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
15550,ERR647595,ERX604031,ERS557915,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Egg,SAMEA2796300,UNIVERSITY OF AMSTERDAM,Alias:Egg|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:29:23Z|INSDC status:public|SRA accession:ERS557915|Sample Name:ERS557915|Title:Zebrafish Egg samples|dev stage:Oocytes,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:25:29:391 1,RID0024,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0024_016.fastq.gz,fastq,6684767188.0,89052017.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:25:29:391 1,0:75.07,A:1523328157;C:1795624453;G:1849675240;T:1516139338;N:0,75,,,,1523328157,1795624453,1849675240,1516139338,0,ERX604031,ERS557915,ERA363845,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.89536,,0.15322,,0.91421,,0.69019,,73,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Zygote,Embryo,Oocyte,Reproductive System
25293,SRR25764131,SRX21486791,SRS18719090,SRP457111,PRJNA1009808,Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq],GSE241754,Transcriptome Analysis,Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.,parent bioproject:PRJNA1009800,pubmed:39402326,,WT egg 0 hpf tRNA seq rep2,GSM7734772,,source name:Unfertilized egg|strain:TLAB strain|tissue:Unfertilized egg|developmental stage:unfertilized egg 0 hpf|genotype:WT|geo loc name:missing|collection date:missing,WT egg 0 hpf tRNA seq rep2,Read demultiplexing and adapter trimming performed with cutadapt v3.5  where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained  and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters   species Drer   cluster id 0.93   min cov 0.001   max mismatches 0.075   control condition Egg   deconv cov ratio 0.4   remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters  and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts,Unfertilized egg,unperturbed growth conditions in E3 medium for zebrafish embryos.,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.,strain:TLAB strain|tissue:Unfertilized egg|developmental stage:unfertilized egg 0 hpf|genotype:WT,GSM7734772,GSM7734772: WT egg 0 hpf tRNA seq rep2; Danio rerio; ncRNA Seq,GSM7734772 r1,GSM7734772,1,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP457111,,,WT_tRNA_egg_2.fastq.gz,fastq,206374994.0,3181706.0,GSM7734772 r1,0:64.86,A:41195250;C:56578032;G:56479855;T:52121365;N:492,64,,,,41195250,56578032,56479855,52121365,492,SRX21486791,SRS18719090,SRA1700461,"Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry",Max Planck Institute of Biochemistry,1,0.28659,,0.02017,,0.9207,,0.48536,,78,,B,,usable mapping rate,illumina,nextseq,5prime,size_fractionation,unknown,bulk,unknown,unknown,,Germany,2023-08-28,Zygote,Embryo,Oocyte,Reproductive System
25294,SRR25764132,SRX21486790,SRS18719089,SRP457111,PRJNA1009808,Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq],GSE241754,Transcriptome Analysis,Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.,parent bioproject:PRJNA1009800,pubmed:39402326,,WT egg 0 hpf tRNA seq rep1,GSM7734771,,source name:Unfertilized egg|strain:TLAB strain|tissue:Unfertilized egg|developmental stage:unfertilized egg 0 hpf|genotype:WT|geo loc name:missing|collection date:missing,WT egg 0 hpf tRNA seq rep1,Read demultiplexing and adapter trimming performed with cutadapt v3.5  where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained  and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters   species Drer   cluster id 0.93   min cov 0.001   max mismatches 0.075   control condition Egg   deconv cov ratio 0.4   remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters  and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts,Unfertilized egg,unperturbed growth conditions in E3 medium for zebrafish embryos.,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.,strain:TLAB strain|tissue:Unfertilized egg|developmental stage:unfertilized egg 0 hpf|genotype:WT,GSM7734771,GSM7734771: WT egg 0 hpf tRNA seq rep1; Danio rerio; ncRNA Seq,GSM7734771 r1,GSM7734771,1,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP457111,,,WT_tRNA_egg_1.fastq.gz,fastq,86021968.0,1304769.0,GSM7734771 r1,0:65.93,A:17511521;C:23474625;G:23300759;T:21734864;N:199,65,,,,17511521,23474625,23300759,21734864,199,SRX21486790,SRS18719089,SRA1700461,"Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry",Max Planck Institute of Biochemistry,1,0.29829,,0.02027,,0.92245,,0.48877,,74,,B,,usable mapping rate,illumina,nextseq,5prime,size_fractionation,unknown,bulk,unknown,unknown,,Germany,2023-08-28,Zygote,Embryo,Oocyte,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
29765,SRR27437485,SRX23109812,SRS20064566,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary BS R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: ovary  BS  rep3,EV04017,EV04017,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV04017.R1.fastq.gz,fastq,576584540.0,4118461.0,EV04017.R1.fastq.gz,0:140,A:149516980;C:91163801;G:169046762;T:166831111;N:25886,140,,,,149516980,91163801,169046762,166831111,25886,SRX23109812,SRS20064566,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.0,,0.0,,1.0,,,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Adult,Adult,Gonad,Reproductive System
