{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", technology = \"bulk\" and tissue_curation = \"Gonad\"", "rows": [[24582, "SRR25462250", "SRX21195051", "SRS18453977", "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.", null, null, null, "PG HE 8mpf 3", "GSM7669027", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing", "PG HE 8mpf 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. 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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.", null, null, null, "PG HE 8mpf 2", "GSM7669026", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing", "PG HE 8mpf 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. 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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.", null, null, null, "PG HE 8mpf 1", "GSM7669025", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing", "PG HE 8mpf 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. 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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.", null, null, null, "PG WT 8mpf 3", "GSM7669024", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing", "PG WT 8mpf 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. 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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.", null, null, null, "PG WT 8mpf 2", "GSM7669023", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing", "PG WT 8mpf 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. 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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.", null, null, null, "PG WT 8mpf 1", "GSM7669022", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing", "PG WT 8mpf 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", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+", "GSM7669022", "GSM7669022: PG WT 8mpf 1; Danio rerio; RNA Seq", "GSM7669022 r1", "GSM7669022", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452270", null, null, "WT_PG_8mpf_1_S9_L003_R1_001.fastq.gz WT_PG_8mpf_1_S9_L003_R2_001.fastq.gz", "fastq fastq", 3375380667.0, 28408784.0, "GSM7669022 r1", "0:59.42 1:59.40", "A:842316103;C:825987175;G:818715765;T:881225528;N:7136096", 59, 59, null, null, 842316103, 825987175, 818715765, 881225528, 7136096, "SRX21195046", "SRS18453972", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.94039, 0.9444, 0.0162, 0.01617, 0.7697, 0.76986, 0.47132, 0.46938, 60, 60, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Adult", "Adult", "Gonad", "Reproductive System"], [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.", null, null, null, "PG HE 50dpf 3", "GSM7669021", null, "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", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452270", null, null, "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, null, null, 1134815259, 1102592573, 1104475707, 1160918938, 17248524, "SRX21195045", "SRS18453971", null, null, "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", null, "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.", null, null, null, "PG HE 50dpf 2", "GSM7669020", null, "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", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452270", null, null, "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, null, null, 982714666, 957212118, 961590362, 1003408448, 10546274, "SRX21195044", "SRS18453970", null, null, "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", null, "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.", null, null, null, "PG HE 50dpf 1", "GSM7669019", null, "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", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452270", null, null, "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, null, null, 1194676445, 1161648051, 1165061360, 1221860864, 21751424, "SRX21195043", "SRS18453969", null, null, "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", null, "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.", null, null, null, "PG WT 50dpf 3", "GSM7669018", null, "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", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452270", null, null, "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, null, null, 1567898375, 1505755791, 1512895523, 1599284546, 18618177, "SRX21195042", "SRS18453968", null, null, "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", null, "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.", null, null, null, "PG WT 50dpf 2", "GSM7669017", null, "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", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452270", null, null, "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, null, null, 991973983, 940499355, 946342572, 1011476708, 17467211, "SRX21195041", "SRS18453967", null, null, "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", null, "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.", null, null, null, "PG WT 50dpf 1", "GSM7669016", null, "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", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452270", null, null, "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, null, null, 1865709287, 1789949400, 1796311820, 1908470411, 34695483, "SRX21195040", "SRS18453966", null, null, "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", null, "United States", "2023-07-31", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [24594, "SRR25462243", "SRX21195038", "SRS18453964", "SRP452269", "PRJNA1000446", "Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish", "GSE239623", "Transcriptome Analysis", "Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study  we created an ybx1 mutant with CRISPR/Cas9  and showed that the folliculogenesis in the mutant ovary ybx1 /  was blocked at pre vitellogenic PV to early vitellogenic EV transition  leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 /  and the control ybx1+/  including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/   however  follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly  partial loss of p21 in heterozygous cdkn1a+/  could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/  females with normal follicle activation  in contrast to the PV EV blockade in ybx1 /  mutant. Interestingly  the follicle cells from the ybx1 /  mutant follicles displayed a poor proliferative activity in vitro; however  the cells from the ybx1 / p21+/  follicles resumed normal proliferation compared to that from the wildtype fish. In summary  we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a  a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade  we further isolated PV follicles from both WT ybx1+/+ and  ybx1 /  zebrafish. post RNA isolation  we then estbalished 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.", null, null, null, "PV  M3", "GSM7669033", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing", "PV  M3", "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", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / ", "GSM7669033", "GSM7669033: PV  M3; Danio rerio; RNA Seq", "GSM7669033 r1", "GSM7669033", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452269", null, null, "PV_M3_R1.fastq.gz PV_M3_R2.fastq.gz", "fastq fastq", 4644457090.0, 23465750.0, "GSM7669033 r1", "0:98.98 1:98.94", "A:1196567358;C:1114203322;G:1109379777;T:1223156356;N:1150277", 98, 98, null, null, 1196567358, 1114203322, 1109379777, 1223156356, 1150277, "SRX21195038", "SRS18453964", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.94849, 0.95248, 0.02727, 0.02708, 0.73602, 0.73718, 0.48396, 