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335 rows where experiment.library_selection = "cDNA", technology = "unknown" and tissue_curation = "Gonad"

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devstage_curation 8

devstage_curation_coarse 5

experiment.platform 3

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Gonad · 335 ✖

technology 1

  • unknown · 335 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • cDNA · 335 ✖
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
5793 5793 ERR1955208 ERX2020800 ERS1697077 ERP017053 PRJEB15333 Transposon driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution ena-STUDY-EMBL EUROPEAN BIOINFORMATICS INSTITUTE-07-09-2016-10:25:55:499-247 Other In order to better understand the features associated with male germline transcription we profiled the RNA expression in a number of germline cell types. These include spermatogonial stem cells spermatocytes and round spermatids in mouse and spermatocytes in rat. We also profiled the transcription in zebrafish testes. As a consequence it became apparent that transposable elements are driving considerable lncRNA expression in the later stages of spermatogenesis. This is particularly apparent in the case of endogenous retroviruses in rodents. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 05 08     Transcriptional profiling of zebrafish testes for analysis of conserved repeat element associations SAMEA104033184 EMBL EUROPEAN BIOINFORMATICS INSTITUTE ENA FIRST PUBLIC:2017 05 10T17:01:28Z|ENA LAST UPDATE:2017 04 28T10:34:37Z|External Id:SAMEA104033184|INSDC center name:EMBL EUROPEAN BIOINFORMATICS INSTITUTE|INSDC first public:2017 05 10T17:01:28Z|INSDC last update:2017 04 28T10:34:37Z|INSDC status:public|Submitter Id:Zebrafish.Testis 2|common name:zebrafish|sample name:Zebrafish.Testis 2|scientific name:Danio rerio|strain:AB|tissue type:testis                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 16 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP017053 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 05 10|ENA LAST UPDATE:2018 11 16 zebrafish_testis_2.conserved.1.fastq.gz zebrafish_testis_2.conserved.2.fastq.gz fastq fastq 46555372886.0 230472143.0 ena RUN EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 16 0:101 1:101 A:12260062264;C:10888457642;G:11605642683;T:11637267744;N:163942553 101 101     12260062264 10888457642 11605642683 11637267744 163942553 ERX2020800 ERS1697077 ERA904389 EMBL EUROPEAN BIOINFORMATICS INSTITUTE|European Nucleotide Archive EMBL EUROPEAN BIOINFORMATICS INSTITUTE 2 0.93165 0.92785 0.29822 0.32141 0.71386 0.71971 0.66173 0.63843 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2017-01-31 Undetermined Undetermined Gonad Reproductive System
5794 5794 ERR1955207 ERX2020799 ERS1697076 ERP017053 PRJEB15333 Transposon driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution ena-STUDY-EMBL EUROPEAN BIOINFORMATICS INSTITUTE-07-09-2016-10:25:55:499-247 Other In order to better understand the features associated with male germline transcription we profiled the RNA expression in a number of germline cell types. These include spermatogonial stem cells spermatocytes and round spermatids in mouse and spermatocytes in rat. We also profiled the transcription in zebrafish testes. As a consequence it became apparent that transposable elements are driving considerable lncRNA expression in the later stages of spermatogenesis. This is particularly apparent in the case of endogenous retroviruses in rodents. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 05 08     Transcriptional profiling of zebrafish testes for analysis of conserved repeat element associations SAMEA104033183 EMBL EUROPEAN BIOINFORMATICS INSTITUTE ENA FIRST PUBLIC:2017 05 10T17:01:28Z|ENA LAST UPDATE:2017 04 28T10:34:37Z|External Id:SAMEA104033183|INSDC center name:EMBL EUROPEAN BIOINFORMATICS INSTITUTE|INSDC first public:2017 05 10T17:01:28Z|INSDC last update:2017 04 28T10:34:37Z|INSDC status:public|Submitter Id:Zebrafish.Testis 1|common name:zebrafish|sample name:Zebrafish.Testis 1|scientific name:Danio rerio|strain:AB|tissue type:testis                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 15 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP017053 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 05 10|ENA LAST UPDATE:2018 11 16 zebrafish_testis_1.conserved.1.fastq.gz zebrafish_testis_1.conserved.2.fastq.gz fastq fastq 41056086708.0 203247954.0 ena RUN EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 15 0:101 1:101 A:10675591750;C:9672762387;G:10139834713;T:10380949257;N:186948601 101 101     10675591750 9672762387 10139834713 10380949257 186948601 ERX2020799 ERS1697076 ERA904389 EMBL EUROPEAN BIOINFORMATICS INSTITUTE|European Nucleotide Archive EMBL EUROPEAN BIOINFORMATICS INSTITUTE 2 0.92308 0.9157 0.30221 0.31293 0.68276 0.68836 0.56114 0.5857 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2017-01-31 Undetermined Undetermined Gonad Reproductive System
25267 25267 SRR25744342 SRX21467662 SRS18702380 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad eif4e1b 3 GSM7730282   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / |geo loc name:missing|collection date:missing Gonad eif4e1b 3 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / GSM7730282 GSM7730282: Gonad eif4e1b 3; Danio rerio; ssRNA seq GSM7730282 r1 GSM7730282 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_HOM3_1.fastq.gz Ovary_HOM3_2.fastq.gz fastq fastq 2170738056.0 10746228.0 GSM7730282 r1 0:101 1:101 A:531993767;C:520631008;G:565772072;T:552334154;N:7055 101 101     531993767 520631008 565772072 552334154 7055 SRX21467662 SRS18702380 SRA1698764 IMP IMP 2 0.77665 0.7702 0.14988 0.14284 0.66716 0.66957 0.49991 0.47425 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25268 25268 SRR25744343 SRX21467661 SRS18702379 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad eif4e1b 2 GSM7730281   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / |geo loc name:missing|collection date:missing Gonad eif4e1b 2 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / GSM7730281 GSM7730281: Gonad eif4e1b 2; Danio rerio; ssRNA seq GSM7730281 r1 GSM7730281 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_HOM2_1.fastq.gz Ovary_HOM2_2.fastq.gz fastq fastq 3459149000.0 17124500.0 GSM7730281 r1 0:101 1:101 A:876732239;C:796603142;G:882912604;T:902886783;N:14232 101 101     876732239 796603142 882912604 902886783 14232 SRX21467661 SRS18702379 SRA1698764 IMP IMP 2 0.81761 0.79589 0.26282 0.24746 0.70607 0.7039 0.50658 0.49236 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25269 25269 SRR25744344 SRX21467660 SRS18702381 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad eif4e1b 1 GSM7730280   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / |geo loc name:missing|collection date:missing Gonad eif4e1b 1 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / GSM7730280 GSM7730280: Gonad eif4e1b 1; Danio rerio; ssRNA seq GSM7730280 r1 GSM7730280 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_HOM1_1.fastq.gz Ovary_HOM1_2.fastq.gz fastq fastq 2189781202.0 10840501.0 GSM7730280 r1 0:101 1:101 A:537591255;C:525448020;G:568979980;T:557754770;N:7177 101 101     537591255 525448020 568979980 557754770 7177 SRX21467660 SRS18702381 SRA1698764 IMP IMP 2 0.7459 0.74191 0.15778 0.15291 0.65543 0.65841 0.48578 0.48291 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25270 25270 SRR25744345 SRX21467659 SRS18702378 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad WT 3 GSM7730279   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+|geo loc name:missing|collection date:missing Gonad WT 3 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+ GSM7730279 GSM7730279: Gonad WT 3; Danio rerio; ssRNA seq GSM7730279 r1 GSM7730279 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_WT3_1.fastq.gz Ovary_WT3_2.fastq.gz fastq fastq 3674041448.0 18188324.0 GSM7730279 r1 0:101 1:101 A:910831144;C:876967044;G:953299105;T:932928913;N:15242 101 101     910831144 876967044 953299105 932928913 15242 SRX21467659 SRS18702378 SRA1698764 IMP IMP 2 0.89093 0.89038 0.09253 0.09348 0.73892 0.73858 0.47115 0.47218 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25271 25271 SRR25744346 SRX21467658 SRS18702377 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad WT 2 GSM7730278   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+|geo loc name:missing|collection date:missing Gonad WT 2 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+ GSM7730278 GSM7730278: Gonad WT 2; Danio rerio; ssRNA seq GSM7730278 r1 GSM7730278 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_WT2_1.fastq.gz Ovary_WT2_2.fastq.gz fastq fastq 3024886370.0 14974685.0 GSM7730278 r1 0:101 1:101 A:744374909;C:727299396;G:782294774;T:770904797;N:12494 101 101     744374909 727299396 782294774 770904797 12494 SRX21467658 SRS18702377 SRA1698764 IMP IMP 2 0.91806 0.91689 0.06949 0.07178 0.74458 0.74474 0.47548 0.47338 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25272 25272 SRR25744347 SRX21467657 SRS18702376 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad WT 1 GSM7730277   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+|geo loc name:missing|collection date:missing Gonad WT 1 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+ GSM7730277 GSM7730277: Gonad WT 1; Danio rerio; ssRNA seq GSM7730277 r1 GSM7730277 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_WT1_2.fastq.gz Ovary_WT1_1.fastq.gz fastq fastq 3571638356.0 17681378.0 GSM7730277 r1 0:101 1:101 A:876280472;C:856417516;G:935896746;T:903028845;N:14777 101 101     876280472 856417516 935896746 903028845 14777 SRX21467657 SRS18702376 SRA1698764 IMP IMP 2 0.89559 0.89353 0.09223 0.09423 0.73052 0.73012 0.47772 0.47408 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
31721 31721 SRR28537217 SRX24137319 SRS20921922 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         ko3   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:ko biological replicate 3|BioSampleModel:Model organism or animal                 ko3 ko3 ko3 ko ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     ko3_1.fq.gz ko3_2.fq.gz fastq fastq 8310654000.0 27702180.0 ko3 1.fq.gz 0:150 1:150 A:2164758632;C:1964255570;G:1984514973;T:2197073890;N:50935 150 150     2164758632 1964255570 1984514973 2197073890 50935 SRX24137319 SRS20921922     Shenzhen Second People's Hospital 2 0.9472 0.94617 0.02506 0.02527 0.74286 0.74535 0.45316 0.45662 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
31722 31722 SRR28537218 SRX24137318 SRS20921924 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         ko2   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:ko biological replicate 2|BioSampleModel:Model organism or animal                 ko2 ko2 ko2 ko ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     ko2_1.fq.gz ko2_2.fq.gz fastq fastq 8095711800.0 26985706.0 ko2 1.fq.gz 0:150 1:150 A:2117986563;C:1909094084;G:1931885806;T:2136732639;N:12708 150 150     2117986563 1909094084 1931885806 2136732639 12708 SRX24137318 SRS20921924     Shenzhen Second People's Hospital 2 0.9483 0.94443 0.02385 0.02347 0.74266 0.74686 0.45568 0.45676 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
31723 31723 SRR28537219 SRX24137317 SRS20921925 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         ko1   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:ko biological replicate 1|BioSampleModel:Model organism or animal                 ko1 ko1 ko1 ko ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     ko1_1.fq.gz ko1_2.fq.gz fastq fastq 9904629000.0 33015430.0 ko1 1.fq.gz 0:150 1:150 A:2565332092;C:2354153391;G:2380645312;T:2604437822;N:60383 150 150     2565332092 2354153391 2380645312 2604437822 60383 SRX24137317 SRS20921925     Shenzhen Second People's Hospital 2 0.94565 0.94416 0.01943 0.01956 0.7559 0.75739 0.456 0.45903 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
31724 31724 SRR28537220 SRX24137316 SRS20921923 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         wt3   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:wt biological replicate 3|BioSampleModel:Model organism or animal                 wt3 wt3 wt3 wt ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     wt3_1.fq.gz wt3_2.fq.gz fastq fastq 10079485500.0 33598285.0 wt3 1.fq.gz 0:150 1:150 A:2607822943;C:2396994959;G:2427407078;T:2647197813;N:62707 150 150     2607822943 2396994959 2427407078 2647197813 62707 SRX24137316 SRS20921923     Shenzhen Second People's Hospital 2 0.94735 0.94594 0.01733 0.01743 0.75635 0.75712 0.44042 0.46348 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
31725 31725 SRR28537221 SRX24137315 SRS20921920 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         wt2   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:wt biological replicate 2|BioSampleModel:Model organism or animal                 wt2 wt2 wt2 wt ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     wt2_2.fq.gz wt2_1.fq.gz fastq fastq 8980086900.0 29933623.0 wt2 1.fq.gz 0:150 1:150 A:2333474507;C:2131182397;G:2149144543;T:2366230132;N:55321 150 150     2333474507 2131182397 2149144543 2366230132 55321 SRX24137315 SRS20921920     Shenzhen Second People's Hospital 2 0.94182 0.94004 0.0187 0.01854 0.75077 0.75132 0.46271 0.46384 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
31726 31726 SRR28537222 SRX24137314 SRS20921921 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         wt1   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:wt biological replicate 1|BioSampleModel:Model organism or animal                 wt1 wt1 wt1 wt ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     wt1_1.fq.gz wt1_2.fq.gz fastq fastq 5436554400.0 18121848.0 wt1 1.fq.gz 0:150 1:150 A:1418897733;C:1287256771;G:1297629578;T:1432736726;N:33592 150 150     1418897733 1287256771 1297629578 1432736726 33592 SRX24137314 SRS20921921     Shenzhen Second People's Hospital 2 0.9407 0.94657 0.02199 0.02152 0.74655 0.74679 0.47086 0.47165 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
