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
24588,SRR25462256,SRX21195045,SRS18453971,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG HE 50dpf 3,GSM7669021,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing,PG HE 50dpf 3,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ ,GSM7669021,GSM7669021: PG HE 50dpf 3; Danio rerio; RNA Seq,GSM7669021 r1,GSM7669021,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_HE_3_S26_L003_R1_001.fastq.gz PG_HE_3_S26_L003_R2_001.fastq.gz,fastq fastq,4520051001.0,22984712.0,GSM7669021 r1,0:98.32 1:98.33,A:1134815259;C:1102592573;G:1104475707;T:1160918938;N:17248524,98,98,,,1134815259,1102592573,1104475707,1160918938,17248524,SRX21195045,SRS18453971,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.93438,0.93937,0.01237,0.01252,0.78208,0.78192,0.48454,0.49474,99,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
24589,SRR25462257,SRX21195044,SRS18453970,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG HE 50dpf 2,GSM7669020,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing,PG HE 50dpf 2,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ ,GSM7669020,GSM7669020: PG HE 50dpf 2; Danio rerio; RNA Seq,GSM7669020 r1,GSM7669020,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_HE_2_S25_L003_R2_001.fastq.gz PG_HE_2_S25_L003_R1_001.fastq.gz,fastq fastq,3915471868.0,19847479.0,GSM7669020 r1,0:98.64 1:98.64,A:982714666;C:957212118;G:961590362;T:1003408448;N:10546274,98,98,,,982714666,957212118,961590362,1003408448,10546274,SRX21195044,SRS18453970,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.93184,0.93552,0.01275,0.01275,0.78356,0.7835,0.49472,0.48841,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
24590,SRR25462258,SRX21195043,SRS18453969,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG HE 50dpf 1,GSM7669019,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing,PG HE 50dpf 1,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ ,GSM7669019,GSM7669019: PG HE 50dpf 1; Danio rerio; RNA Seq,GSM7669019 r1,GSM7669019,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_HE_1_S24_L003_R1_001.fastq.gz PG_HE_1_S24_L003_R2_001.fastq.gz,fastq fastq,4764998144.0,24264412.0,GSM7669019 r1,0:98.18 1:98.20,A:1194676445;C:1161648051;G:1165061360;T:1221860864;N:21751424,98,98,,,1194676445,1161648051,1165061360,1221860864,21751424,SRX21195043,SRS18453969,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.91864,0.92247,0.01213,0.01245,0.7949,0.79584,0.50422,0.50318,100,98,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
24591,SRR25462259,SRX21195042,SRS18453968,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG WT 50dpf 3,GSM7669018,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing,PG WT 50dpf 3,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+,GSM7669018,GSM7669018: PG WT 50dpf 3; Danio rerio; RNA Seq,GSM7669018 r1,GSM7669018,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_WT_3_S23_L003_R1_001.fastq.gz PG_WT_3_S23_L003_R2_001.fastq.gz,fastq fastq,6204452412.0,31480139.0,GSM7669018 r1,0:98.55 1:98.54,A:1567898375;C:1505755791;G:1512895523;T:1599284546;N:18618177,98,98,,,1567898375,1505755791,1512895523,1599284546,18618177,SRX21195042,SRS18453968,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.9312,0.93599,0.01692,0.01686,0.76426,0.76439,0.46519,0.47751,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
24592,SRR25462260,SRX21195041,SRS18453967,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG WT 50dpf 2,GSM7669017,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing,PG WT 50dpf 2,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+,GSM7669017,GSM7669017: PG WT 50dpf 2; Danio rerio; RNA Seq,GSM7669017 r1,GSM7669017,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_WT_2_S22_L003_R1_001.fastq.gz PG_WT_2_S22_L003_R2_001.fastq.gz,fastq fastq,3907759829.0,19906505.0,GSM7669017 r1,0:98.15 1:98.15,A:991973983;C:940499355;G:946342572;T:1011476708;N:17467211,98,98,,,991973983,940499355,946342572,1011476708,17467211,SRX21195041,SRS18453967,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.91435,0.9186,0.02035,0.02032,0.764,0.76321,0.48743,0.48644,97,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
24593,SRR25462261,SRX21195040,SRS18453966,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG WT 50dpf 1,GSM7669016,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing,PG WT 50dpf 1,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+,GSM7669016,GSM7669016: PG WT 50dpf 1; Danio rerio; RNA Seq,GSM7669016 r1,GSM7669016,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_WT_1_S21_L003_R2_001.fastq.gz PG_WT_1_S21_L003_R1_001.fastq.gz,fastq fastq,7395136401.0,37752582.0,GSM7669016 r1,0:97.94 1:97.94,A:1865709287;C:1789949400;G:1796311820;T:1908470411;N:34695483,97,97,,,1865709287,1789949400,1796311820,1908470411,34695483,SRX21195040,SRS18453966,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.9216,0.92737,0.01817,0.01802,0.76601,0.76593,0.48894,0.4975,100,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
29188,SRR8176753,SRX4996870,SRS4031878,SRP480945,PRJNA1055160,Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain,PRJNA1055160,Other,We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf,,pubmed:38529407,,Nadia 30dpf ZZ Gonad Single Cell RNA Seq,Nadia 30dpf ZZ Gonad Single Cell RNA Seq,,strain:Nadia|age:30 dpf provider:John H. Postlethwait  University of Oregon|genotype:ZZ|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: Nadia 30dpf ZZ gonad,Nadia 30dpf ZZ gonad,Nadia 30dpf ZZ gonad,A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP480945,,loader:fastq load.py,,,23587173438.0,167284918.0,1 I1 001.fastq.gz,0:8 1:133,A:6732844252;C:4934497997;G:5685086026;T:6219863789;N:14881374,8,133,,,6732844252,4934497997,5685086026,6219863789,14881374,SRX4996870,SRS4031878,SRA807619,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2018-11-08,Juvenile,Juvenile,Gonad,Reproductive System
29189,SRR8176754,SRX4996869,SRS4031877,SRP480945,PRJNA1055160,Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain,PRJNA1055160,Other,We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf,,pubmed:38529407,,Nadia 30dpf ZW Gonad Single Cell RNA Seq,Nadia 30dpf ZW Gonad Single Cell RNA Seq,,strain:Nadia|age:30 dpf provider:John H. Postlethwait  University of Oregon|genotype:ZW|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: Nadia 30dpf ZW gonad,Nadia 30dpf ZW gonad,Nadia 30dpf ZW gonad,A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP480945,,loader:fastq load.py,,,43358808480.0,307509280.0,2 I1 001.fastq.gz,0:8 1:133,A:12290612367;C:8880655083;G:10261318751;T:11898771792;N:27450487,8,133,,,12290612367,8880655083,10261318751,11898771792,27450487,SRX4996869,SRS4031877,SRA807619,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2018-11-08,Juvenile,Juvenile,Gonad,Reproductive System
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,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,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,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,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,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,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,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,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,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,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,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
34128,SRR31371655,SRX26745254,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,PC3 R1.fq,PC3 R1.fq,CuNPs and melatonin treatment,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,PC3_R1.fq.gz PC3_R2.fq.gz,fastq fastq,8050557450.0,26657475.0,PC3 R1.fq.gz,,,,,,,,,,,,SRX26745254,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34129,SRR31371656,SRX26745253,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,PC2 R1.fq,PC2 R1.fq,CuNPs and melatonin treatment,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,PC2_R1.fq.gz PC2_R2.fq.gz,fastq fastq,7072903722.0,23420211.0,PC2 R1.fq.gz,0:151 1:151,A:1848366962;C:1685927772;G:1702568524;T:1835518466;N:521998,151,151,,,1848366962,1685927772,1702568524,1835518466,521998,SRX26745253,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34130,SRR31371657,SRX26745252,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,PC1 R1.fq,PC1 R1.fq,CuNPs and melatonin treatment,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,PC1_R1.fq.gz PC1_R2.fq.gz,fastq fastq,9551575668.0,31627734.0,PC1 R1.fq.gz,,,,,,,,,,,,SRX26745252,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34131,SRR31371658,SRX26745251,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,PB3 R1.fq,PB3 R1.fq,CuNPs treatment,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,PB3_R1.fq.gz PB3_R2.fq.gz,fastq fastq,6839092000.0,22646000.0,PB3 R1.fq.gz,,,,,,,,,,,,SRX26745251,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34132,SRR31371659,SRX26745250,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,PB2 R1.fq,PB2 R1.fq,CuNPs treatment,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,PB2_R1.fq.gz PB2_R2.fq.gz,fastq fastq,7582292558.0,25106929.0,PB2 R1.fq.gz,,,,,,,,,,,,SRX26745250,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34133,SRR31371660,SRX26745249,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,PB1 R1.fq,PB1 R1.fq,CuNPs treatment,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,PB1_R1.fq.gz PB1_R2.fq.gz,fastq fastq,8122972218.0,26897259.0,PB1 R1.fq.gz,,,,,,,,,,,,SRX26745249,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34134,SRR31371661,SRX26745248,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,CA3 R1.fq,CA3 R1.fq,control,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,CA3_R1.fq.gz CA3_R2.fq.gz,fastq fastq,7638136586.0,25291843.0,CA3 R1.fq.gz,,,,,,,,,,,,SRX26745248,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34135,SRR31371662,SRX26745247,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,CA1 R1.fq,CA1 R1.fq,control,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,CA1_R1.fq.gz CA1_R2.fq.gz,fastq fastq,7499744784.0,24833592.0,CA1 R1.fq.gz,0:151 1:151,A:1951636355;C:1801626786;G:1812560367;T:1933366696;N:554580,151,151,,,1951636355,1801626786,1812560367,1933366696,554580,SRX26745247,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34136,SRR31371663,SRX26745246,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,CA2 R1.fq,CA2 R1.fq,control,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,CA2_R1.fq.gz CA2_R2.fq.gz,fastq fastq,6253035330.0,20705415.0,CA2 R1.fq.gz,,,,,,,,,,,,SRX26745246,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
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,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
41971,SRR5378568,SRX2673830,SRS2073025,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,40CT1,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:male|tissue:testis|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:40 dpf control testis Replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf untreated testis,40CT1,40CT1,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102493,,,C1PF2ACXX_NZGL00075_40SCMT1_GCCAAT_L005_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCMT1_GCCAAT_L005_R2_001.fastq.gz,fastq fastq,3383566200.0,16917831.0,C1PF2ACXX NZGL00075 40SCMT1 GCCAAT L005 R1 001.fastq.gz,0:100 1:100,A:907427604;C:788874979;G:779558006;T:904812741;N:2892870,100,100,,,907427604,788874979,779558006,904812741,2892870,SRX2673830,SRS2073025,SRA549173,University of Otago|Anatomy,University of Otago,2,0.9435,0.94416,0.077,0.07807,0.62992,0.63291,0.49572,0.49386,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41972,SRR5378567,SRX2673829,SRS2073024,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,40CT2,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:male|tissue:testis|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:40 dpf control testis Replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf untreated testis,40CT2,40CT2,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102493,,,C1PF2ACXX_NZGL00075_40SCMT2_CAGATC_L005_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCMT2_CAGATC_L005_R2_001.fastq.gz,fastq fastq,4228737000.0,21143685.0,C1PF2ACXX NZGL00075 40SCMT2 CAGATC L005 R2 001.fastq.gz,0:100 1:100,A:1127980638;C:991852227;G:979335663;T:1125913673;N:3654799,100,100,,,1127980638,991852227,979335663,1125913673,3654799,SRX2673829,SRS2073024,SRA549173,University of Otago|Anatomy,University of Otago,2,0.92133,0.92088,0.07288,0.07187,0.63589,0.63569,0.49565,0.49652,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41973,SRR5378566,SRX2673828,SRS2073023,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,40CT3,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:male|tissue:testis|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:40 dpf control testis Replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf untreated testis,40CT3,40CT3,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102493,,,C1PF2ACXX_NZGL00075_40SCMT3_CTTGTA_L005_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCMT3_CTTGTA_L005_R2_001.fastq.gz,fastq fastq,3573385600.0,17866928.0,C1PF2ACXX NZGL00075 40SCMT3 CTTGTA L005 R1 001.fastq.gz,0:100 1:100,A:959171053;C:833305488;G:821071871;T:956752401;N:3084787,100,100,,,959171053,833305488,821071871,956752401,3084787,SRX2673828,SRS2073023,SRA549173,University of Otago|Anatomy,University of Otago,2,0.94254,0.94306,0.0824,0.08326,0.63035,0.63073,0.48663,0.48853,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41974,SRR5378565,SRX2673827,SRS2073022,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,40MT1,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:male|tissue:testis|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:methyltestoster1 treated|replicate:40 dpf MT treated testis Replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf methyltestoster1 treated testis,40MT1,40MT1,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102493,,,C1PF2ACXX_NZGL00075_40MTMT2_CCGTCC_L005_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40MTMT2_CCGTCC_L005_R2_001.fastq.gz,fastq fastq,3390203000.0,16951015.0,C1PF2ACXX NZGL00075 40MTMT2 CCGTCC L005 R1 001.fastq.gz,0:100 1:100,A:913160038;C:786792863;G:776512460;T:910747347;N:2990292,100,100,,,913160038,786792863,776512460,910747347,2990292,SRX2673827,SRS2073022,SRA549173,University of Otago|Anatomy,University of Otago,2,0.93965,0.93936,0.09767,0.09857,0.62775,0.62842,0.49596,0.49531,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41975,SRR5378564,SRX2673826,SRS2073021,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,40MT2,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:male|tissue:testis|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:methyltestoster1 treated|replicate:40 dpf MT treated testis Replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf methyltestoster1 treated testis,40MT2,40MT2,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102493,,,C1PF2ACXX_NZGL00075_40MTMT3_GTCCGC_L005_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40MTMT3_GTCCGC_L005_R2_001.fastq.gz,fastq fastq,3004824200.0,15024121.0,C1PF2ACXX NZGL00075 40MTMT3 GTCCGC L005 R2 001.fastq.gz,0:100 1:100,A:807437097;C:699588436;G:689637394;T:805597982;N:2563291,100,100,,,807437097,699588436,689637394,805597982,2563291,SRX2673826,SRS2073021,SRA549173,University of Otago|Anatomy,University of Otago,2,0.93696,0.93654,0.09597,0.09569,0.63335,0.63128,0.48899,0.49336,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41976,SRR5378563,SRX2673825,SRS2073020,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,40CO1,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:female|tissue:ovary|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:40 