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205 rows where experiment.library_layout = "SINGLE", experiment.library_strategy = "RNA-Seq" and tissue_curation = "Gonad"

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experiment.library_selection 7

devstage_curation_coarse 5

devstage_curation 5

technology 3

experiment.platform 3

tissue_curation_coarse 1

tissue_curation 1

  • Gonad · 205 ✖

experiment.library_strategy 1

  • RNA-Seq · 205 ✖

experiment.library_source 1

experiment.library_layout 1

  • SINGLE · 205 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
50 50 DRR029944 DRX026962 DRS086502 DRP004756 PRJDB3475 Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish DRP004756 Other To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.     ovulation duirng natural paring zebrafish ovary isolated from adult fish at ovulation duirng natural paring. [RNAseq] SAMD00025434   sample name:6 Ovu|strain:roy|tissue type:ovary|dev stage:adult                 Illumina HiSeq 2500 sequencing of SAMD00025434 DRX026962 6 Ovu 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004756 Illumina HiSeq 2500 sequencing of SAMD00025434       351766656.0 9771296.0 DRR029944 0:36 A:79811727;C:85391142;G:90185809;T:96371771;N:6207 36       79811727 85391142 90185809 96371771 6207 DRX026962 DRS086502 DRA003031 SHIZUOKA|Shizuoka University Shizuoka University 1 0.91956   0.01686   0.76637   0.45997   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
52 52 DRR029942 DRX026960 DRS086500 DRP004756 PRJDB3475 Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish DRP004756 Other To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.     in vivo testosterone treatment zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq replicate] SAMD00025432   sample name:4 Tes rep|strain:roy|tissue type:ovary|dev stage:adult                 Illumina HiSeq 2500 sequencing of SAMD00025432 DRX026960 4 Tes rep 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004756 Illumina HiSeq 2500 sequencing of SAMD00025432       366042528.0 10167848.0 DRR029942 0:36 A:84988522;C:88640326;G:93559022;T:98847003;N:7655 36       84988522 88640326 93559022 98847003 7655 DRX026960 DRS086500 DRA003031 SHIZUOKA|Shizuoka University Shizuoka University 1 0.91602   0.01846   0.76015   0.46475   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
53 53 DRR029941 DRX026959 DRS086499 DRP004756 PRJDB3475 Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish DRP004756 Other To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.     in vivo testosterone treatment zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq] SAMD00025431   sample name:4 Tes|strain:roy|tissue type:ovary|dev stage:adult                 Illumina HiSeq 2500 sequencing of SAMD00025431 DRX026959 4 Tes 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004756 Illumina HiSeq 2500 sequencing of SAMD00025431       1269835992.0 35273222.0 DRR029941 0:36 A:275250658;C:323605136;G:316729009;T:354204170;N:47019 36       275250658 323605136 316729009 354204170 47019 DRX026959 DRS086499 DRA003031 SHIZUOKA|Shizuoka University Shizuoka University 1 0.91467   0.02353   0.75962   0.46861   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
54 54 DRR029940 DRX026958 DRS086498 DRP004756 PRJDB3475 Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish DRP004756 Other To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.     in vivo diethylstilbestrol DES treatment zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq replicate] SAMD00025430   sample name:3 DES rep|strain:roy|tissue type:ovary|dev stage:adult                 Illumina HiSeq 2500 sequencing of SAMD00025430 DRX026958 3 DES rep 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004756 Illumina HiSeq 2500 sequencing of SAMD00025430       658651536.0 18295876.0 DRR029940                       DRX026958 DRS086498 DRA003031 SHIZUOKA|Shizuoka University Shizuoka University 1 0.89964   0.01785   0.76451   0.45872   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
55 55 DRR029939 DRX026957 DRS086497 DRP004756 PRJDB3475 Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish DRP004756 Other To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.     in vivo diethylstilbestrol DES treatment zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq] SAMD00025429   sample name:3 DES|strain:roy|tissue type:ovary|dev stage:adult                 Illumina HiSeq 2500 sequencing of SAMD00025429 DRX026957 3 DES 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004756 Illumina HiSeq 2500 sequencing of SAMD00025429       1202024016.0 33389556.0 DRR029939 0:36 A:263319430;C:305852921;G:298798093;T:334008544;N:45028 36       263319430 305852921 298798093 334008544 45028 DRX026957 DRS086497 DRA003031 SHIZUOKA|Shizuoka University Shizuoka University 1 0.90643   0.02337   0.75008   0.47587   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
56 56 DRR029938 DRX026956 DRS086496 DRP004756 PRJDB3475 Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish DRP004756 Other To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.     in vivo maturation inducing hormone DHP treatment zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq replicate] SAMD00025428   sample name:2 DHP rep|strain:roy|tissue type:ovary|dev stage:adult                 Illumina HiSeq 2500 sequencing of SAMD00025428 DRX026956 2 DHP rep 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004756 Illumina HiSeq 2500 sequencing of SAMD00025428       434243088.0 12062308.0 DRR029938 0:36 A:99859342;C:105890785;G:110526688;T:117957580;N:8693 36       99859342 105890785 110526688 117957580 8693 DRX026956 DRS086496 DRA003031 SHIZUOKA|Shizuoka University Shizuoka University 1 0.91529   0.02061   0.7595   0.45809   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