31837 31837 SRR28709001 SRX24276192 SRS21041156 SRP502090 PRJNA1101048 Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish GSE264143 Transcriptome Analysis Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.       dpf61 Ov mt 3 GSM8212808   source name:Ovary|tissue:Ovary|age:dpf 61|genotype:mutant|geo loc name:missing|collection date:missing dpf61 Ov mt 3 Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample. Ovary   Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples. WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food. tissue:Ovary|age:dpf 61|genotype:mutant GSM8212808 GSM8212808: dpf61 Ov mt 3; Danio rerio; RNA Seq GSM8212808 r1 GSM8212808 1 Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP502090   loader:fastq load.py NS51397.M43_20230510_103430.L001.1.fastq.gz NS51397.M43_20230510_103430.L001.2.fastq.gz fastq fastq 9024444634.0 29882267.0 GSM8212808 r1 0:151 1:151 A:2471288260;C:1931225512;G:2256742565;T:2363378475;N:1809822 151 151     2471288260 1931225512 2256742565 2363378475 1809822 SRX24276192 SRS21041156 SRA1847037 Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences                       B B biological fallback assumption illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-04-16 Juvenile Juvenile Gonad Reproductive System
31838 31838 SRR28709002 SRX24276191 SRS21041154 SRP502090 PRJNA1101048 Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish GSE264143 Transcriptome Analysis Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.       dpf61 Ov mt 2 GSM8212807   source name:Ovary|tissue:Ovary|age:dpf 61|genotype:mutant|geo loc name:missing|collection date:missing dpf61 Ov mt 2 Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample. Ovary   Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples. WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food. tissue:Ovary|age:dpf 61|genotype:mutant GSM8212807 GSM8212807: dpf61 Ov mt 2; Danio rerio; RNA Seq GSM8212807 r1 GSM8212807 1 Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP502090   loader:fastq load.py NS51397.M41_20230510_103430.L001.1.fastq.gz NS51397.M41_20230510_103430.L001.2.fastq.gz fastq fastq 13553131538.0 44877919.0 GSM8212807 r1 0:151 1:151 A:3707129145;C:2878818514;G:3433054125;T:3531357698;N:2772056 151 151     3707129145 2878818514 3433054125 3531357698 2772056 SRX24276191 SRS21041154 SRA1847037 Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences                       B B biological fallback assumption illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-04-16 Juvenile Juvenile Gonad Reproductive System
31839 31839 SRR28709003 SRX24276190 SRS21041155 SRP502090 PRJNA1101048 Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish GSE264143 Transcriptome Analysis Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.       dpf61 Ov mt 1 GSM8212806   source name:Ovary|tissue:Ovary|age:dpf 61|genotype:mutant|geo loc name:missing|collection date:missing dpf61 Ov mt 1 Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample. Ovary   Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples. WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food. tissue:Ovary|age:dpf 61|genotype:mutant GSM8212806 GSM8212806: dpf61 Ov mt 1; Danio rerio; RNA Seq GSM8212806 r1 GSM8212806 1 Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP502090   loader:fastq load.py NS51397.M32_20230510_103430.L001.1.fastq.gz NS51397.M32_20230510_103430.L001.2.fastq.gz fastq fastq 11752803234.0 38916567.0 GSM8212806 r1 0:151 1:151 A:3199511211;C:2525248103;G:2947698766;T:3077964367;N:2380787 151 151     3199511211 2525248103 2947698766 3077964367 2380787 SRX24276190 SRS21041155 SRA1847037 Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences                       B B biological fallback assumption illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-04-16 Juvenile Juvenile Gonad Reproductive System
31840 31840 SRR28709004 SRX24276189 SRS21041153 SRP502090 PRJNA1101048 Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish GSE264143 Transcriptome Analysis Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.       dpf61 Ov wt 3 GSM8212805   source name:Ovary|tissue:Ovary|age:dpf 61|genotype:wildtype|geo loc name:missing|collection date:missing dpf61 Ov wt 3 Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample. Ovary   Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples. WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food. tissue:Ovary|age:dpf 61|genotype:wildtype GSM8212805 GSM8212805: dpf61 Ov wt 3; Danio rerio; RNA Seq GSM8212805 r1 GSM8212805 1 Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP502090   loader:fastq load.py NS51397.M17_20230510_103430.L001.1.fastq.gz NS51397.M17_20230510_103430.L001.2.fastq.gz fastq fastq 16726684646.0 55386373.0 GSM8212805 r1 0:151 1:151 A:4912874254;C:2935821083;G:3844206542;T:5030341800;N:3440967 151 151     4912874254 2935821083 3844206542 5030341800 3440967 SRX24276189 SRS21041153 SRA1847037 Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences                       B B biological fallback assumption illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-04-16 Juvenile Juvenile Gonad Reproductive System
31841 31841 SRR28709005 SRX24276188 SRS21041152 SRP502090 PRJNA1101048 Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish GSE264143 Transcriptome Analysis Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.       dpf61 Ov wt 2 GSM8212804   source name:Ovary|tissue:Ovary|age:dpf 61|genotype:wildtype|geo loc name:missing|collection date:missing dpf61 Ov wt 2 Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample. Ovary   Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples. WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food. tissue:Ovary|age:dpf 61|genotype:wildtype GSM8212804 GSM8212804: dpf61 Ov wt 2; Danio rerio; RNA Seq GSM8212804 r1 GSM8212804 1 Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP502090   loader:fastq load.py NS51397.M14_20230510_103430.L001.1.fastq.gz NS51397.M14_20230510_103430.L001.2.fastq.gz fastq fastq 11600612146.0 38412623.0 GSM8212804 r1 0:151 1:151 A:3087038432;C:2559546168;G:3029729871;T:2921939557;N:2358118 151 151     3087038432 2559546168 3029729871 2921939557 2358118 SRX24276188 SRS21041152 SRA1847037 Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences                       B B biological fallback assumption illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-04-16 Juvenile Juvenile Gonad Reproductive System
31842 31842 SRR28709006 SRX24276187 SRS21041151 SRP502090 PRJNA1101048 Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish GSE264143 Transcriptome Analysis Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.       dpf61 Ov wt 1 GSM8212803   source name:Ovary|tissue:Ovary|age:dpf 61|genotype:wildtype|geo loc name:missing|collection date:missing dpf61 Ov wt 1 Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample. Ovary   Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples. WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food. tissue:Ovary|age:dpf 61|genotype:wildtype GSM8212803 GSM8212803: dpf61 Ov wt 1; Danio rerio; RNA Seq GSM8212803 r1 GSM8212803 1 Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP502090   loader:fastq load.py NS51397.M9_20230510_103430.L001.1.fastq.gz NS51397.M9_20230510_103430.L001.2.fastq.gz fastq fastq 19081987478.0 63185389.0 GSM8212803 r1 0:151 1:151 A:5188307750;C:4048527738;G:4868706940;T:4972575432;N:3869618 151 151     5188307750 4048527738 4868706940 4972575432 3869618 SRX24276187 SRS21041151 SRA1847037 Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences                       B B biological fallback assumption illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-04-16 Juvenile Juvenile Gonad Reproductive System
31843 31843 SRR28709007 SRX24276186 SRS21041150 SRP502090 PRJNA1101048 Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish GSE264143 Transcriptome Analysis Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.       dpf47 Ov mt 3 GSM8212802   source name:Ovary|tissue:Ovary|age:dpf 47|genotype:mutant|geo loc name:missing|collection date:missing dpf47 Ov mt 3 Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample. Ovary   Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples. WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food. tissue:Ovary|age:dpf 47|genotype:mutant GSM8212802 GSM8212802: dpf47 Ov mt 3; Danio rerio; RNA Seq GSM8212802 r1 GSM8212802 1 Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP502090   loader:fastq load.py NS51397.C33_20230510_103430.L001.1.fastq.gz NS51397.C33_20230510_103430.L001.2.fastq.gz fastq fastq 8256087174.0 27338037.0 GSM8212802 r1 0:151 1:151 A:2217123657;C:1857924925;G:2109544983;T:2069850323;N:1643286 151 151     2217123657 1857924925 2109544983 2069850323 1643286 SRX24276186 SRS21041150 SRA1847037 Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences                       B B biological fallback assumption illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-04-16 Juvenile Juvenile Gonad Reproductive System
31844 31844 SRR28709008 SRX24276185 SRS21041149 SRP502090 PRJNA1101048 Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish GSE264143 Transcriptome Analysis Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.       dpf47 Ov mt 2 GSM8212801   source name:Ovary|tissue:Ovary|age:dpf 47|genotype:mutant|geo loc name:missing|collection date:missing dpf47 Ov mt 2 Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample. Ovary   Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples. WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food. tissue:Ovary|age:dpf 47|genotype:mutant GSM8212801 GSM8212801: dpf47 Ov mt 2; Danio rerio; RNA Seq GSM8212801 r1 GSM8212801 1 Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP502090   loader:fastq load.py NS51397.C32_20230510_103430.L001.1.fastq.gz NS51397.C32_20230510_103430.L001.2.fastq.gz fastq fastq 14985320634.0 49620267.0 GSM8212801 r1 0:151 1:151 A:4058920258;C:3245799385;G:3815485722;T:3862070151;N:3045118 151 151     4058920258 3245799385 3815485722 3862070151 3045118 SRX24276185 SRS21041149 SRA1847037 Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences                       B B biological fallback assumption illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-04-16 Juvenile Juvenile Gonad Reproductive System
31845 31845 SRR28709009 SRX24276184 SRS21041147 SRP502090 PRJNA1101048 Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish GSE264143 Transcriptome Analysis Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.       dpf47 Ov mt 1 GSM8212800   source name:Ovary|tissue:Ovary|age:dpf 47|genotype:mutant|geo loc name:missing|collection date:missing dpf47 Ov mt 1 Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample. Ovary   Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples. WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food. tissue:Ovary|age:dpf 47|genotype:mutant GSM8212800 GSM8212800: dpf47 Ov mt 1; Danio rerio; RNA Seq GSM8212800 r1 GSM8212800 1 Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP502090   loader:fastq load.py NS51397.C29_20230510_103430.L001.1.fastq.gz NS51397.C29_20230510_103430.L001.2.fastq.gz fastq fastq 11177741176.0 37012388.0 GSM8212800 r1 0:151 1:151 A:3060199842;C:2374800912;G:2799391711;T:2941063533;N:2285178 151 151     3060199842 2374800912 2799391711 2941063533 2285178 SRX24276184 SRS21041147 SRA1847037 Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences                       B B biological fallback assumption illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-04-16 Juvenile Juvenile Gonad Reproductive System
31846 31846 SRR28709010 SRX24276183 SRS21041146 SRP502090 PRJNA1101048 Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish GSE264143 Transcriptome Analysis Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.       dpf47 Ov wt 3 GSM8212799   source name:Ovary|tissue:Ovary|age:dpf 47|genotype:wildtype|geo loc name:missing|collection date:missing dpf47 Ov wt 3 Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample. Ovary   Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples. WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food. tissue:Ovary|age:dpf 47|genotype:wildtype GSM8212799 GSM8212799: dpf47 Ov wt 3; Danio rerio; RNA Seq GSM8212799 r1 GSM8212799 1 Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP502090   loader:fastq load.py NS51397.C21_20230510_103430.L001.1.fastq.gz NS51397.C21_20230510_103430.L001.2.fastq.gz fastq fastq 13599817718.0 45032509.0 GSM8212799 r1 0:151 1:151 A:3724782410;C:2835413438;G:3575258078;T:3461647906;N:2715886 151 151     3724782410 2835413438 3575258078 3461647906 2715886 SRX24276183 SRS21041146 SRA1847037 Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences                       B B biological fallback assumption illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-04-16 Juvenile Juvenile Gonad Reproductive System
31847 31847 SRR28709011 SRX24276182 SRS21041148 SRP502090 PRJNA1101048 Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish GSE264143 Transcriptome Analysis Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.       dpf47 Ov wt 2 GSM8212798   source name:Ovary|tissue:Ovary|age:dpf 47|genotype:wildtype|geo loc name:missing|collection date:missing dpf47 Ov wt 2 Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample. Ovary   Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples. WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food. tissue:Ovary|age:dpf 47|genotype:wildtype GSM8212798 GSM8212798: dpf47 Ov wt 2; Danio rerio; RNA Seq GSM8212798 r1 GSM8212798 1 Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP502090   loader:fastq load.py NS51397.C20_20230510_103430.L001.1.fastq.gz NS51397.C20_20230510_103430.L001.2.fastq.gz fastq fastq 13632935642.0 45142171.0 GSM8212798 r1 0:151 1:151 A:3708965267;C:2903664830;G:3492295019;T:3525245989;N:2764537 151 151     3708965267 2903664830 3492295019 3525245989 2764537 SRX24276182 SRS21041148 SRA1847037 Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences                       B B biological fallback assumption illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-04-16 Juvenile Juvenile Gonad Reproductive System
31848 31848 SRR28709012 SRX24276181 SRS21041145 SRP502090 PRJNA1101048 Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish GSE264143 Transcriptome Analysis Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.       dpf47 Ov wt 1 GSM8212797   source name:Ovary|tissue:Ovary|age:dpf 47|genotype:wildtype|geo loc name:missing|collection date:missing dpf47 Ov wt 1 Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample. Ovary   Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples. WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food. tissue:Ovary|age:dpf 47|genotype:wildtype GSM8212797 GSM8212797: dpf47 Ov wt 1; Danio rerio; RNA Seq GSM8212797 r1 GSM8212797 1 Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP502090   loader:fastq load.py NS51397.C4_20230510_103430.L001.1.fastq.gz NS51397.C4_20230510_103430.L001.2.fastq.gz fastq fastq 12378485324.0 40988362.0 GSM8212797 r1 0:151 1:151 A:3378421522;C:2638098449;G:3108553273;T:3250895048;N:2517032 151 151     3378421522 2638098449 3108553273 3250895048 2517032 SRX24276181 SRS21041145 SRA1847037 Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences                       B B biological fallback assumption illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-04-16 Juvenile Juvenile Gonad Reproductive System