dpf control ovary Replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf untreated ovary,40CO1,40CO1,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102493,,,C1PF2ACXX_NZGL00075_40SCFO1_CGATGT_L005_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCFO1_CGATGT_L005_R2_001.fastq.gz,fastq fastq,2794786000.0,13973930.0,C1PF2ACXX NZGL00075 40SCFO1 CGATGT L005 R2 001.fastq.gz,0:100 1:100,A:733793512;C:667693170;G:653892765;T:737072945;N:2333608,100,100,,,733793512,667693170,653892765,737072945,2333608,SRX2673825,SRS2073020,SRA549173,University of Otago|Anatomy,University of Otago,2,0.93457,0.93414,0.03501,0.03513,0.74416,0.74306,0.45464,0.46296,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41977,SRR5378562,SRX2673824,SRS2073019,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,40CO2,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:female|tissue:ovary|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:40 dpf control ovary Replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf untreated ovary,40CO2,40CO2,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102493,,,C1PF2ACXX_NZGL00075_40SCFO2_TGACCA_L005_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCFO2_TGACCA_L005_R2_001.fastq.gz,fastq fastq,3496834600.0,17484173.0,C1PF2ACXX NZGL00075 40SCFO2 TGACCA L005 R2 001.fastq.gz,0:100 1:100,A:915245192;C:837105900;G:822612411;T:918931328;N:2939769,100,100,,,915245192,837105900,822612411,918931328,2939769,SRX2673824,SRS2073019,SRA549173,University of Otago|Anatomy,University of Otago,2,0.93222,0.9318,0.03321,0.03282,0.75077,0.74882,0.46269,0.46292,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41978,SRR5378561,SRX2673823,SRS2073018,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,40CO3,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:female|tissue:ovary|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:40 dpf control ovary Replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf untreated ovary,40CO3,40CO3,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102493,,,C1PF2ACXX_NZGL00075_40SCFO3_ACAGTG_L005_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCFO3_ACAGTG_L005_R2_001.fastq.gz,fastq fastq,4130973400.0,20654867.0,C1PF2ACXX NZGL00075 40SCFO3 ACAGTG L005 R2 001.fastq.gz,0:100 1:100,A:1088505082;C:983093552;G:963601484;T:1092305451;N:3467831,100,100,,,1088505082,983093552,963601484,1092305451,3467831,SRX2673823,SRS2073018,SRA549173,University of Otago|Anatomy,University of Otago,2,0.93407,0.93321,0.03906,0.03894,0.74509,0.74393,0.46191,0.45469,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41979,SRR5378560,SRX2673822,SRS2073017,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,60CO1,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:female|tissue:ovary|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:60 dpf control ovary Replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf untreated ovary,60CO1,60CO1,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102493,,,C1PF2ACXX_NZGL00075_60SCFO1_GTGGCC_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFO1_GTGGCC_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFO1_GTGGCC_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFO1_GTGGCC_L004_R2_001.fastq.gz,fastq fastq fastq fastq,3581758800.0,17908794.0,C1PF2ACXX NZGL00075 60SCFO1 GTGGCC L003 R2 001.fastq.gz,0:100 1:100,A:935420703;C:859741152;G:842371309;T:940446466;N:3779170,100,100,,,935420703,859741152,842371309,940446466,3779170,SRX2673822,SRS2073017,SRA549173,University of Otago|Anatomy,University of Otago,2,0.93554,0.93458,0.02697,0.0264,0.75548,0.75398,0.46163,0.45871,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41980,SRR5378559,SRX2673821,SRS2073016,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,60CO2,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:female|tissue:ovary|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:60 dpf control ovary Replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf untreated ovary,60CO2,60CO2,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102493,,,C1PF2ACXX_NZGL00075_60SCFO2_GTTTCG_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFO2_GTTTCG_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFO2_GTTTCG_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFO2_GTTTCG_L004_R2_001.fastq.gz,fastq fastq fastq fastq,3004585400.0,15022927.0,C1PF2ACXX NZGL00075 60SCFO2 GTTTCG L003 R1 001.fastq.gz,0:100 1:100,A:785595086;C:720322210;G:706179659;T:789383440;N:3105005,100,100,,,785595086,720322210,706179659,789383440,3105005,SRX2673821,SRS2073016,SRA549173,University of Otago|Anatomy,University of Otago,2,0.93549,0.93572,0.02626,0.02653,0.75217,0.75463,0.45521,0.457,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41981,SRR5378558,SRX2673820,SRS2073015,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,60CO3,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:female|tissue:ovary|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:60 dpf control ovary Replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf untreated ovary,60CO3,60CO3,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102493,,,C1PF2ACXX_NZGL00075_60SCFO3_CGTACG_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFO3_CGTACG_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFO3_CGTACG_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFO3_CGTACG_L004_R2_001.fastq.gz,fastq fastq fastq fastq,3953476600.0,19767383.0,C1PF2ACXX NZGL00075 60SCFO3 CGTACG L004 R1 001.fastq.gz,0:100 1:100,A:1032933744;C:948238902;G:931243897;T:1036980742;N:4079315,100,100,,,1032933744,948238902,931243897,1036980742,4079315,SRX2673820,SRS2073015,SRA549173,University of Otago|Anatomy,University of Otago,2,0.93441,0.93421,0.02746,0.02731,0.75659,0.75641,0.45685,0.457,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41982,SRR5378557,SRX2673819,SRS2073014,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,60CT1,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:male|tissue:testis|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:60 dpf control testis Replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf untreated testis,60CT1,60CT1,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,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>,SRP102493,,,BC1JJDACXX_NZGL00075_60SCMT1_GAGTGG_L005_R1_001.fastq.gz BC1JJDACXX_NZGL00075_60SCMT1_GAGTGG_L005_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT1_GAGTGG_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT1_GAGTGG_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT1_GAGTGG_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT1_GAGTGG_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,4182954400.0,20914772.0,BC1JJDACXX NZGL00075 60SCMT1 GAGTGG L005 R1 001.fastq.gz,0:100 1:100,A:1126126575;C:969544687;G:954207474;T:1123657066;N:9418598,100,100,,,1126126575,969544687,954207474,1123657066,9418598,SRX2673819,SRS2073014,SRA549173,University of Otago|Anatomy,University of Otago,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41983,SRR5378556,SRX2673818,SRS2073013,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,60CT2,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:male|tissue:testis|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:60 dpf control testis Replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf untreated testis,60CT2,60CT2,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,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>,SRP102493,,,BC1JJDACXX_NZGL00075_60SCMT2_ACTGAT_L005_R1_001.fastq.gz BC1JJDACXX_NZGL00075_60SCMT2_ACTGAT_L005_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT2_ACTGAT_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT2_ACTGAT_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT2_ACTGAT_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT2_ACTGAT_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,4555876800.0,22779384.0,BC1JJDACXX NZGL00075 60SCMT2 ACTGAT L005 R1 001.fastq.gz,0:100 1:100,A:1226376468;C:1056355551;G:1039067674;T:1223922466;N:10154641,100,100,,,1226376468,1056355551,1039067674,1223922466,10154641,SRX2673818,SRS2073013,SRA549173,University of Otago|Anatomy,University of Otago,2,0.93701,0.939,0.09793,0.09845,0.6168,0.61682,0.49149,0.49108,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41984,SRR5378555,SRX2673817,SRS2073012,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,60CT3,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:male|tissue:testis|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:60 dpf control testis Replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf untreated testis,60CT3,60CT3,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,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>,SRP102493,,,BC1JJDACXX_NZGL00075_60SCMT3_ATTCCT_L005_R1_001.fastq.gz BC1JJDACXX_NZGL00075_60SCMT3_ATTCCT_L005_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT3_ATTCCT_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT3_ATTCCT_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT3_ATTCCT_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT3_ATTCCT_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,4716215400.0,23581077.0,C1PF2ACXX NZGL00075 60SCMT3 ATTCCT L004 R1 001.fastq.gz,0:100 1:100,A:1265703574;C:1096707638;G:1081376113;T:1262008670;N:10419405,100,100,,,1265703574,1096707638,1081376113,1262008670,10419405,SRX2673817,SRS2073012,SRA549173,University of Otago|Anatomy,University of Otago,2,0.94129,0.93998,0.08872,0.08824,0.62556,0.62526,0.47605,0.48069,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41985,SRR5378554,SRX2673816,SRS2073011,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,60MT1,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:male|tissue:testis|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:methyltestoster1 treated|replicate:60 dpf MT treated testis Replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf methyltestoster1 treated testis,60MT1,60MT1,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,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>,SRP102493,,,C1PF2ACXX_NZGL00075_60MTMT1_AGTCAA_L005_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60MTMT1_AGTCAA_L005_R2_001.fastq.gz,fastq fastq,2983913800.0,14919569.0,C1PF2ACXX NZGL00075 60MTMT1 AGTCAA L005 R1 001.fastq.gz,0:100 1:100,A:807289133;C:689635666;G:678693228;T:805746458;N:2549315,100,100,,,807289133,689635666,678693228,805746458,2549315,SRX2673816,SRS2073011,SRA549173,University of Otago|Anatomy,University of Otago,2,0.93656,0.93727,0.09689,0.09818,0.61637,0.61671,0.49189,0.49119,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41986,SRR5378553,SRX2673815,SRS2073010,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,60MT2,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:male|tissue:testis|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:methyltestoster1 treated|replicate:60 dpf MT treated testis Replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf methyltestoster1 treated testis,60MT2,60MT2,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,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>,SRP102493,,,C1PF2ACXX_NZGL00075_60MTMT2_AGTTCC_L005_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60MTMT2_AGTTCC_L005_R2_001.fastq.gz,fastq fastq,3535698400.0,17678492.0,C1PF2ACXX NZGL00075 60MTMT2 AGTTCC L005 R1 001.fastq.gz,0:100 1:100,A:953667018;C:819969570;G:806855071;T:952124680;N:3082061,100,100,,,953667018,819969570,806855071,952124680,3082061,SRX2673815,SRS2073010,SRA549173,University of Otago|Anatomy,University of Otago,2,0.94013,0.93993,0.09566,0.09661,0.62591,0.62731,0.48997,0.488,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41987,SRR5378552,SRX2673814,SRS2073009,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,60MT3,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:male|tissue:testis|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:methyltestoster1 treated|replicate:60 dpf MT treated testis Replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf methyltestoster1 treated testis,60MT3,60MT3,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,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>,SRP102493,,,C1PF2ACXX_NZGL00075_60MTMT3_ATGTCA_L005_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60MTMT3_ATGTCA_L005_R2_001.fastq.gz,fastq fastq,3198016000.0,15990080.0,C1PF2ACXX NZGL00075 60MTMT3 ATGTCA L005 R1 001.fastq.gz,0:100 1:100,A:864374636;C:739335019;G:728461692;T:863093537;N:2751116,100,100,,,864374636,739335019,728461692,863093537,2751116,SRX2673814,SRS2073009,SRA549173,University of Otago|Anatomy,University of Otago,2,0.93815,0.93857,0.10501,0.10578,0.61777,0.61968,0.49259,0.48964,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
60599,SRR12432918,SRX8928709,SRS7184991,SRP277140,PRJNA656674,EGFR mutant Danio rerio ovary raw sequence reads,PRJNA656674,Whole Genome Sequencing,The ovaries of 45 dpf zebrafish were separated. Transcriptome analysis between EGFR mutant and wildtype zebrafish was conducted in this project.,,,The zebrafish ovaries isolated from 45 dpf female were analyzed.,Ovary of 45 dpf Danio rerio,zebrafish,,strain:AB|age:45 dpf|dev stage:puberty|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,WT2,5,5,common method,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina iSeq 100,,SRP277140,,,egfraWT2_1.fq.gz egfraWT2_2.fq.gz,fastq fastq,4505046300.0,15016821.0,egfraWT2 1.fq.gz,0:150 1:150,A:1178064156;C:1082694104;G:1073742824;T:1169756132;N:789084,150,150,,,1178064156,1082694104,1073742824,1169756132,789084,SRX8928709,SRS7184991,SRA1111906,"Faculty of Health Sciences, University of Macau|Centre of Reproduction, Development and Aging","Faculty of Health Sciences, University of Macau",2,0.89561,0.8985,0.02356,0.02385,0.74383,0.74953,0.47901,0.47332,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,other,unknown,bulk,unknown,unknown,,China,2020-08-12,Juvenile,Juvenile,Gonad,Reproductive System
60600,SRR12432919,SRX8928708,SRS7184991,SRP277140,PRJNA656674,EGFR mutant Danio rerio ovary raw sequence reads,PRJNA656674,Whole Genome Sequencing,The ovaries of 45 dpf zebrafish were separated. Transcriptome analysis between EGFR mutant and wildtype zebrafish was conducted in this project.,,,The zebrafish ovaries isolated from 45 dpf female were analyzed.,Ovary of 45 dpf Danio rerio,zebrafish,,strain:AB|age:45 dpf|dev stage:puberty|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,WT1,4,4,common method,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina iSeq 100,,SRP277140,,,egfraWT1_2.fq.gz egfraWT1_1.fq.gz,fastq fastq,4315818300.0,14386061.0,egfraWT1 1.fq.gz,0:150 1:150,A:1130385340;C:1035711280;G:1025882601;T:1123083064;N:756015,150,150,,,1130385340,1035711280,1025882601,1123083064,756015,SRX8928708,SRS7184991,SRA1111906,"Faculty of Health Sciences, University of Macau|Centre of Reproduction, Development and Aging","Faculty of Health Sciences, University of Macau",2,0.90084,0.90364,0.02361,0.0238,0.73941,0.74452,0.4717,0.47805,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,other,unknown,bulk,unknown,unknown,,China,2020-08-12,Juvenile,Juvenile,Gonad,Reproductive System
