  strand  number of polyA length reads  followed by the individual measurements lower bounds on polyA tail length,male adults,Ovaries and testes were obtained as described  in Gupta and Mullins 2010.,3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html,Zebrafish embryos or adults grown under standard condition,genotype/variation:wild type|tissue:testis|developmental stage:adult,GSM919971,GSM919971: 3P Seq Testis; Danio rerio; RNA Seq,GSM919971 1,GSM919971: 3P Seq Testis,1,,GEO Accession:GSM919971,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP012376,,,3P_Seq_Testis.fastq,fastq,633839040.0,17606640.0,GSM919971 r1,0:36,A:250493743;C:111846021;G:97558731;T:173764035;N:176510,36,,,,250493743,111846021,97558731,173764035,176510,SRX143565,SRS310286,SRA051955,GEO,Whitehead Institute for Biomedical Research,1,0.56499,,0.1059,,0.72468,,0.46158,,36,,B,,usable mapping rate,illumina,early_illumina,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2012-04-20,Adult,Adult,Gonad,Reproductive System
36362,SRR489487,SRX143564,SRS310285,SRP012376,PRJNA160143,Extensive alternative polyadenylation during zebrafish development,GSE37453,Transcriptome Analysis,The post transcriptional fate of messenger RNAs mRNAs is largely dictated by their three prime' untranslated regions three prime'UTRs  which are defined by cleavage and polyadenylation CPA of pre mRNAs. We used polyA position profiling by sequencing 3P Seq to map polyA sites at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P Seq reads substantially increased and improved existing three prime'UTR annotations  resulting in confidently identified three prime'UTRs for more than 78.79% of the annotated protein coding genes in zebrafish. Most zebrafish genes undergo alternative CPA with more than a thousand genes using different dominant three prime'UTRs at different stages. three prime'UTRs tend to be shortest in the ovaries and longest in the brain. Isoforms with some of the shortest three prime'UTRs are highly expressed in the ovary yet absent in the maternally contributed RNAs of the embryo  perhaps because their three prime'UTRs are too short to accommodate a uridine rich motif required for stability of the maternal mRNA. At two hpf  thousands of unique polyA sites appear at locations lacking a typical polyadenylation signal  which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into the identities  formation  and evolution of zebrafish three prime'UTRs provide a resource for studying gene regulation during vertebrate development. Overall design: 3P Seq was used to map the three prime' ends of protein coding genes in the zebrafish genome,,pubmed:22722342,,3P Seq Ovary,GSM919970,,source name:female adults|genotype/variation:wild type|tissue:ovary|development stage:adult,3P Seq Ovary,For 3P Seq: Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. The BED file is as in Jan et al. GSE24924 For 3P PE Seq: In each read pair  read #1 captured the three prime end of the polyA tail in the antisense orientation  and read #2 captured a portion of the three prime region of the transcript  and occasionally  the beginning of the polyA tail  in the sense orientation. Read #2 began with an adapter of 26 bases. Reads with more than 10 mismatches to the adapter were discarded and the first 26 bases were removed before further processing.  A read pair was considered informative only if read #1 began with Ts and read #2 contained 2–39 terminal As. post leading Ts and terminal As were removed from reads #1 and #2  respectively  they were mapped to the genome using Bowtie  allowing for up to two mismatches and requiring a unique mapping position in the zebrafish genome. The length of the tail encoded in read #2 was defined as the maximum number of trailing As allowing for up to one mismatch. Only cases in which this number was larger than the number of As encoded in the genome at the predicted cleavage position by at least 2 bases were carried forward. Cleavage and polyadenylation position was defined as the last non A base in read #2. The length of the polyA tail at that position was estimated using the corresponding read #1  and defined as the maximal i for which >90% of the bases in the first i bases of read #1 were Ts. This criterion was used to allow for some sequencing errors expected when sequencing long homopolymers. Genome build: danRer7 Supplementary files format and content: The .bed files contain the positions where 3P Seq reads were mapped  and the name of each track is the number of reads mapping to that position. Supplementary files format and content: The bigWig .bw files contain a summary of the number of reads whose three prime ends mapped to each position in the genome. Supplementary files format and content: For the paired end sequencing for mapping polyA tail lengths  the text files contain the following columns : chromosome  position  strand  number of polyA length reads  followed by the individual measurements lower bounds on polyA tail length,female adults,Ovaries and testes were obtained as described  in Gupta and Mullins 2010.,3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html,Zebrafish embryos or adults grown under standard condition,genotype/variation:wild type|tissue:ovary|developmental stage:adult,GSM919970,GSM919970: 3P Seq Ovary; Danio rerio; RNA Seq,GSM919970 1,GSM919970: 3P Seq Ovary,1,,GEO Accession:GSM919970,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP012376,,,3P_Seq_Ovary.fastq,fastq,644470380.0,17901955.0,GSM919970 r1,0:36,A:263871252;C:97757369;G:94972134;T:187683515;N:186110,36,,,,263871252,97757369,94972134,187683515,186110,SRX143564,SRS310285,SRA051955,GEO,Whitehead Institute for Biomedical Research,1,0.51356,,0.04868,,0.821,,0.48788,,36,,B,,usable mapping rate,illumina,early_illumina,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2012-04-20,Adult,Adult,Gonad,Reproductive System
36514,SRR578923,SRX190981,SRS366702,SRP015982,PRJNA176481,Small RNA analysis of Tu And SJD zebrafish strain and their progeny,GSE41299,Transcriptome Analysis,Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .,,pubmed:23335638,,SJD male,GSM1014087,,source name:Testes|sex:male|strain:SJD|development stage:Adult|tissue:Testes,SJD male,Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads  except for libraries Tu Male  Tu P0  SJD Male  SJD P0  SJDxTuF1  TuxSJDF1  TuxSJDF2 and SJDxTuF2  which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts,Testes,,Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps.,Animals were grown under standard conditioni,gender:male|strain:SJD|developmental stage:Adult|tissue:Testes,GSM1014087,GSM1014087: SJD male; Danio rerio; RNA Seq,GSM1014087 1,,1,,GEO Accession:GSM1014087,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP015982,,,SJD_Male.fastq,fastq,869956128.0,24165448.0,GSM1014087 r1,0:36,A:216078167;C:187750746;G:231408128;T:234642875;N:76212,36,,,,216078167,187750746,231408128,234642875,76212,SRX190981,SRS366702,SRA059229,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.27444,,0.19385,,0.92478,,0.49214,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2012-10-03,Adult,Adult,Gonad,Reproductive System
36515,SRR578922,SRX190980,SRS366701,SRP015982,PRJNA176481,Small RNA analysis of Tu And SJD zebrafish strain and their progeny,GSE41299,Transcriptome Analysis,Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .,,pubmed:23335638,,Tu Male,GSM1014086,,source name:Testes|sex:male|strain:Tu|development stage:Adult|tissue:Testes,Tu Male,Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads  except for libraries Tu Male  Tu P0  SJD Male  SJD P0  SJDxTuF1  TuxSJDF1  TuxSJDF2 and SJDxTuF2  which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts,Testes,,Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps.,Animals were grown under standard conditioni,gender:male|strain:Tu|developmental stage:Adult|tissue:Testes,GSM1014086,GSM1014086: Tu Male; Danio rerio; RNA Seq,GSM1014086 1,,1,,GEO Accession:GSM1014086,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP015982,,,,,908421696.0,25233936.0,GSM1014086 r1,0:36,A:222765185;C:198165182;G:240641436;T:246807325;N:42568,36,,,,222765185,198165182,240641436,246807325,42568,SRX190980,SRS366701,SRA059229,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.1451,,0.10199,,0.95128,,0.45517,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2012-10-03,Adult,Adult,Gonad,Reproductive System
36516,SRR578921,SRX190979,SRS366700,SRP015982,PRJNA176481,Small RNA analysis of Tu And SJD zebrafish strain and their progeny,GSE41299,Transcriptome Analysis,Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .,,pubmed:23335638,,TuxSJDF2 Individual 2,GSM1014085,,source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary,TuxSJDF2 Individual 2,Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads  except for libraries Tu Male  Tu P0  SJD Male  SJD P0  SJDxTuF1  TuxSJDF1  TuxSJDF2 and SJDxTuF2  which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts,Ovary,,Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps.,Animals were grown under standard conditioni,gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary,GSM1014085,GSM1014085: TuxSJDF2 Individual 2; Danio rerio; RNA Seq,GSM1014085 1,,1,,GEO Accession:GSM1014085,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP015982,,,,,383509188.0,10653033.0,GSM1014085 r1,0:36,A:105355133;C:85084746;G:89408418;T:103592177;N:68714,36,,,,105355133,85084746,89408418,103592177,68714,SRX190979,SRS366700,SRA059229,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.14582,,0.10997,,0.96175,,0.35151,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2012-10-03,Adult,Adult,Gonad,Reproductive System
