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126 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "cDNA" and tissue_curation = "Gonad"

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technology 3

experiment.platform 3

devstage_curation_coarse 3

devstage_curation 3

tissue_curation_coarse 1

tissue_curation 1

  • Gonad · 126 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • cDNA · 126 ✖

experiment.library_layout 1

  • SINGLE · 126 ✖
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
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
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
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
41343 41343 SRR4243168 SRX2164183 SRS1692128 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 5 GSM2310622   tissue:Testis|age:Adult|genotype:Wild type|incubation:3 days|treatment:control 11KT 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:control GSM2310622 GSM2310622: 11KT 5; Danio rerio; RNA Seq GSM2310622   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:GSM2310622 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP089896     IL-14-08-8_TAGCTT_L001_R1_001.fastq.gz fastq 906867771.0 17781721.0 GSM2310622 r1 0:51 A:248681526;C:208321293;G:202986876;T:246659593;N:218483 51       248681526 208321293 202986876 246659593 218483 SRX2164183 SRS1692128 SRA471529 GEO Reproductive Biology, Biology, Utrecht University 1 0.91216   0.11605   0.65533   0.50523   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-09-14 Adult Adult Gonad Reproductive System
41344 41344 SRR4243167 SRX2164182 SRS1692127 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 4 GSM2310621   tissue:Testis|age:Adult|genotype:Wild type|incubation:3 days|treatment:control 11KT 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:control GSM2310621 GSM2310621: 11KT 4; Danio rerio; RNA Seq GSM2310621   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:GSM2310621 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP089896     IL-14-08-7_GATCAG_L001_R1_001.fastq.gz fastq 810915249.0 15900299.0 GSM2310621 r1 0:51 A:223051661;C:185259732;G:180275369;T:222124161;N:204326 51       223051661 185259732 180275369 222124161 204326 SRX2164182 SRS1692127 SRA471529 GEO Reproductive Biology, Biology, Utrecht University 1 0.91741   0.11127   0.65729   0.52493   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-09-14 Adult Adult Gonad Reproductive System
41345 41345 SRR4243166 SRX2164181 SRS1692126 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 3 GSM2310620   tissue:Testis|age:Adult|genotype:Wild type|incubation:3 days|treatment:control 11KT 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:control GSM2310620 GSM2310620: 11KT 3; Danio rerio; RNA Seq GSM2310620   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:GSM2310620 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP089896     IL-14-08-4_ACTTGA_L001_R1_001.fastq.gz fastq 762603000.0 14953000.0 GSM2310620 r1 0:51 A:208388925;C:174982032;G:171459809;T:207583812;N:188422 51       208388925 174982032 171459809 207583812 188422 SRX2164181 SRS1692126 SRA471529 GEO Reproductive Biology, Biology, Utrecht University 1 0.91126   0.12186   0.669   0.4979   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-09-14 Adult Adult Gonad Reproductive System
41346 41346 SRR4243165 SRX2164180 SRS1692125 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 2 GSM2310619   tissue:Testis|age:Adult|genotype:Wild type|incubation:3 days|treatment:control 11KT 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:control GSM2310619 GSM2310619: 11KT 2; Danio rerio; RNA Seq GSM2310619   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:GSM2310619 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP089896     IL-14-08-3_TTAGGC_L001_R1_001.fastq.gz fastq 693008247.0 13588397.0 GSM2310619 r1 0:51 A:199282612;C:150789916;G:146878078;T:195891642;N:165999 51       199282612 150789916 146878078 195891642 165999 SRX2164180 SRS1692125 SRA471529 GEO Reproductive Biology, Biology, Utrecht University 1 0.8977   0.16323   0.65695   0.52131   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-09-14 Adult Adult Gonad Reproductive System
41347 41347 SRR4243164 SRX2164179 SRS1692124 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 1 GSM2310618   tissue:Testis|age:Adult|genotype:Wild type|incubation:3 days|treatment:control 11KT 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:control GSM2310618 GSM2310618: 11KT 1; Danio rerio; RNA Seq GSM2310618   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:GSM2310618 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP089896     IL-14-08-1_ATCACG_L001_R1_001.fastq.gz fastq 836727216.0 16406416.0 GSM2310618 r1 0:51 A:228522236;C:192582706;G:188473692;T:226939267;N:209315 51       228522236 192582706 188473692 226939267 209315 SRX2164179 SRS1692124 SRA471529 GEO Reproductive Biology, Biology, Utrecht University 1 0.91111   0.11625   0.66249   0.50635   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2016-09-14 Adult Adult Gonad Reproductive System
48812 48812 SRR7341816 SRX4215318 SRS3417596 SRP150521 PRJNA476105 Transcriptome analysis of wildtype and sox3 / zebrafish adult ovary GSE115806 Transcriptome Analysis The goals of this study are to compare the differentially expressed genes between wildtype and sox3 / zebrafish ovaries based on RNA seq data and some of these genes were validated by qRT–PCR. Further the differentially expressed genes were devided into up regulated and down regulated genes for GO and KEGG analysis. Overall design: Ovary mRNA profiles of adult wildtype and sox3 / zebrafish were generated by deep sequencing.   pubmed:30588557   KO mix GSM3190267   source name:Ovary|strain:AB|tissue:Ovary|age:Adult KO mix Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz10 whole genome using HISAT mapped to genes using Bowtie2. fragments per kilo bases per million fragments FPKM were calculated using RSEM. Genome build: GRCz10 Supplementary files format and content: The text files include the Ensembl ID of genes and the FPKM values for each Sample. Ovary   Ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.   strain:AB|tissue:Ovary|age:Adult GSM3190267 GSM3190267: KO mix; Danio rerio; RNA Seq GSM3190267   1 Ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols. GEO Accession:GSM3190267 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP150521     KO-ovary.fq.gz fastq 1173123100.0 23462462.0 GSM3190267 r1 0:50 1:0 A:308426188;C:271468505;G:292019086;T:300532126;N:677195 50 0     308426188 271468505 292019086 300532126 677195 SRX4215318 SRS3417596 SRA721702 GEO Wuhan university 1 0.93261   0.02261   0.76132   0.4585   50   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   China 2018-06-14 Adult Adult Gonad Reproductive System