33663 33663 SRR30502664 SRX25926478 SRS22513929 SRP529840 PRJNA1154960 Deletion of ddx4 ovary specific transcript causes downregulation of sycp1 and derepression of DNA transposons in zebrafish ovaries GSE276129 Transcriptome Analysis Ddx4 DEAD box helicase 4 is a well established marker gene for early stage germlines and is required for the development of germ cells. Alternative splicing of ddx4 produces a long transcript that is exclusively expressed in zebrafish ovaries. The function of this ovary specific transcript ddx4 L remains unclear. In this study using the ddx4 L knockout zebrafish model we found that elimination of ddx4 L results in a decrease in fertilization rate and in the number of mature eggs laid by the female mutants. Transcriptome analysis was performed to identify the underlying changes of gene expression between WT and ddx4 L knockout ovaries. A total of 1134 differentially expressed genes were identified of which 524 were upregulated and 610 were downregulated. Functional enrichment analysis showed that the terms of negative regulation of fertilization sperm egg recognition process and oocyte meiosis might be affected by elimination of ddx4 L. Furthermore we found that Sycp1 a synaptonemal complex protein involved in meiosis and fertility was dramatically decreased in the ddx4 L knockout ovaries at both mRNA and protein levels. Moreover the activities of transposable elements were analyzed based on the RNA seq data. The result showed that elimination of ddx4 L causes the derepression of DNA transposons a subclass of transposable elements in zebrafish ovaries. In conclusion the aforementioned findings indicate that the ovary specific transcript of ddx4 plays an important role in oocyte development and egg quality possibly by maintaining sycp1 expression and repressing DNA transposons. Our work provide novel insights into the functions and regulatory mechanisms of ddx4 in zebrafish oogenesis. Overall design: Ovaries were dissected from three WT and three ddx4 E4? zebrafish at 6 mpf respectively. Six total RNA samples were extracted and subjected to RNA sequencing. Differentially expressed genes DEGs and transposable elements TEs between WT and ddx4 E4? zebrafish ovaries were analyzed.   pubmed:39765722   ddx4E4Δ ovary rep3 GSM8491761   source name:Ovary|tissue:Ovary|genotype:ddx4E4{delta}|geo loc name:missing|collection date:missing ddx4E4Δ ovary rep3 The raw paired end reads were trimmed and quality controlled by SeqPrep https://github.com/jstjohn/SeqPrep and Sickle https://github.com/najoshi/sickle with default parameters. Then clean reads were separately aligned to zebrafish reference genome GRCz11 with orientation mode using HISAT2 http://ccb.jhu.edu/software/hisat2/index.shtml software. The mapped reads of each sample were assembled by StringTie https://ccb.jhu.edu/software/stringtie/index.shtml in a reference based approach. To identify DEGs differential expression genes between the ovaries of WT and ddx4 E4Δ zebrafish the expression level of each transcript was calculated according to the transcripts per million reads TPM method. RSEM http://deweylab.biostat.wisc.edu/rsem/ was used to quantify gene abundances. Essentially differential expression analysis was performed using the DESeq2 software. DEGs with |log2FC|>1 and Q value <= 0.05 were considered to be significantly different expressed genes. Functional enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni corrected P value ≤0.05 compared with the whole transcriptome background. Assembly: GRCz11 Supplementary files format and content: read count.txt is a tab delimited text file for read count numbers of each gene in all six samples. Ovary   Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer’s protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina San Diego CA. About 1μg of high quality total RNA samples OD260/280=1.82.2 RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.   tissue:Ovary|genotype:ddx4E4{delta} GSM8491761 GSM8491761: ddx4E4Δ ovary rep3; Danio rerio; RNA Seq GSM8491761 r1 GSM8491761 1 Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer's protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina San Diego CA. About 1μg of high quality total RNA samples OD260/280=1.82.2 RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP529840     D3_R1.fastq.gz D3_R2.fastq.gz fastq fastq 8532086786.0 28251943.0 GSM8491761 r1 0:151 1:151 A:2175886107;C:2065104971;G:2109654211;T:2181416846;N:24651 151 151     2175886107 2065104971 2109654211 2181416846 24651 SRX25926478 SRS22513929 SRA1960397 Institute of Hydrobiology, Chinese Academy of Sciences Institute of Hydrobiology, Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era full_length random_priming unknown bulk unknown unknown   China 2024-08-31 Adult Adult Gonad Reproductive System
33664 33664 SRR30502665 SRX25926477 SRS22513928 SRP529840 PRJNA1154960 Deletion of ddx4 ovary specific transcript causes downregulation of sycp1 and derepression of DNA transposons in zebrafish ovaries GSE276129 Transcriptome Analysis Ddx4 DEAD box helicase 4 is a well established marker gene for early stage germlines and is required for the development of germ cells. Alternative splicing of ddx4 produces a long transcript that is exclusively expressed in zebrafish ovaries. The function of this ovary specific transcript ddx4 L remains unclear. In this study using the ddx4 L knockout zebrafish model we found that elimination of ddx4 L results in a decrease in fertilization rate and in the number of mature eggs laid by the female mutants. Transcriptome analysis was performed to identify the underlying changes of gene expression between WT and ddx4 L knockout ovaries. A total of 1134 differentially expressed genes were identified of which 524 were upregulated and 610 were downregulated. Functional enrichment analysis showed that the terms of negative regulation of fertilization sperm egg recognition process and oocyte meiosis might be affected by elimination of ddx4 L. Furthermore we found that Sycp1 a synaptonemal complex protein involved in meiosis and fertility was dramatically decreased in the ddx4 L knockout ovaries at both mRNA and protein levels. Moreover the activities of transposable elements were analyzed based on the RNA seq data. The result showed that elimination of ddx4 L causes the derepression of DNA transposons a subclass of transposable elements in zebrafish ovaries. In conclusion the aforementioned findings indicate that the ovary specific transcript of ddx4 plays an important role in oocyte development and egg quality possibly by maintaining sycp1 expression and repressing DNA transposons. Our work provide novel insights into the functions and regulatory mechanisms of ddx4 in zebrafish oogenesis. Overall design: Ovaries were dissected from three WT and three ddx4 E4? zebrafish at 6 mpf respectively. Six total RNA samples were extracted and subjected to RNA sequencing. Differentially expressed genes DEGs and transposable elements TEs between WT and ddx4 E4? zebrafish ovaries were analyzed.   pubmed:39765722   ddx4E4Δ ovary rep2 GSM8491760   source name:Ovary|tissue:Ovary|genotype:ddx4E4{delta}|geo loc name:missing|collection date:missing ddx4E4Δ ovary rep2 The raw paired end reads were trimmed and quality controlled by SeqPrep https://github.com/jstjohn/SeqPrep and Sickle https://github.com/najoshi/sickle with default parameters. Then clean reads were separately aligned to zebrafish reference genome GRCz11 with orientation mode using HISAT2 http://ccb.jhu.edu/software/hisat2/index.shtml software. The mapped reads of each sample were assembled by StringTie https://ccb.jhu.edu/software/stringtie/index.shtml in a reference based approach. To identify DEGs differential expression genes between the ovaries of WT and ddx4 E4Δ zebrafish the expression level of each transcript was calculated according to the transcripts per million reads TPM method. RSEM http://deweylab.biostat.wisc.edu/rsem/ was used to quantify gene abundances. Essentially differential expression analysis was performed using the DESeq2 software. DEGs with |log2FC|>1 and Q value <= 0.05 were considered to be significantly different expressed genes. Functional enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni corrected P value ≤0.05 compared with the whole transcriptome background. Assembly: GRCz11 Supplementary files format and content: read count.txt is a tab delimited text file for read count numbers of each gene in all six samples. Ovary   Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer’s protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina San Diego CA. About 1μg of high quality total RNA samples OD260/280=1.82.2 RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.   tissue:Ovary|genotype:ddx4E4{delta} GSM8491760 GSM8491760: ddx4E4Δ ovary rep2; Danio rerio; RNA Seq GSM8491760 r1 GSM8491760 1 Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer's protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina San Diego CA. About 1μg of high quality total RNA samples OD260/280=1.82.2 RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP529840     D2_R1.fastq.gz D2_R2.fastq.gz fastq fastq 8420834516.0 27883558.0 GSM8491760 r1 0:151 1:151 A:2130607193;C:2053627459;G:2099203008;T:2137372997;N:23859 151 151     2130607193 2053627459 2099203008 2137372997 23859 SRX25926477 SRS22513928 SRA1960397 Institute of Hydrobiology, Chinese Academy of Sciences Institute of Hydrobiology, Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era full_length random_priming unknown bulk unknown unknown   China 2024-08-31 Adult Adult Gonad Reproductive System
33665 33665 SRR30502666 SRX25926476 SRS22513927 SRP529840 PRJNA1154960 Deletion of ddx4 ovary specific transcript causes downregulation of sycp1 and derepression of DNA transposons in zebrafish ovaries GSE276129 Transcriptome Analysis Ddx4 DEAD box helicase 4 is a well established marker gene for early stage germlines and is required for the development of germ cells. Alternative splicing of ddx4 produces a long transcript that is exclusively expressed in zebrafish ovaries. The function of this ovary specific transcript ddx4 L remains unclear. In this study using the ddx4 L knockout zebrafish model we found that elimination of ddx4 L results in a decrease in fertilization rate and in the number of mature eggs laid by the female mutants. Transcriptome analysis was performed to identify the underlying changes of gene expression between WT and ddx4 L knockout ovaries. A total of 1134 differentially expressed genes were identified of which 524 were upregulated and 610 were downregulated. Functional enrichment analysis showed that the terms of negative regulation of fertilization sperm egg recognition process and oocyte meiosis might be affected by elimination of ddx4 L. Furthermore we found that Sycp1 a synaptonemal complex protein involved in meiosis and fertility was dramatically decreased in the ddx4 L knockout ovaries at both mRNA and protein levels. Moreover the activities of transposable elements were analyzed based on the RNA seq data. The result showed that elimination of ddx4 L causes the derepression of DNA transposons a subclass of transposable elements in zebrafish ovaries. In conclusion the aforementioned findings indicate that the ovary specific transcript of ddx4 plays an important role in oocyte development and egg quality possibly by maintaining sycp1 expression and repressing DNA transposons. Our work provide novel insights into the functions and regulatory mechanisms of ddx4 in zebrafish oogenesis. Overall design: Ovaries were dissected from three WT and three ddx4 E4? zebrafish at 6 mpf respectively. Six total RNA samples were extracted and subjected to RNA sequencing. Differentially expressed genes DEGs and transposable elements TEs between WT and ddx4 E4? zebrafish ovaries were analyzed.   pubmed:39765722   ddx4E4Δ ovary rep1 GSM8491759   source name:Ovary|tissue:Ovary|genotype:ddx4E4{delta}|geo loc name:missing|collection date:missing ddx4E4Δ ovary rep1 The raw paired end reads were trimmed and quality controlled by SeqPrep https://github.com/jstjohn/SeqPrep and Sickle https://github.com/najoshi/sickle with default parameters. Then clean reads were separately aligned to zebrafish reference genome GRCz11 with orientation mode using HISAT2 http://ccb.jhu.edu/software/hisat2/index.shtml software. The mapped reads of each sample were assembled by StringTie https://ccb.jhu.edu/software/stringtie/index.shtml in a reference based approach. To identify DEGs differential expression genes between the ovaries of WT and ddx4 E4Δ zebrafish the expression level of each transcript was calculated according to the transcripts per million reads TPM method. RSEM http://deweylab.biostat.wisc.edu/rsem/ was used to quantify gene abundances. Essentially differential expression analysis was performed using the DESeq2 software. DEGs with |log2FC|>1 and Q value <= 0.05 were considered to be significantly different expressed genes. Functional enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni corrected P value ≤0.05 compared with the whole transcriptome background. Assembly: GRCz11 Supplementary files format and content: read count.txt is a tab delimited text file for read count numbers of each gene in all six samples. Ovary   Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer’s protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina San Diego CA. About 1μg of high quality total RNA samples OD260/280=1.82.2 RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.   tissue:Ovary|genotype:ddx4E4{delta} GSM8491759 GSM8491759: ddx4E4Δ ovary rep1; Danio rerio; RNA Seq GSM8491759 r1 GSM8491759 1 Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer's protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina San Diego CA. About 1μg of high quality total RNA samples OD260/280=1.82.2 RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP529840     D1_R1.fastq.gz D1_R2.fastq.gz fastq fastq 8478573292.0 28074746.0 GSM8491759 r1 0:151 1:151 A:2141904837;C:2071392554;G:2116256871;T:2148995183;N:23847 151 151     2141904837 2071392554 2116256871 2148995183 23847 SRX25926476 SRS22513927 SRA1960397 Institute of Hydrobiology, Chinese Academy of Sciences Institute of Hydrobiology, Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era full_length random_priming unknown bulk unknown unknown   China 2024-08-31 Adult Adult Gonad Reproductive System