60601,SRR12432920,SRX8928707,SRS7184991,SRP277140,PRJNA656674,EGFR mutant Danio rerio ovary raw sequence reads,PRJNA656674,Whole Genome Sequencing,The ovaries of 45 dpf zebrafish were separated. Transcriptome analysis between EGFR mutant and wildtype zebrafish was conducted in this project.,,,The zebrafish ovaries isolated from 45 dpf female were analyzed.,Ovary of 45 dpf Danio rerio,zebrafish,,strain:AB|age:45 dpf|dev stage:puberty|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,KO3,3,3,common method,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina iSeq 100,,SRP277140,,,egfraKO3_2.fq.gz egfraKO3_1.fq.gz,fastq fastq,8905879200.0,29686264.0,egfraKO3 1.fq.gz,0:150 1:150,A:2348479134;C:2123503765;G:2100165882;T:2332167190;N:1563229,150,150,,,2348479134,2123503765,2100165882,2332167190,1563229,SRX8928707,SRS7184991,SRA1111906,"Faculty of Health Sciences, University of Macau|Centre of Reproduction, Development and Aging","Faculty of Health Sciences, University of Macau",2,0.89938,0.90015,0.02459,0.02443,0.73959,0.74619,0.47427,0.48032,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,other,unknown,bulk,unknown,unknown,,China,2020-08-12,Juvenile,Juvenile,Gonad,Reproductive System
60602,SRR12432921,SRX8928706,SRS7184991,SRP277140,PRJNA656674,EGFR mutant Danio rerio ovary raw sequence reads,PRJNA656674,Whole Genome Sequencing,The ovaries of 45 dpf zebrafish were separated. Transcriptome analysis between EGFR mutant and wildtype zebrafish was conducted in this project.,,,The zebrafish ovaries isolated from 45 dpf female were analyzed.,Ovary of 45 dpf Danio rerio,zebrafish,,strain:AB|age:45 dpf|dev stage:puberty|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,KO2,2,2,common method,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina iSeq 100,,SRP277140,,,egfraKO2_1.fq.gz egfraKO2_2.fq.gz,fastq fastq,8150314500.0,27167715.0,egfraKO2 1.fq.gz,0:150 1:150,A:2142556905;C:1947068596;G:1929502017;T:2129761480;N:1425502,150,150,,,2142556905,1947068596,1929502017,2129761480,1425502,SRX8928706,SRS7184991,SRA1111906,"Faculty of Health Sciences, University of Macau|Centre of Reproduction, Development and Aging","Faculty of Health Sciences, University of Macau",2,0.89813,0.89911,0.0236,0.0243,0.74562,0.75097,0.47766,0.48014,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,other,unknown,bulk,unknown,unknown,,China,2020-08-12,Juvenile,Juvenile,Gonad,Reproductive System
60603,SRR12432922,SRX8928705,SRS7184991,SRP277140,PRJNA656674,EGFR mutant Danio rerio ovary raw sequence reads,PRJNA656674,Whole Genome Sequencing,The ovaries of 45 dpf zebrafish were separated. Transcriptome analysis between EGFR mutant and wildtype zebrafish was conducted in this project.,,,The zebrafish ovaries isolated from 45 dpf female were analyzed.,Ovary of 45 dpf Danio rerio,zebrafish,,strain:AB|age:45 dpf|dev stage:puberty|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,KO1,1,1,common method,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina iSeq 100,,SRP277140,,,egfraKO1_1.fq.gz egfraKO1_2.fq.gz,fastq fastq,8737229100.0,29124097.0,egfraKO1 1.fq.gz,0:150 1:150,A:2303932995;C:2082372983;G:2062052221;T:2287339032;N:1531869,150,150,,,2303932995,2082372983,2062052221,2287339032,1531869,SRX8928705,SRS7184991,SRA1111906,"Faculty of Health Sciences, University of Macau|Centre of Reproduction, Development and Aging","Faculty of Health Sciences, University of Macau",2,0.89994,0.9013,0.02483,0.02509,0.74497,0.7511,0.47316,0.4729,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,other,unknown,bulk,unknown,unknown,,China,2020-08-12,Juvenile,Juvenile,Gonad,Reproductive System
60604,SRR12432923,SRX8928704,SRS7184991,SRP277140,PRJNA656674,EGFR mutant Danio rerio ovary raw sequence reads,PRJNA656674,Whole Genome Sequencing,The ovaries of 45 dpf zebrafish were separated. Transcriptome analysis between EGFR mutant and wildtype zebrafish was conducted in this project.,,,The zebrafish ovaries isolated from 45 dpf female were analyzed.,Ovary of 45 dpf Danio rerio,zebrafish,,strain:AB|age:45 dpf|dev stage:puberty|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,WT3,6,6,common method,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina iSeq 100,,SRP277140,,,egfraWT3_1.fq.gz egfraWT3_2.fq.gz,fastq fastq,4200074700.0,14000249.0,egfraWT3 1.fq.gz,0:150 1:150,A:1106327217;C:1001998393;G:992359377;T:1098651320;N:738393,150,150,,,1106327217,1001998393,992359377,1098651320,738393,SRX8928704,SRS7184991,SRA1111906,"Faculty of Health Sciences, University of Macau|Centre of Reproduction, Development and Aging","Faculty of Health Sciences, University of Macau",2,0.89695,0.90079,0.02495,0.0254,0.74304,0.74795,0.47396,0.48144,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,other,unknown,bulk,unknown,unknown,,China,2020-08-12,Juvenile,Juvenile,Gonad,Reproductive System
64471,SRR14710793,SRX11048792,SRS9116827,SRP322308,PRJNA734487,polyA+ RNA seq of zebrafish gonad at 25 dpf and 30dpf,GSE175979,Transcriptome Analysis,In this study  we explored the biological process of zebrafish gonad differentiation through PolyA enriched RNA sequencing and found that the differences in the gonads differentiating towards testis or ovary were represented through types and expression levels of different genes. Using the GO enrichment classification  it is found that  in the differentiating ovary  the differentially expressed genes are enriched in processes of material synthesis and metabolic pathway  indicating that oocyte requires the accumulation of maternal RNA  protein  sugar  lipids  vitamins and other substances  which is consistent with its basic function of providing primary materials for early development of fertilized embryo. In addition  during ovarian differentiation  the biological processes associated with the nucleus  mitochondria  and cytoplasmic particles are more active  and the genes associated with sperm egg recognition are also expressed during this period. Unlike the differentiating ovary  when the gonad differentiates into testis  the differentially expressed genes are more enriched in biological regulation and development processes  including morphogenesis  cell proliferation  etc.The cytometers adapted to these biological processes are associated with cell membrane  such as membrane receptors  extra cellular regions  extra cellular matrix  and cell connections  and also associated with nuclear chromatin. In addition  we enriched 14 signaling pathways involved in testis differentiation  and showed the expression heat map of every differentially expressed gene of each pathway. Overall  the study reveals the different biological processes existing in the differentiation of the zebrafish gonads into ovary or testis  helping us to get a comprehensive understanding of the basis on biological events and molecules during this process. Overall design: Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads. Each gonad is placed under a microscope to identify either the testis or the ovary. Six 25 dpf and six 30 dpf undamaged gonads with sound integrity were choosen for PolyA+ RNA sequencing.,,pubmed:36257818,,30dpf testis rep3,GSM5352296,,source name:Gonad|strain:AB|tissue:testis|age:post fertilization day 30|genotype:Tgpiwil1 egfp nos3UTRihb327Tg,30dpf testis rep3,"High throughput sequencing raw image data files were converted to reads using fqtools plus analysis and using FastqC v0.11.8 and sequencing report tool of MultiQC v0.9to evaluate the raw read quality statistics. Reads were mapped to the corresponding reference genome Ensembl v96 with the parameters ""   dta x    rna strandness RF"" and ""   known spliceset infile"" using Hisat2 v2.0.5  and gene annotation was performed in GTF format Ensembl 96. Hisat2 converts the data into BAM format  sorted by Samtools v1.5  and removed duplicates using the Picard MarkDuplicates v2.18.15 tool. HTSeq v0.9.1 was used to read and count the parameter "" t exon i gene id r pos s reverse"". Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample",Gonad,,Gonads were removed  and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample  5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit   N711  Vazyme  and 5ng of amplified cDNA was used for  construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502.,The zebrafish were maintained  raised  and staged according to zebrafish book. The rearing density is 50 larvae/L for age from 5 dpf to 15 dpf  20 fish/L for age 15 dpf to 1 mpf.,strain:AB|tissue:testis|age:post fertilization day 30|genotype:Tgpiwil1 egfp nos3UTRihb327Tg,GSM5352296,GSM5352296: 30dpf testis rep3; Danio rerio; RNA Seq,GSM5352296,,1,Gonads were removed  and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample  5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit   N711  Vazyme  and 5ng of amplified cDNA was used for  construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502.,GEO Accession:GSM5352296,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP322308,,,30d_small_3_r1.fastq.gz 30d_small_3_r2.fastq.gz,fastq fastq,6441017824.0,21853422.0,GSM5352296 r1,0:148.38 1:146.36,A:1763949833;C:1455730529;G:1465555054;T:1755773512;N:8896,148,146,,,1763949833,1455730529,1465555054,1755773512,8896,SRX11048792,SRS9116827,SRA1239593,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.93532,0.93598,0.07225,0.07236,0.6801,0.6854,0.49476,0.4952,93,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-06-02,Juvenile,Juvenile,Gonad,Reproductive System
64472,SRR14710792,SRX11048791,SRS9116826,SRP322308,PRJNA734487,polyA+ RNA seq of zebrafish gonad at 25 dpf and 30dpf,GSE175979,Transcriptome Analysis,In this study  we explored the biological process of zebrafish gonad differentiation through PolyA enriched RNA sequencing and found that the differences in the gonads differentiating towards testis or ovary were represented through types and expression levels of different genes. Using the GO enrichment classification  it is found that  in the differentiating ovary  the differentially expressed genes are enriched in processes of material synthesis and metabolic pathway  indicating that oocyte requires the accumulation of maternal RNA  protein  sugar  lipids  vitamins and other substances  which is consistent with its basic function of providing primary materials for early development of fertilized embryo. In addition  during ovarian differentiation  the biological processes associated with the nucleus  mitochondria  and cytoplasmic particles are more active  and the genes associated with sperm egg recognition are also expressed during this period. Unlike the differentiating ovary  when the gonad differentiates into testis  the differentially expressed genes are more enriched in biological regulation and development processes  including morphogenesis  cell proliferation  etc.The cytometers adapted to these biological processes are associated with cell membrane  such as membrane receptors  extra cellular regions  extra cellular matrix  and cell connections  and also associated with nuclear chromatin. In addition  we enriched 14 signaling pathways involved in testis differentiation  and showed the expression heat map of every differentially expressed gene of each pathway. Overall  the study reveals the different biological processes existing in the differentiation of the zebrafish gonads into ovary or testis  helping us to get a comprehensive understanding of the basis on biological events and molecules during this process. Overall design: Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads. Each gonad is placed under a microscope to identify either the testis or the ovary. Six 25 dpf and six 30 dpf undamaged gonads with sound integrity were choosen for PolyA+ RNA sequencing.,,pubmed:36257818,,30dpf testis rep2,GSM5352295,,source name:Gonad|strain:AB|tissue:testis|age:post fertilization day 30|genotype:Tgpiwil1 egfp nos3UTRihb327Tg,30dpf testis rep2,"High throughput sequencing raw image data files were converted to reads using fqtools plus analysis and using FastqC v0.11.8 and sequencing report tool of MultiQC v0.9to evaluate the raw read quality statistics. Reads were mapped to the corresponding reference genome Ensembl v96 with the parameters ""   dta x    rna strandness RF"" and ""   known spliceset infile"" using Hisat2 v2.0.5  and gene annotation was performed in GTF format Ensembl 96. Hisat2 converts the data into BAM format  sorted by Samtools v1.5  and removed duplicates using the Picard MarkDuplicates v2.18.15 tool. HTSeq v0.9.1 was used to read and count the parameter "" t exon i gene id r pos s reverse"". Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample",Gonad,,Gonads were removed  and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample  5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit   N711  Vazyme  and 5ng of amplified cDNA was used for  construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502.,The zebrafish were maintained  raised  and staged according to zebrafish book. The rearing density is 50 larvae/L for age from 5 dpf to 15 dpf  20 fish/L for age 15 dpf to 1 mpf.,strain:AB|tissue:testis|age:post fertilization day 30|genotype:Tgpiwil1 egfp nos3UTRihb327Tg,GSM5352295,GSM5352295: 30dpf testis rep2; Danio rerio; RNA Seq,GSM5352295,,1,Gonads were removed  and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample  5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit   N711  Vazyme  and 5ng of amplified cDNA was used for  construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502.,GEO Accession:GSM5352295,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP322308,,,30d_small_2_r1.fastq.gz 30d_small_2_r2.fastq.gz,fastq fastq,6853411125.0,23219079.0,GSM5352295 r1,0:148.28 1:146.88,A:1858128706;C:1569075657;G:1580228791;T:1845965296;N:12675,148,146,,,1858128706,1569075657,1580228791,1845965296,12675,SRX11048791,SRS9116826,SRA1239593,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.93587,0.93627,0.05854,0.05886,0.68081,0.68337,0.49214,0.49713,150,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-06-02,Juvenile,Juvenile,Gonad,Reproductive System