48813 48813 SRR7341815 SRX4215317 SRS3417595 SRP150521 PRJNA476105 Transcriptome analysis of wildtype and sox3 / zebrafish adult ovary GSE115806 Transcriptome Analysis The goals of this study are to compare the differentially expressed genes between wildtype and sox3 / zebrafish ovaries based on RNA seq data and some of these genes were validated by qRT–PCR. Further the differentially expressed genes were devided into up regulated and down regulated genes for GO and KEGG analysis. Overall design: Ovary mRNA profiles of adult wildtype and sox3 / zebrafish were generated by deep sequencing.   pubmed:30588557   WT mix GSM3190266   source name:Ovary|strain:AB|tissue:Ovary|age:Adult WT mix Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz10 whole genome using HISAT mapped to genes using Bowtie2. fragments per kilo bases per million fragments FPKM were calculated using RSEM. Genome build: GRCz10 Supplementary files format and content: The text files include the Ensembl ID of genes and the FPKM values for each Sample. Ovary   Ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.   strain:AB|tissue:Ovary|age:Adult GSM3190266 GSM3190266: WT mix; Danio rerio; RNA Seq GSM3190266   1 Ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols. GEO Accession:GSM3190266 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP150521     WT-ovary.fq.gz fastq 1176463600.0 23529272.0 GSM3190266 r1 0:50 1:0 A:311869864;C:270650722;G:289863261;T:303489229;N:590524 50 0     311869864 270650722 289863261 303489229 590524 SRX4215317 SRS3417595 SRA721702 GEO Wuhan university 1 0.93489   0.02765   0.75627   0.46875   50   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   China 2018-06-14 Adult Adult Gonad Reproductive System
48911 48911 SRR7468702 SRX4338471 SRS3499386 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Recovery 5 GSM3243777   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Recovery 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|tissue:Testis GSM3243777 GSM3243777: Testis Recovery 5; Danio rerio; RNA Seq GSM3243777   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:GSM3243777 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_27_ACTTGA_L001_R1_001_HBGRYADXX.fastq.gz fastq 552604890.0 10835390.0 GSM3243777 r1 0:51 A:139121742;C:132482814;G:122480393;T:158489534;N:30407 51       139121742 132482814 122480393 158489534 30407 SRX4338471 SRS3499386 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.92201   0.11734   0.63711   0.47964   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48912 48912 SRR7468703 SRX4338471 SRS3499386 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Recovery 5 GSM3243777   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Recovery 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|tissue:Testis GSM3243777 GSM3243777: Testis Recovery 5; Danio rerio; RNA Seq GSM3243777   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:GSM3243777 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_27_ACTTGA_L002_R1_001_HBGRYADXX.fastq.gz fastq 545267673.0 10691523.0 GSM3243777 r2 0:51 A:137207619;C:130755783;G:120931785;T:156332365;N:40121 51       137207619 130755783 120931785 156332365 40121 SRX4338471 SRS3499386 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.92138   0.11738   0.64098   0.48487   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48913 48913 SRR7468700 SRX4338470 SRS3499384 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Recovery 4 GSM3243776   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Recovery 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|tissue:Testis GSM3243776 GSM3243776: Testis Recovery 4; Danio rerio; RNA Seq GSM3243776   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:GSM3243776 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_22_TTAGGC_L001_R1_001_HBGRYADXX.fastq.gz fastq 350250966.0 6867666.0 GSM3243776 r1 0:51 A:90857323;C:81141631;G:77474341;T:100758696;N:18975 51       90857323 81141631 77474341 100758696 18975 SRX4338470 SRS3499384 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.92353   0.11575   0.64788   0.49422   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48914 48914 SRR7468701 SRX4338470 SRS3499384 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Recovery 4 GSM3243776   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Recovery 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|tissue:Testis GSM3243776 GSM3243776: Testis Recovery 4; Danio rerio; RNA Seq GSM3243776   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:GSM3243776 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_22_TTAGGC_L002_R1_001_HBGRYADXX.fastq.gz fastq 345190491.0 6768441.0 GSM3243776 r2 0:51 A:89503841;C:79992303;G:76416649;T:99253801;N:23897 51       89503841 79992303 76416649 99253801 23897 SRX4338470 SRS3499384 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.92144   0.11503   0.64715   0.4912   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48915 48915 SRR7468698 SRX4338469 SRS3499387 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Recovery 3 GSM3243775   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Recovery 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|tissue:Testis GSM3243775 GSM3243775: Testis Recovery 3; Danio rerio; RNA Seq GSM3243775   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:GSM3243775 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_21_ATCACG_L001_R1_001_HBGRYADXX.fastq.gz fastq 932153673.0 18277523.0 GSM3243775 r1 0:51 A:233867020;C:223302964;G:204457194;T:270472757;N:53738 51       233867020 223302964 204457194 270472757 53738 SRX4338469 SRS3499387 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.9252   0.10721   0.6477   0.48926   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48916 48916 SRR7468699 SRX4338469 SRS3499387 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Recovery 3 GSM3243775   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Recovery 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|tissue:Testis GSM3243775 GSM3243775: Testis Recovery 3; Danio rerio; RNA Seq GSM3243775   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:GSM3243775 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_21_ATCACG_L002_R1_001_HBGRYADXX.fastq.gz fastq 923872752.0 18115152.0 GSM3243775 r2 0:51 A:231644800;C:221350765;G:202799132;T:268008161;N:69894 51       231644800 221350765 202799132 268008161 69894 SRX4338469 SRS3499387 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.92438   0.1075   0.64749   0.49122   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48917 48917 SRR7468696 SRX4338468 SRS3499385 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Recovery 2 GSM3243774   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Recovery 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|tissue:Testis GSM3243774 GSM3243774: Testis Recovery 2; Danio rerio; RNA Seq GSM3243774   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:GSM3243774 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_20_GTGAAA_L001_R1_001_HBGRYADXX.fastq.gz fastq 488463975.0 9577725.0 GSM3243774 r1 0:51 A:124059246;C:115925214;G:108132371;T:140316066;N:31078 51       124059246 115925214 108132371 140316066 31078 SRX4338468 