33666 33666 SRR30502667 SRX25926475 SRS22513926 SRP529840 PRJNA1154960 Deletion of ddx4 ovary specific transcript causes downregulation of sycp1 and derepression of DNA transposons in zebrafish ovaries GSE276129 Transcriptome Analysis Ddx4 DEAD box helicase 4 is a well established marker gene for early stage germlines and is required for the development of germ cells. Alternative splicing of ddx4 produces a long transcript that is exclusively expressed in zebrafish ovaries. The function of this ovary specific transcript ddx4 L remains unclear. In this study using the ddx4 L knockout zebrafish model we found that elimination of ddx4 L results in a decrease in fertilization rate and in the number of mature eggs laid by the female mutants. Transcriptome analysis was performed to identify the underlying changes of gene expression between WT and ddx4 L knockout ovaries. A total of 1134 differentially expressed genes were identified of which 524 were upregulated and 610 were downregulated. Functional enrichment analysis showed that the terms of negative regulation of fertilization sperm egg recognition process and oocyte meiosis might be affected by elimination of ddx4 L. Furthermore we found that Sycp1 a synaptonemal complex protein involved in meiosis and fertility was dramatically decreased in the ddx4 L knockout ovaries at both mRNA and protein levels. Moreover the activities of transposable elements were analyzed based on the RNA seq data. The result showed that elimination of ddx4 L causes the derepression of DNA transposons a subclass of transposable elements in zebrafish ovaries. In conclusion the aforementioned findings indicate that the ovary specific transcript of ddx4 plays an important role in oocyte development and egg quality possibly by maintaining sycp1 expression and repressing DNA transposons. Our work provide novel insights into the functions and regulatory mechanisms of ddx4 in zebrafish oogenesis. Overall design: Ovaries were dissected from three WT and three ddx4 E4? zebrafish at 6 mpf respectively. Six total RNA samples were extracted and subjected to RNA sequencing. Differentially expressed genes DEGs and transposable elements TEs between WT and ddx4 E4? zebrafish ovaries were analyzed.   pubmed:39765722   WT ovary rep3 GSM8491758   source name:Ovary|tissue:Ovary|genotype:WT|geo loc name:missing|collection date:missing WT ovary rep3 The raw paired end reads were trimmed and quality controlled by SeqPrep https://github.com/jstjohn/SeqPrep and Sickle https://github.com/najoshi/sickle with default parameters. Then clean reads were separately aligned to zebrafish reference genome GRCz11 with orientation mode using HISAT2 http://ccb.jhu.edu/software/hisat2/index.shtml software. The mapped reads of each sample were assembled by StringTie https://ccb.jhu.edu/software/stringtie/index.shtml in a reference based approach. To identify DEGs differential expression genes between the ovaries of WT and ddx4 E4Δ zebrafish the expression level of each transcript was calculated according to the transcripts per million reads TPM method. RSEM http://deweylab.biostat.wisc.edu/rsem/ was used to quantify gene abundances. Essentially differential expression analysis was performed using the DESeq2 software. DEGs with |log2FC|>1 and Q value <= 0.05 were considered to be significantly different expressed genes. Functional enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni corrected P value ≤0.05 compared with the whole transcriptome background. Assembly: GRCz11 Supplementary files format and content: read count.txt is a tab delimited text file for read count numbers of each gene in all six samples. Ovary   Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer’s protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina San Diego CA. About 1μg of high quality total RNA samples OD260/280=1.82.2 RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.   tissue:Ovary|genotype:WT GSM8491758 GSM8491758: WT ovary rep3; Danio rerio; RNA Seq GSM8491758 r1 GSM8491758 1 Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer's protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina San Diego CA. About 1μg of high quality total RNA samples OD260/280=1.82.2 RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP529840     W3_R1.fastq.gz W3_R2.fastq.gz fastq fastq 9507568228.0 31482014.0 GSM8491758 r1 0:151 1:151 A:2403365632;C:2318225719;G:2368354059;T:2417595791;N:27027 151 151     2403365632 2318225719 2368354059 2417595791 27027 SRX25926475 SRS22513926 SRA1960397 Institute of Hydrobiology, Chinese Academy of Sciences Institute of Hydrobiology, Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era full_length random_priming unknown bulk unknown unknown   China 2024-08-31 Adult Adult Gonad Reproductive System
33667 33667 SRR30502668 SRX25926474 SRS22513925 SRP529840 PRJNA1154960 Deletion of ddx4 ovary specific transcript causes downregulation of sycp1 and derepression of DNA transposons in zebrafish ovaries GSE276129 Transcriptome Analysis Ddx4 DEAD box helicase 4 is a well established marker gene for early stage germlines and is required for the development of germ cells. Alternative splicing of ddx4 produces a long transcript that is exclusively expressed in zebrafish ovaries. The function of this ovary specific transcript ddx4 L remains unclear. In this study using the ddx4 L knockout zebrafish model we found that elimination of ddx4 L results in a decrease in fertilization rate and in the number of mature eggs laid by the female mutants. Transcriptome analysis was performed to identify the underlying changes of gene expression between WT and ddx4 L knockout ovaries. A total of 1134 differentially expressed genes were identified of which 524 were upregulated and 610 were downregulated. Functional enrichment analysis showed that the terms of negative regulation of fertilization sperm egg recognition process and oocyte meiosis might be affected by elimination of ddx4 L. Furthermore we found that Sycp1 a synaptonemal complex protein involved in meiosis and fertility was dramatically decreased in the ddx4 L knockout ovaries at both mRNA and protein levels. Moreover the activities of transposable elements were analyzed based on the RNA seq data. The result showed that elimination of ddx4 L causes the derepression of DNA transposons a subclass of transposable elements in zebrafish ovaries. In conclusion the aforementioned findings indicate that the ovary specific transcript of ddx4 plays an important role in oocyte development and egg quality possibly by maintaining sycp1 expression and repressing DNA transposons. Our work provide novel insights into the functions and regulatory mechanisms of ddx4 in zebrafish oogenesis. Overall design: Ovaries were dissected from three WT and three ddx4 E4? zebrafish at 6 mpf respectively. Six total RNA samples were extracted and subjected to RNA sequencing. Differentially expressed genes DEGs and transposable elements TEs between WT and ddx4 E4? zebrafish ovaries were analyzed.   pubmed:39765722   WT ovary rep2 GSM8491757   source name:Ovary|tissue:Ovary|genotype:WT|geo loc name:missing|collection date:missing WT ovary rep2 The raw paired end reads were trimmed and quality controlled by SeqPrep https://github.com/jstjohn/SeqPrep and Sickle https://github.com/najoshi/sickle with default parameters. Then clean reads were separately aligned to zebrafish reference genome GRCz11 with orientation mode using HISAT2 http://ccb.jhu.edu/software/hisat2/index.shtml software. The mapped reads of each sample were assembled by StringTie https://ccb.jhu.edu/software/stringtie/index.shtml in a reference based approach. To identify DEGs differential expression genes between the ovaries of WT and ddx4 E4Δ zebrafish the expression level of each transcript was calculated according to the transcripts per million reads TPM method. RSEM http://deweylab.biostat.wisc.edu/rsem/ was used to quantify gene abundances. Essentially differential expression analysis was performed using the DESeq2 software. DEGs with |log2FC|>1 and Q value <= 0.05 were considered to be significantly different expressed genes. Functional enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni corrected P value ≤0.05 compared with the whole transcriptome background. Assembly: GRCz11 Supplementary files format and content: read count.txt is a tab delimited text file for read count numbers of each gene in all six samples. Ovary   Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer’s protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina San Diego CA. About 1μg of high quality total RNA samples OD260/280=1.82.2 RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.   tissue:Ovary|genotype:WT GSM8491757 GSM8491757: WT ovary rep2; Danio rerio; RNA Seq GSM8491757 r1 GSM8491757 1 Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer's protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina San Diego CA. About 1μg of high quality total RNA samples OD260/280=1.82.2 RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP529840     W2_R1.fastq.gz W2_R2.fastq.gz fastq fastq 8515265084.0 28196242.0 GSM8491757 r1 0:151 1:151 A:2152677268;C:2074877248;G:2122308956;T:2165377885;N:23727 151 151     2152677268 2074877248 2122308956 2165377885 23727 SRX25926474 SRS22513925 SRA1960397 Institute of Hydrobiology, Chinese Academy of Sciences Institute of Hydrobiology, Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era full_length random_priming unknown bulk unknown unknown   China 2024-08-31 Adult Adult Gonad Reproductive System
33668 33668 SRR30502669 SRX25926473 SRS22513924 SRP529840 PRJNA1154960 Deletion of ddx4 ovary specific transcript causes downregulation of sycp1 and derepression of DNA transposons in zebrafish ovaries GSE276129 Transcriptome Analysis Ddx4 DEAD box helicase 4 is a well established marker gene for early stage germlines and is required for the development of germ cells. Alternative splicing of ddx4 produces a long transcript that is exclusively expressed in zebrafish ovaries. The function of this ovary specific transcript ddx4 L remains unclear. In this study using the ddx4 L knockout zebrafish model we found that elimination of ddx4 L results in a decrease in fertilization rate and in the number of mature eggs laid by the female mutants. Transcriptome analysis was performed to identify the underlying changes of gene expression between WT and ddx4 L knockout ovaries. A total of 1134 differentially expressed genes were identified of which 524 were upregulated and 610 were downregulated. Functional enrichment analysis showed that the terms of negative regulation of fertilization sperm egg recognition process and oocyte meiosis might be affected by elimination of ddx4 L. Furthermore we found that Sycp1 a synaptonemal complex protein involved in meiosis and fertility was dramatically decreased in the ddx4 L knockout ovaries at both mRNA and protein levels. Moreover the activities of transposable elements were analyzed based on the RNA seq data. The result showed that elimination of ddx4 L causes the derepression of DNA transposons a subclass of transposable elements in zebrafish ovaries. In conclusion the aforementioned findings indicate that the ovary specific transcript of ddx4 plays an important role in oocyte development and egg quality possibly by maintaining sycp1 expression and repressing DNA transposons. Our work provide novel insights into the functions and regulatory mechanisms of ddx4 in zebrafish oogenesis. Overall design: Ovaries were dissected from three WT and three ddx4 E4? zebrafish at 6 mpf respectively. Six total RNA samples were extracted and subjected to RNA sequencing. Differentially expressed genes DEGs and transposable elements TEs between WT and ddx4 E4? zebrafish ovaries were analyzed.   pubmed:39765722   WT ovary rep1 GSM8491756   source name:Ovary|tissue:Ovary|genotype:WT|geo loc name:missing|collection date:missing WT ovary rep1 The raw paired end reads were trimmed and quality controlled by SeqPrep https://github.com/jstjohn/SeqPrep and Sickle https://github.com/najoshi/sickle with default parameters. Then clean reads were separately aligned to zebrafish reference genome GRCz11 with orientation mode using HISAT2 http://ccb.jhu.edu/software/hisat2/index.shtml software. The mapped reads of each sample were assembled by StringTie https://ccb.jhu.edu/software/stringtie/index.shtml in a reference based approach. To identify DEGs differential expression genes between the ovaries of WT and ddx4 E4Δ zebrafish the expression level of each transcript was calculated according to the transcripts per million reads TPM method. RSEM http://deweylab.biostat.wisc.edu/rsem/ was used to quantify gene abundances. Essentially differential expression analysis was performed using the DESeq2 software. DEGs with |log2FC|>1 and Q value <= 0.05 were considered to be significantly different expressed genes. Functional enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni corrected P value ≤0.05 compared with the whole transcriptome background. Assembly: GRCz11 Supplementary files format and content: read count.txt is a tab delimited text file for read count numbers of each gene in all six samples. Ovary   Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer’s protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina San Diego CA. About 1μg of high quality total RNA samples OD260/280=1.82.2 RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.   tissue:Ovary|genotype:WT GSM8491756 GSM8491756: WT ovary rep1; Danio rerio; RNA Seq GSM8491756 r1 GSM8491756 1 Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer's protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina San Diego CA. About 1μg of high quality total RNA samples OD260/280=1.82.2 RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP529840     W1_R1.fastq.gz W1_R2.fastq.gz fastq fastq 8347159200.0 27639600.0 GSM8491756 r1 0:151 1:151 A:2109928092;C:2033967699;G:2079802211;T:2123438464;N:22734 151 151     2109928092 2033967699 2079802211 2123438464 22734 SRX25926473 SRS22513924 SRA1960397 Institute of Hydrobiology, Chinese Academy of Sciences Institute of Hydrobiology, Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era full_length random_priming unknown bulk unknown unknown   China 2024-08-31 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