64473,SRR14710791,SRX11048790,SRS9116825,SRP322308,PRJNA734487,polyA+ RNA seq of zebrafish gonad at 25 dpf and 30dpf,GSE175979,Transcriptome Analysis,In this study  we explored the biological process of zebrafish gonad differentiation through PolyA enriched RNA sequencing and found that the differences in the gonads differentiating towards testis or ovary were represented through types and expression levels of different genes. Using the GO enrichment classification  it is found that  in the differentiating ovary  the differentially expressed genes are enriched in processes of material synthesis and metabolic pathway  indicating that oocyte requires the accumulation of maternal RNA  protein  sugar  lipids  vitamins and other substances  which is consistent with its basic function of providing primary materials for early development of fertilized embryo. In addition  during ovarian differentiation  the biological processes associated with the nucleus  mitochondria  and cytoplasmic particles are more active  and the genes associated with sperm egg recognition are also expressed during this period. Unlike the differentiating ovary  when the gonad differentiates into testis  the differentially expressed genes are more enriched in biological regulation and development processes  including morphogenesis  cell proliferation  etc.The cytometers adapted to these biological processes are associated with cell membrane  such as membrane receptors  extra cellular regions  extra cellular matrix  and cell connections  and also associated with nuclear chromatin. In addition  we enriched 14 signaling pathways involved in testis differentiation  and showed the expression heat map of every differentially expressed gene of each pathway. Overall  the study reveals the different biological processes existing in the differentiation of the zebrafish gonads into ovary or testis  helping us to get a comprehensive understanding of the basis on biological events and molecules during this process. Overall design: Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads. Each gonad is placed under a microscope to identify either the testis or the ovary. Six 25 dpf and six 30 dpf undamaged gonads with sound integrity were choosen for PolyA+ RNA sequencing.,,pubmed:36257818,,30dpf testis rep1,GSM5352294,,source name:Gonad|strain:AB|tissue:testis|age:post fertilization day 30|genotype:Tgpiwil1 egfp nos3UTRihb327Tg,30dpf testis rep1,"High throughput sequencing raw image data files were converted to reads using fqtools plus analysis and using FastqC v0.11.8 and sequencing report tool of MultiQC v0.9to evaluate the raw read quality statistics. Reads were mapped to the corresponding reference genome Ensembl v96 with the parameters ""   dta x    rna strandness RF"" and ""   known spliceset infile"" using Hisat2 v2.0.5  and gene annotation was performed in GTF format Ensembl 96. Hisat2 converts the data into BAM format  sorted by Samtools v1.5  and removed duplicates using the Picard MarkDuplicates v2.18.15 tool. HTSeq v0.9.1 was used to read and count the parameter "" t exon i gene id r pos s reverse"". Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample",Gonad,,Gonads were removed  and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample  5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit   N711  Vazyme  and 5ng of amplified cDNA was used for  construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502.,The zebrafish were maintained  raised  and staged according to zebrafish book. The rearing density is 50 larvae/L for age from 5 dpf to 15 dpf  20 fish/L for age 15 dpf to 1 mpf.,strain:AB|tissue:testis|age:post fertilization day 30|genotype:Tgpiwil1 egfp nos3UTRihb327Tg,GSM5352294,GSM5352294: 30dpf testis rep1; Danio rerio; RNA Seq,GSM5352294,,1,Gonads were removed  and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample  5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit   N711  Vazyme  and 5ng of amplified cDNA was used for  construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502.,GEO Accession:GSM5352294,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP322308,,,30d_small_1_r1.fastq.gz 30d_small_1_r2.fastq.gz,fastq fastq,6855210490.0,23214978.0,GSM5352294 r1,0:148.82 1:146.47,A:1858166240;C:1568142468;G:1583589142;T:1845249501;N:63139,148,146,,,1858166240,1568142468,1583589142,1845249501,63139,SRX11048790,SRS9116825,SRA1239593,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.93541,0.93553,0.06501,0.06502,0.67405,0.6799,0.47785,0.48052,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-06-02,Juvenile,Juvenile,Gonad,Reproductive System
64478,SRR14710786,SRX11048785,SRS9116820,SRP322308,PRJNA734487,polyA+ RNA seq of zebrafish gonad at 25 dpf and 30dpf,GSE175979,Transcriptome Analysis,In this study  we explored the biological process of zebrafish gonad differentiation through PolyA enriched RNA sequencing and found that the differences in the gonads differentiating towards testis or ovary were represented through types and expression levels of different genes. Using the GO enrichment classification  it is found that  in the differentiating ovary  the differentially expressed genes are enriched in processes of material synthesis and metabolic pathway  indicating that oocyte requires the accumulation of maternal RNA  protein  sugar  lipids  vitamins and other substances  which is consistent with its basic function of providing primary materials for early development of fertilized embryo. In addition  during ovarian differentiation  the biological processes associated with the nucleus  mitochondria  and cytoplasmic particles are more active  and the genes associated with sperm egg recognition are also expressed during this period. Unlike the differentiating ovary  when the gonad differentiates into testis  the differentially expressed genes are more enriched in biological regulation and development processes  including morphogenesis  cell proliferation  etc.The cytometers adapted to these biological processes are associated with cell membrane  such as membrane receptors  extra cellular regions  extra cellular matrix  and cell connections  and also associated with nuclear chromatin. In addition  we enriched 14 signaling pathways involved in testis differentiation  and showed the expression heat map of every differentially expressed gene of each pathway. Overall  the study reveals the different biological processes existing in the differentiation of the zebrafish gonads into ovary or testis  helping us to get a comprehensive understanding of the basis on biological events and molecules during this process. Overall design: Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads. Each gonad is placed under a microscope to identify either the testis or the ovary. Six 25 dpf and six 30 dpf undamaged gonads with sound integrity were choosen for PolyA+ RNA sequencing.,,pubmed:36257818,,30dpf ovary rep3,GSM5352289,,source name:Gonad|strain:AB|tissue:ovary|age:post fertilization day 30|genotype:Tgpiwil1 egfp nos3UTRihb327Tg,30dpf ovary rep3,"High throughput sequencing raw image data files were converted to reads using fqtools plus analysis and using FastqC v0.11.8 and sequencing report tool of MultiQC v0.9to evaluate the raw read quality statistics. Reads were mapped to the corresponding reference genome Ensembl v96 with the parameters ""   dta x    rna strandness RF"" and ""   known spliceset infile"" using Hisat2 v2.0.5  and gene annotation was performed in GTF format Ensembl 96. Hisat2 converts the data into BAM format  sorted by Samtools v1.5  and removed duplicates using the Picard MarkDuplicates v2.18.15 tool. HTSeq v0.9.1 was used to read and count the parameter "" t exon i gene id r pos s reverse"". Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample",Gonad,,Gonads were removed  and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample  5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit   N711  Vazyme  and 5ng of amplified cDNA was used for  construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502.,The zebrafish were maintained  raised  and staged according to zebrafish book. The rearing density is 50 larvae/L for age from 5 dpf to 15 dpf  20 fish/L for age 15 dpf to 1 mpf.,strain:AB|tissue:ovary|age:post fertilization day 30|genotype:Tgpiwil1 egfp nos3UTRihb327Tg,GSM5352289,GSM5352289: 30dpf ovary rep3; Danio rerio; RNA Seq,GSM5352289,,1,Gonads were removed  and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample  5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit   N711  Vazyme  and 5ng of amplified cDNA was used for  construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502.,GEO Accession:GSM5352289,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP322308,,,30d_big_3_r1.fastq.gz 30d_big_3_r2.fastq.gz,fastq fastq,6676977482.0,22630370.0,GSM5352289 r1,0:148.67 1:146.37,A:1771343428;C:1564127719;G:1583578290;T:1757913435;N:14610,148,146,,,1771343428,1564127719,1583578290,1757913435,14610,SRX11048785,SRS9116820,SRA1239593,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.93394,0.93568,0.02958,0.02971,0.69747,0.70175,0.48413,0.48655,150,130,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-06-02,Juvenile,Juvenile,Gonad,Reproductive System
64479,SRR14710785,SRX11048784,SRS9116819,SRP322308,PRJNA734487,polyA+ RNA seq of zebrafish gonad at 25 dpf and 30dpf,GSE175979,Transcriptome Analysis,In this study  we explored the biological process of zebrafish gonad differentiation through PolyA enriched RNA sequencing and found that the differences in the gonads differentiating towards testis or ovary were represented through types and expression levels of different genes. Using the GO enrichment classification  it is found that  in the differentiating ovary  the differentially expressed genes are enriched in processes of material synthesis and metabolic pathway  indicating that oocyte requires the accumulation of maternal RNA  protein  sugar  lipids  vitamins and other substances  which is consistent with its basic function of providing primary materials for early development of fertilized embryo. In addition  during ovarian differentiation  the biological processes associated with the nucleus  mitochondria  and cytoplasmic particles are more active  and the genes associated with sperm egg recognition are also expressed during this period. Unlike the differentiating ovary  when the gonad differentiates into testis  the differentially expressed genes are more enriched in biological regulation and development processes  including morphogenesis  cell proliferation  etc.The cytometers adapted to these biological processes are associated with cell membrane  such as membrane receptors  extra cellular regions  extra cellular matrix  and cell connections  and also associated with nuclear chromatin. In addition  we enriched 14 signaling pathways involved in testis differentiation  and showed the expression heat map of every differentially expressed gene of each pathway. Overall  the study reveals the different biological processes existing in the differentiation of the zebrafish gonads into ovary or testis  helping us to get a comprehensive understanding of the basis on biological events and molecules during this process. Overall design: Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads. Each gonad is placed under a microscope to identify either the testis or the ovary. Six 25 dpf and six 30 dpf undamaged gonads with sound integrity were choosen for PolyA+ RNA sequencing.,,pubmed:36257818,,30dpf ovary rep2,GSM5352288,,source name:Gonad|strain:AB|tissue:ovary|age:post fertilization day 30|genotype:Tgpiwil1 egfp nos3UTRihb327Tg,30dpf ovary rep2,"High throughput sequencing raw image data files were converted to reads using fqtools plus analysis and using FastqC v0.11.8 and sequencing report tool of MultiQC v0.9to evaluate the raw read quality statistics. Reads were mapped to the corresponding reference genome Ensembl v96 with the parameters ""   dta x    rna strandness RF"" and ""   known spliceset infile"" using Hisat2 v2.0.5  and gene annotation was performed in GTF format Ensembl 96. Hisat2 converts the data into BAM format  sorted by Samtools v1.5  and removed duplicates using the Picard MarkDuplicates v2.18.15 tool. HTSeq v0.9.1 was used to read and count the parameter "" t exon i gene id r pos s reverse"". Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample",Gonad,,Gonads were removed  and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample  5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit   N711  Vazyme  and 5ng of amplified cDNA was used for  construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502.,The zebrafish were maintained  raised  and staged according to zebrafish book. The rearing density is 50 larvae/L for age from 5 dpf to 15 dpf  20 fish/L for age 15 dpf to 1 mpf.,strain:AB|tissue:ovary|age:post fertilization day 30|genotype:Tgpiwil1 egfp nos3UTRihb327Tg,GSM5352288,GSM5352288: 30dpf ovary rep2; Danio rerio; RNA Seq,GSM5352288,,1,Gonads were removed  and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample  5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit   N711  Vazyme  and 5ng of amplified cDNA was used for  construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502.,GEO Accession:GSM5352288,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP322308,,,30d_big_2_r1.fastq.gz 30d_big_2_r2.fastq.gz,fastq fastq,7002707279.0,23728518.0,GSM5352288 r1,0:148.43 1:146.68,A:1856090857;C:1638464115;G:1660485512;T:1847654247;N:12548,148,146,,,1856090857,1638464115,1660485512,1847654247,12548,SRX11048784,SRS9116819,SRA1239593,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.9285,0.92822,0.0276,0.02823,0.71336,0.71747,0.47571,0.47811,148,129,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-06-02,Juvenile,Juvenile,Gonad,Reproductive System
64480,SRR14710784,SRX11048783,SRS9116818,SRP322308,PRJNA734487,polyA+ RNA seq of zebrafish gonad at 25 dpf and 30dpf,GSE175979,Transcriptome Analysis,In this study  we explored the biological process of zebrafish gonad differentiation through PolyA enriched RNA sequencing and found that the differences in the gonads differentiating towards testis or ovary were represented through types and expression levels of different genes. Using the GO enrichment classification  it is found that  in the differentiating ovary  the differentially expressed genes are enriched in processes of material synthesis and metabolic pathway  indicating that oocyte requires the accumulation of maternal RNA  protein  sugar  lipids  vitamins and other substances  which is consistent with its basic function of providing primary materials for early development of fertilized embryo. In addition  during ovarian differentiation  the biological processes associated with the nucleus  mitochondria  and cytoplasmic particles are more active  and the genes associated with sperm egg recognition are also expressed during this period. Unlike the differentiating ovary  when the gonad differentiates into testis  the differentially expressed genes are more enriched in biological regulation and development processes  including morphogenesis  cell proliferation  etc.The cytometers adapted to these biological processes are associated with cell membrane  such as membrane receptors  extra cellular regions  extra cellular matrix  and cell connections  and also associated with nuclear chromatin. In addition  we enriched 14 signaling pathways involved in testis differentiation  and showed the expression heat map of every differentially expressed gene of each pathway. Overall  the study reveals the different biological processes existing in the differentiation of the zebrafish gonads into ovary or testis  helping us to get a comprehensive understanding of the basis on biological events and molecules during this process. Overall design: Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads. Each gonad is placed under a microscope to identify either the testis or the ovary. Six 25 dpf and six 30 dpf undamaged gonads with sound integrity were choosen for PolyA+ RNA sequencing.,,pubmed:36257818,,30dpf ovary rep1,GSM5352287,,source name:Gonad|strain:AB|tissue:ovary|age:post fertilization day 30|genotype:Tgpiwil1 egfp nos3UTRihb327Tg,30dpf ovary rep1,"High throughput sequencing raw image data files were converted to reads using fqtools plus analysis and using FastqC v0.11.8 and sequencing report tool of MultiQC v0.9to evaluate the raw read quality statistics. Reads were mapped to the corresponding reference genome Ensembl v96 with the parameters ""   dta x    rna strandness RF"" and ""   known spliceset infile"" using Hisat2 v2.0.5  and gene annotation was performed in GTF format Ensembl 96. Hisat2 converts the data into BAM format  sorted by Samtools v1.5  and removed duplicates using the Picard MarkDuplicates v2.18.15 tool. HTSeq v0.9.1 was used to read and count the parameter "" t exon i gene id r pos s reverse"". Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample",Gonad,,Gonads were removed  and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample  5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit   N711  Vazyme  and 5ng of amplified cDNA was used for  construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502.,The zebrafish were maintained  raised  and staged according to zebrafish book. The rearing density is 50 larvae/L for age from 5 dpf to 15 dpf  20 fish/L for age 15 dpf to 1 mpf.,strain:AB|tissue:ovary|age:post fertilization day 30|genotype:Tgpiwil1 egfp nos3UTRihb327Tg,GSM5352287,GSM5352287: 30dpf ovary rep1; Danio rerio; RNA Seq,GSM5352287,,1,Gonads were removed  and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample  5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit   N711  Vazyme  and 5ng of amplified cDNA was used for  construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502.,GEO Accession:GSM5352287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP322308,,,30d_big_1_r1.fastq.gz 30d_big_1_r2.fastq.gz,fastq fastq,7208677502.0,24449023.0,GSM5352287 r1,0:148.54 1:146.31,A:1908199908;C:1687339815;G:1709530623;T:1903592952;N:14204,148,146,,,1908199908,1687339815,1709530623,1903592952,14204,SRX11048783,SRS9116818,SRA1239593,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.92602,0.92821,0.02773,0.02865,0.72224,0.72744,0.47193,0.47411,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-06-02,Juvenile,Juvenile,Gonad,Reproductive System