0.4855, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [24595, "SRR25462244", "SRX21195037", "SRS18453963", "SRP452269", "PRJNA1000446", "Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish", "GSE239623", "Transcriptome Analysis", "Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study  we created an ybx1 mutant with CRISPR/Cas9  and showed that the folliculogenesis in the mutant ovary ybx1 /  was blocked at pre vitellogenic PV to early vitellogenic EV transition  leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 /  and the control ybx1+/  including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/   however  follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly  partial loss of p21 in heterozygous cdkn1a+/  could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/  females with normal follicle activation  in contrast to the PV EV blockade in ybx1 /  mutant. Interestingly  the follicle cells from the ybx1 /  mutant follicles displayed a poor proliferative activity in vitro; however  the cells from the ybx1 / p21+/  follicles resumed normal proliferation compared to that from the wildtype fish. In summary  we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a  a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade  we further isolated PV follicles from both WT ybx1+/+ and  ybx1 /  zebrafish. post RNA isolation  we then estbalished 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.", null, null, null, "PV  M2", "GSM7669032", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing", "PV  M2", "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", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / ", "GSM7669032", "GSM7669032: PV  M2; Danio rerio; RNA Seq", "GSM7669032 r1", "GSM7669032", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452269", null, null, "PV_M2_R1.fastq.gz PV_M2_R2.fastq.gz", "fastq fastq", 2464506276.0, 12449948.0, "GSM7669032 r1", "0:98.99 1:98.96", "A:632587002;C:593372099;G:591579950;T:646214108;N:753117", 98, 98, null, null, 632587002, 593372099, 591579950, 646214108, 753117, "SRX21195037", "SRS18453963", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.94889, 0.9522, 0.02585, 0.02585, 0.73669, 0.73841, 0.48398, 0.48486, 100, 99, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [24596, "SRR25462245", "SRX21195036", "SRS18453962", "SRP452269", "PRJNA1000446", "Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish", "GSE239623", "Transcriptome Analysis", "Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study  we created an ybx1 mutant with CRISPR/Cas9  and showed that the folliculogenesis in the mutant ovary ybx1 /  was blocked at pre vitellogenic PV to early vitellogenic EV transition  leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 /  and the control ybx1+/  including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/   however  follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly  partial loss of p21 in heterozygous cdkn1a+/  could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/  females with normal follicle activation  in contrast to the PV EV blockade in ybx1 /  mutant. Interestingly  the follicle cells from the ybx1 /  mutant follicles displayed a poor proliferative activity in vitro; however  the cells from the ybx1 / p21+/  follicles resumed normal proliferation compared to that from the wildtype fish. In summary  we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a  a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade  we further isolated PV follicles from both WT ybx1+/+ and  ybx1 /  zebrafish. post RNA isolation  we then estbalished 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.", null, null, null, "PV  M1", "GSM7669031", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing", "PV  M1", "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", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / ", "GSM7669031", "GSM7669031: PV  M1; Danio rerio; RNA Seq", "GSM7669031 r1", "GSM7669031", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452269", null, null, "PV_M1_R1.fastq.gz PV_M1_R2.fastq.gz", "fastq fastq", 3634173229.0, 18461903.0, "GSM7669031 r1", "0:98.44 1:98.41", "A:930322973;C:875929476;G:875710056;T:948595199;N:3615525", 98, 98, null, null, 930322973, 875929476, 875710056, 948595199, 3615525, "SRX21195036", "SRS18453962", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.94787, 0.95134, 0.02457, 0.02445, 0.73762, 0.73843, 0.48244, 0.48069, 100, 98, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [24597, "SRR25462246", "SRX21195035", "SRS18453961", "SRP452269", "PRJNA1000446", "Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish", "GSE239623", "Transcriptome Analysis", "Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study  we created an ybx1 mutant with CRISPR/Cas9  and showed that the folliculogenesis in the mutant ovary ybx1 /  was blocked at pre vitellogenic PV to early vitellogenic EV transition  leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 /  and the control ybx1+/  including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/   however  follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly  partial loss of p21 in heterozygous cdkn1a+/  could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/  females with normal follicle activation  in contrast to the PV EV blockade in ybx1 /  mutant. Interestingly  the follicle cells from the ybx1 /  mutant follicles displayed a poor proliferative activity in vitro; however  the cells from the ybx1 / p21+/  follicles resumed normal proliferation compared to that from the wildtype fish. In summary  we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a  a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade  we further isolated PV follicles from both WT ybx1+/+ and  ybx1 /  zebrafish. post RNA isolation  we then estbalished 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.", null, null, null, "PV  WT3", "GSM7669030", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing", "PV  WT3", "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", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+", "GSM7669030", "GSM7669030: PV  WT3; Danio rerio; RNA Seq", "GSM7669030 r1", "GSM7669030", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452269", null, null, "PV_WT3_R2.fastq PV_WT3_R1.fastq", "fastq fastq", 2965772270.0, 14976621.0, "GSM7669030 r1", "0:99.03 1:98.99", "A:759343389;C:716154246;G:713466520;T:775995980;N:812135", 99, 98, null, null, 759343389, 716154246, 713466520, 775995980, 812135, "SRX21195035", "SRS18453961", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.95027, 0.95485, 0.02356, 0.02292, 0.74422, 0.74554, 0.47974, 0.48267, 100, 98, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [24598, "SRR25462247", "SRX21195034", "SRS18453960", "SRP452269", "PRJNA1000446", "Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish", "GSE239623", "Transcriptome Analysis", "Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study  we created an ybx1 mutant with CRISPR/Cas9  and showed that the folliculogenesis in the mutant ovary ybx1 /  was blocked at pre vitellogenic PV to early vitellogenic EV transition  leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 /  and the control ybx1+/  including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/   however  follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly  partial loss of p21 in heterozygous cdkn1a+/  could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/  females with normal follicle activation  in contrast to the PV EV blockade in ybx1 /  mutant. Interestingly  the follicle cells from the ybx1 /  mutant follicles displayed