36517,SRR578920,SRX190978,SRS366699,SRP015982,PRJNA176481,Small RNA analysis of Tu And SJD zebrafish strain and their progeny,GSE41299,Transcriptome Analysis,Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .,,pubmed:23335638,,TuxSJDF2 Individual 1,GSM1014084,,source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary,TuxSJDF2 Individual 1,Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads  except for libraries Tu Male  Tu P0  SJD Male  SJD P0  SJDxTuF1  TuxSJDF1  TuxSJDF2 and SJDxTuF2  which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts,Ovary,,Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps.,Animals were grown under standard conditioni,gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary,GSM1014084,GSM1014084: TuxSJDF2 Individual 1; Danio rerio; RNA Seq,GSM1014084 1,,1,,GEO Accession:GSM1014084,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP015982,,,TuxSJDF1_Individual_1.fastq,fastq,464899752.0,12913882.0,GSM1014084 r1,0:36,A:140830427;C:93401413;G:113254459;T:117332119;N:81334,36,,,,140830427,93401413,113254459,117332119,81334,SRX190978,SRS366699,SRA059229,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.43194,,0.32,,0.93154,,0.3438,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2012-10-03,Adult,Adult,Gonad,Reproductive System
36518,SRR578919,SRX190977,SRS366698,SRP015982,PRJNA176481,Small RNA analysis of Tu And SJD zebrafish strain and their progeny,GSE41299,Transcriptome Analysis,Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .,,pubmed:23335638,,TuxSJDF2,GSM1014083,,source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary,TuxSJDF2,Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads  except for libraries Tu Male  Tu P0  SJD Male  SJD P0  SJDxTuF1  TuxSJDF1  TuxSJDF2 and SJDxTuF2  which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts,Ovary,,Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps.,Animals were grown under standard conditioni,gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary,GSM1014083,GSM1014083: TuxSJDF2; Danio rerio; RNA Seq,GSM1014083 1,,1,,GEO Accession:GSM1014083,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP015982,,,TuxSJDF2.fastq,fastq,1036162620.0,28782295.0,GSM1014083 r1,0:36,A:268457303;C:215700792;G:273583173;T:278046713;N:374639,36,,,,268457303,215700792,273583173,278046713,374639,SRX190977,SRS366698,SRA059229,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.16399,,0.12914,,0.9517,,0.52232,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2012-10-03,Adult,Adult,Gonad,Reproductive System
36519,SRR578918,SRX190976,SRS366697,SRP015982,PRJNA176481,Small RNA analysis of Tu And SJD zebrafish strain and their progeny,GSE41299,Transcriptome Analysis,Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .,,pubmed:23335638,,TuxSJDF1 Individual 2,GSM1014082,,source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary,TuxSJDF1 Individual 2,Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads  except for libraries Tu Male  Tu P0  SJD Male  SJD P0  SJDxTuF1  TuxSJDF1  TuxSJDF2 and SJDxTuF2  which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts,Ovary,,Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps.,Animals were grown under standard conditioni,gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary,GSM1014082,GSM1014082: TuxSJDF1 Individual 2; Danio rerio; RNA Seq,GSM1014082 1,,1,,GEO Accession:GSM1014082,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP015982,,,,,344764980.0,9576805.0,GSM1014082 r1,0:36,A:90252809;C:80943703;G:83338280;T:90171695;N:58493,36,,,,90252809,80943703,83338280,90171695,58493,SRX190976,SRS366697,SRA059229,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.18861,,0.14536,,0.95335,,0.54431,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2012-10-03,Adult,Adult,Gonad,Reproductive System
36520,SRR578917,SRX190975,SRS366696,SRP015982,PRJNA176481,Small RNA analysis of Tu And SJD zebrafish strain and their progeny,GSE41299,Transcriptome Analysis,Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .,,pubmed:23335638,,TuxSJDF1 Individual 1,GSM1014081,,source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary,TuxSJDF1 Individual 1,Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads  except for libraries Tu Male  Tu P0  SJD Male  SJD P0  SJDxTuF1  TuxSJDF1  TuxSJDF2 and SJDxTuF2  which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts,Ovary,,Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps.,Animals were grown under standard conditioni,gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary,GSM1014081,GSM1014081: TuxSJDF1 Individual 1; Danio rerio; RNA Seq,GSM1014081 1,,1,,GEO Accession:GSM1014081,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP015982,,,TuxSJDF2_Individual_1.fastq,fastq,373504320.0,10375120.0,GSM1014081 r1,0:36,A:96550943;C:89937876;G:87356943;T:99426239;N:232319,36,,,,96550943,89937876,87356943,99426239,232319,SRX190975,SRS366696,SRA059229,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.15362,,0.12272,,0.95943,,0.56453,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2012-10-03,Adult,Adult,Gonad,Reproductive System
36521,SRR578916,SRX190974,SRS366695,SRP015982,PRJNA176481,Small RNA analysis of Tu And SJD zebrafish strain and their progeny,GSE41299,Transcriptome Analysis,Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .,,pubmed:23335638,,TuxSJDF1,GSM1014080,,source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary,TuxSJDF1,Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads  except for libraries Tu Male  Tu P0  SJD Male  SJD P0  SJDxTuF1  TuxSJDF1  TuxSJDF2 and SJDxTuF2  which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts,Ovary,,Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps.,Animals were grown under standard conditioni,gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary,GSM1014080,GSM1014080: TuxSJDF1; Danio rerio; RNA Seq,GSM1014080 1,,1,,GEO Accession:GSM1014080,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP015982,,,TuxSJDF1.fastq,fastq,1031108904.0,28641914.0,GSM1014080 r1,0:36,A:270773113;C:213123466;G:267237418;T:279702377;N:272530,36,,,,270773113,213123466,267237418,279702377,272530,SRX190974,SRS366695,SRA059229,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.15469,,0.12537,,0.95457,,0.48819,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2012-10-03,Adult,Adult,Gonad,Reproductive System
36522,SRR578915,SRX190973,SRS366694,SRP015982,PRJNA176481,Small RNA analysis of Tu And SJD zebrafish strain and their progeny,GSE41299,Transcriptome Analysis,Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .,,pubmed:23335638,,Tu P0 Individual 2,GSM1014079,,source name:Ovary|sex:female|strain:Tu|development stage:Adult|tissue:Ovary,Tu P0 Individual 2,Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads  except for libraries Tu Male  Tu P0  SJD Male  SJD P0  SJDxTuF1  TuxSJDF1  TuxSJDF2 and SJDxTuF2  which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts,Ovary,,Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps.,Animals were grown under standard conditioni,gender:female|strain:Tu|developmental stage:Adult|tissue:Ovary,GSM1014079,GSM1014079: Tu P0 Individual 2; Danio rerio; RNA Seq,GSM1014079 1,,1,,GEO Accession:GSM1014079,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP015982,,,,,464586408.0,12905178.0,GSM1014079 r1,0:36,A:150621423;C:99131637;G:92380585;T:122374816;N:77947,36,,,,150621423,99131637,92380585,122374816,77947,SRX190973,SRS366694,SRA059229,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.0937,,0.05289,,0.96546,,0.60026,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2012-10-03,Adult,Adult,Gonad,Reproductive System
36523,SRR578914,SRX190972,SRS366693,SRP015982,PRJNA176481,Small RNA analysis of Tu And SJD zebrafish strain and their progeny,GSE41299,Transcriptome Analysis,Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .,,pubmed:23335638,,Tu P0 Individual 1,GSM1014078,,source name:Ovary|sex:female|strain:Tu|development stage:Adult|tissue:Ovary,Tu P0 Individual 1,Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads  except for libraries Tu Male  Tu P0  SJD Male  SJD P0  SJDxTuF1  TuxSJDF1  TuxSJDF2 and SJDxTuF2  which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts,Ovary,,Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps.,Animals were grown under standard conditioni,gender:female|strain:Tu|developmental stage:Adult|tissue:Ovary,GSM1014078,GSM1014078: Tu P0 Individual 1; Danio rerio; RNA Seq,GSM1014078 1,,1,,GEO Accession:GSM1014078,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP015982,,,,,427172796.0,11865911.0,GSM1014078 r1,0:36,A:135500495;C:91385480;G:87823245;T:112202150;N:261426,36,,,,135500495,91385480,87823245,112202150,261426,SRX190972,SRS366693,SRA059229,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.1368,,0.09652,,0.95142,,0.49555,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2012-10-03,Adult,Adult,Gonad,Reproductive System