67758,SRR17262950,SRX13441050,SRS11340479,SRP351377,PRJNA789855,Single cell transcriptome reveals insights into the development and function of the zebrafish ovary,GSE191137,Transcriptome Analysis,Zebrafish are an established research organism that has made many contributions to our understanding of vertebrate tissue and organ development  yet there are still significant gaps in our understanding of the genes that regulate gonad development  sex  and reproduction. Unlike the development of many organs  such as the brain and heart that form during the first few days of development  zebrafish gonads do not begin to form until the larval stage  =5 dpf. Thus  forward genetic screens have identified very few genes required for gonad development. In addition  bulk RNA sequencing studies which identify genes expressed in the gonads do not have the resolution necessary to define minor cell populations that may play significant roles in development and function of these organs. To overcome these limitations  we have used single cell RNA sequencing to determine the transcriptomes of cells isolated from juvenile zebrafish ovaries. This resulted in the profiles of 10 658 germ cells and 14 431 somatic cells. Our germ cell data represents all developmental stages from germline stem cells to early meiotic oocytes. Our somatic cell data represents all known somatic cell types  including follicle cells  theca cells and interstitial stromal cells. Further analysis revealed an unexpected number of cell subpopulations within these broadly defined cell types. To further define their functional significance  we determined the location of these cell subpopulations within the ovary. Finally  for select examples  we used gene knockout experiments to determine the role of newly identified genes. Our results reveal novel insights into ovarian development and function and the sequencing information will provide a valuable resource for future studies. Overall design: Single cell RNA sequencing of 40 dpf zebrafish ovaries,,pubmed:35588359,,40 dpf zebrafish ovaries cells zx4,GSM5739896,,tissue:40 dpf zebrafish ovaries|cell type:Ovary cells|genotype:AB wildtype,40 dpf zebrafish ovaries cells zx4,A General Transfer Format GTF gene annotation filerelease 96 for the GRCz11 zebrafish genome was downloaded from Ensembl Genome Browser and filtered using the “mkgtf” function in Cell Ranger v3.0.2; 10x Genomic to retain the following attributes: protein coding  lincRNA  and antisense. A genome reference file was generated with Cell Ranger’s “mkref” function using the GRCz11 zebrafish genome obtained from the Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file. GRCz11 zebrafish genome FASTQ file from Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file described above were used to generate the count file using the “count” function in Cell Ranger v3.0.2; 10x Genomic. “expect cells” was setted to 10000 based on estimated cell recovery.  Genome build: GRCz11 Supplementary files format and content: Filtered or raw matrix files generated from Cell Ranger in one zip file.,40 dpf zebrafish ovaries,,Somatic ovary cells were dissociated using a modification of Elkouby and Mullins 2016. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfp transgenic fish Leu et al.  2010 were dissected and stored in a LoBind tube containing 2mL of L15. Tissues were minced with microdissection scissors into < 1 mm pieces. post the tissue had settled to the bottom of the tube  the media was replaced with 5mL of digestive enzyme mixture 3 mg/mL collagenase I Cat.No. C0130; Sigma Aldrich  3 mg/mL collagenase II Cat.No. C6885; Sigma Aldrich  and 1.6 mg/mL hyaluronidase Cat.No. H4272; Sigma Aldrich in L15 and incubated on an orbital rotator at room temperature . The suspension was monitored every 10 mins until a minimal number of cell clumps were observed 30 min.. Cells were centrifuged for 3 mins at 300 x g and resuspended in 5 mL of 5x TrypLE Cat.No. A1217701; Thermo Fisher in L15 and incubated on an orbital rotator at room temperature for 15 min. The trypsin reaction was stopped by adding 500 µL of 2.8 mg/mL trypsin inhibitor in L15 and incubated on an orbital rotator at room temperature for 1 min. The cell suspension was then added to 25 ml of L15 in a 50 ml conical tube to dilute the trypsin and centrifuged for 3 min at 300 x g. The cell pellet was resuspended and washed two times with 5 mL of L15 using a P1000 pipette and centrifuged for 3 mins at 300 x g. The cell pellet was then resuspended and filtered as described above. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly  barcoded 3’ single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell 3’ Library and Gel Bead kit V3 10X Genomics for sequencing according to the manufacturer’s recommendations. All libraries were targeted at 10 000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro capillary gel electrophoresis on a Bioanalyzer 2100 Agilent.  The libraries were quantified by fluorometry on a Qubit instrument LifeTechnologies and by qPCR with a Kapa Library Quant kit Kapa Biosystems prior to sequencing. Libraries were sequenced on a HiSeq 4000 sequencer Illumina with paired end 100 bp reads.,Zebrafish husbandry was performed as previously described Westerfield  2000.,cell type:Ovary cells|genotype:AB wildtype,GSM5739896,GSM5739896: 40 dpf zebrafish ovaries cells zx4; Danio rerio; ssRNA seq,GSM5739896 r1,GSM5739896,1,Somatic ovary cells were dissociated using a modification of Elkouby and Mullins 2016. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfp transgenic fish Leu et al.  2010 were dissected and stored in a LoBind tube containing 2mL of L15. Tissues were minced with microdissection scissors into < 1 mm pieces. post the tissue had settled to the bottom of the tube  the media was replaced with 5mL of digestive enzyme mixture 3 mg/mL collagenase I Cat.No. C0130; Sigma Aldrich  3 mg/mL collagenase II Cat.No. C6885; Sigma Aldrich  and 1.6 mg/mL hyaluronidase Cat.No. H4272; Sigma Aldrich in L15 and incubated on an orbital rotator at room temperature . The suspension was monitored every 10 mins until a minimal number of cell clumps were observed 30 min.. Cells were centrifuged for 3 mins at 300 x g and resuspended in 5 mL of 5x TrypLE Cat.No. A1217701; Thermo Fisher in L15 and incubated on an orbital rotator at room temperature for 15 min. The trypsin reaction was stopped by adding 500 µL of 2.8 mg/mL trypsin inhibitor in L15 and incubated on an orbital rotator at room temperature for 1 min. The cell suspension was then added to 25 ml of L15 in a 50 ml conical tube to dilute the trypsin and centrifuged for 3 min at 300 x g. The cell pellet was resuspended and washed two times with 5 mL of L15 using a P1000 pipette and centrifuged for 3 mins at 300 x g. The cell pellet was then resuspended and filtered as described above. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly  barcoded three prime single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell three prime Library and Gel Bead kit V3 10X Genomics for sequencing according to the manufacturer's recommendations. All libraries were targeted at 10 000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro capillary gel electrophoresis on a Bioanalyzer 2100 Agilent.  The libraries were quantified by fluorometry on a Qubit instrument LifeTechnologies and by qPCR with a Kapa Library Quant kit Kapa Biosystems prior to sequencing. Libraries were sequenced on a HiSeq 4000 sequencer Illumina with paired end 100 bp reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP351377,,,40dpf_ova_2_S1_L001_R1_001.fastq.gz 40dpf_ova_2_S1_L001_R2_001.fastq.gz,fastq fastq,109199255578.0,361586939.0,GSM5739896 r1,0:151 1:151,A:26889567766;C:19012911507;G:17705256458;T:45580417154;N:11102693,151,151,,,26889567766,19012911507,17705256458,45580417154,11102693,SRX13441050,SRS11340479,SRA1345465,"Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis","Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis",2,0.00012,0.84311,5e-05,0.10842,0.99997,0.78486,1.0,0.53946,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-17,Juvenile,Juvenile,Gonad,Reproductive System
67759,SRR17262951,SRX13441049,SRS11340478,SRP351377,PRJNA789855,Single cell transcriptome reveals insights into the development and function of the zebrafish ovary,GSE191137,Transcriptome Analysis,Zebrafish are an established research organism that has made many contributions to our understanding of vertebrate tissue and organ development  yet there are still significant gaps in our understanding of the genes that regulate gonad development  sex  and reproduction. Unlike the development of many organs  such as the brain and heart that form during the first few days of development  zebrafish gonads do not begin to form until the larval stage  =5 dpf. Thus  forward genetic screens have identified very few genes required for gonad development. In addition  bulk RNA sequencing studies which identify genes expressed in the gonads do not have the resolution necessary to define minor cell populations that may play significant roles in development and function of these organs. To overcome these limitations  we have used single cell RNA sequencing to determine the transcriptomes of cells isolated from juvenile zebrafish ovaries. This resulted in the profiles of 10 658 germ cells and 14 431 somatic cells. Our germ cell data represents all developmental stages from germline stem cells to early meiotic oocytes. Our somatic cell data represents all known somatic cell types  including follicle cells  theca cells and interstitial stromal cells. Further analysis revealed an unexpected number of cell subpopulations within these broadly defined cell types. To further define their functional significance  we determined the location of these cell subpopulations within the ovary. Finally  for select examples  we used gene knockout experiments to determine the role of newly identified genes. Our results reveal novel insights into ovarian development and function and the sequencing information will provide a valuable resource for future studies. Overall design: Single cell RNA sequencing of 40 dpf zebrafish ovaries,,pubmed:35588359,,40 dpf zebrafish ovaries cells zx2,GSM5739895,,tissue:40 dpf zebrafish ovaries|cell type:Ovary cells|genotype:AB wildtype,40 dpf zebrafish ovaries cells zx2,A General Transfer Format GTF gene annotation filerelease 96 for the GRCz11 zebrafish genome was downloaded from Ensembl Genome Browser and filtered using the “mkgtf” function in Cell Ranger v3.0.2; 10x Genomic to retain the following attributes: protein coding  lincRNA  and antisense. A genome reference file was generated with Cell Ranger’s “mkref” function using the GRCz11 zebrafish genome obtained from the Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file. GRCz11 zebrafish genome FASTQ file from Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file described above were used to generate the count file using the “count” function in Cell Ranger v3.0.2; 10x Genomic. “expect cells” was setted to 10000 based on estimated cell recovery.  Genome build: GRCz11 Supplementary files format and content: Filtered or raw matrix files generated from Cell Ranger in one zip file.,40 dpf zebrafish ovaries,,Somatic ovary cells were dissociated using a modification of Elkouby and Mullins 2016. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfp transgenic fish Leu et al.  2010 were dissected and stored in a LoBind tube containing 2mL of L15. Tissues were minced with microdissection scissors into < 1 mm pieces. post the tissue had settled to the bottom of the tube  the media was replaced with 5mL of digestive enzyme mixture 3 mg/mL collagenase I Cat.No. C0130; Sigma Aldrich  3 mg/mL collagenase II Cat.No. C6885; Sigma Aldrich  and 1.6 mg/mL hyaluronidase Cat.No. H4272; Sigma Aldrich in L15 and incubated on an orbital rotator at room temperature . The suspension was monitored every 10 mins until a minimal number of cell clumps were observed 30 min.. Cells were centrifuged for 3 mins at 300 x g and resuspended in 5 mL of 5x TrypLE Cat.No. A1217701; Thermo Fisher in L15 and incubated on an orbital rotator at room temperature for 15 min. The trypsin reaction was stopped by adding 500 µL of 2.8 mg/mL trypsin inhibitor in L15 and incubated on an orbital rotator at room temperature for 1 min. The cell suspension was then added to 25 ml of L15 in a 50 ml conical tube to dilute the trypsin and centrifuged for 3 min at 300 x g. The cell pellet was resuspended and washed two times with 5 mL of L15 using a P1000 pipette and centrifuged for 3 mins at 300 x g. The cell pellet was then resuspended and filtered as described above. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly  barcoded 3’ single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell 3’ Library and Gel Bead kit V3 10X Genomics for sequencing according to the manufacturer’s recommendations. All libraries were targeted at 10 000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro capillary gel electrophoresis on a Bioanalyzer 2100 Agilent.  The libraries were quantified by fluorometry on a Qubit instrument LifeTechnologies and by qPCR with a Kapa Library Quant kit Kapa Biosystems prior to sequencing. Libraries were sequenced on a HiSeq 4000 sequencer Illumina with paired end 100 bp reads.,Zebrafish husbandry was performed as previously described Westerfield  2000.,cell type:Ovary cells|genotype:AB wildtype,GSM5739895,GSM5739895: 40 dpf zebrafish ovaries cells zx2; Danio rerio; ssRNA seq,GSM5739895 r1,GSM5739895,1,Somatic ovary cells were dissociated using a modification of Elkouby and Mullins 2016. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfp transgenic fish Leu et al.  2010 were dissected and stored in a LoBind tube containing 2mL of L15. Tissues were minced with microdissection scissors into < 1 mm pieces. post the tissue had settled to the bottom of the tube  the media was replaced with 5mL of digestive enzyme mixture 3 mg/mL collagenase I Cat.No. C0130; Sigma Aldrich  3 mg/mL collagenase II Cat.No. C6885; Sigma Aldrich  and 1.6 mg/mL hyaluronidase Cat.No. H4272; Sigma Aldrich in L15 and incubated on an orbital rotator at room temperature . The suspension was monitored every 10 mins until a minimal number of cell clumps were observed 30 min.. Cells were centrifuged for 3 mins at 300 x g and resuspended in 5 mL of 5x TrypLE Cat.No. A1217701; Thermo Fisher in L15 and incubated on an orbital rotator at room temperature for 15 min. The trypsin reaction was stopped by adding 500 µL of 2.8 mg/mL trypsin inhibitor in L15 and incubated on an orbital rotator at room temperature for 1 min. The cell suspension was then added to 25 ml of L15 in a 50 ml conical tube to dilute the trypsin and centrifuged for 3 min at 300 x g. The cell pellet was resuspended and washed two times with 5 mL of L15 using a P1000 pipette and centrifuged for 3 mins at 300 x g. The cell pellet was then resuspended and filtered as described above. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly  barcoded three prime single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell three prime Library and Gel Bead kit V3 10X Genomics for sequencing according to the manufacturer's recommendations. All libraries were targeted at 10 000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro capillary gel electrophoresis on a Bioanalyzer 2100 Agilent.  The libraries were quantified by fluorometry on a Qubit instrument LifeTechnologies and by qPCR with a Kapa Library Quant kit Kapa Biosystems prior to sequencing. Libraries were sequenced on a HiSeq 4000 sequencer Illumina with paired end 100 bp reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP351377,,,40dpf_ova_1_S146_L004_R2_001.fastq.gz 40dpf_ova_1_S146_L004_R1_001.fastq.gz,fastq fastq,109753922368.0,363423584.0,GSM5739895 r1,0:151 1:151,A:26550231612;C:18985464266;G:18837331344;T:45367377509;N:13517637,151,151,,,26550231612,18985464266,18837331344,45367377509,13517637,SRX13441049,SRS11340478,SRA1345465,"Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis","Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis",2,9e-05,0.84548,8e-05,0.09287,1.0,0.78589,,0.54454,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-17,Juvenile,Juvenile,Gonad,Reproductive System