a poor proliferative activity in vitro; however  the cells from the ybx1 / p21+/  follicles resumed normal proliferation compared to that from the wildtype fish. In summary  we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a  a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade  we further isolated PV follicles from both WT ybx1+/+ and  ybx1 /  zebrafish. post RNA isolation  we then estbalished 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.", null, null, null, "PV  WT2", "GSM7669029", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing", "PV  WT2", "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", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+", "GSM7669029", "GSM7669029: PV  WT2; Danio rerio; RNA Seq", "GSM7669029 r1", "GSM7669029", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452269", null, null, "PV_WT2_R2.fastq PV_WT2_R1.fastq", "fastq fastq", 2021387268.0, 10195384.0, "GSM7669029 r1", "0:99.15 1:99.12", "A:517788644;C:487363563;G:485168383;T:530550229;N:516449", 99, 99, null, null, 517788644, 487363563, 485168383, 530550229, 516449, "SRX21195034", "SRS18453960", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.95113, 0.9544, 0.02394, 0.02364, 0.74168, 0.74363, 0.47881, 0.47499, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [24599, "SRR25462248", "SRX21195033", "SRS18453959", "SRP452269", "PRJNA1000446", "Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish", "GSE239623", "Transcriptome Analysis", "Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study  we created an ybx1 mutant with CRISPR/Cas9  and showed that the folliculogenesis in the mutant ovary ybx1 /  was blocked at pre vitellogenic PV to early vitellogenic EV transition  leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 /  and the control ybx1+/  including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/   however  follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly  partial loss of p21 in heterozygous cdkn1a+/  could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/  females with normal follicle activation  in contrast to the PV EV blockade in ybx1 /  mutant. Interestingly  the follicle cells from the ybx1 /  mutant follicles displayed a poor proliferative activity in vitro; however  the cells from the ybx1 / p21+/  follicles resumed normal proliferation compared to that from the wildtype fish. In summary  we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a  a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade  we further isolated PV follicles from both WT ybx1+/+ and  ybx1 /  zebrafish. post RNA isolation  we then estbalished 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.", null, null, null, "PV  WT1", "GSM7669028", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing", "PV  WT1", "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", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+", "GSM7669028", "GSM7669028: PV  WT1; Danio rerio; RNA Seq", "GSM7669028 r1", "GSM7669028", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452269", null, null, "PV_WT1_R1.fastq PV_WT1_R2.fastq", "fastq fastq", 3244660111.0, 16481925.0, "GSM7669028 r1", "0:98.44 1:98.42", "A:831426044;C:781489498;G:779991004;T:848549246;N:3204319", 98, 98, null, null, 831426044, 781489498, 779991004, 848549246, 3204319, "SRX21195033", "SRS18453959", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.94779, 0.95185, 0.02328, 0.02298, 0.74294, 0.74391, 0.48052, 0.47966, 95, 95, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [30556, "SRR27836071", "SRX23499420", "SRS20351177", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "Rbpms2 mApple crosslinked SR3", "GSM8059038", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing", "Rbpms2 mApple crosslinked SR3", "Basespace illumina platform was used and reads were mapped using tophate2 aligner. Estimation of reference genes and transcript was done using cufflinks and reads were mapped to the genome GRCz10. Reads were aligned with the TopHat Alignment App. GRCz10 CSV file that compiled includes tracking ids  gene loci  and FPKMs for each samples CSV files include tracking and gene id  gene short name  tss id  locus  and FPKM for each sample", "Gonad", null, "RNA was extracted with an Rneasy Mini Kit Qiagen  74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina  20020589", null, "tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype", "GSM8059038", "GSM8059038: Rbpms2 mApple crosslinked SR3; Danio rerio; RNA Seq", "GSM8059038 r1", "GSM8059038", "1", "RNA was extracted with an Rneasy Mini Kit Qiagen  74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina  20020589", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, null, "SR-3_S4_L001_R1_001.fastq.gz SR-3_S4_L001_R2_001.fastq.gz", "fastq fastq", 588252864.0, 3949222.0, "GSM8059038 r1", "0:74.42 1:74.53", "A:116383167;C:176622592;G:176850622;T:118306997;N:89486", 74, 74, null, null, 116383167, 176622592, 176850622, 118306997, 89486, "SRX23499420", "SRS20351177", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [30557, "SRR27836072", "SRX23499419", "SRS20351178", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "Rbpms2 mApple uncrosslinked SR2", "GSM8059037", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing", "Rbpms2 mApple uncrosslinked SR2", "Basespace illumina platform was used and reads were mapped using tophate2 aligner. Estimation of reference genes and transcript was done using cufflinks and reads were mapped to the genome GRCz10. Reads were aligned with the TopHat Alignment App. GRCz10 CSV file that compiled includes tracking ids  gene loci  and FPKMs for each samples CSV files include tracking and gene id  gene short name  tss id  locus  and FPKM for each sample", "Gonad", null, "RNA was extracted with an Rneasy Mini Kit Qiagen  74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina  20020589", null, "tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype", "GSM8059037", "GSM8059037: Rbpms2 mApple uncrosslinked SR2; Danio rerio; RNA Seq", "GSM8059037 r1", "GSM8059037", "1", "RNA was extracted with an Rneasy Mini Kit Qiagen  74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina  20020589", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, null, "SR-2_S3_L001_R1_001.fastq.gz SR-2_S3_L001_R2_001.fastq.gz", "fastq fastq", 547329260.0, 3670350.0, "GSM8059037 r1", "0:74.51 1:74.61", "A:109193152;C:163365002;G:162344228;T:112378069;N:48809", 74, 74, null, null, 109193152, 163365002, 162344228, 112378069, 48809, "SRX23499419", "SRS20351178", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [30558, "SRR27836073", "SRX23499418", "SRS20351176", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "mApple control crosslinked SR8", "GSM8059036", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing", "mApple control crosslinked SR8", "Basespace illumina platform was used and reads were mapped using tophate2 aligner. Estimation of reference genes and transcript was done using cufflinks and reads were mapped to the genome GRCz10. Reads were aligned with the TopHat Alignment App. GRCz10 CSV file that compiled includes tracking ids  gene loci  and FPKMs for each samples CSV files include tracking and gene id  gene short name  tss id  locus  and FPKM for each sample", "Gonad", null, "RNA was extracted with an Rneasy Mini Kit Qiagen  74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina  20020589", null, "tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype", "GSM8059036", "GSM8059036: mApple control crosslinked SR8; Danio rerio; RNA Seq", "GSM8059036 r1", "GSM8059036", "1", "RNA was extracted with an Rneasy Mini Kit Qiagen  