57 57 DRR029937 DRX026955 DRS086495 DRP004756 PRJDB3475 Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish DRP004756 Other To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.     in vivo maturation inducing hormone DHP treatment zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq] SAMD00025427   sample name:2 DHP|strain:roy|tissue type:ovary|dev stage:adult                 Illumina HiSeq 2500 sequencing of SAMD00025427 DRX026955 2 DHP 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004756 Illumina HiSeq 2500 sequencing of SAMD00025427       1463868972.0 40663027.0 DRR029937 0:36 A:316060780;C:369221844;G:372845502;T:405685804;N:55042 36       316060780 369221844 372845502 405685804 55042 DRX026955 DRS086495 DRA003031 SHIZUOKA|Shizuoka University Shizuoka University 1 0.91556   0.01967   0.76621   0.46541   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
58 58 DRR029936 DRX026954 DRS086494 DRP004756 PRJDB3475 Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish DRP004756 Other To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.     in vivo ethanol treatment zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq replicate] SAMD00025426   sample name:1 EtOH rep|strain:roy|tissue type:ovary|dev stage:adult                 Illumina HiSeq 2500 sequencing of SAMD00025426 DRX026954 1 EtOH rep 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004756 Illumina HiSeq 2500 sequencing of SAMD00025426       438020208.0 12167228.0 DRR029936 0:36 A:101672612;C:105602774;G:110120652;T:120615069;N:9101 36       101672612 105602774 110120652 120615069 9101 DRX026954 DRS086494 DRA003031 SHIZUOKA|Shizuoka University Shizuoka University 1 0.90777   0.01929   0.7652   0.45988   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
59 59 DRR029935 DRX026953 DRS086493 DRP004756 PRJDB3475 Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish DRP004756 Other To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.     in vivo ethanol treatment zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq] SAMD00025425   sample name:1 EtOH|strain:roy|tissue type:ovary|dev stage:adult                 Illumina HiSeq 2500 sequencing of SAMD00025425 DRX026953 1 EtOH 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004756 Illumina HiSeq 2500 sequencing of SAMD00025425       1365603372.0 37933427.0 DRR029935 0:36 A:299786286;C:345487829;G:342408447;T:377870789;N:50021 36       299786286 345487829 342408447 377870789 50021 DRX026953 DRS086493 DRA003031 SHIZUOKA|Shizuoka University Shizuoka University 1 0.91103   0.02142   0.75402   0.46574   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
174 174 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
176 176 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
177 177 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
178 178 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
179 179 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
180 180 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
182 182 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
183 183 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
184 184 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
185 185 DRR084187 DRX078018 DRS086512 DRP004758 PRJDB5490 Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish DRP004758 Other Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.     in vivo ethanol treatment zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq replicate1] SAMD00073594   sample name:EtOH|replicate:biological replicate 1                 Illumina HiSeq 2500 sequencing of SAMD00073594 DRX078018 zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq replicate1] 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004758 Illumina HiSeq 2500 sequencing of SAMD00073594       1152032724.0 32000909.0 DRR084187 0:36 A:265166034;C:279617628;G:285136940;T:321928656;N:183466 36       265166034 279617628 285136940 321928656 183466 DRX078018 DRS086512 DRA005484 SHIZUOKA|Shizuoka University Shizuoka University 1 0.90791   0.02405   0.75972   0.48931   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
29259 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
34965 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 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 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
36273 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 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 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 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 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 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 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 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 … 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 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 … female adults Ovaries and testes were obtained as described in Gupta and Mullins 2010. 3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html Zebrafish embryos or adults grown under standard condition genotype/variation:wild type|tissue:ovary|developmental stage:adult GSM919970 GSM919970: 3P Seq Ovary; Danio rerio; RNA Seq GSM919970 1 GSM919970: 3P Seq Ovary 1   GEO Accession:GSM919970 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP012376     3P_Seq_Ovary.fastq fastq 644470380.0 17901955.0 GSM919970 r1 0:36 A:263871252;C:97757369;G:94972134;T:187683515;N:186110 36       263871252 97757369 94972134 187683515 186110 SRX143564 SRS310285 SRA051955 GEO Whitehead Institute for Biomedical Research 1 0.51356   0.04868   0.821   0.48788   36   B   usable mapping rate illumina early_illumina 3prime cdna_unspecified unknown bulk unknown unknown   United States 2012-04-20 Adult Adult Gonad Reproductive System
36514 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 36533 SRR578904 SRX190962 SRS366683 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   SJD P0 GSM1014068   source name:Ovary|sex:female|strain:SJD|development stage:Adult|tissue:Ovary SJD P0 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:SJD|developmental stage:Adult|tissue:Ovary GSM1014068 GSM1014068: SJD P0; Danio rerio; RNA Seq GSM1014068 1   1   GEO Accession:GSM1014068 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982     SJD_P0.fastq fastq 837950832.0 23276412.0 GSM1014068 r1 0:36 A:217386642;C:179519865;G:217337232;T:223633685;N:73408 36       217386642 179519865 217337232 223633685 73408 SRX190962 SRS366683 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.26607   0.21631   0.93789   0.46928   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