29776,SRR27437496,SRX23109801,SRS20064555,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary DM R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: ovary  DM  rep3,EV04016,EV04016,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV04016.R1.fastq.gz,fastq,635752880.0,4541092.0,EV04016.R1.fastq.gz,0:140,A:160072248;C:143996869;G:189137330;T:142516059;N:30374,140,,,,160072248,143996869,189137330,142516059,30374,SRX23109801,SRS20064555,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,1e-05,,0.0,,0.99997,,1.0,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Adult,Adult,Gonad,Reproductive System
29777,SRR27437497,SRX23109800,SRS20064554,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary mock R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: ovary  mock  rep3,EV04015,EV04015,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV04015.R1.fastq.gz,fastq,489700680.0,3497862.0,EV04015.R1.fastq.gz,0:140,A:126641754;C:126582886;G:130564204;T:105889815;N:22021,140,,,,126641754,126582886,130564204,105889815,22021,SRX23109800,SRS20064554,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,6e-05,,0.0,,0.99983,,0.55555,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Adult,Adult,Gonad,Reproductive System
29786,SRR27435871,SRX23108225,SRS20063062,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary BS R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: ovary  BS  rep4,EV08003,EV08003,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08003.R1.fastq.gz,fastq,571689580.0,4083497.0,EV08003.R1.fastq.gz,0:140,A:141414131;C:88722455;G:138790445;T:202723075;N:39474,140,,,,141414131,88722455,138790445,202723075,39474,SRX23108225,SRS20063062,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,3e-05,,0.0,,0.99991,,0.75,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Adult,Adult,Gonad,Reproductive System
29797,SRR27435882,SRX23108214,SRS20063050,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary DM R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: ovary  DM  rep4,EV08002,EV08002,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08002.R1.fastq.gz,fastq,668593800.0,4775670.0,EV08002.R1.fastq.gz,0:140,A:164584224;C:175789134;G:175538168;T:152637106;N:45168,140,,,,164584224,175789134,175538168,152637106,45168,SRX23108214,SRS20063050,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.00525,,2e-05,,0.99192,,0.63501,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Adult,Adult,Gonad,Reproductive System
29798,SRR27435883,SRX23108213,SRS20063051,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary mock R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: ovary  mock  rep4,EV08001,EV08001,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08001.R1.fastq.gz,fastq,753247460.0,5380339.0,EV08001.R1.fastq.gz,0:140,A:183862675;C:196453674;G:197604061;T:175275086;N:51964,140,,,,183862675,196453674,197604061,175275086,51964,SRX23108213,SRS20063051,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.00754,,4e-05,,0.98957,,0.51048,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Adult,Adult,Gonad,Reproductive System
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
36424,SRR516545,SRX156307,SRS347187,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   unfertilized egg,D. rerio unfertilized egg,D. rerio unfertilized egg,,,,,,,,,,,CAGE   D. rerio unfertilized egg,CAGE   D. rerio unfertilized egg run2,D. rerio unfertilized egg,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<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>,SRP013950,,,,,115273233.0,4269379.0,CAGE   D. rerio unfertilized egg run1,0:27,A:29909511;C:24823784;G:32519899;T:28020039;N:0,27,,,,29909511,24823784,32519899,28020039,0,SRX156307,SRS347187,SRA055273,University of Bergen,ZEPROME consortium,1,0.49872,,0.07655,,0.81673,,0.80445,,27,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2012-06-28,Zygote,Embryo,Oocyte,Reproductive System
36425,SRR516546,SRX156307,SRS347187,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   unfertilized egg,D. rerio unfertilized egg,D. rerio unfertilized egg,,,,,,,,,,,CAGE   D. rerio unfertilized egg,CAGE   D. rerio unfertilized egg run2,D. rerio unfertilized egg,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<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>,SRP013950,,,,,112673943.0,4173109.0,CAGE   D. rerio unfertilized egg run2,0:27,A:28315221;C:24199098;G:32599482;T:27560142;N:0,27,,,,28315221,24199098,32599482,27560142,0,SRX156307,SRS347187,SRA055273,University of Bergen,ZEPROME consortium,1,0.46201,,0.06422,,0.82118,,0.82184,,27,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2012-06-28,Zygote,Embryo,Oocyte,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