74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina  20020589", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, null, "SR-8_S6_L001_R1_001.fastq.gz SR-8_S6_L001_R2_001.fastq.gz", "fastq fastq", 474378287.0, 3180744.0, "GSM8059036 r1", "0:74.52 1:74.62", "A:90310344;C:145884340;G:146185172;T:91942086;N:56345", 74, 74, null, null, 90310344, 145884340, 146185172, 91942086, 56345, "SRX23499418", "SRS20351176", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [30559, "SRR27836074", "SRX23499417", "SRS20351175", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "mApple control uncrosslinked SR6", "GSM8059035", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing", "mApple control uncrosslinked SR6", "Basespace illumina platform was used and reads were mapped using tophate2 aligner. Estimation of reference genes and transcript was done using cufflinks and reads were mapped to the genome GRCz10. Reads were aligned with the TopHat Alignment App. GRCz10 CSV file that compiled includes tracking ids  gene loci  and FPKMs for each samples CSV files include tracking and gene id  gene short name  tss id  locus  and FPKM for each sample", "Gonad", null, "RNA was extracted with an Rneasy Mini Kit Qiagen  74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina  20020589", null, "tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype", "GSM8059035", "GSM8059035: mApple control uncrosslinked SR6; Danio rerio; RNA Seq", "GSM8059035 r1", "GSM8059035", "1", "RNA was extracted with an Rneasy Mini Kit Qiagen  74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina  20020589", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, null, "SR-6_S5_L001_R1_001.fastq.gz SR-6_S5_L001_R2_001.fastq.gz", "fastq fastq", 1667210566.0, 11187841.0, "GSM8059035 r1", "0:74.46 1:74.56", "A:348153529;C:480420209;G:474792496;T:363567978;N:276354", 74, 74, null, null, 348153529, 480420209, 474792496, 363567978, 276354, "SRX23499417", "SRS20351175", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [30560, "SRR27836075", "SRX23499416", "SRS20351174", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 mutant 4  21 dpf", "GSM8059034", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing", "rbpms2 mutant 4  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM", "GSM8059034", "GSM8059034: rbpms2 mutant 4  21 dpf; Danio rerio; RNA Seq", "GSM8059034 r1", "GSM8059034", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-DM_4_S8_L001_R1_001.fastq.gz rbpms2-d21-DM_4_S8_L001_R2_001.fastq.gz", "fastq fastq", 2533252722.0, 24835811.0, "GSM8059034 r1", "0:51 1:51", "A:767895104;C:496128064;G:502250517;T:766951391;N:27646", 51, 51, null, null, 767895104, 496128064, 502250517, 766951391, 27646, "SRX23499416", "SRS20351174", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [30561, "SRR27836076", "SRX23499416", "SRS20351174", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 mutant 4  21 dpf", "GSM8059034", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing", "rbpms2 mutant 4  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM", "GSM8059034", "GSM8059034: rbpms2 mutant 4  21 dpf; Danio rerio; RNA Seq", "GSM8059034 r1", "GSM8059034", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-DM_4_S8_L002_R1_001.fastq.gz rbpms2-d21-DM_4_S8_L002_R2_001.fastq.gz", "fastq fastq", 2500214514.0, 24511907.0, "GSM8059034 r2", "0:51 1:51", "A:757980090;C:489633622;G:495839519;T:756737989;N:23294", 51, 51, null, null, 757980090, 489633622, 495839519, 756737989, 23294, "SRX23499416", "SRS20351174", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [30562, "SRR27836077", "SRX23499415", "SRS20351173", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 mutant 3  21 dpf", "GSM8059033", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing", "rbpms2 mutant 3  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM", "GSM8059033", "GSM8059033: rbpms2 mutant 3  21 dpf; Danio rerio; RNA Seq", "GSM8059033 r1", "GSM8059033", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-DM_3_S7_L001_R1_001.fastq.gz rbpms2-d21-DM_3_S7_L001_R2_001.fastq.gz", "fastq fastq", 2383569354.0, 23368327.0, "GSM8059033 r1", "0:51 1:51", "A:705650487;C:468856307;G:473479720;T:735556568;N:26272", 51, 51, null, null, 705650487, 468856307, 473479720, 735556568, 26272, "SRX23499415", "SRS20351173", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [30563, "SRR27836078", "SRX23499415", "SRS20351173", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 mutant 3  21 dpf", "GSM8059033", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing", "rbpms2 mutant 3  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM", "GSM8059033", "GSM8059033: rbpms2 mutant 3  21 dpf; Danio rerio; RNA Seq", "GSM8059033 r1", "GSM8059033", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-DM_3_S7_L002_R1_001.fastq.gz rbpms2-d21-DM_3_S7_L002_R2_001.fastq.gz", "fastq fastq", 2324856114.0, 22792707.0, "GSM8059033 r2", "0:51 1:51", "A:688232198;C:457346277;G:462034541;T:717221485;N:21613", 51, 51, null, null, 688232198, 457346277, 462034541, 717221485, 21613, "SRX23499415", "SRS20351173", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [30564, "SRR27836079", "SRX23499414", "SRS20351172", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 mutant 1  21 dpf", "GSM8059032", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing", "rbpms2 mutant 1  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM", "GSM8059032", "GSM8059032: rbpms2 mutant 1  21 dpf; Danio rerio; RNA Seq", "GSM8059032 r1", "GSM8059032", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-DM_1_S5_L001_R1_001.fastq.gz rbpms2-d21-DM_1_S5_L001_R2_001.fastq.gz", "fastq fastq", 2412458100.0, 23651550.0, "GSM8059032 r1", "0:51 1:51", "A:726246267;C:465733066;G:465377798;T:755071663;N:29306", 51, 51, null, null, 726246267, 465733066, 465377798, 755071663, 29306, "SRX23499414", "SRS20351172", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [30565, "SRR27836080", "SRX23499414", "SRS20351172", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 mutant 1  21 dpf", "GSM8059032", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing", "rbpms2 mutant 1  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM", "GSM8059032", "GSM8059032: rbpms2 mutant 1  21 dpf; Danio rerio; RNA Seq", "GSM8059032 r1", "GSM8059032", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-DM_1_S5_L002_R1_001.fastq.gz rbpms2-d21-DM_1_S5_L002_R2_001.fastq.gz", "fastq fastq", 2363898144.0, 23175472.0, "GSM8059032 r2", "0:51 1:51", "A:711756208;C:456236364;G:456088591;T:739792903;N:24078", 51, 51, null, null, 711756208, 456236364, 456088591, 739792903, 24078, "SRX23499414", "SRS20351172", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [30566, "SRR27836081", "SRX23499413", "SRS20351171", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 wildtype 3  21 dpf", "GSM8059031", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing", "rbpms2 wildtype 3  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype", "GSM8059031", "GSM8059031: rbpms2 wildtype 3  21 dpf; Danio rerio; RNA Seq", "GSM8059031 r1", "GSM8059031", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-WT_3_S3_L001_R1_001.fastq.gz rbpms2-d21-WT_3_S3_L001_R2_001.fastq.gz", "fastq fastq", 2048418162.0, 20082531.0, "GSM8059031 r1", "0:51 1:51", "A:612611264;C:409068349;G:413909657;T:612805097;N:23795", 51, 51, null, null, 612611264, 409068349, 413909657, 612805097, 23795, "SRX23499413", "SRS20351171", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [30567, "SRR27836082", "SRX23499413", "SRS20351171", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 wildtype 3  21 dpf", "GSM8059031", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing", "rbpms2 