40708 40708 SRR3420428 SRX1660366 SRS1360334 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG01296 testis   strain:TUAB|age:adult|sex:pooled male and female|tissue:Testis|BioSampleModel:Model organism or animal                 AG01296 testis AG01296 testis 1 1     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>75</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG01296_SEQ0273_R1.fastq.gz fastq 708117840.0 9317340.0 AG01296 run 1 0:76 A:188728168;C:160744436;G:154540381;T:204071817;N:33038 76       188728168 160744436 154540381 204071817 33038 SRX1660366 SRS1360334 SRA395141 Yale University|Giraldez Lab Yale University 1 0.93648   0.13514   0.61302   0.4884   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Adult Adult Gonad Reproductive System
41175 41175 SRR3923687 SRX1950218 SRS1564979 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane+Fsh 6 GSM2236119   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane+Fsh 6 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236119 GSM2236119: Trilostane+Fsh 6; Danio rerio; RNA Seq GSM2236119   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236119 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq19_H9PG8ADXX_CTGAAGCT-GTACTGAC_L001_R1_001.fastq.gz fastq 541196550.0 10823931.0 GSM2236119 r1 0:50 A:129904818;C:128871362;G:125784183;T:151841105;N:4795082 50       129904818 128871362 125784183 151841105 4795082 SRX1950218 SRS1564979 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.83528   0.26943   0.65632   0.56402   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41176 41176 SRR3923688 SRX1950218 SRS1564979 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane+Fsh 6 GSM2236119   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane+Fsh 6 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236119 GSM2236119: Trilostane+Fsh 6; Danio rerio; RNA Seq GSM2236119   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236119 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq19_H9PG8ADXX_CTGAAGCT-GTACTGAC_L002_R1_001.fastq.gz fastq 540752550.0 10815051.0 GSM2236119 r2 0:50 A:129870926;C:128702724;G:125668527;T:151723226;N:4787147 50       129870926 128702724 125668527 151723226 4787147 SRX1950218 SRS1564979 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.83561   0.26923   0.65658   0.5633   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41177 41177 SRR3923685 SRX1950217 SRS1564978 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane+Fsh 5 GSM2236118   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane+Fsh 5 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236118 GSM2236118: Trilostane+Fsh 5; Danio rerio; RNA Seq GSM2236118   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236118 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq18_H9PG8ADXX_ATTCAGAA-GTACTGAC_L001_R1_001.fastq.gz fastq 536259700.0 10725194.0 GSM2236118 r1 0:50 A:132683158;C:124371530;G:118570874;T:155804755;N:4829383 50       132683158 124371530 118570874 155804755 4829383 SRX1950217 SRS1564978 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.86166   0.28405   0.66085   0.56844   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41178 41178 SRR3923686 SRX1950217 SRS1564978 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane+Fsh 5 GSM2236118   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane+Fsh 5 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236118 GSM2236118: Trilostane+Fsh 5; Danio rerio; RNA Seq GSM2236118   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236118 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq18_H9PG8ADXX_ATTCAGAA-GTACTGAC_L002_R1_001.fastq.gz fastq 536614850.0 10732297.0 GSM2236118 r2 0:50 A:132824083;C:124387998;G:118657068;T:155922787;N:4822914 50       132824083 124387998 118657068 155922787 4822914 SRX1950217 SRS1564978 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.86253   0.2872   0.66176   0.56675   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41179 41179 SRR3923683 SRX1950216 SRS1564977 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane+Fsh 4 GSM2236117   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane+Fsh 4 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236117 GSM2236117: Trilostane+Fsh 4; Danio rerio; RNA Seq GSM2236117   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236117 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq16_H9PG8ADXX_CGCTCATT-GTACTGAC_L001_R1_001.fastq.gz fastq 427009700.0 8540194.0 GSM2236117 r1 0:50 A:104823398;C:99767068;G:94526860;T:124062805;N:3829569 50       104823398 99767068 94526860 124062805 3829569 SRX1950216 SRS1564977 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.86391   0.29478   0.65476   0.47031   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41180 41180 SRR3923684 SRX1950216 SRS1564977 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane+Fsh 4 GSM2236117   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane+Fsh 4 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236117 GSM2236117: Trilostane+Fsh 4; Danio rerio; RNA Seq GSM2236117   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236117 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq16_H9PG8ADXX_CGCTCATT-GTACTGAC_L002_R1_001.fastq.gz fastq 425476900.0 8509538.0 GSM2236117 r2 0:50 A:104473554;C:99368446;G:94196508;T:123623942;N:3814450 50       104473554 99368446 94196508 123623942 3814450 SRX1950216 SRS1564977 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.86395   0.29677   0.65736   0.46962   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41181 41181 SRR3923681 SRX1950215 