37921,SRR1554495,SRX685396,SRS686645,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF4Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97410|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary2,ZF4Ovary2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP039502,,,ZF4_Ovary_3.fq.gz,fastq,1225610154.0,12134754.0,Ovary2 Run3,0:101,A:347141358;C:303255805;G:280185540;T:294456010;N:571441,101,,,,347141358,303255805,280185540,294456010,571441,SRX685396,SRS686645,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,2e-05,,1e-05,,1.0,,,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37922,SRR1554492,SRX685395,SRS686644,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97409|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis2,ZF2Testis2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP039502,,,ZF2_Testis_3.fq.gz,fastq,1192024422.0,11802222.0,Testis2 Run3,0:101,A:373380865;C:276125943;G:251033102;T:290931637;N:552875,101,,,,373380865,276125943,251033102,290931637,552875,SRX685395,SRS686644,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,3e-05,,1e-05,,0.99997,,0.0,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37925,SRR1554483,SRX685391,SRS686559,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF3Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary1,ZF3Ovary2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP039502,,,ZF3_Ovary_3.fq.gz,fastq,347516154.0,3440754.0,Ovary1 Run3,0:101,A:107805981;C:80183725;G:73617313;T:85763181;N:145954,101,,,,107805981,80183725,73617313,85763181,145954,SRX685391,SRS686559,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,5e-05,,4e-05,,1.0,,,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37926,SRR1554480,SRX685390,SRS686542,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97405|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis1,ZF1Testis2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP039502,,,ZF1_Testis_3.fq.gz,fastq,1184228636.0,11725036.0,Testis1 Run3,0:101,A:340636900;C:278505979;G:259975802;T:304564724;N:545231,101,,,,340636900,278505979,259975802,304564724,545231,SRX685390,SRS686542,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,1e-05,,0.0,,1.0,,,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37929,SRR1554493,SRX683354,SRS686645,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF4Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97410|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary2,ZF4Ovary1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF4_Ovary_1.fq.gz,fastq,476104278.0,9335378.0,Ovary2 Run1,0:51,A:111060704;C:120863975;G:129849761;T:114224677;N:105161,51,,,,111060704,120863975,129849761,114224677,105161,SRX683354,SRS686645,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.00027,,8e-05,,0.99945,,0.8125,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37930,SRR1554494,SRX683354,SRS686645,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF4Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97410|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary2,ZF4Ovary1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF4_Ovary_2.fq.gz,fastq,561956352.0,11018752.0,Ovary2 Run2,0:51,A:129925815;C:148479658;G:148478706;T:132824290;N:2247883,51,,,,129925815,148479658,148478706,132824290,2247883,SRX683354,SRS686645,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.00022,,0.0001,,0.99967,,0.6875,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37931,SRR1554490,SRX683353,SRS686644,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97409|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis2,ZF2Testis1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF2_Testis_1.fq.gz,fastq,586152231.0,11493181.0,Testis2 Run1,0:51,A:145360493;C:148943988;G:151402108;T:140286245;N:159397,51,,,,145360493,148943988,151402108,140286245,159397,SRX683353,SRS686644,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,8e-05,,2e-05,,0.99985,,0.57142,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37932,SRR1554491,SRX683353,SRS686644,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97409|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis2,ZF2Testis1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF2_Testis_2.fq.gz,fastq,697016337.0,13666987.0,Testis2 Run2,0:51,A:172082858;C:184634425;G:173370430;T:163527914;N:3400710,51,,,,172082858,184634425,173370430,163527914,3400710,SRX683353,SRS686644,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,8e-05,,2e-05,,0.99985,,0.57142,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37937,SRR1554481,SRX683080,SRS686559,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF3Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary1,ZF3Ovary1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF3_Ovary_1.fq.gz,fastq,116086965.0,2276215.0,Ovary1 