36524,SRR578913,SRX190971,SRS366692,SRP015982,PRJNA176481,Small RNA analysis of Tu And SJD zebrafish strain and their progeny,GSE41299,Transcriptome Analysis,Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .,,pubmed:23335638,,Tu P0,GSM1014077,,source name:Ovary|sex:female|strain:Tu|development stage:Adult|tissue:Ovary,Tu P0,Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads  except for libraries Tu Male  Tu P0  SJD Male  SJD P0  SJDxTuF1  TuxSJDF1  TuxSJDF2 and SJDxTuF2  which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts,Ovary,,Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps.,Animals were grown under standard conditioni,gender:female|strain:Tu|developmental stage:Adult|tissue:Ovary,GSM1014077,GSM1014077: Tu P0; Danio rerio; RNA Seq,GSM1014077 1,,1,,GEO Accession:GSM1014077,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP015982,,,,,967772772.0,26882577.0,GSM1014077 r1,0:36,A:227085973;C:218180545;G:249458631;T:273002038;N:45585,36,,,,227085973,218180545,249458631,273002038,45585,SRX190971,SRS366692,SRA059229,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.14418,,0.1135,,0.95818,,0.51074,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2012-10-03,Adult,Adult,Gonad,Reproductive System
36525,SRR578912,SRX190970,SRS366691,SRP015982,PRJNA176481,Small RNA analysis of Tu And SJD zebrafish strain and their progeny,GSE41299,Transcriptome Analysis,Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .,,pubmed:23335638,,SJDxTuF2 Individual 2,GSM1014076,,source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary,SJDxTuF2 Individual 2,Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads  except for libraries Tu Male  Tu P0  SJD Male  SJD P0  SJDxTuF1  TuxSJDF1  TuxSJDF2 and SJDxTuF2  which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts,Ovary,,Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps.,Animals were grown under standard conditioni,gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary,GSM1014076,GSM1014076: SJDxTuF2 Individual 2; Danio rerio; RNA Seq,GSM1014076 1,,1,,GEO Accession:GSM1014076,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP015982,,,,,347475024.0,9652084.0,GSM1014076 r1,0:36,A:91189258;C:81789488;G:84551251;T:89882775;N:62252,36,,,,91189258,81789488,84551251,89882775,62252,SRX190970,SRS366691,SRA059229,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.15872,,0.12439,,0.95848,,0.56717,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2012-10-03,Adult,Adult,Gonad,Reproductive System
36526,SRR578911,SRX190969,SRS366690,SRP015982,PRJNA176481,Small RNA analysis of Tu And SJD zebrafish strain and their progeny,GSE41299,Transcriptome Analysis,Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .,,pubmed:23335638,,SJDxTuF2 Individual 1,GSM1014075,,source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary,SJDxTuF2 Individual 1,Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads  except for libraries Tu Male  Tu P0  SJD Male  SJD P0  SJDxTuF1  TuxSJDF1  TuxSJDF2 and SJDxTuF2  which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts,Ovary,,Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps.,Animals were grown under standard conditioni,gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary,GSM1014075,GSM1014075: SJDxTuF2 Individual 1; Danio rerio; RNA Seq,GSM1014075 1,,1,,GEO Accession:GSM1014075,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP015982,,,,,400137228.0,11114923.0,GSM1014075 r1,0:36,A:107143937;C:91495000;G:94706504;T:106722021;N:69766,36,,,,107143937,91495000,94706504,106722021,69766,SRX190969,SRS366690,SRA059229,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.15753,,0.12463,,0.95538,,0.5649,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2012-10-03,Adult,Adult,Gonad,Reproductive System
36527,SRR578910,SRX190968,SRS366689,SRP015982,PRJNA176481,Small RNA analysis of Tu And SJD zebrafish strain and their progeny,GSE41299,Transcriptome Analysis,Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .,,pubmed:23335638,,SJDxTuF2,GSM1014074,,source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary,SJDxTuF2,Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads  except for libraries Tu Male  Tu P0  SJD Male  SJD P0  SJDxTuF1  TuxSJDF1  TuxSJDF2 and SJDxTuF2  which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts,Ovary,,Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps.,Animals were grown under standard conditioni,gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary,GSM1014074,GSM1014074: SJDxTuF2; Danio rerio; RNA Seq,GSM1014074 1,,1,,GEO Accession:GSM1014074,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP015982,,,SJDxTuF2.fastq,fastq,958492116.0,26624781.0,GSM1014074 r1,0:36,A:261275440;C:193944805;G:248348765;T:254793050;N:130056,36,,,,261275440,193944805,248348765,254793050,130056,SRX190968,SRS366689,SRA059229,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.20051,,0.16387,,0.94653,,0.53263,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2012-10-03,Adult,Adult,Gonad,Reproductive System
36528,SRR578909,SRX190967,SRS366688,SRP015982,PRJNA176481,Small RNA analysis of Tu And SJD zebrafish strain and their progeny,GSE41299,Transcriptome Analysis,Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .,,pubmed:23335638,,SJDxTuF1 Individual 2,GSM1014073,,source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary,SJDxTuF1 Individual 2,Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads  except for libraries Tu Male  Tu P0  SJD Male  SJD P0  SJDxTuF1  TuxSJDF1  TuxSJDF2 and SJDxTuF2  which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts,Ovary,,Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps.,Animals were grown under standard conditioni,gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary,GSM1014073,GSM1014073: SJDxTuF1 Individual 2; Danio rerio; RNA Seq,GSM1014073 1,,1,,GEO Accession:GSM1014073,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP015982,,,,,435761532.0,12104487.0,GSM1014073 r1,0:36,A:120580697;C:105605593;G:91379055;T:117787426;N:408761,36,,,,120580697,105605593,91379055,117787426,408761,SRX190967,SRS366688,SRA059229,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.07215,,0.05695,,0.97557,,0.48838,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2012-10-03,Adult,Adult,Gonad,Reproductive System
36529,SRR578908,SRX190966,SRS366687,SRP015982,PRJNA176481,Small RNA analysis of Tu And SJD zebrafish strain and their progeny,GSE41299,Transcriptome Analysis,Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .,,pubmed:23335638,,SJDxTuF1 Individual 1,GSM1014072,,source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary,SJDxTuF1 Individual 1,Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads  except for libraries Tu Male  Tu P0  SJD Male  SJD P0  SJDxTuF1  TuxSJDF1  TuxSJDF2 and SJDxTuF2  which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts,Ovary,,Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps.,Animals were grown under standard conditioni,gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary,GSM1014072,GSM1014072: SJDxTuF1 Individual 1; Danio rerio; RNA Seq,GSM1014072 1,,1,,GEO Accession:GSM1014072,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP015982,,,,,378296532.0,10508237.0,GSM1014072 r1,0:36,A:109216358;C:76585213;G:90165899;T:102085771;N:243291,36,,,,109216358,76585213,90165899,102085771,243291,SRX190966,SRS366687,SRA059229,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.13684,,0.10794,,0.96335,,0.49651,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2012-10-03,Adult,Adult,Gonad,Reproductive System
36530,SRR578907,SRX190965,SRS366686,SRP015982,PRJNA176481,Small RNA analysis of Tu And SJD zebrafish strain and their progeny,GSE41299,Transcriptome Analysis,Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .,,pubmed:23335638,,SJDxTuF1,GSM1014071,,source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary,SJDxTuF1,Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads  except for libraries Tu Male  Tu P0  SJD Male  SJD P0  SJDxTuF1  TuxSJDF1  TuxSJDF2 and SJDxTuF2  which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts,Ovary,,Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps.,Animals were grown under standard conditioni,gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary,GSM1014071,GSM1014071: SJDxTuF1; Danio rerio; RNA Seq,GSM1014071 1,,1,,GEO Accession:GSM1014071,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP015982,,,,,1047688380.0,29102455.0,GSM1014071 r1,0:36,A:277032474;C:213232299;G:269309034;T:288068877;N:45696,36,,,,277032474,213232299,269309034,288068877,45696,SRX190965,SRS366686,SRA059229,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.1858,,0.15153,,0.95006,,0.51345,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2012-10-03,Adult,Adult,Gonad,Reproductive System