SRS3499385 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.92666   0.10881   0.6406   0.48975   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48918 48918 SRR7468697 SRX4338468 SRS3499385 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Recovery 2 GSM3243774   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Recovery 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|tissue:Testis GSM3243774 GSM3243774: Testis Recovery 2; Danio rerio; RNA Seq GSM3243774   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:GSM3243774 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_20_GTGAAA_L002_R1_001_HBGRYADXX.fastq.gz fastq 483820986.0 9486686.0 GSM3243774 r2 0:51 A:122808323;C:114849749;G:107201486;T:138922696;N:38732 51       122808323 114849749 107201486 138922696 38732 SRX4338468 SRS3499385 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.92627   0.10747   0.6369   0.49158   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48919 48919 SRR7468694 SRX4338467 SRS3499381 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Recovery 1 GSM3243773   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Recovery 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|tissue:Testis GSM3243773 GSM3243773: Testis Recovery 1; Danio rerio; RNA Seq GSM3243773   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:GSM3243773 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_19_GTCCGC_L001_R1_001_HBGRYADXX.fastq.gz fastq 320008476.0 6274676.0 GSM3243773 r1 0:51 A:82056407;C:75200770;G:70054966;T:92678428;N:17905 51       82056407 75200770 70054966 92678428 17905 SRX4338467 SRS3499381 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.92363   0.11205   0.63901   0.49533   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48920 48920 SRR7468695 SRX4338467 SRS3499381 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Recovery 1 GSM3243773   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Recovery 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|tissue:Testis GSM3243773 GSM3243773: Testis Recovery 1; Danio rerio; RNA Seq GSM3243773   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:GSM3243773 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_19_GTCCGC_L002_R1_001_HBGRYADXX.fastq.gz fastq 316706379.0 6209929.0 GSM3243773 r2 0:51 A:81144248;C:74436278;G:69378013;T:91724817;N:23023 51       81144248 74436278 69378013 91724817 23023 SRX4338467 SRS3499381 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.92209   0.11247   0.641   0.49169   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48921 48921 SRR7468692 SRX4338466 SRS3499380 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Depletion 5 GSM3243772   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Depletion 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|tissue:Testis GSM3243772 GSM3243772: Testis Depletion 5; Danio rerio; RNA Seq GSM3243772   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:GSM3243772 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_15_CCGTCC_L001_R1_001_HBGRYADXX.fastq.gz fastq 361757892.0 7093292.0 GSM3243772 r1 0:51 A:91765393;C:86319849;G:81580662;T:102070154;N:21834 51       91765393 86319849 81580662 102070154 21834 SRX4338466 SRS3499380 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.91403   0.09146   0.70303   0.47815   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48922 48922 SRR7468693 SRX4338466 SRS3499380 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Depletion 5 GSM3243772   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Depletion 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|tissue:Testis GSM3243772 GSM3243772: Testis Depletion 5; Danio rerio; RNA Seq GSM3243772   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:GSM3243772 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_15_CCGTCC_L002_R1_001_HBGRYADXX.fastq.gz fastq 358933155.0 7037905.0 GSM3243772 r2 0:51 A:90971855;C:85661708;G:81025594;T:101247515;N:26483 51       90971855 85661708 81025594 101247515 26483 SRX4338466 SRS3499380 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.91352   0.09218   0.70587   0.47689   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48923 48923 SRR7468690 SRX4338465 SRS3499373 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Depletion 4 GSM3243771   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Depletion 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|tissue:Testis GSM3243771 GSM3243771: Testis Depletion 4; Danio rerio; RNA Seq GSM3243771   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:GSM3243771 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_13_ATGTCA_L001_R1_001_HBGRYADXX.fastq.gz fastq 362189301.0 7101751.0 GSM3243771 r1 0:51 A:93944703;C:84574406;G:80766474;T:102881135;N:22583 51       93944703 84574406 80766474 102881135 22583 SRX4338465 SRS3499373 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.9175   0.13669   0.69331   0.47497   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48924 48924 SRR7468691 SRX4338465 SRS3499373 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Depletion 4 GSM3243771   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Depletion 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|tissue:Testis GSM3243771 GSM3243771: Testis Depletion 4; Danio rerio; RNA Seq GSM3243771   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:GSM3243771 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_13_ATGTCA_L002_R1_001_HBGRYADXX.fastq.gz fastq 357458796.0 7008996.0 GSM3243771 r2 0:51 A:92666882;C:83501967;G:79751404;T:101511030;N:27513 51       92666882 83501967 79751404 101511030 27513 SRX4338465 SRS3499373 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.91688   0.13791   0.69589   0.48069   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48925 48925 SRR7468688 SRX4338464 SRS3499374 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Depletion 3 GSM3243770   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Depletion 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|tissue:Testis GSM3243770 GSM3243770: Testis Depletion 3; Danio rerio; RNA Seq GSM3243770   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:GSM3243770 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_12_AGTTCC_L001_R1_001_HBGRYADXX.fastq.gz fastq 360587850.0 7070350.0 GSM3243770 r1 0:51 A:93351341;C:83525699;G:80405894;T:103285803;N:19113 51       93351341 83525699 80405894 103285803 19113 SRX4338464 SRS3499374 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.91686   0.15015   0.68749   0.48342   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48926 48926 SRR7468689 SRX4338464 SRS3499374 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Depletion 3 GSM3243770   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Depletion 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|tissue:Testis GSM3243770 GSM3243770: Testis Depletion 3; Danio rerio; RNA Seq GSM3243770   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:GSM3243770 