wildtype 3  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype", "GSM8059031", "GSM8059031: rbpms2 wildtype 3  21 dpf; Danio rerio; RNA Seq", "GSM8059031 r1", "GSM8059031", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-WT_3_S3_L002_R1_001.fastq.gz rbpms2-d21-WT_3_S3_L002_R2_001.fastq.gz", "fastq fastq", 2018915070.0, 19793285.0, "GSM8059031 r2", "0:51 1:51", "A:603776465;C:403221066;G:408169193;T:603728354;N:19992", 51, 51, null, null, 603776465, 403221066, 408169193, 603728354, 19992, "SRX23499413", "SRS20351171", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [30568, "SRR27836083", "SRX23499412", "SRS20351179", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 wildtype 2  21 dpf", "GSM8059030", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing", "rbpms2 wildtype 2  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype", "GSM8059030", "GSM8059030: rbpms2 wildtype 2  21 dpf; Danio rerio; RNA Seq", "GSM8059030 r1", "GSM8059030", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-WT_2_S2_L001_R1_001.fastq.gz rbpms2-d21-WT_2_S2_L001_R2_001.fastq.gz", "fastq fastq", 1927777866.0, 18899783.0, "GSM8059030 r1", "0:51 1:51", "A:589122616;C:372230241;G:374787285;T:591617780;N:19944", 51, 51, null, null, 589122616, 372230241, 374787285, 591617780, 19944, "SRX23499412", "SRS20351179", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [30569, "SRR27836084", "SRX23499412", "SRS20351179", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 wildtype 2  21 dpf", "GSM8059030", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing", "rbpms2 wildtype 2  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype", "GSM8059030", "GSM8059030: rbpms2 wildtype 2  21 dpf; Danio rerio; RNA Seq", "GSM8059030 r1", "GSM8059030", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-WT_2_S2_L002_R1_001.fastq.gz rbpms2-d21-WT_2_S2_L002_R2_001.fastq.gz", "fastq fastq", 1901436570.0, 18641535.0, "GSM8059030 r2", "0:51 1:51", "A:581077435;C:367152917;G:369822980;T:583366137;N:17101", 51, 51, null, null, 581077435, 367152917, 369822980, 583366137, 17101, "SRX23499412", "SRS20351179", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [30570, "SRR27836085", "SRX23499411", "SRS20351170", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 wildtype 1  21 dpf", "GSM8059029", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing", "rbpms2 wildtype 1  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype", "GSM8059029", "GSM8059029: rbpms2 wildtype 1  21 dpf; Danio rerio; RNA Seq", "GSM8059029 r1", "GSM8059029", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-WT_1_S1_L001_R1_001.fastq.gz rbpms2-d21-WT_1_S1_L001_R2_001.fastq.gz", "fastq fastq", 1878693222.0, 18418561.0, "GSM8059029 r1", "0:51 1:51", "A:581058368;C:356028122;G:360378733;T:581204723;N:23276", 51, 51, null, null, 581058368, 356028122, 360378733, 581204723, 23276, "SRX23499411", "SRS20351170", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [30571, "SRR27836086", "SRX23499411", "SRS20351170", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 wildtype 1  21 dpf", "GSM8059029", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing", "rbpms2 wildtype 1  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype", "GSM8059029", "GSM8059029: rbpms2 wildtype 1  21 dpf; Danio rerio; RNA Seq", "GSM8059029 r1", "GSM8059029", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-WT_1_S1_L002_R1_001.fastq.gz rbpms2-d21-WT_1_S1_L002_R2_001.fastq.gz", "fastq fastq", 1861916160.0, 18254080.0, "GSM8059029 r2", "0:51 1:51", "A:575859972;C:352771580;G:357641601;T:575624138;N:18869", 51, 51, null, null, 575859972, 352771580, 357641601, 575624138, 18869, "SRX23499411", "SRS20351170", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [32476, "SRR29270149", "SRX24787634", "SRS21505104", "SRP511487", "PRJNA1119569", "RNA seq of zebrafish foxl2l mutant", "PRJNA1119569", "Other", "Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.", null, null, null, null, "foxl2l Mut 20 1", null, "strain:AB|age:20|collection date:2023 06 10|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "foxl2l Mut 20 1", "E10", "E10", "50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme  NR604 01", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP511487", null, null, "foxl2l_Mut-20-1_S162_R1.fastq.gz foxl2l_Mut-20-1_S162_R2.fastq.gz", "fastq fastq", 8940963680.0, 29605840.0, "foxl2l Mut 20 1 S162 R1.fastq.gz", "0:151 1:151", "A:2232167098;C:2229744850;G:2271326718;T:2207692629;N:32385", 151, 151, null, null, 2232167098, 2229744850, 2271326718, 2207692629, 32385, "SRX24787634", "SRS21505104", "SRA1887976", "Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology", "Institute of Hydrobiology, Chinese Academy of Sciences", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "China", "2024-06-03", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [32477, "SRR29270150", "SRX24787633", "SRS21505103", "SRP511487", "PRJNA1119569", "RNA seq of zebrafish foxl2l mutant", "PRJNA1119569", "Other", "Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. 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This is particularly salient in aquatic ecosystems  where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end  zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that  in males  nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction  resulting in viable spermatozoa but with reduced motility. Moreover  in females we observed an alteration in oocyte stages frequencies during oogenesis  possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure  meiosis and DNA double strand break formation and repair progression  and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall  our results demonstrate that acute exposure to NPs can compromise reproductive fitness  underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples", null, "pubmed:39556913", null, "Zebrafish  Testicle  Plastic  Replicate 3  Animal 3", "GSM8583344", null, "source name:testicles|tissue:testicles|cell line:germline|genotype:WT|treatment:Plastic|geo loc name:missing|collection date:missing", "Zebrafish  Testicle  Plastic  Replicate 3  Animal 3", "Anaconda The sequencing quality was checked before performing the assembly. 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This is particularly salient in aquatic ecosystems  where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end  zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that  in males  nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction  resulting in viable spermatozoa but with reduced motility. Moreover  in females we observed an alteration in oocyte stages frequencies during oogenesis  possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure  meiosis and DNA double strand break formation and repair progression  and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall  our results demonstrate that acute exposure to NPs can compromise reproductive fitness  underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples", null, "pubmed:39556913", null, "Zebrafish  Testicle  Plastic  Replicate 3  Animal 1", "GSM8583343", null, "source name:testicles|tissue:testicles|cell line:germline|genotype:WT|treatment:Plastic|geo loc name:missing|collection date:missing", "Zebrafish  Testicle  Plastic  Replicate 3  Animal 1", "Anaconda The sequencing quality was checked before performing the assembly. STAR bioconda was used for the assembly smartools bioconda was used to generate the intermediate files Sam and Bam Counts were obtained from the bam intermediate file Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample", "testicles", "Half