38055 38055 SRR1524249 SRX661014 SRS665988 SRP044781 PRJNA255848 Danio rerio Transcriptome PRJNA255848 Transcriptome Analysis Transcriptome analysis of 12 zebrafish tissues parent bioproject:PRJNA255979 pubmed:27189481 Zebrafish testis Zebrafish testis F Dr 10   strain:AB|age:5 month|biomaterial provider:INRA|sex:male|tissue:Testis|BioSampleModel:Model organism or animal                 Zebrafish testis F Dr 10 F Dr 10 Total RNA was qualified using an Agilent BioAnalyzer and 1 µg was used for polyA selection and library construction with Illumina's TruSeq stranded total RNA sample preparation kit according to the manufacturer's instructions TruSeq stranded total RNA SamplePrep Guide RevC     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP044781     F_Dr_10_CAGATC_L003_R2.fastq.gz F_Dr_10_CAGATC_L003_R1.fastq.gz fastq fastq 11979537200.0 59897686.0 F Dr 10 files 0:100 1:100 A:3163301263;C:2775393678;G:2795402967;T:3125382350;N:120056942 100 100     3163301263 2775393678 2795402967 3125382350 120056942 SRX661014 SRS665988 SRA176464 INRA|Fish Physiology and Genomics INRA PhyloFish 2 0.86011 0.88922 0.11073 0.11591 0.67359 0.67596 0.4986 0.50073 100 100 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   France 2014-07-25 Adult Adult Gonad Reproductive System
38056 38056 SRR1524248 SRX661013 SRS665989 SRP044781 PRJNA255848 Danio rerio Transcriptome PRJNA255848 Transcriptome Analysis Transcriptome analysis of 12 zebrafish tissues parent bioproject:PRJNA255979 pubmed:27189481 Zebrafish ovary Zebrafish ovary F Dr 1   strain:AB|age:5 month|biomaterial provider:INRA|sex:female|tissue:Ovary|BioSampleModel:Model organism or animal                 Zebrafish ovary F Dr 1 F Dr 1 Total RNA was qualified using an Agilent BioAnalyzer and 1 µg was used for polyA selection and library construction with Illumina's TruSeq stranded total RNA sample preparation kit according to the manufacturer's instructions TruSeq stranded total RNA SamplePrep Guide RevC     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP044781     F_Dr_1_ATCACG_L008_R2.fastq.gz F_Dr_1_ATCACG_L008_R1.fastq.gz fastq fastq 4405297200.0 22026486.0 F Dr 1 files 0:100 1:100 A:1143385640;C:1055537748;G:1050116650;T:1145226897;N:11030265 100 100     1143385640 1055537748 1050116650 1145226897 11030265 SRX661013 SRS665989 SRA176464 INRA|Fish Physiology and Genomics INRA PhyloFish 2 0.9327 0.93326 0.01849 0.01893 0.76773 0.77029 0.47583 0.47445 100 100 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   France 2015-07-24 Adult Adult Gonad Reproductive System
39859 39859 SRR2177445 SRX1161440 SRS1042403 SRP062685 PRJNA293388 Danio rerio Transcriptome or Gene expression PRJNA293388 Other Differential Expression between testis and ovary in two months of fish     Differential Expression between testis and ovary in two months of fish   T   isolate:Danio rerio testis|age:2 months|sex:male|tissue:testis|biomaterial provider:Department of Biology and Biotechnology|BioSampleModel:Model organism or animal                 Danio rerio transcriptome sequencing T 1 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062685     T_R1.fastq.gz T_R2.fastq.gz fastq fastq 7616200600.0 38081003.0 T 0:100 1:100 A:2018574469;C:1797807061;G:1758967564;T:2040674119;N:177387 100 100     2018574469 1797807061 1758967564 2040674119 177387 SRX1161440 SRS1042403 SRA290385 Shanghai Ocean University|Department of Biology and Biotechnology Shanghai Ocean University 2 0.946 0.93541 0.0936 0.09298 0.62929 0.63343 0.49102 0.48875 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2016-08-01 Juvenile Juvenile Gonad Reproductive System
39860 39860 SRR2177444 SRX1161439 SRS1042402 SRP062685 PRJNA293388 Danio rerio Transcriptome or Gene expression PRJNA293388 Other Differential Expression between testis and ovary in two months of fish     Differential Expression between testis and ovary in two months of fish   O   isolate:Danio rerio ovary|age:2 months|sex:female|tissue:ovary|biomaterial provider:Department of Biology and Biotechnology|BioSampleModel:Model organism or animal                 Danio rerio transcriptome sequencing O 1 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062685     O_R1.fastq.gz O_R2.fastq.gz fastq fastq 6602802000.0 33014010.0 O 0:100 1:100 A:1705654028;C:1598182709;G:1559109823;T:1739704779;N:150661 100 100     1705654028 1598182709 1559109823 1739704779 150661 SRX1161439 SRS1042402 SRA290385 Shanghai Ocean University|Department of Biology and Biotechnology Shanghai Ocean University 2 0.94263 0.93359 0.02018 0.02017 0.74842 0.75087 0.47643 0.47578 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2016-08-01 Juvenile Juvenile Gonad Reproductive System
39861 39861 SRR2177451 SRX1161443 SRS1042406 SRP062686 PRJNA293487 Danio rerio Digital Gene Expression Sequencing PRJNA293487 Other Differential expression between WT and CD82a from Morpholino treated embyro of Danio rerio     Differential expression between WT and CD82a Morpholino treated embyro of Danio rerio   control   isolate:Danio rerio embyro|dev stage:embyro|sex:missing|tissue:ovary|BioSampleModel:Model organism or animal                 Danio rerio Digital Gene Expression Sequencing control 1 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062686     control_R1.fastq.gz control_R2.fastq.gz fastq fastq 1381289200.0 6906446.0 control 0:100 1:100 A:362182510;C:331106787;G:327770778;T:360198909;N:30216 100 100     362182510 331106787 327770778 360198909 30216 SRX1161443 SRS1042406 SRA290388 Shanghai Ocean University|Department of Biology and Biotechnology Shanghai Ocean University 2 0.95634 0.95016 0.06922 0.06922 0.7013 0.70368 0.46985 0.47013 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2016-08-21 Undetermined Embryo Gonad Reproductive System
39862 39862 SRR2177447 SRX1161442 SRS1042404 SRP062686 PRJNA293487 Danio rerio Digital Gene Expression Sequencing PRJNA293487 Other Differential expression between WT and CD82a from Morpholino treated embyro of Danio rerio     Differential expression between WT and CD82a Morpholino treated embyro of Danio rerio   ATG   isolate:Danio rerio embyro|dev stage:embyro|sex:missing|tissue:ovary|BioSampleModel:Model organism or animal                 Danio rerio Digital Gene Expression Sequencing ATG 1 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062686     ATG_R1.fastq.gz ATG_R2.fastq.gz fastq fastq 1278088000.0 6390440.0 ATG 0:100 1:100 A:335532626;C:305947212;G:302508524;T:334072046;N:27592 100 100     335532626 305947212 302508524 334072046 27592 SRX1161442 SRS1042404 SRA290388 Shanghai Ocean University|Department of Biology and Biotechnology Shanghai Ocean University 2 0.95535 0.94653 0.07264 0.07271 0.70402 0.7082 0.46712 0.46962 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2016-08-21 Undetermined Embryo Gonad Reproductive System
39938 39938 SRR2541826 SRX1297648 SRS1095788 SRP064360 PRJNA297460 Female Reproductive Impacts of Dietary Methylmercury in Yellow Perch Perca flavescens and Zebrafish Danio rerio GSE73615 Transcriptome Analysis This study sought to evaluate the effects of dietary MeHg exposure on adult female yellow perch Perca flavescens and zebrafish Danio rerio reproduction by relating controlled exposures with subsequent reproductive effects. Yellow perch were used in the study for their socioeconomic and ecological importance within the Great Lakes basin and the use of zebrafish allowed for a detailed analysis of the molecular effects of MeHg. MeHg exposures at environmentally relevant levels were done in zebrafish for a full life cycle mimicking a realistic exposure scenario and in adult yellow perch for twenty weeks capturing early seasonal ovarian development. In zebrafish several genes involved in reproductive processes were shown to be dysregulated by RNA seq and QPCR but no significant phenotypic or physiological changes were observed with ovarian staging fecundity or embryo mortality. Yellow perch did not appear to be affected by MeHg either at a molecular level as assessed by QPCR of eight genes in the pituitary liver and ovary tissue or a physiological level as seen with ovarian somatic index circulating estradiol and ovarian staging. Lack of impact in yellow perch limits the usefulness of zebrafish as a model and suggests that the reproductive sensitivity to environmentally relevant levels of MeHg differs between yellow perch and zebrafish. Overall design: 12 samples of total RNA isolated from adult zebrafish ovaries were analyzed. Each exposure group 1 3 and 10 ppm MeHg had three replicates as did the vehicle control. Each sample was comprised of pooled total RNA of up to 6 individual fish.   pubmed:29272799   zfish 10ppm R3 GSM1899557   source name:ovary|tissue:ovary|strain:EK|mehg exposure:10 ppm zfish 10ppm R3 Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat The alignment output from TopHat was converted into a transcriptome using Cufflinks v. 2.2.1 and alignment data was confirmed using RNAseQC against the Zv9 reference transcriptome of zebrafish Sample specific transcriptomes were assembled using Cufflinks with the Zv9 transcriptome as a reference to correct fragment biases by better identifying the start/end point of each exon Transcriptomes from each sample were merged into an ovary specific transcriptome using Cuffmerge Differential expression was conducted with Cuffdiff using pooled dispersion geometric normalization and the merged ovary transcriptome. Genome build: UCSC Zv9 Supplementary files format and content: Cuffdiff outputs FPKM files which show expression values. Included in ovary.zip ovary Ovaries were flash frozen in RNA later and placed on dry ice immediately post dissection until proper storage at 80C. High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Adult EK female zebrafish were exposed to MeHg 0 1 3 or 10 ppm with ethanol as the vehicle for an entire life cycle starting with maternal exposure. Fish were exposed until euthanized. tissue:ovary|strain:EK|mehg exposure:10 ppm GSM1899557 GSM1899557: zfish 10ppm R3; Danio rerio; RNA Seq GSM1899557   1 High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. GEO Accession:GSM1899557 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP064360     run448.R3-10ppm_AGTTCC_L003_R1.fastq.gz run448.R3-10ppm_AGTTCC_L003_R2.fastq.gz fastq fastq 1525386436.0 7551418.0 GSM1899557 r1 0:101 1:101 A:413205816;C:348712240;G:344513814;T:414908557;N:4046009 101 101     413205816 348712240 344513814 414908557 4046009 SRX1297648 SRS1095788 SRA302185 GEO School of Freshwater Sciences, University of Wisconsin-Milwaukee 2 0.92358 0.92408 0.02862 0.02882 0.73898 0.74014 0.46916 0.46537 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2015-09-30 Adult Adult Gonad Reproductive System
39939 39939 SRR2541825 SRX1297647 SRS1095789 SRP064360 PRJNA297460 Female Reproductive Impacts of Dietary Methylmercury in Yellow Perch Perca flavescens and Zebrafish Danio rerio GSE73615 Transcriptome Analysis This study sought to evaluate the effects of dietary MeHg exposure on adult female yellow perch Perca flavescens and zebrafish Danio rerio reproduction by relating controlled exposures with subsequent reproductive effects. Yellow perch were used in the study for their socioeconomic and ecological importance within the Great Lakes basin and the use of zebrafish allowed for a detailed analysis of the molecular effects of MeHg. MeHg exposures at environmentally relevant levels were done in zebrafish for a full life cycle mimicking a realistic exposure scenario and in adult yellow perch for twenty weeks capturing early seasonal ovarian development. In zebrafish several genes involved in reproductive processes were shown to be dysregulated by RNA seq and QPCR but no significant phenotypic or physiological changes were observed with ovarian staging fecundity or embryo mortality. Yellow perch did not appear to be affected by MeHg either at a molecular level as assessed by QPCR of eight genes in the pituitary liver and ovary tissue or a physiological level as seen with ovarian somatic index circulating estradiol and ovarian staging. Lack of impact in yellow perch limits the usefulness of zebrafish as a model and suggests that the reproductive sensitivity to environmentally relevant levels of MeHg differs between yellow perch and zebrafish. Overall design: 12 samples of total RNA isolated from adult zebrafish ovaries were analyzed. Each exposure group 1 3 and 10 ppm MeHg had three replicates as did the vehicle control. Each sample was comprised of pooled total RNA of up to 6 individual fish.   pubmed:29272799   zfish 10ppm R2 GSM1899556   source name:ovary|tissue:ovary|strain:EK|mehg exposure:10 ppm zfish 10ppm R2 Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat The alignment output from TopHat was converted into a transcriptome using Cufflinks v. 2.2.1 and alignment data was confirmed using RNAseQC against the Zv9 reference transcriptome of zebrafish Sample specific transcriptomes were assembled using Cufflinks with the Zv9 transcriptome as a reference to correct fragment biases by better identifying the start/end point of each exon Transcriptomes from each sample were merged into an ovary specific transcriptome using Cuffmerge Differential expression was conducted with Cuffdiff using pooled dispersion geometric normalization and the merged ovary transcriptome. Genome build: UCSC Zv9 Supplementary files format and content: Cuffdiff outputs FPKM files which show expression values. Included in ovary.zip ovary Ovaries were flash frozen in RNA later and placed on dry ice immediately post dissection until proper storage at 80C. High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Adult EK female zebrafish were exposed to MeHg 0 1 3 or 10 ppm with ethanol as the vehicle for an entire life cycle starting with maternal exposure. Fish were exposed until euthanized. tissue:ovary|strain:EK|mehg exposure:10 ppm GSM1899556 GSM1899556: zfish 10ppm R2; Danio rerio; RNA Seq GSM1899556   1 High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. GEO Accession:GSM1899556 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP064360     run448.R2-10ppm_TAGCTT_L003_R2.fastq.gz run448.R2-10ppm_TAGCTT_L003_R1.fastq.gz fastq fastq 2061452016.0 10205208.0 GSM1899556 r1 0:101 1:101 A:557864095;C:473236506;G:465541615;T:559336990;N:5472810 101 101     557864095 473236506 465541615 559336990 5472810 SRX1297647 SRS1095789 SRA302185 GEO School of Freshwater Sciences, University of Wisconsin-Milwaukee 2 0.91738 0.91678 0.02538 0.0255 0.74454 0.74546 0.45899 0.4623 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2015-09-30 Adult Adult Gonad Reproductive System