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_12_AGTTCC_L002_R1_001_HBGRYADXX.fastq.gz fastq 355171395.0 6964145.0 GSM3243770 r2 0:51 A:91888828;C:82308089;G:79253121;T:101695969;N:25388 51       91888828 82308089 79253121 101695969 25388 SRX4338464 SRS3499374 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.91616   0.14982   0.68745   0.4751   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48927 48927 SRR7468686 SRX4338463 SRS3499378 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Depletion 2 GSM3243769   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Depletion 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|tissue:Testis GSM3243769 GSM3243769: Testis Depletion 2; Danio rerio; RNA Seq GSM3243769   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:GSM3243769 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_11_AGTCAA_L001_R1_001_HBGRYADXX.fastq.gz fastq 292081947.0 5727097.0 GSM3243769 r1 0:51 A:72873171;C:69857310;G:66617588;T:82718171;N:15707 51       72873171 69857310 66617588 82718171 15707 SRX4338463 SRS3499378 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.93   0.08674   0.65819   0.50939   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48928 48928 SRR7468687 SRX4338463 SRS3499378 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Depletion 2 GSM3243769   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Depletion 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|tissue:Testis GSM3243769 GSM3243769: Testis Depletion 2; Danio rerio; RNA Seq GSM3243769   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:GSM3243769 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_11_AGTCAA_L002_R1_001_HBGRYADXX.fastq.gz fastq 287484450.0 5636950.0 GSM3243769 r2 0:51 A:71715008;C:68762533;G:65604930;T:81381185;N:20794 51       71715008 68762533 65604930 81381185 20794 SRX4338463 SRS3499378 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.92956   0.0864   0.6589   0.49904   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48929 48929 SRR7468684 SRX4338462 SRS3499376 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Depletion 1 GSM3243768   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Depletion 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|tissue:Testis GSM3243768 GSM3243768: Testis Depletion 1; Danio rerio; RNA Seq GSM3243768   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:GSM3243768 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_10_CTTGTA_L001_R1_001_HBGRYADXX.fastq.gz fastq 321374715.0 6301465.0 GSM3243768 r1 0:51 A:82362320;C:75071563;G:70755128;T:93167038;N:18666 51       82362320 75071563 70755128 93167038 18666 SRX4338462 SRS3499376 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.9178   0.15168   0.64386   0.47826   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48930 48930 SRR7468685 SRX4338462 SRS3499376 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Depletion 1 GSM3243768   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Depletion 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|tissue:Testis GSM3243768 GSM3243768: Testis Depletion 1; Danio rerio; RNA Seq GSM3243768   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:GSM3243768 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_10_CTTGTA_L002_R1_001_HBGRYADXX.fastq.gz fastq 317659365.0 6228615.0 GSM3243768 r2 0:51 A:81382955;C:74232035;G:69983462;T:92037129;N:23784 51       81382955 74232035 69983462 92037129 23784 SRX4338462 SRS3499376 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.91676   0.15228   0.64425   0.4778   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48931 48931 SRR7468682 SRX4338461 SRS3499379 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Control 5 GSM3243767   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Control 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|tissue:Testis GSM3243767 GSM3243767: Testis Control 5; Danio rerio; RNA Seq GSM3243767   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:GSM3243767 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_5_CAGATC_L001_R1_001_HBGRYADXX.fastq.gz fastq 1807367325.0 35438575.0 GSM3243767 r1 0:51 A:452670863;C:426888853;G:402222075;T:525465400;N:120134 51       452670863 426888853 402222075 525465400 120134 SRX4338461 SRS3499379 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.92398   0.10727   0.63847   0.48929   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48932 48932 SRR7468683 SRX4338461 SRS3499379 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Control 5 GSM3243767   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Control 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|tissue:Testis GSM3243767 GSM3243767: Testis Control 5; Danio rerio; RNA Seq GSM3243767   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:GSM3243767 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_5_CAGATC_L002_R1_001_HBGRYADXX.fastq.gz fastq 1788601008.0 35070608.0 GSM3243767 r2 0:51 A:447675880;C:422557474;G:398397059;T:519829628;N:140967 51       447675880 422557474 398397059 519829628 140967 SRX4338461 SRS3499379 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.92324   0.10891   0.63954   0.4884   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48933 48933 SRR7468680 SRX4338460 SRS3499377 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Control 4 GSM3243766   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Control 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|tissue:Testis GSM3243766 GSM3243766: Testis Control 4; Danio rerio; RNA Seq GSM3243766   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:GSM3243766 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_4_GCCAAT_L001_R1_001_HBGRYADXX.fastq.gz fastq 432263454.0 8475754.0 GSM3243766 r1 0:51 A:108617721;C:101534969;G:96731457;T:125354102;N:25205 51       108617721 101534969 96731457 125354102 25205 SRX4338460 SRS3499377 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.92566   0.11169   0.64062   0.48877   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48934 48934 SRR7468681 SRX4338460 SRS3499377 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Control 4 GSM3243766   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Control 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|tissue:Testis GSM3243766 GSM3243766: Testis Control 4; Danio rerio; RNA Seq GSM3243766   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:GSM3243766 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_4_GCCAAT_L002_R1_001_HBGRYADXX.fastq.gz fastq 427837980.0 8388980.0 GSM3243766 r2 0:51 A:107459455;C:100505057;G:95801183;T:124040216;N:32069 51       107459455 100505057 95801183 124040216 32069 SRX4338460 SRS3499377 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.92497   0.11054   0.6422   0.49028   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48935 48935 SRR7468678 SRX4338459 SRS3499375 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Control 3 GSM3243765   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Control 