SRS1564976 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane+Fsh 3 GSM2236116   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane+Fsh 3 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236116 GSM2236116: Trilostane+Fsh 3; Danio rerio; RNA Seq GSM2236116   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236116 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq8_H9PG8ADXX_TCCGCGAA-CAGGACGT_L001_R1_001.fastq.gz fastq 547479650.0 10949593.0 GSM2236116 r1 0:50 A:132619117;C:134226431;G:118412018;T:157542627;N:4679457 50       132619117 134226431 118412018 157542627 4679457 SRX1950215 SRS1564976 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.9055   0.32136   0.66793   0.60282   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41182 41182 SRR3923682 SRX1950215 SRS1564976 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane+Fsh 3 GSM2236116   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane+Fsh 3 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236116 GSM2236116: Trilostane+Fsh 3; Danio rerio; RNA Seq GSM2236116   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236116 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq8_H9PG8ADXX_TCCGCGAA-CAGGACGT_L002_R1_001.fastq.gz fastq 548145550.0 10962911.0 GSM2236116 r2 0:50 A:132852947;C:134322795;G:118563196;T:157723665;N:4682947 50       132852947 134322795 118563196 157723665 4682947 SRX1950215 SRS1564976 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.90629   0.3224   0.67079   0.59076   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41183 41183 SRR3923679 SRX1950214 SRS1564975 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane+Fsh 2 GSM2236115   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane+Fsh 2 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236115 GSM2236115: Trilostane+Fsh 2; Danio rerio; RNA Seq GSM2236115   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236115 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq6_H9PG8ADXX_TAATGCGC-CAGGACGT_L001_R1_001.fastq.gz fastq 483539450.0 9670789.0 GSM2236115 r1 0:50 A:113342249;C:121843102;G:107743374;T:136575001;N:4035724 50       113342249 121843102 107743374 136575001 4035724 SRX1950214 SRS1564975 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.91137   0.3309   0.67945   0.55402   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41184 41184 SRR3923680 SRX1950214 SRS1564975 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane+Fsh 2 GSM2236115   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane+Fsh 2 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236115 GSM2236115: Trilostane+Fsh 2; Danio rerio; RNA Seq GSM2236115   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236115 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq6_H9PG8ADXX_TAATGCGC-CAGGACGT_L002_R1_001.fastq.gz fastq 483032050.0 9660641.0 GSM2236115 r2 0:50 A:113263999;C:121692767;G:107625313;T:136421502;N:4028469 50       113263999 121692767 107625313 136421502 4028469 SRX1950214 SRS1564975 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.9125   0.32793   0.68138   0.54622   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41185 41185 SRR3923677 SRX1950213 SRS1564974 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane+Fsh 1 GSM2236114   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane+Fsh 1 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236114 GSM2236114: Trilostane+Fsh 1; Danio rerio; RNA Seq GSM2236114   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236114 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq4_H9PG8ADXX_GAGATTCC-CAGGACGT_L001_R1_001.fastq.gz fastq 657366700.0 13147334.0 GSM2236114 r1 0:50 A:167604847;C:149043342;G:139125980;T:195616217;N:5976314 50       167604847 149043342 139125980 195616217 5976314 SRX1950213 SRS1564974 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.85723   0.34006   0.65415   0.46117   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41186 41186 SRR3923678 SRX1950213 SRS1564974 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane+Fsh 1 GSM2236114   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane+Fsh 1 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236114 GSM2236114: Trilostane+Fsh 1; Danio rerio; RNA Seq GSM2236114   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236114 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq4_H9PG8ADXX_GAGATTCC-CAGGACGT_L002_R1_001.fastq.gz fastq 657335800.0 13146716.0 GSM2236114 r2 0:50 A:167683325;C:148965849;G:139104499;T:195605431;N:5976696 50       167683325 148965849 139104499 195605431 5976696 SRX1950213 SRS1564974 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.85828   0.33726   0.65212   0.46064   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41187 41187 SRR3923675 SRX1950212 SRS1564973 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane 6 GSM2236113   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane 6 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236113 GSM2236113: Trilostane 6; Danio rerio; RNA Seq GSM2236113   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236113 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq23_H9PG8ADXX_TCTCGCGC-GTACTGAC_L001_R1_001.fastq.gz fastq 473414850.0 9468297.0 GSM2236113 r1 0:50 A:115132784;C:111560620;G:107691623;T:134806360;N:4223463 50       115132784 111560620 107691623 134806360 4223463 SRX1950212 SRS1564973 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.82776   0.27832   0.65922   0.56166   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41188 41188 SRR3923676 SRX1950212 SRS1564973 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane 6 GSM2236113   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane 6 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236113 GSM2236113: Trilostane 6; Danio rerio; RNA Seq GSM2236113   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236113 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq23_H9PG8ADXX_TCTCGCGC-GTACTGAC_L002_R1_001.fastq.gz fastq 471843300.0 