36531,SRR578906,SRX190964,SRS366685,SRP015982,PRJNA176481,Small RNA analysis of Tu And SJD zebrafish strain and their progeny,GSE41299,Transcriptome Analysis,Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .,,pubmed:23335638,,SJD P0 Individual 2,GSM1014070,,source name:Ovary|sex:female|strain:SJD|development stage:Adult|tissue:Ovary,SJD P0 Individual 2,Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads  except for libraries Tu Male  Tu P0  SJD Male  SJD P0  SJDxTuF1  TuxSJDF1  TuxSJDF2 and SJDxTuF2  which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts,Ovary,,Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps.,Animals were grown under standard conditioni,gender:female|strain:SJD|developmental stage:Adult|tissue:Ovary,GSM1014070,GSM1014070: SJD P0 Individual 2; Danio rerio; RNA Seq,GSM1014070 1,,1,,GEO Accession:GSM1014070,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP015982,,,SJD_P0_Individual_2.fastq,fastq,392951772.0,10915327.0,GSM1014070 r1,0:36,A:126709476;C:82393458;G:82997127;T:100597122;N:254589,36,,,,126709476,82393458,82997127,100597122,254589,SRX190964,SRS366685,SRA059229,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.12786,,0.10199,,0.95724,,0.52026,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2012-10-03,Adult,Adult,Gonad,Reproductive System
36532,SRR578905,SRX190963,SRS366684,SRP015982,PRJNA176481,Small RNA analysis of Tu And SJD zebrafish strain and their progeny,GSE41299,Transcriptome Analysis,Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .,,pubmed:23335638,,SJD P0 Individual 1,GSM1014069,,source name:Ovary|sex:female|strain:SJD|development stage:Adult|tissue:Ovary,SJD P0 Individual 1,Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads  except for libraries Tu Male  Tu P0  SJD Male  SJD P0  SJDxTuF1  TuxSJDF1  TuxSJDF2 and SJDxTuF2  which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts,Ovary,,Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps.,Animals were grown under standard conditioni,gender:female|strain:SJD|developmental stage:Adult|tissue:Ovary,GSM1014069,GSM1014069: SJD P0 Individual 1; Danio rerio; RNA Seq,GSM1014069 1,,1,,GEO Accession:GSM1014069,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP015982,,,SJD_P0_Individual_1.fastq,fastq,379882512.0,10552292.0,GSM1014069 r1,0:36,A:122444116;C:80302064;G:76948943;T:99839311;N:348078,36,,,,122444116,80302064,76948943,99839311,348078,SRX190963,SRS366684,SRA059229,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.21364,,0.16206,,0.94268,,0.45306,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2012-10-03,Adult,Adult,Gonad,Reproductive System
36533,SRR578904,SRX190962,SRS366683,SRP015982,PRJNA176481,Small RNA analysis of Tu And SJD zebrafish strain and their progeny,GSE41299,Transcriptome Analysis,Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .,,pubmed:23335638,,SJD P0,GSM1014068,,source name:Ovary|sex:female|strain:SJD|development stage:Adult|tissue:Ovary,SJD P0,Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads  except for libraries Tu Male  Tu P0  SJD Male  SJD P0  SJDxTuF1  TuxSJDF1  TuxSJDF2 and SJDxTuF2  which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts,Ovary,,Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps.,Animals were grown under standard conditioni,gender:female|strain:SJD|developmental stage:Adult|tissue:Ovary,GSM1014068,GSM1014068: SJD P0; Danio rerio; RNA Seq,GSM1014068 1,,1,,GEO Accession:GSM1014068,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP015982,,,SJD_P0.fastq,fastq,837950832.0,23276412.0,GSM1014068 r1,0:36,A:217386642;C:179519865;G:217337232;T:223633685;N:73408,36,,,,217386642,179519865,217337232,223633685,73408,SRX190962,SRS366683,SRA059229,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.26607,,0.21631,,0.93789,,0.46928,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2012-10-03,Adult,Adult,Gonad,Reproductive System
40708,SRR3420428,SRX1660366,SRS1360334,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG01296 testis,,strain:TUAB|age:adult|sex:pooled male and female|tissue:Testis|BioSampleModel:Model organism or animal,,,,,,,,,AG01296 testis,AG01296 testis,1,1,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>75</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AG01296_SEQ0273_R1.fastq.gz,fastq,708117840.0,9317340.0,AG01296 run 1,0:76,A:188728168;C:160744436;G:154540381;T:204071817;N:33038,76,,,,188728168,160744436,154540381,204071817,33038,SRX1660366,SRS1360334,SRA395141,Yale University|Giraldez Lab,Yale University,1,0.93648,,0.13514,,0.61302,,0.4884,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Adult,Adult,Gonad,Reproductive System
40962,SRR3470786,SRX1738401,SRS1418771,SRP074244,PRJNA320266,Dietary intake influences fertility and offspring development in zebrafish.,GSE81007,Transcriptome Analysis,We report that increased nutrient availability increases breeding success and egg production. RNA seq analysis revealed that parental diet altered the expression of metabolic genes in the unfertilized eggs. Offspring from the differentially fed parents showed altered survival and energy expenditure as adults. Overall design: RNA from unfertilized eggs post two parental diets.,,pubmed:27870856,,60mg arm 3,GSM2140605,,source name:Unfertilized eggs|strain:In house AB/Pet shop|tissue:Unfertilized eggs|FISH age:9 mpf|treatment arm:60 mg,60mg arm 3,Sequence reads were filtered for quality using trimgalore. Reads were then mapped to the zebrafish genome using tophat v2.0.9  then assembled and merged with cufflinks v2.2.0 and cuffmerge  respectively. Differentially expressed transcripts were determined using cuffdiff v2.2.0. Gene ontology was assessed using BinGO 3.0.3  a plugin for cytoscape v3.3.0. Genome build: Zv9,Unfertilized eggs,Zebrafish were fed either 5 mg or 60 mg Artemia each day for eight weeks.,The eggs were transferred to tube containing RA1 buffer Macherey Nagel  cat. 740955.250 with b mercaptoethanol  and stored at  80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel  cat. 740955.250 and bound and eluted with columns 17   23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish were maintained under standard conditions,strain:In house AB/Pet shop|tissue:Unfertilized eggs|FISH age:9 mpf|treatment arm:60 mg,GSM2140605,GSM2140605: 60mg arm 3; Danio rerio; RNA Seq,GSM2140605,,1,The eggs were transferred to tube containing RA1 buffer Macherey Nagel  cat. 740955.250 with b mercaptoethanol  and stored at  80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel  cat. 740955.250 and bound and eluted with columns 17   23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2140605,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP074244,,,60mg-arm-3.fastq.gz,fastq,2353067800.0,23530678.0,GSM2140605 r1,0:100,A:550921675;C:559384489;G:553530174;T:689218350;N:13112,100,,,,550921675,559384489,553530174,689218350,13112,SRX1738401,SRS1418771,SRA422860,GEO,"Chromosome Structure and Development Group, Department of Pathology, University of Otago",1,0.95538,,0.04454,,0.7512,,0.62731,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2016-05-02,Multi-stage,Multi-stage,Oocyte,Reproductive System
40963,SRR3470785,SRX1738399,SRS1418770,SRP074244,PRJNA320266,Dietary intake influences fertility and offspring development in zebrafish.,GSE81007,Transcriptome Analysis,We report that increased nutrient availability increases breeding success and egg production. RNA seq analysis revealed that parental diet altered the expression of metabolic genes in the unfertilized eggs. Offspring from the differentially fed parents showed altered survival and energy expenditure as adults. Overall design: RNA from unfertilized eggs post two parental diets.,,pubmed:27870856,,60mg arm 2,GSM2140604,,source name:Unfertilized eggs|strain:In house AB/Pet shop|tissue:Unfertilized eggs|FISH age:9 mpf|treatment arm:60 mg,60mg arm 2,Sequence reads were filtered for quality using trimgalore. Reads were then mapped to the zebrafish genome using tophat v2.0.9  then assembled and merged with cufflinks v2.2.0 and cuffmerge  respectively. Differentially expressed transcripts were determined using cuffdiff v2.2.0. Gene ontology was assessed using BinGO 3.0.3  a plugin for cytoscape v3.3.0. Genome build: Zv9,Unfertilized eggs,Zebrafish were fed either 5 mg or 60 mg Artemia each day for eight weeks.,The eggs were transferred to tube containing RA1 buffer Macherey Nagel  cat. 740955.250 with b mercaptoethanol  and stored at  80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel  cat. 740955.250 and bound and eluted with columns 17   23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish were maintained under standard conditions,strain:In house AB/Pet shop|tissue:Unfertilized eggs|FISH age:9 mpf|treatment arm:60 mg,GSM2140604,GSM2140604: 60mg arm 2; Danio rerio; RNA Seq,GSM2140604,,1,The eggs were transferred to tube containing RA1 buffer Macherey Nagel  cat. 740955.250 with b mercaptoethanol  and stored at  80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel  cat. 740955.250 and bound and eluted with columns 17   23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2140604,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP074244,,,60mg-arm-2.fastq.gz,fastq,2552419200.0,25524192.0,GSM2140604 r1,0:100,A:598028827;C:604381782;G:600136410;T:749858137;N:14044,100,,,,598028827,604381782,600136410,749858137,14044,SRX1738399,SRS1418770,SRA422860,GEO,"Chromosome Structure and Development Group, Department of Pathology, University of Otago",1,0.95953,,0.04033,,0.75408,,0.63549,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2016-05-02,Multi-stage,Multi-stage,Oocyte,Reproductive System