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|tissue:Testis GSM3243765 GSM3243765: Testis Control 3; Danio rerio; RNA Seq GSM3243765   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:GSM3243765 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_3_ACAGTG_L001_R1_001_HBGRYADXX.fastq.gz fastq 318864342.0 6252242.0 GSM3243765 r1 0:51 A:79540177;C:75401356;G:70862416;T:93041977;N:18416 51       79540177 75401356 70862416 93041977 18416 SRX4338459 SRS3499375 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.92501   0.10543   0.64421   0.49318   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48936 48936 SRR7468679 SRX4338459 SRS3499375 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Control 3 GSM3243765   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Control 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|tissue:Testis GSM3243765 GSM3243765: Testis Control 3; Danio rerio; RNA Seq GSM3243765   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:GSM3243765 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_3_ACAGTG_L002_R1_001_HBGRYADXX.fastq.gz fastq 315012924.0 6176724.0 GSM3243765 r2 0:51 A:78549739;C:74486878;G:70065256;T:91887178;N:23873 51       78549739 74486878 70065256 91887178 23873 SRX4338459 SRS3499375 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.92419   0.10379   0.64648   0.4907   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48937 48937 SRR7468676 SRX4338458 SRS3499372 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Control 2 GSM3243764   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Control 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|tissue:Testis GSM3243764 GSM3243764: Testis Control 2; Danio rerio; RNA Seq GSM3243764   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:GSM3243764 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_2_TGACCA_L001_R1_001_HBGRYADXX.fastq.gz fastq 281993331.0 5529281.0 GSM3243764 r1 0:51 A:74248995;C:65166680;G:61565290;T:80996003;N:16363 51       74248995 65166680 61565290 80996003 16363 SRX4338458 SRS3499372 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.90812   0.08809   0.66565   0.48223   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48938 48938 SRR7468677 SRX4338458 SRS3499372 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Control 2 GSM3243764   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Control 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|tissue:Testis GSM3243764 GSM3243764: Testis Control 2; Danio rerio; RNA Seq GSM3243764   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:GSM3243764 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_2_TGACCA_L002_R1_001_HBGRYADXX.fastq.gz fastq 276786486.0 5427186.0 GSM3243764 r2 0:51 A:72819016;C:63966270;G:60500151;T:79480832;N:20217 51       72819016 63966270 60500151 79480832 20217 SRX4338458 SRS3499372 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.90907   0.08776   0.66655   0.4778   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48939 48939 SRR7468674 SRX4338457 SRS3499371 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Control 1 GSM3243763   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Control 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|tissue:Testis GSM3243763 GSM3243763: Testis Control 1; Danio rerio; RNA Seq GSM3243763   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:GSM3243763 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_1_CGATGT_L001_R1_001_HCW5HADXX.fastq.gz fastq 259844133.0 5094983.0 GSM3243763 r1 0:51 A:64723559;C:62030280;G:57788866;T:75237104;N:64324 51       64723559 62030280 57788866 75237104 64324 SRX4338457 SRS3499371 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.92325   0.10831   0.64037   0.4947   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
48940 48940 SRR7468675 SRX4338457 SRS3499371 SRP151935 PRJNA479503 Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens GSE116611 Transcriptome Analysis post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples   pubmed:31597660;pubmed:33589679   Testis Control 1 GSM3243763   source name:Testis|age:Adult|genotype:Wild type|tissue:Testis Testis Control 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|tissue:Testis GSM3243763 GSM3243763: Testis Control 1; Danio rerio; RNA Seq GSM3243763   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:GSM3243763 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP151935     ZFG-14-10_1_CGATGT_L002_R1_001_HCW5HADXX.fastq.gz fastq 261354039.0 5124589.0 GSM3243763 r2 0:51 A:65170681;C:62378065;G:58090323;T:75693405;N:21565 51       65170681 62378065 58090323 75693405 21565 SRX4338457 SRS3499371 SRA732862 GEO Reproductive Biology, Biology, Utrecht University 1 0.92347   0.10704   0.63907   0.48949   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Netherlands 2018-07-03 Adult Adult Gonad Reproductive System
63889 63889 SRR14213377 SRX10579922 SRS8684390 SRP314470 PRJNA721381 RNA Seq from zebrafish adult tissues GSE171906 Transcriptome Analysis The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.   pubmed:34556579   Testis3 GSM5237146   source name:zebrafish testis|genotype:wild type|tissue:testis|strain:TLAB Testis3 Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 102. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM zebrafish testis   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:wild type|tissue:testis|strain:TLAB GSM5237146 GSM5237146: Testis3; Danio rerio; RNA Seq GSM5237146   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM5237146 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP314470     Testis3.fastq fastq 16904264700.0 169042647.0 GSM5237146 r1 0:100 A:4166427594;C:4293244634;G:4116245208;T:4327700322;N:646942 100       4166427594 4293244634 4116245208 4327700322 646942 SRX10579922 SRS8684390 SRA1217576 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.94648   0.14489   0.64329   0.5145   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2021-04-12 Undetermined Undetermined Gonad Reproductive System
63890 63890 SRR14213376 SRX10579921 SRS8684389 SRP314470 PRJNA721381 RNA Seq from zebrafish adult tissues GSE171906 Transcriptome Analysis The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.   pubmed:34556579   Testis2 GSM5237145   source name:zebrafish testis|genotype:wild type|tissue:testis|strain:TLAB Testis2 Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 102. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM zebrafish testis   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:wild type|tissue:testis|strain:TLAB GSM5237145 GSM5237145: Testis2; Danio rerio; RNA Seq GSM5237145   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM5237145 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP314470     Testis2.fastq fastq 2130746600.0 21307466.0 GSM5237145 r1 0:100 A:517817182;C:547187586;G:517803772;T:547856602;N:81458 100       517817182 547187586 517803772 547856602 81458 SRX10579921 SRS8684389 SRA1217576 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.95272   0.13195   0.64112   0.50616   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2021-04-12 Undetermined Undetermined Gonad Reproductive System