39940 39940 SRR2541824 SRX1297646 SRS1095790 SRP064360 PRJNA297460 Female Reproductive Impacts of Dietary Methylmercury in Yellow Perch Perca flavescens and Zebrafish Danio rerio GSE73615 Transcriptome Analysis This study sought to evaluate the effects of dietary MeHg exposure on adult female yellow perch Perca flavescens and zebrafish Danio rerio reproduction by relating controlled exposures with subsequent reproductive effects. Yellow perch were used in the study for their socioeconomic and ecological importance within the Great Lakes basin and the use of zebrafish allowed for a detailed analysis of the molecular effects of MeHg. MeHg exposures at environmentally relevant levels were done in zebrafish for a full life cycle mimicking a realistic exposure scenario and in adult yellow perch for twenty weeks capturing early seasonal ovarian development. In zebrafish several genes involved in reproductive processes were shown to be dysregulated by RNA seq and QPCR but no significant phenotypic or physiological changes were observed with ovarian staging fecundity or embryo mortality. Yellow perch did not appear to be affected by MeHg either at a molecular level as assessed by QPCR of eight genes in the pituitary liver and ovary tissue or a physiological level as seen with ovarian somatic index circulating estradiol and ovarian staging. Lack of impact in yellow perch limits the usefulness of zebrafish as a model and suggests that the reproductive sensitivity to environmentally relevant levels of MeHg differs between yellow perch and zebrafish. Overall design: 12 samples of total RNA isolated from adult zebrafish ovaries were analyzed. Each exposure group 1 3 and 10 ppm MeHg had three replicates as did the vehicle control. Each sample was comprised of pooled total RNA of up to 6 individual fish.   pubmed:29272799   zfish 10ppm R1 GSM1899555   source name:ovary|tissue:ovary|strain:EK|mehg exposure:10 ppm zfish 10ppm R1 Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat The alignment output from TopHat was converted into a transcriptome using Cufflinks v. 2.2.1 and alignment data was confirmed using RNAseQC against the Zv9 reference transcriptome of zebrafish Sample specific transcriptomes were assembled using Cufflinks with the Zv9 transcriptome as a reference to correct fragment biases by better identifying the start/end point of each exon Transcriptomes from each sample were merged into an ovary specific transcriptome using Cuffmerge Differential expression was conducted with Cuffdiff using pooled dispersion geometric normalization and the merged ovary transcriptome. Genome build: UCSC Zv9 Supplementary files format and content: Cuffdiff outputs FPKM files which show expression values. Included in ovary.zip ovary Ovaries were flash frozen in RNA later and placed on dry ice immediately post dissection until proper storage at 80C. High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Adult EK female zebrafish were exposed to MeHg 0 1 3 or 10 ppm with ethanol as the vehicle for an entire life cycle starting with maternal exposure. Fish were exposed until euthanized. tissue:ovary|strain:EK|mehg exposure:10 ppm GSM1899555 GSM1899555: zfish 10ppm R1; Danio rerio; RNA Seq GSM1899555   1 High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. GEO Accession:GSM1899555 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP064360     run448.R1-10ppm_ACAGTG_L003_R1.fastq.gz run448.R1-10ppm_ACAGTG_L003_R2.fastq.gz fastq fastq 1475061368.0 7302284.0 GSM1899555 r1 0:101 1:101 A:403049360;C:333664323;G:329533549;T:405032089;N:3782047 101 101     403049360 333664323 329533549 405032089 3782047 SRX1297646 SRS1095790 SRA302185 GEO School of Freshwater Sciences, University of Wisconsin-Milwaukee 2 0.92141 0.92125 0.02731 0.02754 0.74568 0.74665 0.44728 0.44698 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2015-09-30 Adult Adult Gonad Reproductive System
39941 39941 SRR2541823 SRX1297645 SRS1095791 SRP064360 PRJNA297460 Female Reproductive Impacts of Dietary Methylmercury in Yellow Perch Perca flavescens and Zebrafish Danio rerio GSE73615 Transcriptome Analysis This study sought to evaluate the effects of dietary MeHg exposure on adult female yellow perch Perca flavescens and zebrafish Danio rerio reproduction by relating controlled exposures with subsequent reproductive effects. Yellow perch were used in the study for their socioeconomic and ecological importance within the Great Lakes basin and the use of zebrafish allowed for a detailed analysis of the molecular effects of MeHg. MeHg exposures at environmentally relevant levels were done in zebrafish for a full life cycle mimicking a realistic exposure scenario and in adult yellow perch for twenty weeks capturing early seasonal ovarian development. In zebrafish several genes involved in reproductive processes were shown to be dysregulated by RNA seq and QPCR but no significant phenotypic or physiological changes were observed with ovarian staging fecundity or embryo mortality. Yellow perch did not appear to be affected by MeHg either at a molecular level as assessed by QPCR of eight genes in the pituitary liver and ovary tissue or a physiological level as seen with ovarian somatic index circulating estradiol and ovarian staging. Lack of impact in yellow perch limits the usefulness of zebrafish as a model and suggests that the reproductive sensitivity to environmentally relevant levels of MeHg differs between yellow perch and zebrafish. Overall design: 12 samples of total RNA isolated from adult zebrafish ovaries were analyzed. Each exposure group 1 3 and 10 ppm MeHg had three replicates as did the vehicle control. Each sample was comprised of pooled total RNA of up to 6 individual fish.   pubmed:29272799   zfish 3ppm R3 GSM1899554   source name:ovary|tissue:ovary|strain:EK|mehg exposure:3 ppm zfish 3ppm R3 Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat The alignment output from TopHat was converted into a transcriptome using Cufflinks v. 2.2.1 and alignment data was confirmed using RNAseQC against the Zv9 reference transcriptome of zebrafish Sample specific transcriptomes were assembled using Cufflinks with the Zv9 transcriptome as a reference to correct fragment biases by better identifying the start/end point of each exon Transcriptomes from each sample were merged into an ovary specific transcriptome using Cuffmerge Differential expression was conducted with Cuffdiff using pooled dispersion geometric normalization and the merged ovary transcriptome. Genome build: UCSC Zv9 Supplementary files format and content: Cuffdiff outputs FPKM files which show expression values. Included in ovary.zip ovary Ovaries were flash frozen in RNA later and placed on dry ice immediately post dissection until proper storage at 80C. High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Adult EK female zebrafish were exposed to MeHg 0 1 3 or 10 ppm with ethanol as the vehicle for an entire life cycle starting with maternal exposure. Fish were exposed until euthanized. tissue:ovary|strain:EK|mehg exposure:3 ppm GSM1899554 GSM1899554: zfish 3ppm R3; Danio rerio; RNA Seq GSM1899554   1 High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. GEO Accession:GSM1899554 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP064360     run448.R3-3ppm_AGTCAA_L003_R1.fastq.gz run448.R3-3ppm_AGTCAA_L003_R2.fastq.gz fastq fastq 1898187940.0 9396970.0 GSM1899554 r1 0:101 1:101 A:507383899;C:441122897;G:435564865;T:509043014;N:5073265 101 101     507383899 441122897 435564865 509043014 5073265 SRX1297645 SRS1095791 SRA302185 GEO School of Freshwater Sciences, University of Wisconsin-Milwaukee 2 0.91769 0.91792 0.02307 0.0232 0.75004 0.75085 0.45931 0.46055 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2015-09-30 Adult Adult Gonad Reproductive System
39942 39942 SRR2541822 SRX1297644 SRS1095792 SRP064360 PRJNA297460 Female Reproductive Impacts of Dietary Methylmercury in Yellow Perch Perca flavescens and Zebrafish Danio rerio GSE73615 Transcriptome Analysis This study sought to evaluate the effects of dietary MeHg exposure on adult female yellow perch Perca flavescens and zebrafish Danio rerio reproduction by relating controlled exposures with subsequent reproductive effects. Yellow perch were used in the study for their socioeconomic and ecological importance within the Great Lakes basin and the use of zebrafish allowed for a detailed analysis of the molecular effects of MeHg. MeHg exposures at environmentally relevant levels were done in zebrafish for a full life cycle mimicking a realistic exposure scenario and in adult yellow perch for twenty weeks capturing early seasonal ovarian development. In zebrafish several genes involved in reproductive processes were shown to be dysregulated by RNA seq and QPCR but no significant phenotypic or physiological changes were observed with ovarian staging fecundity or embryo mortality. Yellow perch did not appear to be affected by MeHg either at a molecular level as assessed by QPCR of eight genes in the pituitary liver and ovary tissue or a physiological level as seen with ovarian somatic index circulating estradiol and ovarian staging. Lack of impact in yellow perch limits the usefulness of zebrafish as a model and suggests that the reproductive sensitivity to environmentally relevant levels of MeHg differs between yellow perch and zebrafish. Overall design: 12 samples of total RNA isolated from adult zebrafish ovaries were analyzed. Each exposure group 1 3 and 10 ppm MeHg had three replicates as did the vehicle control. Each sample was comprised of pooled total RNA of up to 6 individual fish.   pubmed:29272799   zfish 3ppm R2 GSM1899553   source name:ovary|tissue:ovary|strain:EK|mehg exposure:3 ppm zfish 3ppm R2 Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat The alignment output from TopHat was converted into a transcriptome using Cufflinks v. 2.2.1 and alignment data was confirmed using RNAseQC against the Zv9 reference transcriptome of zebrafish Sample specific transcriptomes were assembled using Cufflinks with the Zv9 transcriptome as a reference to correct fragment biases by better identifying the start/end point of each exon Transcriptomes from each sample were merged into an ovary specific transcriptome using Cuffmerge Differential expression was conducted with Cuffdiff using pooled dispersion geometric normalization and the merged ovary transcriptome. Genome build: UCSC Zv9 Supplementary files format and content: Cuffdiff outputs FPKM files which show expression values. Included in ovary.zip ovary Ovaries were flash frozen in RNA later and placed on dry ice immediately post dissection until proper storage at 80C. High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Adult EK female zebrafish were exposed to MeHg 0 1 3 or 10 ppm with ethanol as the vehicle for an entire life cycle starting with maternal exposure. Fish were exposed until euthanized. tissue:ovary|strain:EK|mehg exposure:3 ppm GSM1899553 GSM1899553: zfish 3ppm R2; Danio rerio; RNA Seq GSM1899553   1 High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. GEO Accession:GSM1899553 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP064360     run448.R2-3ppm_ACTTGA_L003_R1.fastq.gz run448.R2-3ppm_ACTTGA_L003_R2.fastq.gz fastq fastq 1880260844.0 9308222.0 GSM1899553 r1 0:101 1:101 A:498380487;C:441827552;G:435112269;T:499919155;N:5021381 101 101     498380487 441827552 435112269 499919155 5021381 SRX1297644 SRS1095792 SRA302185 GEO School of Freshwater Sciences, University of Wisconsin-Milwaukee 2 0.92603 0.92442 0.02246 0.02276 0.74237 0.7429 0.46927 0.46745 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2015-09-30 Adult Adult Gonad Reproductive System
39943 39943 SRR2541821 SRX1297643 SRS1095793 SRP064360 PRJNA297460 Female Reproductive Impacts of Dietary Methylmercury in Yellow Perch Perca flavescens and Zebrafish Danio rerio GSE73615 Transcriptome Analysis This study sought to evaluate the effects of dietary MeHg exposure on adult female yellow perch Perca flavescens and zebrafish Danio rerio reproduction by relating controlled exposures with subsequent reproductive effects. Yellow perch were used in the study for their socioeconomic and ecological importance within the Great Lakes basin and the use of zebrafish allowed for a detailed analysis of the molecular effects of MeHg. MeHg exposures at environmentally relevant levels were done in zebrafish for a full life cycle mimicking a realistic exposure scenario and in adult yellow perch for twenty weeks capturing early seasonal ovarian development. In zebrafish several genes involved in reproductive processes were shown to be dysregulated by RNA seq and QPCR but no significant phenotypic or physiological changes were observed with ovarian staging fecundity or embryo mortality. Yellow perch did not appear to be affected by MeHg either at a molecular level as assessed by QPCR of eight genes in the pituitary liver and ovary tissue or a physiological level as seen with ovarian somatic index circulating estradiol and ovarian staging. Lack of impact in yellow perch limits the usefulness of zebrafish as a model and suggests that the reproductive sensitivity to environmentally relevant levels of MeHg differs between yellow perch and zebrafish. Overall design: 12 samples of total RNA isolated from adult zebrafish ovaries were analyzed. Each exposure group 1 3 and 10 ppm MeHg had three replicates as did the vehicle control. Each sample was comprised of pooled total RNA of up to 6 individual fish.   pubmed:29272799   zfish 3ppm R1 GSM1899552   source name:ovary|tissue:ovary|strain:EK|mehg exposure:3 ppm zfish 3ppm R1 Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat The alignment output from TopHat was converted into a transcriptome using Cufflinks v. 2.2.1 and alignment data was confirmed using RNAseQC against the Zv9 reference transcriptome of zebrafish Sample specific transcriptomes were assembled using Cufflinks with the Zv9 transcriptome as a reference to correct fragment biases by better identifying the start/end point of each exon Transcriptomes from each sample were merged into an ovary specific transcriptome using Cuffmerge Differential expression was conducted with Cuffdiff using pooled dispersion geometric normalization and the merged ovary transcriptome. Genome build: UCSC Zv9 Supplementary files format and content: Cuffdiff outputs FPKM files which show expression values. Included in ovary.zip ovary Ovaries were flash frozen in RNA later and placed on dry ice immediately post dissection until proper storage at 80C. High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Adult EK female zebrafish were exposed to MeHg 0 1 3 or 10 ppm with ethanol as the vehicle for an entire life cycle starting with maternal exposure. Fish were exposed until euthanized. tissue:ovary|strain:EK|mehg exposure:3 ppm GSM1899552 GSM1899552: zfish 3ppm R1; Danio rerio; RNA Seq GSM1899552   1 High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. GEO Accession:GSM1899552 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP064360     run448.R1-3ppm_TGACCA_L003_R1.fastq.gz run448.R1-3ppm_TGACCA_L003_R2.fastq.gz fastq fastq 925049304.0 4579452.0 GSM1899552 r1 0:101 1:101 A:250171132;C:212335569;G:209416615;T:250637787;N:2488201 101 101     250171132 212335569 209416615 250637787 2488201 SRX1297643 SRS1095793 SRA302185 GEO School of Freshwater Sciences, University of Wisconsin-Milwaukee 2 0.9192 0.91889 0.02566 0.02562 0.74673 0.74694 0.46327 0.46316 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2015-09-30 Adult Adult Gonad Reproductive System