67760,SRR17262952,SRX13441048,SRS11340477,SRP351377,PRJNA789855,Single cell transcriptome reveals insights into the development and function of the zebrafish ovary,GSE191137,Transcriptome Analysis,Zebrafish are an established research organism that has made many contributions to our understanding of vertebrate tissue and organ development  yet there are still significant gaps in our understanding of the genes that regulate gonad development  sex  and reproduction. Unlike the development of many organs  such as the brain and heart that form during the first few days of development  zebrafish gonads do not begin to form until the larval stage  =5 dpf. Thus  forward genetic screens have identified very few genes required for gonad development. In addition  bulk RNA sequencing studies which identify genes expressed in the gonads do not have the resolution necessary to define minor cell populations that may play significant roles in development and function of these organs. To overcome these limitations  we have used single cell RNA sequencing to determine the transcriptomes of cells isolated from juvenile zebrafish ovaries. This resulted in the profiles of 10 658 germ cells and 14 431 somatic cells. Our germ cell data represents all developmental stages from germline stem cells to early meiotic oocytes. Our somatic cell data represents all known somatic cell types  including follicle cells  theca cells and interstitial stromal cells. Further analysis revealed an unexpected number of cell subpopulations within these broadly defined cell types. To further define their functional significance  we determined the location of these cell subpopulations within the ovary. Finally  for select examples  we used gene knockout experiments to determine the role of newly identified genes. Our results reveal novel insights into ovarian development and function and the sequencing information will provide a valuable resource for future studies. Overall design: Single cell RNA sequencing of 40 dpf zebrafish ovaries,,pubmed:35588359,,40 dpf zebrafish ovaries cells  sorted germ cells,GSM5739894,,tissue:40 dpf zebrafish ovaries|cell type:Germ cells|genotype:AB wildtype,40 dpf zebrafish ovaries cells  sorted germ cells,A General Transfer Format GTF gene annotation filerelease 96 for the GRCz11 zebrafish genome was downloaded from Ensembl Genome Browser and filtered using the “mkgtf” function in Cell Ranger v3.0.2; 10x Genomic to retain the following attributes: protein coding  lincRNA  and antisense. A genome reference file was generated with Cell Ranger’s “mkref” function using the GRCz11 zebrafish genome obtained from the Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file. GRCz11 zebrafish genome FASTQ file from Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file described above were used to generate the count file using the “count” function in Cell Ranger v3.0.2; 10x Genomic. “expect cells” was setted to 10000 based on estimated cell recovery.  Genome build: GRCz11 Supplementary files format and content: Filtered or raw matrix files generated from Cell Ranger in one zip file.,40 dpf zebrafish ovaries,,Germ cells were dissociated from the somatic gonad using a modification of Blokhina et al.  2019. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfpuc02 transgenic fish Leu et al.  2010 and stored in a LoBind tube Cat.No. 0030108302; Eppendorf containing 2 mL of L15 mediumCat.No. L5520; Sigma Aldrich. The tissue was minced with small scissors into <1 mm pieces. 200 µL of 20 mg/mL of type 2 collagenase in L15  Cat.No. NC9870009; Worthington were added and incubated on an orbital rotator at 28°C for 35 min. The cell suspension was then gently passed through a 23g needle five times to break up large cell clumps. 200 µL of 7 mg/mL trypsin Cat.No. LS003708; Worthington in L15 were added and incubated on an orbital rotator for 10 min or until a minimal amount of cell clumps was observed. The trypsin reaction was stopped by adding 500 µL of 20 mg/mL trypsin Inhibitor Cat.No. 100612; MP Biomedicals in L15. The cells were centrifuged for 3 min at 300 x g and the supernatant carefully removed. The cells were then resuspended and washed two times with 5 mL of L15 using  a P1000 pipette tip and then centrifuged for 3 min at 300 x g. Cells were then resuspended in 1 mL L15 and filtered through a 100 µm nylon filter Cat.No. 431752; Corning and then through a 40 µm nylon filter Cat.No. 431750; Corning to remove cell clumps. The filtrate was centrifuged for 3 min at 300 x g and resuspended in 1 mL of 50 mg/mL BSA Cat.No. A8806; Sigma Aldrich in Phosphate Buffered Saline. Cell viability and number were assessed using propidium iodine Cat. No. P1304MP; Thermo Fisher and Hoechst 33342 Cat.No. H3570; Thermo Fisher staining on a Fuchs Rosenthal hemocytometer Cat.No. DHC F01; Incyto. Following cell dissociation of Tgpiwil1:egfp transgenic ovaries  GFP+ germ cells were sorted using a MoFlo Astrios EQ Cell Sorter Beckman Coulter with a 70 µm nozzle. Cells were sorted using side scatter and GFP purify to identify single germ cells. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly  barcoded 3’ single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell 3’ Library and Gel Bead kit V3 10X Genomics for sequencing according to the manufacturer’s recommendations. All libraries were targeted at 10 000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro capillary gel electrophoresis on a Bioanalyzer 2100 Agilent.  The libraries were quantified by fluorometry on a Qubit instrument LifeTechnologies and by qPCR with a Kapa Library Quant kit Kapa Biosystems prior to sequencing. Libraries were sequenced on a HiSeq 4000 sequencer Illumina with paired end 100 bp reads.,Zebrafish husbandry was performed as previously described Westerfield  2000.,cell type:Germ cells|genotype:AB wildtype,GSM5739894,GSM5739894: 40 dpf zebrafish ovaries cells  sorted germ cells; Danio rerio; ssRNA seq,GSM5739894 r1,GSM5739894,1,Germ cells were dissociated from the somatic gonad using a modification of Blokhina et al.  2019. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfpuc02 transgenic fish Leu et al.  2010 and stored in a LoBind tube Cat.No. 0030108302; Eppendorf containing 2 mL of L15 mediumCat.No. L5520; Sigma Aldrich. The tissue was minced with small scissors into <1 mm pieces. 200 µL of 20 mg/mL of type 2 collagenase in L15  Cat.No. NC9870009; Worthington were added and incubated on an orbital rotator at 28°C for 35 min. The cell suspension was then gently passed through a 23g needle five times to break up large cell clumps. 200 µL of 7 mg/mL trypsin Cat.No. LS003708; Worthington in L15 were added and incubated on an orbital rotator for 10 min or until a minimal amount of cell clumps was observed. The trypsin reaction was stopped by adding 500 µL of 20 mg/mL trypsin Inhibitor Cat.No. 100612; MP Biomedicals in L15. The cells were centrifuged for 3 min at 300 x g and the supernatant carefully removed. The cells were then resuspended and washed two times with 5 mL of L15 using  a P1000 pipette tip and then centrifuged for 3 min at 300 x g. Cells were then resuspended in 1 mL L15 and filtered through a 100 µm nylon filter Cat.No. 431752; Corning and then through a 40 µm nylon filter Cat.No. 431750; Corning to remove cell clumps. The filtrate was centrifuged for 3 min at 300 x g and resuspended in 1 mL of 50 mg/mL BSA Cat.No. A8806; Sigma Aldrich in Phosphate Buffered Saline. Cell viability and number were assessed using propidium iodine Cat. No. P1304MP; Thermo Fisher and Hoechst 33342 Cat.No. H3570; Thermo Fisher staining on a Fuchs Rosenthal hemocytometer Cat.No. DHC F01; Incyto. Following cell dissociation of Tgpiwil1:egfp transgenic ovaries  GFP+ germ cells were sorted using a MoFlo Astrios EQ Cell Sorter Beckman Coulter with a 70 µm nozzle. Cells were sorted using side scatter and GFP purify to identify single germ cells. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly  barcoded three prime single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell three prime Library and Gel Bead kit V3 10X Genomics for sequencing according to the manufacturer's recommendations. All libraries were targeted at 10 000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro capillary gel electrophoresis on a Bioanalyzer 2100 Agilent.  The libraries were quantified by fluorometry on a Qubit instrument LifeTechnologies and by qPCR with a Kapa Library Quant kit Kapa Biosystems prior to sequencing. Libraries were sequenced on a HiSeq 4000 sequencer Illumina with paired end 100 bp reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP351377,,,40d_Germ_S67_L007_R1_001.fastq.gz 40d_Germ_S67_L007_R2_001.fastq.gz,fastq fastq,97157899800.0,321714900.0,GSM5739894 r1,0:151 1:151,A:25130180865;C:15016964022;G:17255588720;T:39751154898;N:4011295,151,151,,,25130180865,15016964022,17255588720,39751154898,4011295,SRX13441048,SRS11340477,SRA1345465,"Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis","Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis",2,0.00058,0.83872,0.00016,0.05616,0.99989,0.77873,0.4,0.51521,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-17,Juvenile,Juvenile,Gonad,Reproductive System
68139,SRR17630961,SRX13799339,SRS11681628,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,scRNA seq TCDD testes   rep 2,GSM5820556,,tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,scRNA seq TCDD testes   rep 2,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820556,GSM5820556: scRNA seq TCDD testes   rep 2; Danio rerio; RNA Seq,GSM5820556 r1,GSM5820556,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,loader:fastq load.py,SC_T2_S5_L001_I1_001.fastq.gz SC_T2_S5_L001_R1_001.fastq.gz SC_T2_S5_L001_R2_001.fastq.gz,fastq fastq fastq,11262679659.0,88682517.0,GSM5820556 r1,0:8 1:28 2:91,A:2329833844;C:1736580490;G:2028746154;T:1974513391;N:435168,8,28,91,,2329833844,1736580490,2028746154,1974513391,435168,SRX13799339,SRS11681628,SRA1357269,University of Florida,University of Florida,1,0.89663,,0.23137,,0.75166,,0.55299,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68140,SRR17630962,SRX13799339,SRS11681628,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,scRNA seq TCDD testes   rep 2,GSM5820556,,tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,scRNA seq TCDD testes   rep 2,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820556,GSM5820556: scRNA seq TCDD testes   rep 2; Danio rerio; RNA Seq,GSM5820556 r1,GSM5820556,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,loader:fastq load.py,SC_T2_S5_L002_I1_001.fastq.gz SC_T2_S5_L002_R1_001.fastq.gz SC_T2_S5_L002_R2_001.fastq.gz,fastq fastq fastq,11384315052.0,89640276.0,GSM5820556 r2,0:8 1:28 2:91,A:2351124750;C:1758531934;G:2054452297;T:1992620872;N:535263,8,28,91,,2351124750,1758531934,2054452297,1992620872,535263,SRX13799339,SRS11681628,SRA1357269,University of Florida,University of Florida,1,0.89836,,0.23263,,0.7543,,0.55738,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68141,SRR17630963,SRX13799338,SRS11681627,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,scRNA seq TCDD testes   rep 1,GSM5820555,,tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,scRNA seq TCDD testes   rep 1,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820555,GSM5820555: scRNA seq TCDD testes   rep 1; Danio rerio; RNA Seq,GSM5820555 r1,GSM5820555,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,loader:fastq load.py,SC_T1_S4_L001_I1_001.fastq.gz SC_T1_S4_L001_R1_001.fastq.gz SC_T1_S4_L001_R2_001.fastq.gz,fastq fastq fastq,10978768873.0,86446999.0,GSM5820555 r1,0:8 1:28 2:91,A:2363149906;C:1616901304;G:1945888469;T:1940298056;N:439174,8,28,91,,2363149906,1616901304,1945888469,1940298056,439174,SRX13799338,SRS11681627,SRA1357269,University of Florida,University of Florida,1,0.87562,,0.208,,0.75511,,0.5329,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68142,SRR17630964,SRX13799338,SRS11681627,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,scRNA seq TCDD testes   rep 1,GSM5820555,,tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,scRNA seq TCDD testes   rep 1,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820555,GSM5820555: scRNA seq TCDD testes   rep 1; Danio rerio; RNA Seq,GSM5820555 r1,GSM5820555,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,loader:fastq load.py,SC_T1_S4_L002_I1_001.fastq.gz SC_T1_S4_L002_R1_001.fastq.gz SC_T1_S4_L002_R2_001.fastq.gz,fastq fastq fastq,11084990022.0,87283386.0,GSM5820555 r2,0:8 1:28 2:91,A:2382115862;C:1635424114;G:1968060449;T:1956671635;N:516066,8,28,91,,2382115862,1635424114,1968060449,1956671635,516066,SRX13799338,SRS11681627,SRA1357269,University of Florida,University of Florida,1,0.8745,,0.20808,,0.7585,,0.52692,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68143,SRR17630965,SRX13799337,SRS11681626,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,scRNA seq control testes   rep 3,GSM5820554,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,scRNA seq control testes   rep 3,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820554,GSM5820554: scRNA seq control testes   rep 3; Danio rerio; RNA Seq,GSM5820554 r1,GSM5820554,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,loader:fastq load.py,SC_C3_S3_L001_I1_001.fastq.gz SC_C3_S3_L001_R1_001.fastq.gz SC_C3_S3_L001_R2_001.fastq.gz,fastq fastq fastq,11736916836.0,92416668.0,GSM5820554 r1,0:8 1:28 2:91,A:2491182657;C:1749727321;G:2001921423;T:2166620469;N:464918,8,28,91,,2491182657,1749727321,2001921423,2166620469,464918,SRX13799337,SRS11681626,SRA1357269,University of Florida,University of Florida,1,0.89927,,0.17983,,0.71601,,0.52261,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68144,SRR17630966,SRX13799337,SRS11681626,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,scRNA seq control testes   rep 3,GSM5820554,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,scRNA seq control testes   rep 3,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820554,GSM5820554: scRNA seq control testes   rep 3; Danio rerio; RNA Seq,GSM5820554 r1,GSM5820554,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,loader:fastq load.py,SC_C3_S3_L002_I1_001.fastq.gz SC_C3_S3_L002_R1_001.fastq.gz SC_C3_S3_L002_R2_001.fastq.gz,fastq fastq fastq,11862480339.0,93405357.0,GSM5820554 r2,0:8 1:28 2:91,A:2515246562;C:1770645118;G:2026263526;T:2187182415;N:549866,8,28,91,,2515246562,1770645118,2026263526,2187182415,549866,SRX13799337,SRS11681626,SRA1357269,University of Florida,University of Florida,1,0.89922,,0.1803,,0.71419,,0.52093,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68145,SRR17630967,SRX13799336,SRS11681625,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,scRNA seq control testes   rep 