63891 63891 SRR14213375 SRX10579920 SRS8684388 SRP314470 PRJNA721381 RNA Seq from zebrafish adult tissues GSE171906 Transcriptome Analysis The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.   pubmed:34556579   Testis1 GSM5237144   source name:zebrafish testis|genotype:wild type|tissue:testis|strain:TLAB Testis1 Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 102. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM zebrafish testis   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:wild type|tissue:testis|strain:TLAB GSM5237144 GSM5237144: Testis1; Danio rerio; RNA Seq GSM5237144   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM5237144 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP314470     Testis1.fastq fastq 1989342600.0 19893426.0 GSM5237144 r1 0:100 A:511252873;C:487112155;G:465774401;T:525127484;N:75687 100       511252873 487112155 465774401 525127484 75687 SRX10579920 SRS8684388 SRA1217576 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.94514   0.11483   0.63341   0.49832   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2021-04-12 Undetermined Undetermined Gonad Reproductive System
67554 67554 SRR17210893 SRX13390812 SRS11294344 SRP350440 PRJNA788302 PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis GSE190741 Other The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126   pubmed:35477799   RNAseq PCB126 10nM Rep6 GSM5730194   source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 10nM RNAseq PCB126 10nM Rep6 DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups testis Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue. Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.   tissue:testis|developmental stage:Adult|treatment:PCB126 10nM GSM5730194 GSM5730194: RNAseq PCB126 10nM Rep6; Danio rerio; RNA Seq GSM5730194   1 Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform. GEO Accession:GSM5730194 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP350440     4170_mix-T24_S18_R1_001.fastq.gz fastq 1912515249.0 37500299.0 GSM5730194 r1 0:51 1:0 A:477251176;C:466929755;G:439380761;T:528825431;N:128126 51 0     477251176 466929755 439380761 528825431 128126 SRX13390812 SRS11294344 SRA1342092 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.95015   0.10454   0.64922   0.53267   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-12-12 Adult Adult Gonad Reproductive System
67555 67555 SRR17210892 SRX13390811 SRS11294345 SRP350440 PRJNA788302 PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis GSE190741 Other The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126   pubmed:35477799   RNAseq PCB126 10nM Rep5 GSM5730193   source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 10nM RNAseq PCB126 10nM Rep5 DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups testis Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue. Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.   tissue:testis|developmental stage:Adult|treatment:PCB126 10nM GSM5730193 GSM5730193: RNAseq PCB126 10nM Rep5; Danio rerio; RNA Seq GSM5730193   1 Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform. GEO Accession:GSM5730193 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP350440     4170_mix-T23_S17_R1_001.fastq.gz fastq 1344965778.0 26371878.0 GSM5730193 r1 0:51 1:0 A:347349418;C:318051347;G:301879882;T:377595413;N:89718 51 0     347349418 318051347 301879882 377595413 89718 SRX13390811 SRS11294345 SRA1342092 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.94726   0.10386   0.64948   0.5434   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-12-12 Adult Adult Gonad Reproductive System
67556 67556 SRR17210891 SRX13390810 SRS11294343 SRP350440 PRJNA788302 PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis GSE190741 Other The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126   pubmed:35477799   RNAseq PCB126 10nM Rep4 GSM5730192   source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 10nM RNAseq PCB126 10nM Rep4 DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups testis Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue. Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.   tissue:testis|developmental stage:Adult|treatment:PCB126 10nM GSM5730192 GSM5730192: RNAseq PCB126 10nM Rep4; Danio rerio; RNA Seq GSM5730192   1 Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform. GEO Accession:GSM5730192 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP350440     4170_mix-T21_S16_R1_001.fastq.gz fastq 2077575474.0 40736774.0 GSM5730192 r1 0:51 1:0 A:507322408;C:503941476;G:510925051;T:555250063;N:136476 51 0     507322408 503941476 510925051 555250063 136476 SRX13390810 SRS11294343 SRA1342092 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.95021   0.06976   0.6464   0.50296   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-12-12 Adult Adult Gonad Reproductive System
67557 67557 SRR17210890 SRX13390809 SRS11294342 SRP350440 PRJNA788302 PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis GSE190741 Other The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126   pubmed:35477799   RNAseq PCB126 10nM Rep3 GSM5730191   source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 10nM RNAseq PCB126 10nM Rep3 DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups testis Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue. Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.   tissue:testis|developmental stage:Adult|treatment:PCB126 10nM GSM5730191 GSM5730191: RNAseq PCB126 10nM Rep3; Danio rerio; RNA Seq GSM5730191   1 Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform. GEO Accession:GSM5730191 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP350440     4170_mix-T19_S15_R1_001.fastq.gz fastq 1514204127.0 29690277.0 GSM5730191 r1 0:51 1:0 A:362659383;C:370554761;G:356314539;T:424574865;N:100579 51 0     362659383 370554761 356314539 424574865 100579 SRX13390809 SRS11294342 SRA1342092 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.95191   0.07368   0.62509   0.48965   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-12-12 Adult Adult Gonad Reproductive System
67558 67558 SRR17210889 SRX13390808 SRS11294341 SRP350440 PRJNA788302 PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis GSE190741 Other The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126   pubmed:35477799   RNAseq PCB126 10nM Rep2 GSM5730190   source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 10nM RNAseq PCB126 10nM Rep2 DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups testis Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue. Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.   tissue:testis|developmental stage:Adult|treatment:PCB126 10nM GSM5730190 GSM5730190: RNAseq PCB126 10nM Rep2; Danio rerio; RNA Seq GSM5730190   1 Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform. GEO Accession:GSM5730190 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP350440     4170_mix-T18_S14_R1_001.fastq.gz fastq 1381687155.0 27091905.0 GSM5730190 r1 0:51 1:0 A:333912162;C:335458932;G:326378401;T:385845588;N:92072 51 0     333912162 335458932 326378401 385845588 92072 SRX13390808 SRS11294341 SRA1342092 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.95313   0.07433   0.63177   0.50475   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-12-12 Adult Adult Gonad Reproductive System