39944 39944 SRR2541820 SRX1297642 SRS1095794 SRP064360 PRJNA297460 Female Reproductive Impacts of Dietary Methylmercury in Yellow Perch Perca flavescens and Zebrafish Danio rerio GSE73615 Transcriptome Analysis This study sought to evaluate the effects of dietary MeHg exposure on adult female yellow perch Perca flavescens and zebrafish Danio rerio reproduction by relating controlled exposures with subsequent reproductive effects. Yellow perch were used in the study for their socioeconomic and ecological importance within the Great Lakes basin and the use of zebrafish allowed for a detailed analysis of the molecular effects of MeHg. MeHg exposures at environmentally relevant levels were done in zebrafish for a full life cycle mimicking a realistic exposure scenario and in adult yellow perch for twenty weeks capturing early seasonal ovarian development. In zebrafish several genes involved in reproductive processes were shown to be dysregulated by RNA seq and QPCR but no significant phenotypic or physiological changes were observed with ovarian staging fecundity or embryo mortality. Yellow perch did not appear to be affected by MeHg either at a molecular level as assessed by QPCR of eight genes in the pituitary liver and ovary tissue or a physiological level as seen with ovarian somatic index circulating estradiol and ovarian staging. Lack of impact in yellow perch limits the usefulness of zebrafish as a model and suggests that the reproductive sensitivity to environmentally relevant levels of MeHg differs between yellow perch and zebrafish. Overall design: 12 samples of total RNA isolated from adult zebrafish ovaries were analyzed. Each exposure group 1 3 and 10 ppm MeHg had three replicates as did the vehicle control. Each sample was comprised of pooled total RNA of up to 6 individual fish.   pubmed:29272799   zfish 1ppm R3 GSM1899551   source name:ovary|tissue:ovary|strain:EK|mehg exposure:1 ppm zfish 1ppm R3 Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat The alignment output from TopHat was converted into a transcriptome using Cufflinks v. 2.2.1 and alignment data was confirmed using RNAseQC against the Zv9 reference transcriptome of zebrafish Sample specific transcriptomes were assembled using Cufflinks with the Zv9 transcriptome as a reference to correct fragment biases by better identifying the start/end point of each exon Transcriptomes from each sample were merged into an ovary specific transcriptome using Cuffmerge Differential expression was conducted with Cuffdiff using pooled dispersion geometric normalization and the merged ovary transcriptome. Genome build: UCSC Zv9 Supplementary files format and content: Cuffdiff outputs FPKM files which show expression values. Included in ovary.zip ovary Ovaries were flash frozen in RNA later and placed on dry ice immediately post dissection until proper storage at 80C. High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Adult EK female zebrafish were exposed to MeHg 0 1 3 or 10 ppm with ethanol as the vehicle for an entire life cycle starting with maternal exposure. Fish were exposed until euthanized. tissue:ovary|strain:EK|mehg exposure:1 ppm GSM1899551 GSM1899551: zfish 1ppm R3; Danio rerio; RNA Seq GSM1899551   1 High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. GEO Accession:GSM1899551 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP064360     run448.R3-1ppm_CTTGTA_L003_R1.fastq.gz run448.R3-1ppm_CTTGTA_L003_R2.fastq.gz fastq fastq 1556667752.0 7706276.0 GSM1899551 r1 0:101 1:101 A:412970247;C:364917642;G:360505525;T:414110434;N:4163904 101 101     412970247 364917642 360505525 414110434 4163904 SRX1297642 SRS1095794 SRA302185 GEO School of Freshwater Sciences, University of Wisconsin-Milwaukee 2 0.92592 0.92449 0.02137 0.02149 0.74761 0.74984 0.45524 0.46255 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2015-09-30 Adult Adult Gonad Reproductive System
39945 39945 SRR2541819 SRX1297641 SRS1095795 SRP064360 PRJNA297460 Female Reproductive Impacts of Dietary Methylmercury in Yellow Perch Perca flavescens and Zebrafish Danio rerio GSE73615 Transcriptome Analysis This study sought to evaluate the effects of dietary MeHg exposure on adult female yellow perch Perca flavescens and zebrafish Danio rerio reproduction by relating controlled exposures with subsequent reproductive effects. Yellow perch were used in the study for their socioeconomic and ecological importance within the Great Lakes basin and the use of zebrafish allowed for a detailed analysis of the molecular effects of MeHg. MeHg exposures at environmentally relevant levels were done in zebrafish for a full life cycle mimicking a realistic exposure scenario and in adult yellow perch for twenty weeks capturing early seasonal ovarian development. In zebrafish several genes involved in reproductive processes were shown to be dysregulated by RNA seq and QPCR but no significant phenotypic or physiological changes were observed with ovarian staging fecundity or embryo mortality. Yellow perch did not appear to be affected by MeHg either at a molecular level as assessed by QPCR of eight genes in the pituitary liver and ovary tissue or a physiological level as seen with ovarian somatic index circulating estradiol and ovarian staging. Lack of impact in yellow perch limits the usefulness of zebrafish as a model and suggests that the reproductive sensitivity to environmentally relevant levels of MeHg differs between yellow perch and zebrafish. Overall design: 12 samples of total RNA isolated from adult zebrafish ovaries were analyzed. Each exposure group 1 3 and 10 ppm MeHg had three replicates as did the vehicle control. Each sample was comprised of pooled total RNA of up to 6 individual fish.   pubmed:29272799   zfish 1ppm R2 GSM1899550   source name:ovary|tissue:ovary|strain:EK|mehg exposure:1 ppm zfish 1ppm R2 Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat The alignment output from TopHat was converted into a transcriptome using Cufflinks v. 2.2.1 and alignment data was confirmed using RNAseQC against the Zv9 reference transcriptome of zebrafish Sample specific transcriptomes were assembled using Cufflinks with the Zv9 transcriptome as a reference to correct fragment biases by better identifying the start/end point of each exon Transcriptomes from each sample were merged into an ovary specific transcriptome using Cuffmerge Differential expression was conducted with Cuffdiff using pooled dispersion geometric normalization and the merged ovary transcriptome. Genome build: UCSC Zv9 Supplementary files format and content: Cuffdiff outputs FPKM files which show expression values. Included in ovary.zip ovary Ovaries were flash frozen in RNA later and placed on dry ice immediately post dissection until proper storage at 80C. High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Adult EK female zebrafish were exposed to MeHg 0 1 3 or 10 ppm with ethanol as the vehicle for an entire life cycle starting with maternal exposure. Fish were exposed until euthanized. tissue:ovary|strain:EK|mehg exposure:1 ppm GSM1899550 GSM1899550: zfish 1ppm R2; Danio rerio; RNA Seq GSM1899550   1 High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. GEO Accession:GSM1899550 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP064360     run448.R2-1ppm_CAGATC_L003_R1.fastq.gz run448.R2-1ppm_CAGATC_L003_R2.fastq.gz fastq fastq 1357272138.0 6719169.0 GSM1899550 r1 0:101 1:101 A:370072564;C:307253846;G:304254621;T:372060230;N:3630877 101 101     370072564 307253846 304254621 372060230 3630877 SRX1297641 SRS1095795 SRA302185 GEO School of Freshwater Sciences, University of Wisconsin-Milwaukee 2 0.92432 0.92425 0.02923 0.02922 0.73953 0.73981 0.45918 0.45644 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2015-09-30 Adult Adult Gonad Reproductive System
39946 39946 SRR2541818 SRX1297640 SRS1095796 SRP064360 PRJNA297460 Female Reproductive Impacts of Dietary Methylmercury in Yellow Perch Perca flavescens and Zebrafish Danio rerio GSE73615 Transcriptome Analysis This study sought to evaluate the effects of dietary MeHg exposure on adult female yellow perch Perca flavescens and zebrafish Danio rerio reproduction by relating controlled exposures with subsequent reproductive effects. Yellow perch were used in the study for their socioeconomic and ecological importance within the Great Lakes basin and the use of zebrafish allowed for a detailed analysis of the molecular effects of MeHg. MeHg exposures at environmentally relevant levels were done in zebrafish for a full life cycle mimicking a realistic exposure scenario and in adult yellow perch for twenty weeks capturing early seasonal ovarian development. In zebrafish several genes involved in reproductive processes were shown to be dysregulated by RNA seq and QPCR but no significant phenotypic or physiological changes were observed with ovarian staging fecundity or embryo mortality. Yellow perch did not appear to be affected by MeHg either at a molecular level as assessed by QPCR of eight genes in the pituitary liver and ovary tissue or a physiological level as seen with ovarian somatic index circulating estradiol and ovarian staging. Lack of impact in yellow perch limits the usefulness of zebrafish as a model and suggests that the reproductive sensitivity to environmentally relevant levels of MeHg differs between yellow perch and zebrafish. Overall design: 12 samples of total RNA isolated from adult zebrafish ovaries were analyzed. Each exposure group 1 3 and 10 ppm MeHg had three replicates as did the vehicle control. Each sample was comprised of pooled total RNA of up to 6 individual fish.   pubmed:29272799   zfish 1ppm R1 GSM1899549   source name:ovary|tissue:ovary|strain:EK|mehg exposure:1 ppm zfish 1ppm R1 Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat The alignment output from TopHat was converted into a transcriptome using Cufflinks v. 2.2.1 and alignment data was confirmed using RNAseQC against the Zv9 reference transcriptome of zebrafish Sample specific transcriptomes were assembled using Cufflinks with the Zv9 transcriptome as a reference to correct fragment biases by better identifying the start/end point of each exon Transcriptomes from each sample were merged into an ovary specific transcriptome using Cuffmerge Differential expression was conducted with Cuffdiff using pooled dispersion geometric normalization and the merged ovary transcriptome. Genome build: UCSC Zv9 Supplementary files format and content: Cuffdiff outputs FPKM files which show expression values. Included in ovary.zip ovary Ovaries were flash frozen in RNA later and placed on dry ice immediately post dissection until proper storage at 80C. High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Adult EK female zebrafish were exposed to MeHg 0 1 3 or 10 ppm with ethanol as the vehicle for an entire life cycle starting with maternal exposure. Fish were exposed until euthanized. tissue:ovary|strain:EK|mehg exposure:1 ppm GSM1899549 GSM1899549: zfish 1ppm R1; Danio rerio; RNA Seq GSM1899549   1 High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. GEO Accession:GSM1899549 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP064360     run448.R1-1ppm_CGATGT_L003_R1.fastq.gz run448.R1-1ppm_CGATGT_L003_R2.fastq.gz fastq fastq 2389310540.0 11828270.0 GSM1899549 r1 0:101 1:101 A:636881481;C:557085654;G:551199582;T:638074409;N:6069414 101 101     636881481 557085654 551199582 638074409 6069414 SRX1297640 SRS1095796 SRA302185 GEO School of Freshwater Sciences, University of Wisconsin-Milwaukee 2 0.92963 0.92829 0.02114 0.02117 0.74809 0.74917 0.45534 0.45205 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2015-09-30 Adult Adult Gonad Reproductive System