40964,SRR3470784,SRX1738397,SRS1418769,SRP074244,PRJNA320266,Dietary intake influences fertility and offspring development in zebrafish.,GSE81007,Transcriptome Analysis,We report that increased nutrient availability increases breeding success and egg production. RNA seq analysis revealed that parental diet altered the expression of metabolic genes in the unfertilized eggs. Offspring from the differentially fed parents showed altered survival and energy expenditure as adults. Overall design: RNA from unfertilized eggs post two parental diets.,,pubmed:27870856,,60mg arm 1,GSM2140603,,source name:Unfertilized eggs|strain:In house AB/Pet shop|tissue:Unfertilized eggs|FISH age:9 mpf|treatment arm:60 mg,60mg arm 1,Sequence reads were filtered for quality using trimgalore. Reads were then mapped to the zebrafish genome using tophat v2.0.9  then assembled and merged with cufflinks v2.2.0 and cuffmerge  respectively. Differentially expressed transcripts were determined using cuffdiff v2.2.0. Gene ontology was assessed using BinGO 3.0.3  a plugin for cytoscape v3.3.0. Genome build: Zv9,Unfertilized eggs,Zebrafish were fed either 5 mg or 60 mg Artemia each day for eight weeks.,The eggs were transferred to tube containing RA1 buffer Macherey Nagel  cat. 740955.250 with b mercaptoethanol  and stored at  80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel  cat. 740955.250 and bound and eluted with columns 17   23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish were maintained under standard conditions,strain:In house AB/Pet shop|tissue:Unfertilized eggs|FISH age:9 mpf|treatment arm:60 mg,GSM2140603,GSM2140603: 60mg arm 1; Danio rerio; RNA Seq,GSM2140603,,1,The eggs were transferred to tube containing RA1 buffer Macherey Nagel  cat. 740955.250 with b mercaptoethanol  and stored at  80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel  cat. 740955.250 and bound and eluted with columns 17   23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2140603,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP074244,,,60mg-arm-1.fastq.gz,fastq,2471843300.0,24718433.0,GSM2140603 r1,0:100,A:578536744;C:593318438;G:586674975;T:713299111;N:14032,100,,,,578536744,593318438,586674975,713299111,14032,SRX1738397,SRS1418769,SRA422860,GEO,"Chromosome Structure and Development Group, Department of Pathology, University of Otago",1,0.95474,,0.04276,,0.75625,,0.61194,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2016-05-02,Multi-stage,Multi-stage,Oocyte,Reproductive System
40965,SRR3470783,SRX1738395,SRS1418767,SRP074244,PRJNA320266,Dietary intake influences fertility and offspring development in zebrafish.,GSE81007,Transcriptome Analysis,We report that increased nutrient availability increases breeding success and egg production. RNA seq analysis revealed that parental diet altered the expression of metabolic genes in the unfertilized eggs. Offspring from the differentially fed parents showed altered survival and energy expenditure as adults. Overall design: RNA from unfertilized eggs post two parental diets.,,pubmed:27870856,,5mg arm 3,GSM2140602,,source name:Unfertilized eggs|strain:In house AB/Pet shop|tissue:Unfertilized eggs|FISH age:9 mpf|treatment arm:5 mg,5mg arm 3,Sequence reads were filtered for quality using trimgalore. Reads were then mapped to the zebrafish genome using tophat v2.0.9  then assembled and merged with cufflinks v2.2.0 and cuffmerge  respectively. Differentially expressed transcripts were determined using cuffdiff v2.2.0. Gene ontology was assessed using BinGO 3.0.3  a plugin for cytoscape v3.3.0. Genome build: Zv9,Unfertilized eggs,Zebrafish were fed either 5 mg or 60 mg Artemia each day for eight weeks.,The eggs were transferred to tube containing RA1 buffer Macherey Nagel  cat. 740955.250 with b mercaptoethanol  and stored at  80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel  cat. 740955.250 and bound and eluted with columns 17   23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish were maintained under standard conditions,strain:In house AB/Pet shop|tissue:Unfertilized eggs|FISH age:9 mpf|treatment arm:5 mg,GSM2140602,GSM2140602: 5mg arm 3; Danio rerio; RNA Seq,GSM2140602,,1,The eggs were transferred to tube containing RA1 buffer Macherey Nagel  cat. 740955.250 with b mercaptoethanol  and stored at  80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel  cat. 740955.250 and bound and eluted with columns 17   23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2140602,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP074244,,,5mg-arm-3.fastq.gz,fastq,2562336500.0,25623365.0,GSM2140602 r1,0:100,A:599122965;C:614407524;G:605967391;T:742824547;N:14073,100,,,,599122965,614407524,605967391,742824547,14073,SRX1738395,SRS1418767,SRA422860,GEO,"Chromosome Structure and Development Group, Department of Pathology, University of Otago",1,0.95071,,0.0461,,0.74483,,0.61788,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2016-05-02,Multi-stage,Multi-stage,Oocyte,Reproductive System
40966,SRR3470782,SRX1738393,SRS1418765,SRP074244,PRJNA320266,Dietary intake influences fertility and offspring development in zebrafish.,GSE81007,Transcriptome Analysis,We report that increased nutrient availability increases breeding success and egg production. RNA seq analysis revealed that parental diet altered the expression of metabolic genes in the unfertilized eggs. Offspring from the differentially fed parents showed altered survival and energy expenditure as adults. Overall design: RNA from unfertilized eggs post two parental diets.,,pubmed:27870856,,5mg arm 2,GSM2140601,,source name:Unfertilized eggs|strain:In house AB/Pet shop|tissue:Unfertilized eggs|FISH age:9 mpf|treatment arm:5 mg,5mg arm 2,Sequence reads were filtered for quality using trimgalore. Reads were then mapped to the zebrafish genome using tophat v2.0.9  then assembled and merged with cufflinks v2.2.0 and cuffmerge  respectively. Differentially expressed transcripts were determined using cuffdiff v2.2.0. Gene ontology was assessed using BinGO 3.0.3  a plugin for cytoscape v3.3.0. Genome build: Zv9,Unfertilized eggs,Zebrafish were fed either 5 mg or 60 mg Artemia each day for eight weeks.,The eggs were transferred to tube containing RA1 buffer Macherey Nagel  cat. 740955.250 with b mercaptoethanol  and stored at  80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel  cat. 740955.250 and bound and eluted with columns 17   23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish were maintained under standard conditions,strain:In house AB/Pet shop|tissue:Unfertilized eggs|FISH age:9 mpf|treatment arm:5 mg,GSM2140601,GSM2140601: 5mg arm 2; Danio rerio; RNA Seq,GSM2140601,,1,The eggs were transferred to tube containing RA1 buffer Macherey Nagel  cat. 740955.250 with b mercaptoethanol  and stored at  80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel  cat. 740955.250 and bound and eluted with columns 17   23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2140601,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP074244,,,5mg-arm-2.fastq.gz,fastq,2841710700.0,28417107.0,GSM2140601 r1,0:100,A:663485391;C:679416584;G:665850494;T:832942768;N:15463,100,,,,663485391,679416584,665850494,832942768,15463,SRX1738393,SRS1418765,SRA422860,GEO,"Chromosome Structure and Development Group, Department of Pathology, University of Otago",1,0.94998,,0.04837,,0.75442,,0.63571,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2016-05-02,Multi-stage,Multi-stage,Oocyte,Reproductive System
40967,SRR3470781,SRX1738391,SRS1418764,SRP074244,PRJNA320266,Dietary intake influences fertility and offspring development in zebrafish.,GSE81007,Transcriptome Analysis,We report that increased nutrient availability increases breeding success and egg production. RNA seq analysis revealed that parental diet altered the expression of metabolic genes in the unfertilized eggs. Offspring from the differentially fed parents showed altered survival and energy expenditure as adults. Overall design: RNA from unfertilized eggs post two parental diets.,,pubmed:27870856,,5mg arm 1,GSM2140600,,source name:Unfertilized eggs|strain:In house AB/Pet shop|tissue:Unfertilized eggs|FISH age:9 mpf|treatment arm:5 mg,5mg arm 1,Sequence reads were filtered for quality using trimgalore. Reads were then mapped to the zebrafish genome using tophat v2.0.9  then assembled and merged with cufflinks v2.2.0 and cuffmerge  respectively. Differentially expressed transcripts were determined using cuffdiff v2.2.0. Gene ontology was assessed using BinGO 3.0.3  a plugin for cytoscape v3.3.0. Genome build: Zv9,Unfertilized eggs,Zebrafish were fed either 5 mg or 60 mg Artemia each day for eight weeks.,The eggs were transferred to tube containing RA1 buffer Macherey Nagel  cat. 740955.250 with b mercaptoethanol  and stored at  80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel  cat. 740955.250 and bound and eluted with columns 17   23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish were maintained under standard conditions,strain:In house AB/Pet shop|tissue:Unfertilized eggs|FISH age:9 mpf|treatment arm:5 mg,GSM2140600,GSM2140600: 5mg arm 1; Danio rerio; RNA Seq,GSM2140600,,1,The eggs were transferred to tube containing RA1 buffer Macherey Nagel  cat. 740955.250 with b mercaptoethanol  and stored at  80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel  cat. 740955.250 and bound and eluted with columns 17   23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2140600,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP074244,,,5mg-arm-1.fastq.gz,fastq,2409548800.0,24095488.0,GSM2140600 r1,0:100,A:519836883;C:638777587;G:641445656;T:609475335;N:13339,100,,,,519836883,638777587,641445656,609475335,13339,SRX1738391,SRS1418764,SRA422860,GEO,"Chromosome Structure and Development Group, Department of Pathology, University of Otago",1,0.88003,,0.04264,,0.76138,,0.66721,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2016-05-02,Multi-stage,Multi-stage,Oocyte,Reproductive System