Run1,0:51,A:29237121;C:30235277;G:29264328;T:27320814;N:29425,51,,,,29237121,30235277,29264328,27320814,29425,SRX683080,SRS686559,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.00022,,9e-05,,0.99967,,0.65,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37938,SRR1554482,SRX683080,SRS686559,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF3Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary1,ZF3Ovary1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF3_Ovary_2.fq.gz,fastq,138905844.0,2723644.0,Ovary1 Run2,0:51,A:34695180;C:38015933;G:33434207;T:32057083;N:703441,51,,,,34695180,38015933,33434207,32057083,703441,SRX683080,SRS686559,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.00016,,5e-05,,0.99977,,0.42857,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37939,SRR1554478,SRX683062,SRS686542,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97405|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis1,ZF1Testis1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF1_Testis_1.fq.gz,fastq,655515750.0,12853250.0,Testis1 Run1,0:51,A:152422885;C:163771947;G:179144090;T:159997538;N:179290,51,,,,152422885,163771947,179144090,159997538,179290,SRX683062,SRS686542,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.0011,,0.00053,,0.99829,,0.67777,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37940,SRR1554479,SRX683062,SRS686542,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97405|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis1,ZF1Testis1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF1_Testis_2.fq.gz,fastq,777594399.0,15246949.0,Testis1 Run2,0:51,A:180116528;C:202508153;G:204833105;T:186435696;N:3700917,51,,,,180116528,202508153,204833105,186435696,3700917,SRX683062,SRS686542,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.00073,,0.00032,,0.99898,,0.62745,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37997,SRR1265760,SRX529154,SRS598851,SRP041544,PRJNA245824,Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish,GSE57169,Transcriptome Analysis,The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.,,pubmed:26574018,,Testis Replicate 3 sRNAseq,GSM1376643,,source name:Testis|gender:male|tissue:Testis|genetic background:Wild type   Singapore strain,Testis Replicate 3 sRNAseq,Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.,Testis,N/A,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,Fishes were purchased from a local supplier and acclimatized before tissue extraction.,gender:Male|tissue:Testis|genetic background:Wild type   Singapore strain,GSM1376643,GSM1376643: Testis Replicate 3 sRNAseq; Danio rerio; miRNA Seq,GSM1376643,,1,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,GEO Accession:GSM1376643,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP041544,,,MZT004_GCCAAT_L004_R1.fastq.gz,fastq,1096387628.0,14426153.0,GSM1376643 r1,0:76,A:268706118;C:286539627;G:262643519;T:278353167;N:145197,76,,,,268706118,286539627,262643519,278353167,145197,SRX529154,SRS598851,SRA160430,GEO,"Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore",1,0.00659,,0.00333,,0.99845,,0.7331,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Singapore,2014-04-29,Undetermined,Embryo,Gonad,Reproductive System
37998,SRR1265759,SRX529153,SRS598850,SRP041544,PRJNA245824,Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish,GSE57169,Transcriptome Analysis,The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.,,pubmed:26574018,,Testis Replicate 2 sRNAseq,GSM1376642,,source name:Testis|gender:male|tissue:Testis|genetic background:Wild type   Singapore strain,Testis Replicate 2 sRNAseq,Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.,Testis,N/A,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,Fishes were purchased from a local supplier and acclimatized before tissue extraction.,gender:Male|tissue:Testis|genetic background:Wild type   Singapore strain,GSM1376642,GSM1376642: Testis Replicate 2 sRNAseq; Danio rerio; miRNA Seq,GSM1376642,,1,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,GEO Accession:GSM1376642,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP041544,,,MZT003_ACAGTG_L004_R1.fastq.gz,fastq,1562745896.0,20562446.0,GSM1376642 r1,0:76,A:381752411;C:387452090;G:395892335;T:397438930;N:210130,76,,,,381752411,387452090,395892335,397438930,210130,SRX529153,SRS598850,SRA160430,GEO,"Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore",1,0.01222,,0.00651,,0.99788,,0.69591,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Singapore,2014-04-29,Undetermined,Embryo,Gonad,Reproductive System