67559 67559 SRR17210888 SRX13390807 SRS11294340 SRP350440 PRJNA788302 PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis GSE190741 Other The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126   pubmed:35477799   RNAseq PCB126 10nM Rep1 GSM5730189   source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 10nM RNAseq PCB126 10nM Rep1 DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups testis Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue. Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.   tissue:testis|developmental stage:Adult|treatment:PCB126 10nM GSM5730189 GSM5730189: RNAseq PCB126 10nM Rep1; Danio rerio; RNA Seq GSM5730189   1 Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform. GEO Accession:GSM5730189 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP350440     4170_mix-T17_S13_R1_001.fastq.gz fastq 1508524920.0 29578920.0 GSM5730189 r1 0:51 1:0 A:393426431;C:349348415;G:337538750;T:428110887;N:100437 51 0     393426431 349348415 337538750 428110887 100437 SRX13390807 SRS11294340 SRA1342092 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.94765   0.0935   0.64743   0.53646   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-12-12 Adult Adult Gonad Reproductive System
67560 67560 SRR17210887 SRX13390806 SRS11294338 SRP350440 PRJNA788302 PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis GSE190741 Other The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126   pubmed:35477799   RNAseq PCB126 3nM Rep6 GSM5730188   source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 3nM RNAseq PCB126 3nM Rep6 DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups testis Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue. Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.   tissue:testis|developmental stage:Adult|treatment:PCB126 3nM GSM5730188 GSM5730188: RNAseq PCB126 3nM Rep6; Danio rerio; RNA Seq GSM5730188   1 Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform. GEO Accession:GSM5730188 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP350440     4170_mix-T16_S12_R1_001.fastq.gz fastq 1840726935.0 36092685.0 GSM5730188 r1 0:51 1:0 A:466997928;C:437493060;G:421124744;T:514986449;N:124754 51 0     466997928 437493060 421124744 514986449 124754 SRX13390806 SRS11294338 SRA1342092 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.9474   0.0984   0.64165   0.51348   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-12-12 Adult Adult Gonad Reproductive System
67561 67561 SRR17210886 SRX13390805 SRS11294339 SRP350440 PRJNA788302 PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis GSE190741 Other The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126   pubmed:35477799   RNAseq PCB126 3nM Rep5 GSM5730187   source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 3nM RNAseq PCB126 3nM Rep5 DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups testis Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue. Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.   tissue:testis|developmental stage:Adult|treatment:PCB126 3nM GSM5730187 GSM5730187: RNAseq PCB126 3nM Rep5; Danio rerio; RNA Seq GSM5730187   1 Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform. GEO Accession:GSM5730187 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP350440     4170_mix-T15_S11_R1_001.fastq.gz fastq 1384282545.0 27142795.0 GSM5730187 r1 0:51 1:0 A:325552702;C:343473865;G:329054590;T:386110707;N:90681 51 0     325552702 343473865 329054590 386110707 90681 SRX13390805 SRS11294339 SRA1342092 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.95623   0.06621   0.63345   0.49688   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-12-12 Adult Adult Gonad Reproductive System
67562 67562 SRR17210885 SRX13390804 SRS11294337 SRP350440 PRJNA788302 PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis GSE190741 Other The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126   pubmed:35477799   RNAseq PCB126 3nM Rep4 GSM5730186   source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 3nM RNAseq PCB126 3nM Rep4 DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups testis Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue. Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.   tissue:testis|developmental stage:Adult|treatment:PCB126 3nM GSM5730186 GSM5730186: RNAseq PCB126 3nM Rep4; Danio rerio; RNA Seq GSM5730186   1 Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform. GEO Accession:GSM5730186 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP350440     4170_mix-T14_S10_R1_001.fastq.gz fastq 2099071260.0 41158260.0 GSM5730186 r1 0:51 1:0 A:525168723;C:513155313;G:482406202;T:578202593;N:138429 51 0     525168723 513155313 482406202 578202593 138429 SRX13390804 SRS11294337 SRA1342092 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.94639   0.10285   0.64942   0.50757   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-12-12 Adult Adult Gonad Reproductive System
67563 67563 SRR17210884 SRX13390803 SRS11294336 SRP350440 PRJNA788302 PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis GSE190741 Other The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126   pubmed:35477799   RNAseq PCB126 3nM Rep3 GSM5730185   source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 3nM RNAseq PCB126 3nM Rep3 DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups testis Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue. Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.   tissue:testis|developmental stage:Adult|treatment:PCB126 3nM GSM5730185 GSM5730185: RNAseq PCB126 3nM Rep3; Danio rerio; RNA Seq GSM5730185   1 Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform. GEO Accession:GSM5730185 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP350440     4170_mix-T13_S9_R1_001.fastq.gz fastq 1877300055.0 36809805.0 GSM5730185 r1 0:51 1:0 A:447373671;C:463401185;G:439915337;T:526483226;N:126636 51 0     447373671 463401185 439915337 526483226 126636 SRX13390803 SRS11294336 SRA1342092 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.95301   0.06979   0.64319   0.49994   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-12-12 Adult Adult Gonad Reproductive System