41175,SRR3923687,SRX1950218,SRS1564979,SRP078537,PRJNA329141,Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis,GSE84436,Transcriptome Analysis,Spermatogonial stem cells are quiescent  undergo self renewal or differentiating divisions  thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH  through the production of Sertoli cell derived factors  and by Leydig cell released androgens. Here  we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo  using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions  RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß  Hedgehog  Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover  Fsh had a marked impact on metabolic genes  such as lactate and fatty acid metabolism  or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3  a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh  providing promising leads for future work  as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.,,pubmed:27566230,,Trilostane+Fsh 6,GSM2236119,,source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,Trilostane+Fsh 6,Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq  and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.,Testis,,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,,tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,GSM2236119,GSM2236119: Trilostane+Fsh 6; Danio rerio; RNA Seq,GSM2236119,,1,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,GEO Accession:GSM2236119,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP078537,,,Seq19_H9PG8ADXX_CTGAAGCT-GTACTGAC_L001_R1_001.fastq.gz,fastq,541196550.0,10823931.0,GSM2236119 r1,0:50,A:129904818;C:128871362;G:125784183;T:151841105;N:4795082,50,,,,129904818,128871362,125784183,151841105,4795082,SRX1950218,SRS1564979,SRA440585,GEO,"Reproductive Biology, Biology, Utrecht University",1,0.83528,,0.26943,,0.65632,,0.56402,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2016-07-14,Adult,Adult,Gonad,Reproductive System
41176,SRR3923688,SRX1950218,SRS1564979,SRP078537,PRJNA329141,Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis,GSE84436,Transcriptome Analysis,Spermatogonial stem cells are quiescent  undergo self renewal or differentiating divisions  thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH  through the production of Sertoli cell derived factors  and by Leydig cell released androgens. Here  we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo  using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions  RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß  Hedgehog  Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover  Fsh had a marked impact on metabolic genes  such as lactate and fatty acid metabolism  or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3  a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh  providing promising leads for future work  as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.,,pubmed:27566230,,Trilostane+Fsh 6,GSM2236119,,source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,Trilostane+Fsh 6,Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq  and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.,Testis,,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,,tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,GSM2236119,GSM2236119: Trilostane+Fsh 6; Danio rerio; RNA Seq,GSM2236119,,1,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,GEO Accession:GSM2236119,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP078537,,,Seq19_H9PG8ADXX_CTGAAGCT-GTACTGAC_L002_R1_001.fastq.gz,fastq,540752550.0,10815051.0,GSM2236119 r2,0:50,A:129870926;C:128702724;G:125668527;T:151723226;N:4787147,50,,,,129870926,128702724,125668527,151723226,4787147,SRX1950218,SRS1564979,SRA440585,GEO,"Reproductive Biology, Biology, Utrecht University",1,0.83561,,0.26923,,0.65658,,0.5633,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2016-07-14,Adult,Adult,Gonad,Reproductive System
41177,SRR3923685,SRX1950217,SRS1564978,SRP078537,PRJNA329141,Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis,GSE84436,Transcriptome Analysis,Spermatogonial stem cells are quiescent  undergo self renewal or differentiating divisions  thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH  through the production of Sertoli cell derived factors  and by Leydig cell released androgens. Here  we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo  using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions  RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß  Hedgehog  Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover  Fsh had a marked impact on metabolic genes  such as lactate and fatty acid metabolism  or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3  a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh  providing promising leads for future work  as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.,,pubmed:27566230,,Trilostane+Fsh 5,GSM2236118,,source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,Trilostane+Fsh 5,Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq  and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.,Testis,,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,,tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,GSM2236118,GSM2236118: Trilostane+Fsh 5; Danio rerio; RNA Seq,GSM2236118,,1,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,GEO Accession:GSM2236118,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP078537,,,Seq18_H9PG8ADXX_ATTCAGAA-GTACTGAC_L001_R1_001.fastq.gz,fastq,536259700.0,10725194.0,GSM2236118 r1,0:50,A:132683158;C:124371530;G:118570874;T:155804755;N:4829383,50,,,,132683158,124371530,118570874,155804755,4829383,SRX1950217,SRS1564978,SRA440585,GEO,"Reproductive Biology, Biology, Utrecht University",1,0.86166,,0.28405,,0.66085,,0.56844,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2016-07-14,Adult,Adult,Gonad,Reproductive System
41178,SRR3923686,SRX1950217,SRS1564978,SRP078537,PRJNA329141,Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis,GSE84436,Transcriptome Analysis,Spermatogonial stem cells are quiescent  undergo self renewal or differentiating divisions  thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH  through the production of Sertoli cell derived factors  and by Leydig cell released androgens. Here  we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo  using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions  RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß  Hedgehog  Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover  Fsh had a marked impact on metabolic genes  such as lactate and fatty acid metabolism  or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3  a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh  providing promising leads for future work  as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.,,pubmed:27566230,,Trilostane+Fsh 5,GSM2236118,,source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,Trilostane+Fsh 5,Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq  and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.,Testis,,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,,tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,GSM2236118,GSM2236118: Trilostane+Fsh 5; Danio rerio; RNA Seq,GSM2236118,,1,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,GEO Accession:GSM2236118,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP078537,,,Seq18_H9PG8ADXX_ATTCAGAA-GTACTGAC_L002_R1_001.fastq.gz,fastq,536614850.0,10732297.0,GSM2236118 r2,0:50,A:132824083;C:124387998;G:118657068;T:155922787;N:4822914,50,,,,132824083,124387998,118657068,155922787,4822914,SRX1950217,SRS1564978,SRA440585,GEO,"Reproductive Biology, Biology, Utrecht University",1,0.86253,,0.2872,,0.66176,,0.56675,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2016-07-14,Adult,Adult,Gonad,Reproductive System
41179,SRR3923683,SRX1950216,SRS1564977,SRP078537,PRJNA329141,Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis,GSE84436,Transcriptome Analysis,Spermatogonial stem cells are quiescent  undergo self renewal or differentiating divisions  thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH  through the production of Sertoli cell derived factors  and by Leydig cell released androgens. Here  we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo  using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions  RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß  Hedgehog  Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover  Fsh had a marked impact on metabolic genes  such as lactate and fatty acid metabolism  or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3  a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh  providing promising leads for future work  as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.,,pubmed:27566230,,Trilostane+Fsh 4,GSM2236117,,source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,Trilostane+Fsh 4,Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq  and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.,Testis,,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,,tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,GSM2236117,GSM2236117: Trilostane+Fsh 4; Danio rerio; RNA Seq,GSM2236117,,1,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,GEO Accession:GSM2236117,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP078537,,,Seq16_H9PG8ADXX_CGCTCATT-GTACTGAC_L001_R1_001.fastq.gz,fastq,427009700.0,8540194.0,GSM2236117 r1,0:50,A:104823398;C:99767068;G:94526860;T:124062805;N:3829569,50,,,,104823398,99767068,94526860,124062805,3829569,SRX1950216,SRS1564977,SRA440585,GEO,"Reproductive Biology, Biology, Utrecht University",1,0.86391,,0.29478,,0.65476,,0.47031,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2016-07-14,Adult,Adult,Gonad,Reproductive System