37999,SRR1265758,SRX529152,SRS598849,SRP041544,PRJNA245824,Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish,GSE57169,Transcriptome Analysis,The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.,,pubmed:26574018,,Testis Replicate 1 sRNAseq,GSM1376641,,source name:Testis|gender:male|tissue:Testis|genetic background:Wild type   Singapore strain,Testis Replicate 1 sRNAseq,Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.,Testis,N/A,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,Fishes were purchased from a local supplier and acclimatized before tissue extraction.,gender:Male|tissue:Testis|genetic background:Wild type   Singapore strain,GSM1376641,GSM1376641: Testis Replicate 1 sRNAseq; Danio rerio; miRNA Seq,GSM1376641,,1,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,GEO Accession:GSM1376641,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP041544,,,MZT001_TGACCA_L004_R1.fastq.gz,fastq,1368892316.0,18011741.0,GSM1376641 r1,0:76,A:335715713;C:358829703;G:326742789;T:347419137;N:184974,76,,,,335715713,358829703,326742789,347419137,184974,SRX529152,SRS598849,SRA160430,GEO,"Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore",1,0.00032,,3e-05,,0.99943,,0.69387,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Singapore,2014-04-29,Undetermined,Embryo,Gonad,Reproductive System
38000,SRR1265757,SRX529151,SRS598848,SRP041544,PRJNA245824,Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish,GSE57169,Transcriptome Analysis,The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.,,pubmed:26574018,,Ovary Replicate 3 sRNAseq,GSM1376640,,source name:Ovary|gender:female|tissue:Ovary|genetic background:Wild type   Singapore strain,Ovary Replicate 3 sRNAseq,Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.,Ovary,N/A,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,Fishes were purchased from a local supplier and acclimatized before tissue extraction.,gender:Female|tissue:Ovary|genetic background:Wild type   Singapore strain,GSM1376640,GSM1376640: Ovary Replicate 3 sRNAseq; Danio rerio; miRNA Seq,GSM1376640,,1,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,GEO Accession:GSM1376640,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP041544,,,MZO006_GATCAG_L008_R1.fastq.gz,fastq,1411005984.0,27666784.0,GSM1376640 r1,0:51,A:326542153;C:314421825;G:411019622;T:358847379;N:175005,51,,,,326542153,314421825,411019622,358847379,175005,SRX529151,SRS598848,SRA160430,GEO,"Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore",1,0.00638,,0.00068,,0.99513,,0.75483,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Singapore,2014-04-29,Undetermined,Embryo,Gonad,Reproductive System
38001,SRR1265756,SRX529150,SRS598847,SRP041544,PRJNA245824,Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish,GSE57169,Transcriptome Analysis,The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.,,pubmed:26574018,,Ovary Replicate 2 sRNAseq,GSM1376639,,source name:Ovary|gender:female|tissue:Ovary|genetic background:Wild type   Singapore strain,Ovary Replicate 2 sRNAseq,Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.,Ovary,N/A,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,Fishes were purchased from a local supplier and acclimatized before tissue extraction.,gender:Female|tissue:Ovary|genetic background:Wild type   Singapore strain,GSM1376639,GSM1376639: Ovary Replicate 2 sRNAseq; Danio rerio; miRNA Seq,GSM1376639,,1,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,GEO Accession:GSM1376639,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP041544,,,MZO005_ACTTGA_L008_R1.fastq.gz,fastq,765419424.0,15008224.0,GSM1376639 r1,0:51,A:179455664;C:170237021;G:221342071;T:194287721;N:96947,51,,,,179455664,170237021,221342071,194287721,96947,SRX529150,SRS598847,SRA160430,GEO,"Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore",1,0.02512,,0.00355,,0.98212,,0.67744,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Singapore,2014-04-29,Undetermined,Embryo,Gonad,Reproductive System
38002,SRR1265755,SRX529149,SRS598846,SRP041544,PRJNA245824,Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish,GSE57169,Transcriptome Analysis,The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.,,pubmed:26574018,,Ovary Replicate 1 sRNAseq,GSM1376638,,source name:Ovary|gender:female|tissue:Ovary|genetic background:Wild type   Singapore strain,Ovary Replicate 1 sRNAseq,Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.,Ovary,N/A,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,Fishes were purchased from a local supplier and acclimatized before tissue extraction.,gender:Female|tissue:Ovary|genetic background:Wild type   Singapore strain,GSM1376638,GSM1376638: Ovary Replicate 1 sRNAseq; Danio rerio; miRNA Seq,GSM1376638,,1,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,GEO Accession:GSM1376638,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP041544,,,MZO004_CAGATC_L008_R1.fastq.gz,fastq,487558674.0,9559974.0,GSM1376638 r1,0:51,A:114833813;C:108951811;G:140408702;T:123302557;N:61791,51,,,,114833813,108951811,140408702,123302557,61791,SRX529149,SRS598846,SRA160430,GEO,"Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore",1,0.00298,,0.0004,,0.99644,,0.84584,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Singapore,2014-04-29,Undetermined,Embryo,Gonad,Reproductive System