67564 67564 SRR17210883 SRX13390802 SRS11294335 SRP350440 PRJNA788302 PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis GSE190741 Other The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126   pubmed:35477799   RNAseq PCB126 3nM Rep2 GSM5730184   source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 3nM RNAseq PCB126 3nM Rep2 DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups testis Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue. Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.   tissue:testis|developmental stage:Adult|treatment:PCB126 3nM GSM5730184 GSM5730184: RNAseq PCB126 3nM Rep2; Danio rerio; RNA Seq GSM5730184   1 Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform. GEO Accession:GSM5730184 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP350440     4170_mix-T11_S8_R1_001.fastq.gz fastq 1788165621.0 35062071.0 GSM5730184 r1 0:51 1:0 A:420221044;C:445407082;G:423493165;T:498924231;N:120099 51 0     420221044 445407082 423493165 498924231 120099 SRX13390802 SRS11294335 SRA1342092 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.95488   0.06451   0.63126   0.49662   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-12-12 Adult Adult Gonad Reproductive System
67565 67565 SRR17210882 SRX13390801 SRS11294334 SRP350440 PRJNA788302 PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis GSE190741 Other The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126   pubmed:35477799   RNAseq PCB126 3nM Rep1 GSM5730183   source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 3nM RNAseq PCB126 3nM Rep1 DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups testis Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue. Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.   tissue:testis|developmental stage:Adult|treatment:PCB126 3nM GSM5730183 GSM5730183: RNAseq PCB126 3nM Rep1; Danio rerio; RNA Seq GSM5730183   1 Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform. GEO Accession:GSM5730183 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP350440     4170_mix-T9_S7_R1_001.fastq.gz fastq 1855410702.0 36380602.0 GSM5730183 r1 0:51 1:0 A:459292963;C:465999847;G:421852734;T:508143917;N:121241 51 0     459292963 465999847 421852734 508143917 121241 SRX13390801 SRS11294334 SRA1342092 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.95181   0.07794   0.65141   0.51342   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-12-12 Adult Adult Gonad Reproductive System
67566 67566 SRR17210881 SRX13390800 SRS11294333 SRP350440 PRJNA788302 PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis GSE190741 Other The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126   pubmed:35477799   RNAseq DMSO Rep6 GSM5730182   source name:testis|tissue:testis|developmental stage:Adult|treatment:DMSO RNAseq DMSO Rep6 DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups testis Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue. Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.   tissue:testis|developmental stage:Adult|treatment:DMSO GSM5730182 GSM5730182: RNAseq DMSO Rep6; Danio rerio; RNA Seq GSM5730182   1 Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform. GEO Accession:GSM5730182 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP350440     4170_mix-T8_S6_R1_001.fastq.gz fastq 1923223464.0 37710264.0 GSM5730182 r1 0:51 1:0 A:451684628;C:481126641;G:454781274;T:535502647;N:128274 51 0     451684628 481126641 454781274 535502647 128274 SRX13390800 SRS11294333 SRA1342092 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.95508   0.07375   0.63183   0.49887   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-12-12 Adult Adult Gonad Reproductive System
67567 67567 SRR17210880 SRX13390799 SRS11294332 SRP350440 PRJNA788302 PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis GSE190741 Other The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126   pubmed:35477799   RNAseq DMSO Rep5 GSM5730181   source name:testis|tissue:testis|developmental stage:Adult|treatment:DMSO RNAseq DMSO Rep5 DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups testis Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue. Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.   tissue:testis|developmental stage:Adult|treatment:DMSO GSM5730181 GSM5730181: RNAseq DMSO Rep5; Danio rerio; RNA Seq GSM5730181   1 Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform. GEO Accession:GSM5730181 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP350440     4170_mix-T6_S5_R1_001.fastq.gz fastq 1752584247.0 34364397.0 GSM5730181 r1 0:51 1:0 A:413763719;C:434326065;G:412787803;T:491589762;N:116898 51 0     413763719 434326065 412787803 491589762 116898 SRX13390799 SRS11294332 SRA1342092 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.95515   0.06656   0.63859   0.49877   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-12-12 Adult Adult Gonad Reproductive System
67568 67568 SRR17210879 SRX13390798 SRS11294331 SRP350440 PRJNA788302 PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis GSE190741 Other The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126   pubmed:35477799   RNAseq DMSO Rep4 GSM5730180   source name:testis|tissue:testis|developmental stage:Adult|treatment:DMSO RNAseq DMSO Rep4 DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups testis Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue. Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.   tissue:testis|developmental stage:Adult|treatment:DMSO GSM5730180 GSM5730180: RNAseq DMSO Rep4; Danio rerio; RNA Seq GSM5730180   1 Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform. GEO Accession:GSM5730180 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP350440     4170_mix-T5_S4_R1_001.fastq.gz fastq 1783559199.0 34971749.0 GSM5730180 r1 0:51 1:0 A:426389805;C:442827488;G:416807133;T:497417118;N:117655 51 0     426389805 442827488 416807133 497417118 117655 SRX13390798 SRS11294331 SRA1342092 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.95322   0.0736   0.6354   0.49805   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-12-12 Adult Adult Gonad Reproductive System
67569 67569 SRR17210878 SRX13390797 SRS11294329 SRP350440 PRJNA788302 PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis GSE190741 Other The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126   pubmed:35477799   RNAseq DMSO Rep3 GSM5730179   source name:testis|tissue:testis|developmental stage:Adult|treatment:DMSO RNAseq DMSO Rep3 DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups testis Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue. Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.   tissue:testis|developmental stage:Adult|treatment:DMSO GSM5730179 GSM5730179: RNAseq DMSO Rep3; Danio rerio; RNA Seq GSM5730179   1 Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform. GEO Accession:GSM5730179 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP350440     4170_mix-T4_S3_R1_001.fastq.gz fastq 1907367207.0 37399357.0 GSM5730179 r1 0:51 1:0 A:508707164;C:436434670;G:414734236;T:547363631;N:127506 51 0     508707164 436434670 414734236 547363631 127506 SRX13390797 SRS11294329 SRA1342092 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.50915   0.03593   0.70147   0.49838   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-12-12 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");;