9436866.0 GSM2236113 r2 0:50 A:114789047;C:111198690;G:107327397;T:134316769;N:4211397 50       114789047 111198690 107327397 134316769 4211397 SRX1950212 SRS1564973 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.82475   0.28061   0.65914   0.56084   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41189 41189 SRR3923673 SRX1950211 SRS1564972 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane 5 GSM2236112   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane 5 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236112 GSM2236112: Trilostane 5; Danio rerio; RNA Seq GSM2236112   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236112 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq22_H9PG8ADXX_CGGCTATG-GTACTGAC_L001_R1_001.fastq.gz fastq 454002550.0 9080051.0 GSM2236112 r1 0:50 A:110121161;C:107184608;G:104060594;T:128567586;N:4068601 50       110121161 107184608 104060594 128567586 4068601 SRX1950211 SRS1564972 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.8315   0.27748   0.66985   0.56656   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41190 41190 SRR3923674 SRX1950211 SRS1564972 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane 5 GSM2236112   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane 5 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236112 GSM2236112: Trilostane 5; Danio rerio; RNA Seq GSM2236112   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236112 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq22_H9PG8ADXX_CGGCTATG-GTACTGAC_L002_R1_001.fastq.gz fastq 447723500.0 8954470.0 GSM2236112 r2 0:50 A:108647571;C:105645041;G:102638902;T:126784624;N:4007362 50       108647571 105645041 102638902 126784624 4007362 SRX1950211 SRS1564972 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.83099   0.27799   0.66967   0.56426   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41191 41191 SRR3923671 SRX1950210 SRS1564971 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane 4 GSM2236111   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane 4 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236111 GSM2236111: Trilostane 4; Danio rerio; RNA Seq GSM2236111   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236111 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq12_H9PG8ADXX_ATTACTCG-GTACTGAC_L001_R1_001.fastq.gz fastq 446491050.0 8929821.0 GSM2236111 r1 0:50 A:111285929;C:103826231;G:97244947;T:130091134;N:4042809 50       111285929 103826231 97244947 130091134 4042809 SRX1950210 SRS1564971 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.87061   0.31363   0.65111   0.55604   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41192 41192 SRR3923672 SRX1950210 SRS1564971 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane 4 GSM2236111   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane 4 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236111 GSM2236111: Trilostane 4; Danio rerio; RNA Seq GSM2236111   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236111 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq12_H9PG8ADXX_ATTACTCG-GTACTGAC_L002_R1_001.fastq.gz fastq 445907350.0 8918147.0 GSM2236111 r2 0:50 A:111197446;C:103593829;G:97120345;T:129958338;N:4037392 50       111197446 103593829 97120345 129958338 4037392 SRX1950210 SRS1564971 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.86953   0.31237   0.65206   0.54599   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41193 41193 SRR3923669 SRX1950209 SRS1564970 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane 3 GSM2236110   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane 3 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236110 GSM2236110: Trilostane 3; Danio rerio; RNA Seq GSM2236110   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236110 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq10_H9PG8ADXX_AGCGATAG-CAGGACGT_L001_R1_001.fastq.gz fastq 521947750.0 10438955.0 GSM2236110 r1 0:50 A:129320589;C:122268528;G:110282626;T:155469988;N:4606019 50       129320589 122268528 110282626 155469988 4606019 SRX1950209 SRS1564970 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.89087   0.3421   0.67123   0.59545   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41194 41194 SRR3923670 SRX1950209 SRS1564970 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane 3 GSM2236110   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane 3 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236110 GSM2236110: Trilostane 3; Danio rerio; RNA Seq GSM2236110   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236110 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq10_H9PG8ADXX_AGCGATAG-CAGGACGT_L002_R1_001.fastq.gz fastq 516602850.0 10332057.0 GSM2236110 r2 0:50 A:128042316;C:121000293;G:109144625;T:153860728;N:4554888 50       128042316 121000293 109144625 153860728 4554888 SRX1950209 SRS1564970 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.89032   0.34188   0.67397   0.59669   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41195 41195 SRR3923667 SRX1950208 SRS1564969 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane 2 GSM2236109   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane 2 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236109 GSM2236109: Trilostane 2; Danio rerio; RNA Seq GSM2236109   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236109 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq5_H9PG8ADXX_GAATTCGT-CAGGACGT_L001_R1_001.fastq.gz fastq 623611800.0 12472236.0 GSM2236109 r1 0:50 A:158989142;C:142414377;G:130317763;T:186223237;N:5667281 50       158989142 142414377 130317763 186223237 5667281 SRX1950208 SRS1564969 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.87898   0.32511   0.64934   0.46995   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41196 41196 SRR3923668 SRX1950208 SRS1564969 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane 2 GSM2236109   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane 2 