39947 39947 SRR2541817 SRX1297639 SRS1095797 SRP064360 PRJNA297460 Female Reproductive Impacts of Dietary Methylmercury in Yellow Perch Perca flavescens and Zebrafish Danio rerio GSE73615 Transcriptome Analysis This study sought to evaluate the effects of dietary MeHg exposure on adult female yellow perch Perca flavescens and zebrafish Danio rerio reproduction by relating controlled exposures with subsequent reproductive effects. Yellow perch were used in the study for their socioeconomic and ecological importance within the Great Lakes basin and the use of zebrafish allowed for a detailed analysis of the molecular effects of MeHg. MeHg exposures at environmentally relevant levels were done in zebrafish for a full life cycle mimicking a realistic exposure scenario and in adult yellow perch for twenty weeks capturing early seasonal ovarian development. In zebrafish several genes involved in reproductive processes were shown to be dysregulated by RNA seq and QPCR but no significant phenotypic or physiological changes were observed with ovarian staging fecundity or embryo mortality. Yellow perch did not appear to be affected by MeHg either at a molecular level as assessed by QPCR of eight genes in the pituitary liver and ovary tissue or a physiological level as seen with ovarian somatic index circulating estradiol and ovarian staging. Lack of impact in yellow perch limits the usefulness of zebrafish as a model and suggests that the reproductive sensitivity to environmentally relevant levels of MeHg differs between yellow perch and zebrafish. Overall design: 12 samples of total RNA isolated from adult zebrafish ovaries were analyzed. Each exposure group 1 3 and 10 ppm MeHg had three replicates as did the vehicle control. Each sample was comprised of pooled total RNA of up to 6 individual fish.   pubmed:29272799   zfish 0ppm R3 GSM1899548   source name:ovary|tissue:ovary|strain:EK|mehg exposure:0 ppm zfish 0ppm R3 Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat The alignment output from TopHat was converted into a transcriptome using Cufflinks v. 2.2.1 and alignment data was confirmed using RNAseQC against the Zv9 reference transcriptome of zebrafish Sample specific transcriptomes were assembled using Cufflinks with the Zv9 transcriptome as a reference to correct fragment biases by better identifying the start/end point of each exon Transcriptomes from each sample were merged into an ovary specific transcriptome using Cuffmerge Differential expression was conducted with Cuffdiff using pooled dispersion geometric normalization and the merged ovary transcriptome. Genome build: UCSC Zv9 Supplementary files format and content: Cuffdiff outputs FPKM files which show expression values. Included in ovary.zip ovary Ovaries were flash frozen in RNA later and placed on dry ice immediately post dissection until proper storage at 80C. High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Adult EK female zebrafish were exposed to MeHg 0 1 3 or 10 ppm with ethanol as the vehicle for an entire life cycle starting with maternal exposure. Fish were exposed until euthanized. tissue:ovary|strain:EK|mehg exposure:0 ppm GSM1899548 GSM1899548: zfish 0ppm R3; Danio rerio; RNA Seq GSM1899548   1 High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. GEO Accession:GSM1899548 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP064360     run448.R3-control_GGCTAC_L003_R1.fastq.gz run448.R3-control_GGCTAC_L003_R2.fastq.gz fastq fastq 1772836840.0 8776420.0 GSM1899548 r1 0:101 1:101 A:479859924;C:405519938;G:400658916;T:482250457;N:4547605 101 101     479859924 405519938 400658916 482250457 4547605 SRX1297639 SRS1095797 SRA302185 GEO School of Freshwater Sciences, University of Wisconsin-Milwaukee 2 0.91754 0.91556 0.02431 0.02395 0.74998 0.75012 0.45157 0.45334 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2015-09-30 Adult Adult Gonad Reproductive System
39948 39948 SRR2541816 SRX1297638 SRS1095798 SRP064360 PRJNA297460 Female Reproductive Impacts of Dietary Methylmercury in Yellow Perch Perca flavescens and Zebrafish Danio rerio GSE73615 Transcriptome Analysis This study sought to evaluate the effects of dietary MeHg exposure on adult female yellow perch Perca flavescens and zebrafish Danio rerio reproduction by relating controlled exposures with subsequent reproductive effects. Yellow perch were used in the study for their socioeconomic and ecological importance within the Great Lakes basin and the use of zebrafish allowed for a detailed analysis of the molecular effects of MeHg. MeHg exposures at environmentally relevant levels were done in zebrafish for a full life cycle mimicking a realistic exposure scenario and in adult yellow perch for twenty weeks capturing early seasonal ovarian development. In zebrafish several genes involved in reproductive processes were shown to be dysregulated by RNA seq and QPCR but no significant phenotypic or physiological changes were observed with ovarian staging fecundity or embryo mortality. Yellow perch did not appear to be affected by MeHg either at a molecular level as assessed by QPCR of eight genes in the pituitary liver and ovary tissue or a physiological level as seen with ovarian somatic index circulating estradiol and ovarian staging. Lack of impact in yellow perch limits the usefulness of zebrafish as a model and suggests that the reproductive sensitivity to environmentally relevant levels of MeHg differs between yellow perch and zebrafish. Overall design: 12 samples of total RNA isolated from adult zebrafish ovaries were analyzed. Each exposure group 1 3 and 10 ppm MeHg had three replicates as did the vehicle control. Each sample was comprised of pooled total RNA of up to 6 individual fish.   pubmed:29272799   zfish 0ppm R2 GSM1899547   source name:ovary|tissue:ovary|strain:EK|mehg exposure:0 ppm zfish 0ppm R2 Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat The alignment output from TopHat was converted into a transcriptome using Cufflinks v. 2.2.1 and alignment data was confirmed using RNAseQC against the Zv9 reference transcriptome of zebrafish Sample specific transcriptomes were assembled using Cufflinks with the Zv9 transcriptome as a reference to correct fragment biases by better identifying the start/end point of each exon Transcriptomes from each sample were merged into an ovary specific transcriptome using Cuffmerge Differential expression was conducted with Cuffdiff using pooled dispersion geometric normalization and the merged ovary transcriptome. Genome build: UCSC Zv9 Supplementary files format and content: Cuffdiff outputs FPKM files which show expression values. Included in ovary.zip ovary Ovaries were flash frozen in RNA later and placed on dry ice immediately post dissection until proper storage at 80C. High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Adult EK female zebrafish were exposed to MeHg 0 1 3 or 10 ppm with ethanol as the vehicle for an entire life cycle starting with maternal exposure. Fish were exposed until euthanized. tissue:ovary|strain:EK|mehg exposure:0 ppm GSM1899547 GSM1899547: zfish 0ppm R2; Danio rerio; RNA Seq GSM1899547   1 High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. GEO Accession:GSM1899547 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP064360     run448.R2-Control_GCCAAT_L003_R1.fastq.gz run448.R2-Control_GCCAAT_L003_R2.fastq.gz fastq fastq 2017976768.0 9989984.0 GSM1899547 r1 0:101 1:101 A:547376937;C:460360988;G:455866526;T:548980455;N:5391862 101 101     547376937 460360988 455866526 548980455 5391862 SRX1297638 SRS1095798 SRA302185 GEO School of Freshwater Sciences, University of Wisconsin-Milwaukee 2 0.92332 0.92209 0.02739 0.02702 0.73996 0.74038 0.4541 0.4604 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2015-09-30 Adult Adult Gonad Reproductive System
39949 39949 SRR2541815 SRX1297637 SRS1095799 SRP064360 PRJNA297460 Female Reproductive Impacts of Dietary Methylmercury in Yellow Perch Perca flavescens and Zebrafish Danio rerio GSE73615 Transcriptome Analysis This study sought to evaluate the effects of dietary MeHg exposure on adult female yellow perch Perca flavescens and zebrafish Danio rerio reproduction by relating controlled exposures with subsequent reproductive effects. Yellow perch were used in the study for their socioeconomic and ecological importance within the Great Lakes basin and the use of zebrafish allowed for a detailed analysis of the molecular effects of MeHg. MeHg exposures at environmentally relevant levels were done in zebrafish for a full life cycle mimicking a realistic exposure scenario and in adult yellow perch for twenty weeks capturing early seasonal ovarian development. In zebrafish several genes involved in reproductive processes were shown to be dysregulated by RNA seq and QPCR but no significant phenotypic or physiological changes were observed with ovarian staging fecundity or embryo mortality. Yellow perch did not appear to be affected by MeHg either at a molecular level as assessed by QPCR of eight genes in the pituitary liver and ovary tissue or a physiological level as seen with ovarian somatic index circulating estradiol and ovarian staging. Lack of impact in yellow perch limits the usefulness of zebrafish as a model and suggests that the reproductive sensitivity to environmentally relevant levels of MeHg differs between yellow perch and zebrafish. Overall design: 12 samples of total RNA isolated from adult zebrafish ovaries were analyzed. Each exposure group 1 3 and 10 ppm MeHg had three replicates as did the vehicle control. Each sample was comprised of pooled total RNA of up to 6 individual fish.   pubmed:29272799   zfish 0ppm R1 GSM1899546   source name:ovary|tissue:ovary|strain:EK|mehg exposure:0 ppm zfish 0ppm R1 Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat The alignment output from TopHat was converted into a transcriptome using Cufflinks v. 2.2.1 and alignment data was confirmed using RNAseQC against the Zv9 reference transcriptome of zebrafish Sample specific transcriptomes were assembled using Cufflinks with the Zv9 transcriptome as a reference to correct fragment biases by better identifying the start/end point of each exon Transcriptomes from each sample were merged into an ovary specific transcriptome using Cuffmerge Differential expression was conducted with Cuffdiff using pooled dispersion geometric normalization and the merged ovary transcriptome. Genome build: UCSC Zv9 Supplementary files format and content: Cuffdiff outputs FPKM files which show expression values. Included in ovary.zip ovary Ovaries were flash frozen in RNA later and placed on dry ice immediately post dissection until proper storage at 80C. High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Adult EK female zebrafish were exposed to MeHg 0 1 3 or 10 ppm with ethanol as the vehicle for an entire life cycle starting with maternal exposure. Fish were exposed until euthanized. tissue:ovary|strain:EK|mehg exposure:0 ppm GSM1899546 GSM1899546: zfish 0ppm R1; Danio rerio; RNA Seq GSM1899546   1 High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. GEO Accession:GSM1899546 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP064360     run448.R1-Control_ATCACG_L003_R1.fastq.gz run448.R1-Control_ATCACG_L003_R2.fastq.gz fastq fastq 1434701566.0 7102483.0 GSM1899546 r1 0:101 1:101 A:386588261;C:329851910;G:325632344;T:388752449;N:3876602 101 101     386588261 329851910 325632344 388752449 3876602 SRX1297637 SRS1095799 SRA302185 GEO School of Freshwater Sciences, University of Wisconsin-Milwaukee 2 0.92604 0.92477 0.02578 0.02547 0.74736 0.74803 0.46467 0.46823 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2015-09-30 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
41691 41691 SRR5122169 SRX2437319 SRS1872017 SRP095411 PRJNA358209 Identification of a specific 13 miRNA expression signature during follicle activation in Zebrafish GSE92639 Transcriptome Analysis Purpose: We aimed to investigate important miRNA events and to define specific miRNA expression signature underlying the follicle activation of zebrafish. Methods: By using small and regular RNA sequencing we performed transcriptomic analyses of PG primary growth stage I; inactive and PV pre vitellogenic stage II; activated follicles to decipher important miRNA and gene events underlying follicle activation of zebrafish. We identified differentially expressed miRNAs for subsequent qPCR validation and miRNA::target gene prediction. Interaction of candidate miRNA:: target gene pairs were further validated by luciferase reporter assay. Global gene networks involved during PG to PV transition were also assessed by Gene Ontology as well as KEGG pathway analyses. Results and Conclusion: Our expression results indicated that PG follicles can be well differentiated from PV follicles by simply using a specific 13 miRNA expression signature let 7a 7b 7c 5p 7d 5p 7h 7i; miR 21 23a 27c 3p 107a 3p 125b 5p 145 3p 202 5p. Besides we validated interactions of let 7i::atg4a miR 202 5p::c23h20orf24 and miR 144::ybx1 by luciferase reporter assay. Purpose: we aimed to investigate important miRNA events and to define specific miRNA expression signature underlying the follicle activation of zebrafish Overall design: To identify differentially expressed miRNAs and its potential downstream targets during follicle activation of zebrafish we carried out transcriptomic profiling by both small and regular RNA sequencing. By intersecting gene lists of the online predicted targets and RNA seq derived differentially expressed transcripts with a reciprocal expression pattern of miRNAs we shortlisted 6 pairs of miRNA::target gene for validation using luciferase reporter assay.   pubmed:29228146   PG regular RNA seq 2 GSM2433871   tissue:Ovarian follicle|strain:AB|cell type:Pre vitellogenic follicle|age:from ovary of 3 month zebrafish PG regular RNA seq 2 For the RNA seq data all the pair end reads were mapped to the zebrafish genome using TopHat version 2.0.11. Genome annotation files with GTF format for known genes were downloaded from Ensembl. FPKM and RPKM values were calculated for each miRNA and gene respectively using Cufflinks software version 2.2.1 with default parameters. Genome build: Zv9 Ensembl release 79 Supplementary files format and content: tab delimited text files include FFKM for each mRNA transcript; tab delimited text files include RFKM for each miRNA. Ovarian follicle Ovaries from 3 mpf adult zebrafish were dissected in 60% medium of Leibovitz L 15 and follicles PG PV were sorted out according to the size and morphology. RNA was extracted with miRNeasy and RNAeasy extraction kits Qiagen RNA Seq libraries were constructed according to Illumima TrueSeq and small RNA seq protocol and sequenced with the Illumina Hiseq 2000 Single end sequencing and pair end sequencing were used for small RNA seq library and RNA seq library respectively AB fish was housed under a stable flow through condition at 28°C on a 14L:10D photoperiod with the light on at 0800 and off at 2200. Fish were fed regularly twice a day with live brine shrimp with supplement of commercial tropical fish food at a fixed time basis. strain:AB|cell type:Pre vitellogenic follicle|age:from ovary of 3 month zebrafish GSM2433871 GSM2433871: PG regular RNA seq 2; Danio rerio; RNA Seq GSM2433871   1 RNA was extracted with miRNeasy and RNAeasy extraction kits Qiagen RNA Seq libraries were constructed according to Illumima TrueSeq and small RNA seq protocol and sequenced with the Illumina Hiseq 2000 Single end sequencing and pair end sequencing were used for small RNA seq library and RNA seq library respectively GEO Accession:GSM2433871 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP095411     PV_R1.fq.gz PV_R2.fq.gz fastq fastq 2307127000.0 11535635.0 GSM2433871 r1 0:100 1:100 A:597372023;C:545149879;G:583291176;T:581083195;N:230727 100 100     597372023 545149879 583291176 581083195 230727 SRX2437319 SRS1872017 SRA505873 GEO Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institute of Health 2 0.96274 0.96482 0.022 0.02152 0.74328 0.74383 0.48438 0.48484 100 100 B B biological fallback assumption illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   United States 2016-12-20 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");;