41180,SRR3923684,SRX1950216,SRS1564977,SRP078537,PRJNA329141,Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis,GSE84436,Transcriptome Analysis,Spermatogonial stem cells are quiescent  undergo self renewal or differentiating divisions  thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH  through the production of Sertoli cell derived factors  and by Leydig cell released androgens. Here  we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo  using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions  RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß  Hedgehog  Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover  Fsh had a marked impact on metabolic genes  such as lactate and fatty acid metabolism  or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3  a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh  providing promising leads for future work  as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.,,pubmed:27566230,,Trilostane+Fsh 4,GSM2236117,,source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,Trilostane+Fsh 4,Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq  and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.,Testis,,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,,tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,GSM2236117,GSM2236117: Trilostane+Fsh 4; Danio rerio; RNA Seq,GSM2236117,,1,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,GEO Accession:GSM2236117,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP078537,,,Seq16_H9PG8ADXX_CGCTCATT-GTACTGAC_L002_R1_001.fastq.gz,fastq,425476900.0,8509538.0,GSM2236117 r2,0:50,A:104473554;C:99368446;G:94196508;T:123623942;N:3814450,50,,,,104473554,99368446,94196508,123623942,3814450,SRX1950216,SRS1564977,SRA440585,GEO,"Reproductive Biology, Biology, Utrecht University",1,0.86395,,0.29677,,0.65736,,0.46962,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2016-07-14,Adult,Adult,Gonad,Reproductive System
41181,SRR3923681,SRX1950215,SRS1564976,SRP078537,PRJNA329141,Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis,GSE84436,Transcriptome Analysis,Spermatogonial stem cells are quiescent  undergo self renewal or differentiating divisions  thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH  through the production of Sertoli cell derived factors  and by Leydig cell released androgens. Here  we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo  using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions  RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß  Hedgehog  Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover  Fsh had a marked impact on metabolic genes  such as lactate and fatty acid metabolism  or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3  a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh  providing promising leads for future work  as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.,,pubmed:27566230,,Trilostane+Fsh 3,GSM2236116,,source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,Trilostane+Fsh 3,Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq  and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.,Testis,,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,,tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,GSM2236116,GSM2236116: Trilostane+Fsh 3; Danio rerio; RNA Seq,GSM2236116,,1,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,GEO Accession:GSM2236116,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP078537,,,Seq8_H9PG8ADXX_TCCGCGAA-CAGGACGT_L001_R1_001.fastq.gz,fastq,547479650.0,10949593.0,GSM2236116 r1,0:50,A:132619117;C:134226431;G:118412018;T:157542627;N:4679457,50,,,,132619117,134226431,118412018,157542627,4679457,SRX1950215,SRS1564976,SRA440585,GEO,"Reproductive Biology, Biology, Utrecht University",1,0.9055,,0.32136,,0.66793,,0.60282,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2016-07-14,Adult,Adult,Gonad,Reproductive System
41182,SRR3923682,SRX1950215,SRS1564976,SRP078537,PRJNA329141,Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis,GSE84436,Transcriptome Analysis,Spermatogonial stem cells are quiescent  undergo self renewal or differentiating divisions  thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH  through the production of Sertoli cell derived factors  and by Leydig cell released androgens. Here  we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo  using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions  RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß  Hedgehog  Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover  Fsh had a marked impact on metabolic genes  such as lactate and fatty acid metabolism  or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3  a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh  providing promising leads for future work  as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.,,pubmed:27566230,,Trilostane+Fsh 3,GSM2236116,,source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,Trilostane+Fsh 3,Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq  and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.,Testis,,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,,tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,GSM2236116,GSM2236116: Trilostane+Fsh 3; Danio rerio; RNA Seq,GSM2236116,,1,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,GEO Accession:GSM2236116,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP078537,,,Seq8_H9PG8ADXX_TCCGCGAA-CAGGACGT_L002_R1_001.fastq.gz,fastq,548145550.0,10962911.0,GSM2236116 r2,0:50,A:132852947;C:134322795;G:118563196;T:157723665;N:4682947,50,,,,132852947,134322795,118563196,157723665,4682947,SRX1950215,SRS1564976,SRA440585,GEO,"Reproductive Biology, Biology, Utrecht University",1,0.90629,,0.3224,,0.67079,,0.59076,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2016-07-14,Adult,Adult,Gonad,Reproductive System
41183,SRR3923679,SRX1950214,SRS1564975,SRP078537,PRJNA329141,Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis,GSE84436,Transcriptome Analysis,Spermatogonial stem cells are quiescent  undergo self renewal or differentiating divisions  thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH  through the production of Sertoli cell derived factors  and by Leydig cell released androgens. Here  we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo  using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions  RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß  Hedgehog  Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover  Fsh had a marked impact on metabolic genes  such as lactate and fatty acid metabolism  or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3  a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh  providing promising leads for future work  as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.,,pubmed:27566230,,Trilostane+Fsh 2,GSM2236115,,source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,Trilostane+Fsh 2,Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq  and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.,Testis,,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,,tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,GSM2236115,GSM2236115: Trilostane+Fsh 2; Danio rerio; RNA Seq,GSM2236115,,1,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,GEO Accession:GSM2236115,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP078537,,,Seq6_H9PG8ADXX_TAATGCGC-CAGGACGT_L001_R1_001.fastq.gz,fastq,483539450.0,9670789.0,GSM2236115 r1,0:50,A:113342249;C:121843102;G:107743374;T:136575001;N:4035724,50,,,,113342249,121843102,107743374,136575001,4035724,SRX1950214,SRS1564975,SRA440585,GEO,"Reproductive Biology, Biology, Utrecht University",1,0.91137,,0.3309,,0.67945,,0.55402,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2016-07-14,Adult,Adult,Gonad,Reproductive System