of the fish were exposed to polystyrene nanoplastics each 24 hours added in the water during 96 hours accute exposure. The rest were used as controls  so no plastics were added in the water.", "Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment", "Adult zebrafish were maintained at the animal house under standard conditions", "tissue:testicles|cell line:germline|genotype:WT|treatment:Plastic", "GSM8583343", "GSM8583343: Zebrafish  Testicle  Plastic  Replicate 3  Animal 1; Danio rerio; RNA Seq", "GSM8583343 r1", "GSM8583343", "1", "Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP539687", null, null, "M6_C2_R3_A1_EKRN230074902-1A_HWT7HDSX7_L3_1.fq M6_C2_R3_A1_EKRN230074902-1A_HWT7HDSX7_L3_2.fq", "fastq fastq", 21334650000.0, 71115500.0, "GSM8583343 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX26435350", "SRS22952030", "SRA1994234", "UAB (Universidad Aut\u00f3noma de Barcelona)", "UAB (Universidad Aut\u00f3noma de Barcelona)", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Spain", "2024-10-20", "Adult", "Adult", "Gonad", "Reproductive System"], [34096, "SRR31050911", "SRX26435349", "SRS22952029", "SRP539687", "PRJNA1175381", "Short term polystyrene nanoplastic exposure alters zebrafish male and female germline and reproductive outcomes  unveiling pollutant impacted molecular pathways", "GSE279916", "Transcriptome Analysis", "Nanoplastics pollution is a rising environmental concern whose impacts on biodiversity and human health are far from being understood. This is particularly salient in aquatic ecosystems  where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end  zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that  in males  nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction  resulting in viable spermatozoa but with reduced motility. Moreover  in females we observed an alteration in oocyte stages frequencies during oogenesis  possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure  meiosis and DNA double strand break formation and repair progression  and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall  our results demonstrate that acute exposure to NPs can compromise reproductive fitness  underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples", null, "pubmed:39556913", null, "Zebrafish  Testicle  Plastic  Replicate 2  Animal 2", "GSM8583342", null, "source name:testicles|tissue:testicles|cell line:germline|genotype:WT|treatment:Plastic|geo loc name:missing|collection date:missing", "Zebrafish  Testicle  Plastic  Replicate 2  Animal 2", "Anaconda The sequencing quality was checked before performing the assembly. STAR bioconda was used for the assembly smartools bioconda was used to generate the intermediate files Sam and Bam Counts were obtained from the bam intermediate file Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample", "testicles", "Half of the fish were exposed to polystyrene nanoplastics each 24 hours added in the water during 96 hours accute exposure. The rest were used as controls  so no plastics were added in the water.", "Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment", "Adult zebrafish were maintained at the animal house under standard conditions", "tissue:testicles|cell line:germline|genotype:WT|treatment:Plastic", "GSM8583342", "GSM8583342: Zebrafish  Testicle  Plastic  Replicate 2  Animal 2; Danio rerio; RNA Seq", "GSM8583342 r1", "GSM8583342", "1", "Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP539687", null, null, "M6_C2_R2_A2_EKRN230074901-1A_HWT7HDSX7_L2_1.fq M6_C2_R2_A2_EKRN230074901-1A_HWT7HDSX7_L2_2.fq", "fastq fastq", 23956812900.0, 79856043.0, "GSM8583342 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX26435349", "SRS22952029", "SRA1994234", "UAB (Universidad Aut\u00f3noma de Barcelona)", "UAB (Universidad Aut\u00f3noma de Barcelona)", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Spain", "2024-10-20", "Adult", "Adult", "Gonad", "Reproductive System"], [34097, "SRR31050912", "SRX26435348", "SRS22952028", "SRP539687", "PRJNA1175381", "Short term polystyrene nanoplastic exposure alters zebrafish male and female germline and reproductive outcomes  unveiling pollutant impacted molecular pathways", "GSE279916", "Transcriptome Analysis", "Nanoplastics pollution is a rising environmental concern whose impacts on biodiversity and human health are far from being understood. This is particularly salient in aquatic ecosystems  where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end  zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that  in males  nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction  resulting in viable spermatozoa but with reduced motility. Moreover  in females we observed an alteration in oocyte stages frequencies during oogenesis  possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure  meiosis and DNA double strand break formation and repair progression  and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall  our results demonstrate that acute exposure to NPs can compromise reproductive fitness  underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples", null, "pubmed:39556913", null, "Zebrafish  Testicle  Control  Replicate 3  Animal 1", "GSM8583341", null, "source name:testicles|tissue:testicles|cell line:germline|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing", "Zebrafish  Testicle  Control  Replicate 3  Animal 1", "Anaconda The sequencing quality was checked before performing the assembly. STAR bioconda was used for the assembly smartools bioconda was used to generate the intermediate files Sam and Bam Counts were obtained from the bam intermediate file Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample", "testicles", "Half of the fish were exposed to polystyrene nanoplastics each 24 hours added in the water during 96 hours accute exposure. The rest were used as controls  so no plastics were added in the water.", "Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment", "Adult zebrafish were maintained at the animal house under standard conditions", "tissue:testicles|cell line:germline|genotype:WT|treatment:Control", "GSM8583341", "GSM8583341: Zebrafish  Testicle  Control  Replicate 3  Animal 1; Danio rerio; RNA Seq", "GSM8583341 r1", "GSM8583341", "1", "Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP539687", null, null, "M6_C1_R3_A1_EKRN230074898-1A_HWT7HDSX7_L2_1.fq M6_C1_R3_A1_EKRN230074898-1A_HWT7HDSX7_L2_2.fq", "fastq fastq", 17143802100.0, 57146007.0, "GSM8583341 r1", "0:150 1:150", "A:4588084574;C:4015807096;G:4039433882;T:4500279277;N:197271", 150, 150, null, null, 4588084574, 4015807096, 4039433882, 4500279277, 197271, "SRX26435348", "SRS22952028", "SRA1994234", "UAB (Universidad Aut\u00f3noma de Barcelona)", "UAB (Universidad Aut\u00f3noma de Barcelona)", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Spain", "2024-10-20", "Adult", "Adult", "Gonad", "Reproductive System"], [34098, "SRR31050913", "SRX26435347", "SRS22952027", "SRP539687", "PRJNA1175381", "Short term polystyrene nanoplastic exposure alters zebrafish male and female germline and reproductive outcomes  unveiling pollutant impacted molecular pathways", "GSE279916", "Transcriptome Analysis", "Nanoplastics pollution is a rising environmental concern whose impacts on biodiversity and human health are far from being understood. This is particularly salient in aquatic ecosystems  where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end  zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that  in males  nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction  resulting in viable spermatozoa but with reduced motility. Moreover  in females we observed