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236109 GSM2236109: Trilostane 2; Danio rerio; RNA Seq GSM2236109   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236109 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq5_H9PG8ADXX_GAATTCGT-CAGGACGT_L002_R1_001.fastq.gz fastq 625185750.0 12503715.0 GSM2236109 r2 0:50 A:159471869;C:142727575;G:130621469;T:186687783;N:5677054 50       159471869 142727575 130621469 186687783 5677054 SRX1950208 SRS1564969 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.8789   0.32679   0.65285   0.47033   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41197 41197 SRR3923665 SRX1950207 SRS1564968 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane 1 GSM2236108   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane 1 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236108 GSM2236108: Trilostane 1; Danio rerio; RNA Seq GSM2236108   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236108 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq2_H9PG8ADXX_TCCGGAGA-CAGGACGT_L001_R1_001.fastq.gz fastq 437247150.0 8744943.0 GSM2236108 r1 0:50 A:96525256;C:120572709;G:101663845;T:115083503;N:3401837 50       96525256 120572709 101663845 115083503 3401837 SRX1950207 SRS1564968 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.92907   0.28985   0.7189   0.66088   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41198 41198 SRR3923666 SRX1950207 SRS1564968 SRP078537 PRJNA329141 Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis GSE84436 Transcriptome Analysis Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.   pubmed:27566230   Trilostane 1 GSM2236108   source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours Trilostane 1 Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample. Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours GSM2236108 GSM2236108: Trilostane 1; Danio rerio; RNA Seq GSM2236108   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2236108 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP078537     Seq2_H9PG8ADXX_TCCGGAGA-CAGGACGT_L002_R1_001.fastq.gz fastq 438228650.0 8764573.0 GSM2236108 r2 0:50 A:96748886;C:120843515;G:101940166;T:115290259;N:3405824 50       96748886 120843515 101940166 115290259 3405824 SRX1950207 SRS1564968 SRA440585 GEO Reproductive Biology, Biology, Utrecht University 1 0.92905   0.29162   0.72214   0.64838   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-07-14 Adult Adult Gonad Reproductive System
41338 41338 SRR4243173 SRX2164188 SRS1692133 SRP089896 PRJNA343041 Antagonistic regulation of spermatogonial differentiation in zebrafish Danio rerio by Igf3 and Amh GSE86944 Transcriptome Analysis Fsh mediated regulation of zebrafish spermatogenesis includes modulating the expression of testicular growth factors. Here we study if and how two Sertoli cell derived Fsh responsive growth factors anti Müllerian hormone Amh; inhibiting steroidogenesis and germ cell differentiation and insulin like growth factor 3 Igf3; stimulating germ cell differentiation cooperate in regulating spermatogonial development. In dose response and time course experiments with primary testis tissue cultures Fsh upregulated igf3 transcript levels and down regulated amh transcript levels; igf3 transcript levels were more rapidly up regulated and responded to lower Fsh concentrations than were required to decrease amh mRNA levels. Quantification of immunoreactive Amh and Igf3 on testis sections showed that Fsh increased slightly Igf3 staining but decreased clearly Amh staining. Studying the direct interaction of the two growth factors showed that Amh compromised Igf3 stimulated proliferation of type A both undifferentiated [Aund] and differentiating [Adiff] spermatogonia. Also the proliferation of those Sertoli cells associated with Aund spermatogonia was reduced by Amh. To gain more insight into how Amh inhibits germ cell development we examined Amh induced changes in testicular gene expression by RNA sequencing. The majority 69% of the differentially expressed genes was down regulated by Amh including several stimulators of spermatogenesis such as igf3 and steroidogenesis related genes. At the same time Amh increased the expression of inhibitory signals such as inha and id3 or facilitated prostaglandin E2 PGE2 signaling. Evaluating one of the potentially inhibitory signals we indeed found in tissue culture experiments that PGE2 promoted the accumulation of Aund at the expense of Adiff and B spermatogonia. Our data suggest that an important aspect of Fsh bioactivity in stimulating spermatogenesis is implemented by restricting the different inhibitory effects of Amh and by counterbalancing them with stimulatory signals such…   pubmed:28645700   11KT+Amh 5 GSM2310627   tissue:Testis|age:Adult|genotype:Wild type|incubation:3 days|treatment:Amh 11KT+Amh 5 Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   age:Adult|genotype:Wild type|incubation:3 days|treatment:Amh GSM2310627 GSM2310627: 11KT+Amh 5; Danio rerio; RNA Seq GSM2310627   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2310627 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP089896     IL-14-08-16_GAGTGG_L001_R1_001.fastq.gz fastq 1170392472.0 22948872.0 GSM2310627 r1 0:51 A:321032122;C:268515709;G:261725129;T:318830744;N:288768 51       321032122 268515709 261725129 318830744 288768 SRX2164188 SRS1692133 SRA471529 GEO Reproductive Biology, Biology, Utrecht University 1 0.91255   0.11667   0.65137   0.50826   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-09-14 Adult Adult Gonad Reproductive System