41184,SRR3923680,SRX1950214,SRS1564975,SRP078537,PRJNA329141,Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis,GSE84436,Transcriptome Analysis,Spermatogonial stem cells are quiescent  undergo self renewal or differentiating divisions  thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH  through the production of Sertoli cell derived factors  and by Leydig cell released androgens. Here  we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo  using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions  RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß  Hedgehog  Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover  Fsh had a marked impact on metabolic genes  such as lactate and fatty acid metabolism  or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3  a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh  providing promising leads for future work  as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.,,pubmed:27566230,,Trilostane+Fsh 2,GSM2236115,,source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,Trilostane+Fsh 2,Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq  and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.,Testis,,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,,tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,GSM2236115,GSM2236115: Trilostane+Fsh 2; Danio rerio; RNA Seq,GSM2236115,,1,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,GEO Accession:GSM2236115,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP078537,,,Seq6_H9PG8ADXX_TAATGCGC-CAGGACGT_L002_R1_001.fastq.gz,fastq,483032050.0,9660641.0,GSM2236115 r2,0:50,A:113263999;C:121692767;G:107625313;T:136421502;N:4028469,50,,,,113263999,121692767,107625313,136421502,4028469,SRX1950214,SRS1564975,SRA440585,GEO,"Reproductive Biology, Biology, Utrecht University",1,0.9125,,0.32793,,0.68138,,0.54622,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2016-07-14,Adult,Adult,Gonad,Reproductive System
41185,SRR3923677,SRX1950213,SRS1564974,SRP078537,PRJNA329141,Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis,GSE84436,Transcriptome Analysis,Spermatogonial stem cells are quiescent  undergo self renewal or differentiating divisions  thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH  through the production of Sertoli cell derived factors  and by Leydig cell released androgens. Here  we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo  using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions  RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß  Hedgehog  Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover  Fsh had a marked impact on metabolic genes  such as lactate and fatty acid metabolism  or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3  a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh  providing promising leads for future work  as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.,,pubmed:27566230,,Trilostane+Fsh 1,GSM2236114,,source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,Trilostane+Fsh 1,Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq  and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.,Testis,,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,,tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,GSM2236114,GSM2236114: Trilostane+Fsh 1; Danio rerio; RNA Seq,GSM2236114,,1,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,GEO Accession:GSM2236114,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP078537,,,Seq4_H9PG8ADXX_GAGATTCC-CAGGACGT_L001_R1_001.fastq.gz,fastq,657366700.0,13147334.0,GSM2236114 r1,0:50,A:167604847;C:149043342;G:139125980;T:195616217;N:5976314,50,,,,167604847,149043342,139125980,195616217,5976314,SRX1950213,SRS1564974,SRA440585,GEO,"Reproductive Biology, Biology, Utrecht University",1,0.85723,,0.34006,,0.65415,,0.46117,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2016-07-14,Adult,Adult,Gonad,Reproductive System
41186,SRR3923678,SRX1950213,SRS1564974,SRP078537,PRJNA329141,Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis,GSE84436,Transcriptome Analysis,Spermatogonial stem cells are quiescent  undergo self renewal or differentiating divisions  thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH  through the production of Sertoli cell derived factors  and by Leydig cell released androgens. Here  we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo  using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions  RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß  Hedgehog  Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover  Fsh had a marked impact on metabolic genes  such as lactate and fatty acid metabolism  or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3  a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh  providing promising leads for future work  as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.,,pubmed:27566230,,Trilostane+Fsh 1,GSM2236114,,source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,Trilostane+Fsh 1,Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq  and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.,Testis,,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,,tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,GSM2236114,GSM2236114: Trilostane+Fsh 1; Danio rerio; RNA Seq,GSM2236114,,1,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,GEO Accession:GSM2236114,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP078537,,,Seq4_H9PG8ADXX_GAGATTCC-CAGGACGT_L002_R1_001.fastq.gz,fastq,657335800.0,13146716.0,GSM2236114 r2,0:50,A:167683325;C:148965849;G:139104499;T:195605431;N:5976696,50,,,,167683325,148965849,139104499,195605431,5976696,SRX1950213,SRS1564974,SRA440585,GEO,"Reproductive Biology, Biology, Utrecht University",1,0.85828,,0.33726,,0.65212,,0.46064,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2016-07-14,Adult,Adult,Gonad,Reproductive System
41187,SRR3923675,SRX1950212,SRS1564973,SRP078537,PRJNA329141,Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis,GSE84436,Transcriptome Analysis,Spermatogonial stem cells are quiescent  undergo self renewal or differentiating divisions  thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH  through the production of Sertoli cell derived factors  and by Leydig cell released androgens. Here  we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo  using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions  RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß  Hedgehog  Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover  Fsh had a marked impact on metabolic genes  such as lactate and fatty acid metabolism  or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3  a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh  providing promising leads for future work  as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.,,pubmed:27566230,,Trilostane 6,GSM2236113,,source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,Trilostane 6,Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq  and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.,Testis,,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,,tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,GSM2236113,GSM2236113: Trilostane 6; Danio rerio; RNA Seq,GSM2236113,,1,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,GEO Accession:GSM2236113,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP078537,,,Seq23_H9PG8ADXX_TCTCGCGC-GTACTGAC_L001_R1_001.fastq.gz,fastq,473414850.0,9468297.0,GSM2236113 r1,0:50,A:115132784;C:111560620;G:107691623;T:134806360;N:4223463,50,,,,115132784,111560620,107691623,134806360,4223463,SRX1950212,SRS1564973,SRA440585,GEO,"Reproductive Biology, Biology, Utrecht University",1,0.82776,,0.27832,,0.65922,,0.56166,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2016-07-14,Adult,Adult,Gonad,Reproductive System
41188,SRR3923676,SRX1950212,SRS1564973,SRP078537,PRJNA329141,Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis,GSE84436,Transcriptome Analysis,Spermatogonial stem cells are quiescent  undergo self renewal or differentiating divisions  thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH  through the production of Sertoli cell derived factors  and by Leydig cell released androgens. Here  we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo  using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions  RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß  Hedgehog  Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover  Fsh had a marked impact on metabolic genes  such as lactate and fatty acid metabolism  or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3  a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh  providing promising leads for future work  as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.,,pubmed:27566230,,Trilostane 6,GSM2236113,,source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,Trilostane 6,Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq  and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.,Testis,,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,,tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours,GSM2236113,GSM2236113: Trilostane 6; Danio rerio; RNA Seq,GSM2236113,,1,Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina  Inc. according to the manufacturer’s instructions,GEO Accession:GSM2236113,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP078537,,,Seq23_H9PG8ADXX_TCTCGCGC-GTACTGAC_L002_R1_001.fastq.gz,fastq,471843300.0,9436866.0,GSM2236113 r2,0:50,A:114789047;C:111198690;G:107327397;T:134316769;N:4211397,50,,,,114789047,111198690,107327397,134316769,4211397,SRX1950212,SRS1564973,SRA440585,GEO,"Reproductive Biology, Biology, Utrecht University",1,0.82475,,0.28061,,0.65914,,0.56084,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2016-07-14,Adult,Adult,Gonad,Reproductive System