2,GSM5820553,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,scRNA seq control testes   rep 2,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820553,GSM5820553: scRNA seq control testes   rep 2; Danio rerio; RNA Seq,GSM5820553 r1,GSM5820553,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,loader:fastq load.py,SC_C2_S2_L001_I1_001.fastq.gz SC_C2_S2_L001_R1_001.fastq.gz SC_C2_S2_L001_R2_001.fastq.gz,fastq fastq fastq,11597196897.0,91316511.0,GSM5820553 r1,0:8 1:28 2:91,A:2441188567;C:1731265684;G:2062239362;T:2074648513;N:460375,8,28,91,,2441188567,1731265684,2062239362,2074648513,460375,SRX13799336,SRS11681625,SRA1357269,University of Florida,University of Florida,1,0.87524,,0.22302,,0.75893,,0.55047,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68146,SRR17630968,SRX13799336,SRS11681625,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,scRNA seq control testes   rep 2,GSM5820553,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,scRNA seq control testes   rep 2,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820553,GSM5820553: scRNA seq control testes   rep 2; Danio rerio; RNA Seq,GSM5820553 r1,GSM5820553,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,loader:fastq load.py,SC_C2_S2_L002_I1_001.fastq.gz SC_C2_S2_L002_R1_001.fastq.gz SC_C2_S2_L002_R2_001.fastq.gz,fastq fastq fastq,11724309038.0,92317394.0,GSM5820553 r2,0:8 1:28 2:91,A:2464546352;C:1753014248;G:2088164317;T:2094592155;N:565782,8,28,91,,2464546352,1753014248,2088164317,2094592155,565782,SRX13799336,SRS11681625,SRA1357269,University of Florida,University of Florida,1,0.87809,,0.22205,,0.75272,,0.55306,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68147,SRR17630969,SRX13799335,SRS11681624,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,scRNA seq control testes   rep 1,GSM5820552,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,scRNA seq control testes   rep 1,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820552,GSM5820552: scRNA seq control testes   rep 1; Danio rerio; RNA Seq,GSM5820552 r1,GSM5820552,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,loader:fastq load.py,SC_C1_S1_L001_I1_001.fastq.gz SC_C1_S1_L001_R1_001.fastq.gz SC_C1_S1_L001_R2_001.fastq.gz,fastq fastq fastq,11845124392.0,93268696.0,GSM5820552 r1,0:8 1:28 2:91,A:2554285232;C:1757437977;G:2060709302;T:2114543968;N:474857,8,28,91,,2554285232,1757437977,2060709302,2114543968,474857,SRX13799335,SRS11681624,SRA1357269,University of Florida,University of Florida,1,0.89006,,0.16375,,0.74714,,0.51816,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68148,SRR17630970,SRX13799335,SRS11681624,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,scRNA seq control testes   rep 1,GSM5820552,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,scRNA seq control testes   rep 1,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820552,GSM5820552: scRNA seq control testes   rep 1; Danio rerio; RNA Seq,GSM5820552 r1,GSM5820552,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,loader:fastq load.py,SC_C1_S1_L002_I1_001.fastq.gz SC_C1_S1_L002_R1_001.fastq.gz SC_C1_S1_L002_R2_001.fastq.gz,fastq fastq fastq,11974253293.0,94285459.0,GSM5820552 r2,0:8 1:28 2:91,A:2577816465;C:1779883368;G:2086781140;T:2134925822;N:569974,8,28,91,,2577816465,1779883368,2086781140,2134925822,569974,SRX13799335,SRS11681624,SRA1357269,University of Florida,University of Florida,1,0.89007,,0.16458,,0.74986,,0.52005,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68149,SRR17630939,SRX13799350,SRS11681639,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,dissociated bulk seq control testes   rep 3 compared to intact control testes,GSM5820567,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,dissociated bulk seq control testes   rep 3 compared to intact control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820567,GSM5820567: dissociated bulk seq control testes   rep 3 compared to intact control testes; Danio rerio; RNA Seq,GSM5820567 r1,GSM5820567,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,I_C3_S14_L001_R1_001.fastq.gz,fastq,1847371623.0,36222973.0,GSM5820567 r1,0:51 1:0,A:535632392;C:366862698;G:429979337;T:514873991;N:23205,51,0,,,535632392,366862698,429979337,514873991,23205,SRX13799350,SRS11681639,SRA1357269,University of Florida,University of Florida,1,0.87212,,0.1857,,0.69372,,0.56886,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68150,SRR17630940,SRX13799350,SRS11681639,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,dissociated bulk seq control testes   rep 3 compared to intact control testes,GSM5820567,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,dissociated bulk seq control testes   rep 3 compared to intact control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820567,GSM5820567: dissociated bulk seq control testes   rep 3 compared to intact control testes; Danio rerio; RNA Seq,GSM5820567 r1,GSM5820567,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,I_C3_S14_L002_R1_001.fastq.gz,fastq,1823230824.0,35749624.0,GSM5820567 r2,0:51 1:0,A:529009592;C:361883074;G:424030274;T:508289743;N:18141,51,0,,,529009592,361883074,424030274,508289743,18141,SRX13799350,SRS11681639,SRA1357269,University of Florida,University of Florida,1,0.8708,,0.18714,,0.6955,,0.5716,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68151,SRR17630941,SRX13799349,SRS11681638,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,dissociated bulk seq control testes   rep 2 compared to intact control testes,GSM5820566,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,dissociated bulk seq control testes   rep 2 compared to intact control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820566,GSM5820566: dissociated bulk seq control testes   rep 2 compared to intact control testes; Danio rerio; RNA Seq,GSM5820566 r1,GSM5820566,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,I_C2_S13_L001_R1_001.fastq.gz,fastq,536561208.0,10520808.0,GSM5820566 r1,0:51 1:0,A:163430759;C:106016694;G:122059136;T:145048023;N:6596,51,0,,,163430759,106016694,122059136,145048023,6596,SRX13799349,SRS11681638,SRA1357269,University of Florida,University of Florida,1,0.83573,,0.2005,,0.71056,,0.52825,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68152,SRR17630942,SRX13799349,SRS11681638,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,dissociated bulk seq control testes   rep 2 compared to intact control testes,GSM5820566,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,dissociated bulk seq control testes   rep 2 compared to intact control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820566,GSM5820566: dissociated bulk seq control testes   rep 2 compared to intact control testes; Danio rerio; RNA Seq,GSM5820566 r1,GSM5820566,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,I_C2_S13_L002_R1_001.fastq.gz,fastq,530978238.0,10411338.0,GSM5820566 r2,0:51 1:0,A:161875304;C:104815309;G:120705456;T:143576873;N:5296,51,0,,,161875304,104815309,120705456,143576873,5296,SRX13799349,SRS11681638,SRA1357269,University of Florida,University of Florida,1,0.83663,,0.19964,,0.71104,,0.54143,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68153,SRR17630943,SRX13799348,SRS11681637,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,dissociated bulk seq control testes   rep 1 compared to intact control testes,GSM5820565,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,dissociated bulk seq control testes   rep 1 compared to intact control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820565,GSM5820565: dissociated bulk seq control testes   rep 1 compared to intact control testes; Danio rerio; RNA Seq,GSM5820565 r1,GSM5820565,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,I_C1_S12_L001_R1_001.fastq.gz,fastq,523779282.0,10270182.0,GSM5820565 r1,0:51 1:0,A:155891194;C:103400919;G:120028554;T:144451616;N:6999,51,0,,,155891194,103400919,120028554,144451616,6999,SRX13799348,SRS11681637,SRA1357269,University of Florida,University of Florida,1,0.85957,,0.19557,,0.69501,,0.56637,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68154,SRR17630944,SRX13799348,SRS11681637,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,dissociated bulk seq control testes   rep 1 compared to intact control testes,GSM5820565,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,dissociated bulk seq control testes   rep 1 compared to intact control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820565,GSM5820565: dissociated bulk seq control testes   rep 1 compared to intact control testes; Danio rerio; RNA Seq,GSM5820565 r1,GSM5820565,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,I_C1_S12_L002_R1_001.fastq.gz,fastq,516901983.0,10135333.0,GSM5820565 r2,0:51 1:0,A:153923180;C:101966413;G:118359254;T:142647450;N:5686,51,0,,,153923180,101966413,118359254,142647450,5686,SRX13799348,SRS11681637,SRA1357269,University of Florida,University of Florida,1,0.85795,,0.19403,,0.69627,,0.57159,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68155,SRR17630945,SRX13799347,SRS11681636,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq intact control testes   rep 3,GSM5820564,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,bulk seq intact control testes   rep 3,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,GSM5820564,GSM5820564: bulk seq intact control testes   rep 3; Danio rerio; RNA Seq,GSM5820564 r1,GSM5820564,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,D_C3_S16_L001_R1_001.fastq.gz,fastq,1673456880.0,32812880.0,GSM5820564 r1,0:51 1:0,A:496655744;C:334242155;G:387205466;T:455330132;N:23383,51,0,,,496655744,334242155,387205466,455330132,23383,SRX13799347,SRS11681636,SRA1357269,University of Florida,University of Florida,1,0.8707,,0.22045,,0.71078,,0.60605,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68156,SRR17630946,SRX13799347,SRS11681636,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq intact control testes   rep 3,GSM5820564,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,bulk seq intact control testes   rep 3,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,GSM5820564,GSM5820564: bulk seq intact control testes   rep 3; Danio rerio; RNA Seq,GSM5820564 r1,GSM5820564,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,D_C3_S16_L002_R1_001.fastq.gz,fastq,1647184587.0,32297737.0,GSM5820564 r2,0:51 1:0,A:489182217;C:328774657;G:380849646;T:448358863;N:19204,51,0,,,489182217,328774657,380849646,448358863,19204,SRX13799347,SRS11681636,SRA1357269,University of Florida,University of Florida,1,0.87032,,0.22081,,0.71261,,0.60917,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68157,SRR17630947,SRX13799346,SRS11681635,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq TCDD testes rep 2to be compared to scRNA seq TCDD testes,GSM5820561,,tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq TCDD testes rep 2to be compared  to scRNA seq TCDD testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820561,GSM5820561: bulk seq TCDD testes rep 2to be compared  to scRNA seq TCDD testes; Danio rerio; RNA Seq,GSM5820561 r1,GSM5820561,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_T2_S7_L001_R1_001.fastq.gz,fastq,1583815608.0,31055208.0,GSM5820561 r1,0:51 1:0,A:447529477;C:312467507;G:374130013;T:449667219;N:21392,51,0,,,447529477,312467507,374130013,449667219,21392,SRX13799346,SRS11681635,SRA1357269,University of Florida,University of Florida,1,0.86982,,0.25275,,0.70774,,0.5721,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68158,SRR17630948,SRX13799346,SRS11681635,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq TCDD testes rep 2to be compared to scRNA seq TCDD testes,GSM5820561,,tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq TCDD testes rep 2to be compared  to scRNA seq TCDD testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820561,GSM5820561: bulk seq TCDD testes rep 2to be compared  to scRNA seq TCDD testes; Danio rerio; RNA Seq,GSM5820561 r1,GSM5820561,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_T2_S7_L002_R1_001.fastq.gz,fastq,1564087941.0,30668391.0,GSM5820561 r2,0:51 1:0,A:442209708;C:308400147;G:369229792;T:444230646;N:17648,51,0,,,442209708,308400147,369229792,444230646,17648,SRX13799346,SRS11681635,SRA1357269,University of Florida,University of Florida,1,0.87035,,0.2527,,0.70682,,0.57673,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68159,SRR17630949,SRX13799345,SRS11681634,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq intact control testes   rep 2,GSM5820563,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,bulk seq intact control testes   rep 2,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,GSM5820563,GSM5820563: bulk seq intact control testes   rep 2; Danio rerio; RNA Seq,GSM5820563 r1,GSM5820563,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,D_C2_S15_L001_R1_001.fastq.gz,fastq,1493724669.0,29288719.0,GSM5820563 r1,0:51 1:0,A:445588125;C:289131502;G:340459665;T:418525850;N:19527,51,0,,,445588125,289131502,340459665,418525850,19527,SRX13799345,SRS11681634,SRA1357269,University of Florida,University of Florida,1,0.85779,,0.20343,,0.69887,,0.56808,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68160,SRR17630950,SRX13799345,SRS11681634,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq intact control testes   rep 2,GSM5820563,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,bulk seq intact control testes   rep 2,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,GSM5820563,GSM5820563: bulk seq intact control testes   rep 2; Danio rerio; RNA Seq,GSM5820563 r1,GSM5820563,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,D_C2_S15_L002_R1_001.fastq.gz,fastq,1475012565.0,28921815.0,GSM5820563 r2,0:51 1:0,A:440339743;C:285301590;G:335922618;T:413432380;N:16234,51,0,,,440339743,285301590,335922618,413432380,16234,SRX13799345,SRS11681634,SRA1357269,University of Florida,University of Florida,1,0.85783,,0.20221,,0.70102,,0.57116,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68161,SRR17630957,SRX13799344,SRS11681633,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq intact control testes   rep 1,GSM5820562,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,bulk seq intact control testes   rep 1,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,GSM5820562,GSM5820562: bulk seq intact control testes   rep 1; Danio rerio; RNA Seq,GSM5820562 r1,GSM5820562,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,D_C1_S2_L001_R1_001.fastq.gz,fastq,1783515696.0,34970896.0,GSM5820562 r1,0:51 1:0,A:503613569;C:361648917;G:420357217;T:497872153;N:23840,51,0,,,503613569,361648917,420357217,497872153,23840,SRX13799344,SRS11681633,SRA1357269,University of Florida,University of Florida,1,0.88797,,0.22692,,0.69522,,0.57676,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68162,SRR17630958,SRX13799344,SRS11681633,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq intact control testes   rep 1,GSM5820562,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,bulk seq intact control testes   rep 1,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,GSM5820562,GSM5820562: bulk seq intact control testes   rep 1; Danio rerio; RNA Seq,GSM5820562 r1,GSM5820562,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,D_C1_S2_L002_R1_001.fastq.gz,fastq,1758067563.0,34471913.0,GSM5820562 r2,0:51 1:0,A:496669418;C:356271536;G:414028881;T:491077933;N:19795,51,0,,,496669418,356271536,414028881,491077933,19795,SRX13799344,SRS11681633,SRA1357269,University of Florida,University of Florida,1,0.88843,,0.22792,,0.69619,,0.57488,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68163,SRR17630951,SRX13799343,SRS11681632,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes,GSM5820560,,tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820560,GSM5820560: bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes; Danio