41339 41339 SRR4243172 SRX2164187 SRS1692132 SRP089896 PRJNA343041 Antagonistic regulation of spermatogonial differentiation in zebrafish Danio rerio by Igf3 and Amh GSE86944 Transcriptome Analysis Fsh mediated regulation of zebrafish spermatogenesis includes modulating the expression of testicular growth factors. Here we study if and how two Sertoli cell derived Fsh responsive growth factors anti Müllerian hormone Amh; inhibiting steroidogenesis and germ cell differentiation and insulin like growth factor 3 Igf3; stimulating germ cell differentiation cooperate in regulating spermatogonial development. In dose response and time course experiments with primary testis tissue cultures Fsh upregulated igf3 transcript levels and down regulated amh transcript levels; igf3 transcript levels were more rapidly up regulated and responded to lower Fsh concentrations than were required to decrease amh mRNA levels. Quantification of immunoreactive Amh and Igf3 on testis sections showed that Fsh increased slightly Igf3 staining but decreased clearly Amh staining. Studying the direct interaction of the two growth factors showed that Amh compromised Igf3 stimulated proliferation of type A both undifferentiated [Aund] and differentiating [Adiff] spermatogonia. Also the proliferation of those Sertoli cells associated with Aund spermatogonia was reduced by Amh. To gain more insight into how Amh inhibits germ cell development we examined Amh induced changes in testicular gene expression by RNA sequencing. The majority 69% of the differentially expressed genes was down regulated by Amh including several stimulators of spermatogenesis such as igf3 and steroidogenesis related genes. At the same time Amh increased the expression of inhibitory signals such as inha and id3 or facilitated prostaglandin E2 PGE2 signaling. Evaluating one of the potentially inhibitory signals we indeed found in tissue culture experiments that PGE2 promoted the accumulation of Aund at the expense of Adiff and B spermatogonia. Our data suggest that an important aspect of Fsh bioactivity in stimulating spermatogenesis is implemented by restricting the different inhibitory effects of Amh and by counterbalancing them with stimulatory signals such…   pubmed:28645700   11KT+Amh 4 GSM2310626   tissue:Testis|age:Adult|genotype:Wild type|incubation:3 days|treatment:Amh 11KT+Amh 4 Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   age:Adult|genotype:Wild type|incubation:3 days|treatment:Amh GSM2310626 GSM2310626: 11KT+Amh 4; Danio rerio; RNA Seq GSM2310626   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2310626 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP089896     IL-14-08-15_CGTACG_L001_R1_001.fastq.gz fastq 1020609348.0 20011948.0 GSM2310626 r1 0:51 A:280659283;C:233389387;G:227016796;T:279291132;N:252750 51       280659283 233389387 227016796 279291132 252750 SRX2164187 SRS1692132 SRA471529 GEO Reproductive Biology, Biology, Utrecht University 1 0.91619   0.10708   0.66125   0.51479   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-09-14 Adult Adult Gonad Reproductive System
41340 41340 SRR4243171 SRX2164186 SRS1692131 SRP089896 PRJNA343041 Antagonistic regulation of spermatogonial differentiation in zebrafish Danio rerio by Igf3 and Amh GSE86944 Transcriptome Analysis Fsh mediated regulation of zebrafish spermatogenesis includes modulating the expression of testicular growth factors. Here we study if and how two Sertoli cell derived Fsh responsive growth factors anti Müllerian hormone Amh; inhibiting steroidogenesis and germ cell differentiation and insulin like growth factor 3 Igf3; stimulating germ cell differentiation cooperate in regulating spermatogonial development. In dose response and time course experiments with primary testis tissue cultures Fsh upregulated igf3 transcript levels and down regulated amh transcript levels; igf3 transcript levels were more rapidly up regulated and responded to lower Fsh concentrations than were required to decrease amh mRNA levels. Quantification of immunoreactive Amh and Igf3 on testis sections showed that Fsh increased slightly Igf3 staining but decreased clearly Amh staining. Studying the direct interaction of the two growth factors showed that Amh compromised Igf3 stimulated proliferation of type A both undifferentiated [Aund] and differentiating [Adiff] spermatogonia. Also the proliferation of those Sertoli cells associated with Aund spermatogonia was reduced by Amh. To gain more insight into how Amh inhibits germ cell development we examined Amh induced changes in testicular gene expression by RNA sequencing. The majority 69% of the differentially expressed genes was down regulated by Amh including several stimulators of spermatogenesis such as igf3 and steroidogenesis related genes. At the same time Amh increased the expression of inhibitory signals such as inha and id3 or facilitated prostaglandin E2 PGE2 signaling. Evaluating one of the potentially inhibitory signals we indeed found in tissue culture experiments that PGE2 promoted the accumulation of Aund at the expense of Adiff and B spermatogonia. Our data suggest that an important aspect of Fsh bioactivity in stimulating spermatogenesis is implemented by restricting the different inhibitory effects of Amh and by counterbalancing them with stimulatory signals such…   pubmed:28645700   11KT+Amh 3 GSM2310625   tissue:Testis|age:Adult|genotype:Wild type|incubation:3 days|treatment:Amh 11KT+Amh 3 Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   age:Adult|genotype:Wild type|incubation:3 days|treatment:Amh GSM2310625 GSM2310625: 11KT+Amh 3; Danio rerio; RNA Seq GSM2310625   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2310625 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP089896     IL-14-08-12_GTTTCG_L001_R1_001.fastq.gz fastq 903981069.0 17725119.0 GSM2310625 r1 0:51 A:248045770;C:207394369;G:201577494;T:246739594;N:223842 51       248045770 207394369 201577494 246739594 223842 SRX2164186 SRS1692131 SRA471529 GEO Reproductive Biology, Biology, Utrecht University 1 0.9133   0.11386   0.66782   0.50462   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-09-14 Adult Adult Gonad Reproductive System