an alteration in oocyte stages frequencies during oogenesis  possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure  meiosis and DNA double strand break formation and repair progression  and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall  our results demonstrate that acute exposure to NPs can compromise reproductive fitness  underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples", null, "pubmed:39556913", null, "Zebrafish  Testicle  Control  Replicate 2  Animal 2", "GSM8583340", null, "source name:testicles|tissue:testicles|cell line:germline|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing", "Zebrafish  Testicle  Control  Replicate 2  Animal 2", "Anaconda The sequencing quality was checked before performing the assembly. STAR bioconda was used for the assembly smartools bioconda was used to generate the intermediate files Sam and Bam Counts were obtained from the bam intermediate file Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample", "testicles", "Half of the fish were exposed to polystyrene nanoplastics each 24 hours added in the water during 96 hours accute exposure. The rest were used as controls  so no plastics were added in the water.", "Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment", "Adult zebrafish were maintained at the animal house under standard conditions", "tissue:testicles|cell line:germline|genotype:WT|treatment:Control", "GSM8583340", "GSM8583340: Zebrafish  Testicle  Control  Replicate 2  Animal 2; Danio rerio; RNA Seq", "GSM8583340 r1", "GSM8583340", "1", "Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP539687", null, null, "M6_C1_R2_A2_1.fq M6_C1_R2_A2_2.fq", "fastq fastq", 17289440100.0, 57631467.0, "GSM8583340 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX26435347", "SRS22952027", "SRA1994234", "UAB (Universidad Aut\u00f3noma de Barcelona)", "UAB (Universidad Aut\u00f3noma de Barcelona)", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Spain", "2024-10-20", "Adult", "Adult", "Gonad", "Reproductive System"], [34099, "SRR31050914", "SRX26435346", "SRS22952026", "SRP539687", "PRJNA1175381", "Short term polystyrene nanoplastic exposure alters zebrafish male and female germline and reproductive outcomes  unveiling pollutant impacted molecular pathways", "GSE279916", "Transcriptome Analysis", "Nanoplastics pollution is a rising environmental concern whose impacts on biodiversity and human health are far from being understood. This is particularly salient in aquatic ecosystems  where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end  zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that  in males  nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction  resulting in viable spermatozoa but with reduced motility. Moreover  in females we observed an alteration in oocyte stages frequencies during oogenesis  possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure  meiosis and DNA double strand break formation and repair progression  and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall  our results demonstrate that acute exposure to NPs can compromise reproductive fitness  underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples", null, "pubmed:39556913", null, "Zebrafish  Testicle  Control  Replicate 1  Animal 2", "GSM8583339", null, "source name:testicles|tissue:testicles|cell line:germline|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing", "Zebrafish  Testicle  Control  Replicate 1  Animal 2", "Anaconda The sequencing quality was checked before performing the assembly. STAR bioconda was used for the assembly smartools bioconda was used to generate the intermediate files Sam and Bam Counts were obtained from the bam intermediate file Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample", "testicles", "Half of the fish were exposed to polystyrene nanoplastics each 24 hours added in the water during 96 hours accute exposure. The rest were used as controls  so no plastics were added in the water.", "Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment", "Adult zebrafish were maintained at the animal house under standard conditions", "tissue:testicles|cell line:germline|genotype:WT|treatment:Control", "GSM8583339", "GSM8583339: Zebrafish  Testicle  Control  Replicate 1  Animal 2; Danio rerio; RNA Seq", "GSM8583339 r1", "GSM8583339", "1", "Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP539687", null, null, "M6_C1_R1_A2_EKRN230074896-1A_HWT7HDSX7_L2_1.fq M6_C1_R1_A2_EKRN230074896-1A_HWT7HDSX7_L2_2.fq", "fastq fastq", 19275937200.0, 64253124.0, "GSM8583339 r1", "0:150 1:150", "A:5148413409;C:4525316389;G:4541110001;T:5060873310;N:224091", 150, 150, null, null, 5148413409, 4525316389, 4541110001, 5060873310, 224091, "SRX26435346", "SRS22952026", "SRA1994234", "UAB (Universidad Aut\u00f3noma de Barcelona)", "UAB (Universidad Aut\u00f3noma de Barcelona)", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Spain", "2024-10-20", "Adult", "Adult", "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.", null, null, null, "LB023 mutant B", "LB023 Mut B", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "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, null, null, 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", null, "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.", null, null, null, "LB023 mutant C", "LB023 Mut C", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "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, null, null, 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", null, "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.", null, null, null, "LB023 wildtype sibling control D", "LB023 WT D", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "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, null, null, 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", null, "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.", null, null, null, "adad1 mutant E", "adad1 Mut E", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "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, null, null, 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", null, "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.", null, null, null, "adad1 mutant F", "adad1 Mut F", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "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, null, null, 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", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76361, "SRR24844105", "SRX20608296", "SRS17908189", "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.", null, null, null, "adad1 wildtype sibling control A", "adad1 WT A", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:WildtypeA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 wildtype sibling: male testes", "adad1 WT A", "adad1 WT A", "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "adad1-WT-A_R1_001.fastq.gz adad1-WT-A_R2_001.fastq.gz", "fastq fastq", 8011954200.0, 26706514.0, "adad1 WT A R1 001.fastq.gz", "0:150 1:150", "A:2090202005;C:1898897650;G:2026356221;T:1996371474;N:126850", 150, 150, null, null, 2090202005, 1898897650, 2026356221, 1996371474, 126850, "SRX20608296", "SRS17908189", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.91189, 0.91021, 0.06102, 0.06139, 0.68525, 0.68718, 0.50676, 0.50889, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76362, "SRR24844106", "SRX20608295", "SRS17908186", "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.", null, null, null, "adad1 wildtype sibling control B", "adad1 WT B", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:WildtypeB|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 wildtype