rerio; RNA Seq,GSM5820560 r1,GSM5820560,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_T1_S6_L001_R1_001.fastq.gz,fastq,3525780042.0,69132942.0,GSM5820560 r1,0:51 1:0,A:1025376436;C:691776192;G:829134506;T:979443851;N:49057,51,0,,,1025376436,691776192,829134506,979443851,49057,SRX13799343,SRS11681632,SRA1357269,University of Florida,University of Florida,1,0.86505,,0.30929,,0.72074,,0.6373,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68164,SRR17630952,SRX13799343,SRS11681632,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes,GSM5820560,,tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820560,GSM5820560: bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes; Danio rerio; RNA Seq,GSM5820560 r1,GSM5820560,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_T1_S6_L002_R1_001.fastq.gz,fastq,3479799156.0,68231356.0,GSM5820560 r2,0:51 1:0,A:1012622841;C:682305804;G:817948602;T:966881210;N:40699,51,0,,,1012622841,682305804,817948602,966881210,40699,SRX13799343,SRS11681632,SRA1357269,University of Florida,University of Florida,1,0.86392,,0.30933,,0.71863,,0.63706,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68165,SRR17630953,SRX13799342,SRS11681631,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq control testes rep 2  to be compared to scRNA seq control testes,GSM5820558,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq control testes rep 2  to be compared to  scRNA seq control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820558,GSM5820558: bulk seq control testes rep 2  to be compared to  scRNA seq control testes; Danio rerio; RNA Seq,GSM5820558 r1,GSM5820558,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_C2_S8_L001_R1_001.fastq.gz,fastq,1264687137.0,24797787.0,GSM5820558 r1,0:51 1:0,A:361072135;C:254984535;G:302043978;T:346569617;N:16872,51,0,,,361072135,254984535,302043978,346569617,16872,SRX13799342,SRS11681631,SRA1357269,University of Florida,University of Florida,1,0.86972,,0.31888,,0.71561,,0.6242,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68166,SRR17630954,SRX13799342,SRS11681631,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq control testes rep 2  to be compared to scRNA seq control testes,GSM5820558,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq control testes rep 2  to be compared to  scRNA seq control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820558,GSM5820558: bulk seq control testes rep 2  to be compared to  scRNA seq control testes; Danio rerio; RNA Seq,GSM5820558 r1,GSM5820558,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_C2_S8_L002_R1_001.fastq.gz,fastq,1247134620.0,24453620.0,GSM5820558 r2,0:51 1:0,A:356333809;C:251264657;G:297639103;T:341883185;N:13866,51,0,,,356333809,251264657,297639103,341883185,13866,SRX13799342,SRS11681631,SRA1357269,University of Florida,University of Florida,1,0.8683,,0.31544,,0.71332,,0.62605,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68167,SRR17630955,SRX13799341,SRS11681630,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq control testes rep 3  to be compared to scRNA seq control testes,GSM5820559,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq control testes rep 3  to be compared to  scRNA seq control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820559,GSM5820559: bulk seq control testes rep 3  to be compared to  scRNA seq control testes; Danio rerio; RNA Seq,GSM5820559 r1,GSM5820559,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_C3_S5_L001_R1_001.fastq.gz,fastq,1298470557.0,25460207.0,GSM5820559 r1,0:51 1:0,A:370125548;C:258465981;G:307735443;T:362125609;N:17976,51,0,,,370125548,258465981,307735443,362125609,17976,SRX13799341,SRS11681630,SRA1357269,University of Florida,University of Florida,1,0.87017,,0.23168,,0.7049,,0.43404,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68168,SRR17630956,SRX13799341,SRS11681630,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq control testes rep 3  to be compared to scRNA seq control testes,GSM5820559,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq control testes rep 3  to be compared to  scRNA seq control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820559,GSM5820559: bulk seq control testes rep 3  to be compared to  scRNA seq control testes; Danio rerio; RNA Seq,GSM5820559 r1,GSM5820559,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_C3_S5_L002_R1_001.fastq.gz,fastq,1282277445.0,25142695.0,GSM5820559 r2,0:51 1:0,A:365706822;C:255117242;G:303741803;T:357696714;N:14864,51,0,,,365706822,255117242,303741803,357696714,14864,SRX13799341,SRS11681630,SRA1357269,University of Florida,University of Florida,1,0.86967,,0.23412,,0.70447,,0.60084,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68169,SRR17630959,SRX13799340,SRS11681629,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq control testes rep 1 to be compared to scRNA seq control testes,GSM5820557,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq control testes rep 1 to be compared to scRNA seq control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820557,GSM5820557: bulk seq control testes rep 1 to be compared to scRNA seq control testes; Danio rerio; RNA Seq,GSM5820557 r1,GSM5820557,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_C1_S4_L001_R1_001.fastq.gz,fastq,363711651.0,7131601.0,GSM5820557 r1,0:51 1:0,A:101645255;C:77359657;G:89895787;T:94805817;N:5135,51,0,,,101645255,77359657,89895787,94805817,5135,SRX13799340,SRS11681629,SRA1357269,University of Florida,University of Florida,1,0.86049,,0.29611,,0.72293,,0.54071,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68170,SRR17630960,SRX13799340,SRS11681629,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq control testes rep 1 to be compared to scRNA seq control testes,GSM5820557,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq control testes rep 1 to be compared to scRNA seq control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820557,GSM5820557: bulk seq control testes rep 1 to be compared to scRNA seq control testes; Danio rerio; RNA Seq,GSM5820557 r1,GSM5820557,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_C1_S4_L002_R1_001.fastq.gz,fastq,358349460.0,7026460.0,GSM5820557 r2,0:51 1:0,A:100176173;C:76199709;G:88532838;T:93436578;N:4162,51,0,,,100176173,76199709,88532838,93436578,4162,SRX13799340,SRS11681629,SRA1357269,University of Florida,University of Florida,1,0.86034,,0.29588,,0.72346,,0.54277,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
76356,SRR24844103,SRX20608301,SRS17908187,SRP441411,PRJNA980839,Adad1 knockout and misense mutant RNAseq,PRJNA980839,Other,The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice  Adad1 is necessary for sperm differentiation  however its function outside of mammals has not been investigated. Here  through an N ethyl N nitrosourea ENU based forward genetic screen  we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish  however germ cells populated the gonad  proliferated  and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes  the spermatocytes failed to progress beyond the zygotene stage. Thus  Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay  and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings  suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1  we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification  pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.,,,,LB023 mutant B,LB023 Mut B,,strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense MutantB|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of Danio rerio adad1 missense mutant: male testes,LB023 Mut B,LB023 Mut B,Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age  5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences  NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP441411,,,LB023-Mut-B_R1_001.fastq.gz LB023-Mut-B_R2_001.fastq.gz,fastq fastq,5532352200.0,18441174.0,LB023 Mut B R1 001.fastq.gz,0:150 1:150,A:1408144772;C:1348146392;G:1440174663;T:1335799503;N:86870,150,150,,,1408144772,1348146392,1440174663,1335799503,86870,SRX20608301,SRS17908187,SRA1650047,University of Massachusetts Boston|Biology,University of Massachusetts Boston,2,0.93072,0.9289,0.0921,0.09129,0.73129,0.73143,0.55139,0.54723,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2023-06-07,Juvenile,Juvenile,Gonad,Reproductive System
76357,SRR24844100,SRX20608300,SRS17908192,SRP441411,PRJNA980839,Adad1 knockout and misense mutant RNAseq,PRJNA980839,Other,The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice  Adad1 is necessary for sperm differentiation  however its function outside of mammals has not been investigated. Here  through an N ethyl N nitrosourea ENU based forward genetic screen  we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish  however germ cells populated the gonad  proliferated  and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes  the spermatocytes failed to progress beyond the zygotene stage. Thus  Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay  and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings  suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1  we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification  pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.,,,,LB023 mutant C,LB023 Mut C,,strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense MutantC|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of Danio rerio adad1 missense mutant: male testes,LB023 Mut C,LB023 Mut C,Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age  5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences  NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP441411,,,LB023-Mut-C_R2_001.fastq.gz LB023-Mut-C_R1_001.fastq.gz,fastq fastq,6159317100.0,20531057.0,LB023 Mut C R1 001.fastq.gz,0:150 1:150,A:1639865405;C:1424690953;G:1522945570;T:1571725037;N:90135,150,150,,,1639865405,1424690953,1522945570,1571725037,90135,SRX20608300,SRS17908192,SRA1650047,University of Massachusetts Boston|Biology,University of Massachusetts Boston,2,0.92565,0.92502,0.07339,0.0724,0.70832,0.70924,0.50224,0.49923,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2023-06-07,Juvenile,Juvenile,Gonad,Reproductive System
76358,SRR24844101,SRX20608299,SRS17908193,SRP441411,PRJNA980839,Adad1 knockout and misense mutant RNAseq,PRJNA980839,Other,The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice  Adad1 is necessary for sperm differentiation  however its function outside of mammals has not been investigated. Here  through an N ethyl N nitrosourea ENU based forward genetic screen  we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish  however germ cells populated the gonad  proliferated  and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes  the spermatocytes failed to progress beyond the zygotene stage. Thus  Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay  and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings  suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1  we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification  pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.,,,,LB023 wildtype sibling control D,LB023 WT D,,strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense WildtypeD|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of Danio rerio adad1 missense wildtype sibling: male testes,LB023 WT D,LB023 WT D,Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age  5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences  NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP441411,,,LB023-WT-D_R2_001.fastq.gz LB023-WT-D_R1_001.fastq.gz,fastq fastq,5436242700.0,18120809.0,LB023 WT D R1 001.fastq.gz,0:150 1:150,A:1448689171;C:1252673824;G:1358298822;T:1376497051;N:83832,150,150,,,1448689171,1252673824,1358298822,1376497051,83832,SRX20608299,SRS17908193,SRA1650047,University of Massachusetts Boston|Biology,University of Massachusetts Boston,2,0.91802,0.91762,0.09407,0.09394,0.70916,0.7108,0.54977,0.55217,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2023-06-07,Juvenile,Juvenile,Gonad,Reproductive System
76359,SRR24844102,SRX20608298,SRS17908191,SRP441411,PRJNA980839,Adad1 knockout and misense mutant RNAseq,PRJNA980839,Other,The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice  Adad1 is necessary for sperm differentiation  however its function outside of mammals has not been investigated. Here  through an N ethyl N nitrosourea ENU based forward genetic screen  we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish  however germ cells populated the gonad  proliferated  and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes  the spermatocytes failed to progress beyond the zygotene stage. Thus  Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay  and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings  suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1  we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification  pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.,,,,adad1 mutant E,adad1 Mut E,,strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:MutantE|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of Danio rerio adad1 mutant: male testes,adad1 Mut E,adad1 Mut E,Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age  5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences  NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP441411,,,adad1-Mut-E_R2_001.fastq.gz adad1-Mut-E_R1_001.fastq.gz,fastq fastq,4958837100.0,16529457.0,adad1 Mut E R1 001.fastq.gz,0:150 1:150,A:1311870356;C:1151609197;G:1254712533;T:1240567756;N:77258,150,150,,,1311870356,1151609197,1254712533,1240567756,77258,SRX20608298,SRS17908191,SRA1650047,University of Massachusetts Boston|Biology,University of Massachusetts Boston,2,0.901,0.90124,0.11096,0.11139,0.71851,0.71967,0.5526,0.57121,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2023-06-07,Juvenile,Juvenile,Gonad,Reproductive System
76360,SRR24844104,SRX20608297,SRS17908190,SRP441411,PRJNA980839,Adad1 knockout and misense mutant RNAseq,PRJNA980839,Other,The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice  Adad1 is necessary for sperm differentiation  however its function outside of mammals has not been investigated. Here  through an N ethyl N nitrosourea ENU based forward genetic screen  we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish  however germ cells populated the gonad  proliferated  and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes  the spermatocytes failed to progress beyond the zygotene stage. Thus  Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay  and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings  suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1  we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification  pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.,,,,adad1 mutant F,adad1 Mut F,,strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:MutantF|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of Danio rerio adad1 mutant: male testes,adad1 Mut F,adad1 Mut F,Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age  5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences  NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP441411,,,adad1-Mut-F_R1_001.fastq.gz adad1-Mut-F_R2_001.fastq.gz,fastq fastq,5780694600.0,19268982.0,adad1 Mut F R1 001.fastq.gz,0:150 1:150,A:1502665613;C:1371103253;G:1490414769;T:1416422204;N:88761,150,150,,,1502665613,1371103253,1490414769,1416422204,88761,SRX20608297,SRS17908190,SRA1650047,University of Massachusetts Boston|Biology,University of Massachusetts Boston,2,0.89657,0.89588,0.10966,0.10896,0.72671,0.72728,0.57267,0.55033,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2023-06-07,Juvenile,Juvenile,Gonad,Reproductive System