41341 41341 SRR4243170 SRX2164185 SRS1692130 SRP089896 PRJNA343041 Antagonistic regulation of spermatogonial differentiation in zebrafish Danio rerio by Igf3 and Amh GSE86944 Transcriptome Analysis Fsh mediated regulation of zebrafish spermatogenesis includes modulating the expression of testicular growth factors. Here we study if and how two Sertoli cell derived Fsh responsive growth factors anti Müllerian hormone Amh; inhibiting steroidogenesis and germ cell differentiation and insulin like growth factor 3 Igf3; stimulating germ cell differentiation cooperate in regulating spermatogonial development. In dose response and time course experiments with primary testis tissue cultures Fsh upregulated igf3 transcript levels and down regulated amh transcript levels; igf3 transcript levels were more rapidly up regulated and responded to lower Fsh concentrations than were required to decrease amh mRNA levels. Quantification of immunoreactive Amh and Igf3 on testis sections showed that Fsh increased slightly Igf3 staining but decreased clearly Amh staining. Studying the direct interaction of the two growth factors showed that Amh compromised Igf3 stimulated proliferation of type A both undifferentiated [Aund] and differentiating [Adiff] spermatogonia. Also the proliferation of those Sertoli cells associated with Aund spermatogonia was reduced by Amh. To gain more insight into how Amh inhibits germ cell development we examined Amh induced changes in testicular gene expression by RNA sequencing. The majority 69% of the differentially expressed genes was down regulated by Amh including several stimulators of spermatogenesis such as igf3 and steroidogenesis related genes. At the same time Amh increased the expression of inhibitory signals such as inha and id3 or facilitated prostaglandin E2 PGE2 signaling. Evaluating one of the potentially inhibitory signals we indeed found in tissue culture experiments that PGE2 promoted the accumulation of Aund at the expense of Adiff and B spermatogonia. Our data suggest that an important aspect of Fsh bioactivity in stimulating spermatogenesis is implemented by restricting the different inhibitory effects of Amh and by counterbalancing them with stimulatory signals such…   pubmed:28645700   11KT+Amh 2 GSM2310624   tissue:Testis|age:Adult|genotype:Wild type|incubation:3 days|treatment:Amh 11KT+Amh 2 Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   age:Adult|genotype:Wild type|incubation:3 days|treatment:Amh GSM2310624 GSM2310624: 11KT+Amh 2; Danio rerio; RNA Seq GSM2310624   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2310624 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP089896     IL-14-08-11_GTGGCC_L001_R1_001.fastq.gz fastq 818454171.0 16048121.0 GSM2310624 r1 0:51 A:224174167;C:188064997;G:183412696;T:222602796;N:199515 51       224174167 188064997 183412696 222602796 199515 SRX2164185 SRS1692130 SRA471529 GEO Reproductive Biology, Biology, Utrecht University 1 0.91371   0.11249   0.66074   0.52081   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-09-14 Adult Adult Gonad Reproductive System
41342 41342 SRR4243169 SRX2164184 SRS1692129 SRP089896 PRJNA343041 Antagonistic regulation of spermatogonial differentiation in zebrafish Danio rerio by Igf3 and Amh GSE86944 Transcriptome Analysis Fsh mediated regulation of zebrafish spermatogenesis includes modulating the expression of testicular growth factors. Here we study if and how two Sertoli cell derived Fsh responsive growth factors anti Müllerian hormone Amh; inhibiting steroidogenesis and germ cell differentiation and insulin like growth factor 3 Igf3; stimulating germ cell differentiation cooperate in regulating spermatogonial development. In dose response and time course experiments with primary testis tissue cultures Fsh upregulated igf3 transcript levels and down regulated amh transcript levels; igf3 transcript levels were more rapidly up regulated and responded to lower Fsh concentrations than were required to decrease amh mRNA levels. Quantification of immunoreactive Amh and Igf3 on testis sections showed that Fsh increased slightly Igf3 staining but decreased clearly Amh staining. Studying the direct interaction of the two growth factors showed that Amh compromised Igf3 stimulated proliferation of type A both undifferentiated [Aund] and differentiating [Adiff] spermatogonia. Also the proliferation of those Sertoli cells associated with Aund spermatogonia was reduced by Amh. To gain more insight into how Amh inhibits germ cell development we examined Amh induced changes in testicular gene expression by RNA sequencing. The majority 69% of the differentially expressed genes was down regulated by Amh including several stimulators of spermatogenesis such as igf3 and steroidogenesis related genes. At the same time Amh increased the expression of inhibitory signals such as inha and id3 or facilitated prostaglandin E2 PGE2 signaling. Evaluating one of the potentially inhibitory signals we indeed found in tissue culture experiments that PGE2 promoted the accumulation of Aund at the expense of Adiff and B spermatogonia. Our data suggest that an important aspect of Fsh bioactivity in stimulating spermatogenesis is implemented by restricting the different inhibitory effects of Amh and by counterbalancing them with stimulatory signals such…   pubmed:28645700   11KT+Amh 1 GSM2310623   tissue:Testis|age:Adult|genotype:Wild type|incubation:3 days|treatment:Amh 11KT+Amh 1 Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample Testis   Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions   age:Adult|genotype:Wild type|incubation:3 days|treatment:Amh GSM2310623 GSM2310623: 11KT+Amh 1; Danio rerio; RNA Seq GSM2310623   1 Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions GEO Accession:GSM2310623 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP089896     IL-14-08-9_GGCTAC_L001_R1_001.fastq.gz fastq 1030828830.0 20212330.0 GSM2310623 r1 0:51 A:282285319;C:237657119;G:230237273;T:280396581;N:252538 51       282285319 237657119 230237273 280396581 252538 SRX2164184 SRS1692129 SRA471529 GEO Reproductive Biology, Biology, Utrecht University 1 0.90885   0.11549   0.65869   0.49547   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-09-14 Adult Adult Gonad Reproductive System

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