sibling: male testes", "adad1 WT B", "adad1 WT 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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "adad1-WT-B_R1_001.fastq.gz adad1-WT-B_R2_001.fastq.gz", "fastq fastq", 7492292100.0, 24974307.0, "adad1 WT B R1 001.fastq.gz", "0:150 1:150", "A:1943185783;C:1771813934;G:1904551325;T:1872624369;N:116689", 150, 150, null, null, 1943185783, 1771813934, 1904551325, 1872624369, 116689, "SRX20608295", "SRS17908186", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.90916, 0.90763, 0.11162, 0.11123, 0.67399, 0.6743, 0.52068, 0.52927, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76363, "SRR24844107", "SRX20608294", "SRS17908185", "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.", null, null, null, "adad1 wildtype sibling control C", "adad1 WT C", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:WildtypeC|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 wildtype sibling: male testes", "adad1 WT C", "adad1 WT 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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "adad1-WT-C_R2_001.fastq.gz adad1-WT-C_R1_001.fastq.gz", "fastq fastq", 7521501900.0, 25071673.0, "adad1 WT C R1 001.fastq.gz", "0:150 1:150", "A:1804312038;C:1905161135;G:2076680572;T:1735230886;N:117269", 150, 150, null, null, 1804312038, 1905161135, 2076680572, 1735230886, 117269, "SRX20608294", "SRS17908185", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.91415, 0.91424, 0.1126, 0.11157, 0.72861, 0.72924, 0.60581, 0.59123, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76364, "SRR24844111", "SRX20608293", "SRS17908188", "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.", null, null, null, "adad1 wildtype sibling control D", "adad1 WT D", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:WildtypeD|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 wildtype sibling: male testes", "adad1 WT D", "adad1 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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "adad1-WT-D_R2_001.fastq.gz adad1-WT-D_R1_001.fastq.gz", "fastq fastq", 6723661500.0, 22412205.0, "adad1 WT D R1 001.fastq.gz", "0:150 1:150", "A:1762783841;C:1577461245;G:1700257202;T:1683053935;N:105277", 150, 150, null, null, 1762783841, 1577461245, 1700257202, 1683053935, 105277, "SRX20608293", "SRS17908188", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.90669, 0.90515, 0.1057, 0.1054, 0.7055, 0.70648, 0.53378, 0.53859, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76365, "SRR24844108", "SRX20608292", "SRS17908183", "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.", null, null, null, "LB023 wildtype sibling control C", "LB023 WT C", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense WildtypeC|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 missense wildtype sibling: male testes", "LB023 WT C", "LB023 WT 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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "LB023-WT-C_R1_001.fastq.gz LB023-WT-C_R2_001.fastq.gz", "fastq fastq", 6931350600.0, 23104502.0, "LB023 WT C R1 001.fastq.gz", "0:150 1:150", "A:1738105921;C:1615563430;G:1915220365;T:1662351851;N:109033", 150, 150, null, null, 1738105921, 1615563430, 1915220365, 1662351851, 109033, "SRX20608292", "SRS17908183", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.85918, 0.86008, 0.0973, 0.0972, 0.75621, 0.75617, 0.51414, 0.52127, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76366, "SRR24844109", "SRX20608291", "SRS17908182", "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.", null, null, null, "LB023 wildtype sibling control B", "LB023 WT B", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense WildtypeB|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 missense wildtype sibling: male testes", "LB023 WT B", "LB023 WT 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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "LB023-WT-B_R1_001.fastq.gz LB023-WT-B_R2_001.fastq.gz", "fastq fastq", 6486567300.0, 21621891.0, "LB023 WT B R1 001.fastq.gz", "0:150 1:150", "A:1659315544;C:1565803285;G:1669608945;T:1591739895;N:99631", 150, 150, null, null, 1659315544, 1565803285, 1669608945, 1591739895, 99631, "SRX20608291", "SRS17908182", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.92214, 0.92196, 0.09064, 0.09079, 0.70092, 0.70207, 0.54638, 0.55145, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76367, "SRR24844110", "SRX20608290", "SRS17908184", "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.", null, null, null, "LB023 wildtype sibling control A", "LB023 WT A", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense WildtypeA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 missense wildtype sibling: male testes", "LB023 WT A", "LB023 WT A", "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "LB023-WT-A_R1_001.fastq.gz LB023-WT-A_R2_001.fastq.gz", "fastq fastq", 7085531700.0, 23618439.0, "LB023 WT A R1 001.fastq.gz", "0:150 1:150", "A:1870324648;C:1666204540;G:1769576825;T:1779314498;N:111189", 150, 150, null, null, 1870324648, 1666204540, 1769576825, 1779314498, 111189, "SRX20608290", "SRS17908184", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.91831, 0.91753, 0.06037, 0.06044, 0.70307, 0.70368, 0.51531, 0.51099, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76368, "SRR24844112", "SRX20608289", "SRS17908179", "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.", null, null, null, "LB023 mutant F", "LB023 Mut F", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense MutantF|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 missense mutant: male testes", "LB023 Mut F", "LB023 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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "LB023-Mut-F_R1_001.fastq.gz LB023-Mut-F_R2_001.fastq.gz", "fastq fastq", 7753356600.0, 25844522.0, "LB023 Mut F R1 001.fastq.gz", "0:150 1:150", "A:2031483621;C:1809017944;G:1970064517;T:1942669709;N:120809", 150, 150, null, null, 2031483621, 1809017944, 1970064517, 1942669709, 120809, "SRX20608289", "SRS17908179", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.87475, 0.87314, 0.09092, 0.09089, 0.75373, 0.75434, 0.5602, 0.56521, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76369, "SRR24844113", "SRX20608288", "SRS17908178", "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.", null, null, null, "LB023 mutant E", "LB023 Mut E", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense MutantE|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 missense mutant: male testes", "LB023 Mut E", "LB023 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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "LB023-Mut-E_R1_001.fastq.gz LB023-Mut-E_R2_001.fastq.gz", "fastq fastq", 4532652000.0, 15108840.0, "LB023 Mut E R1 001.fastq.gz", "0:150 1:150", "A:1199854650;C:1037858889;G:1150707006;T:1144159494;N:71961", 150, 150, null, null, 1199854650, 1037858889, 1150707006, 1144159494, 71961, "SRX20608288", "SRS17908178", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.87501, 0.87504, 0.08393, 0.08384, 0.76021, 0.76055, 0.54045, 0.54351, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76370, "SRR24844114", "SRX20608287", "SRS17908181", "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.", null, null, null, "adad1 mutant C", "adad1 Mut C", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:MutantC|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 mutant: male testes", "adad1 Mut C", "adad1 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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "adad1-Mut-C_R1_001.fastq.gz adad1-Mut-C_R2_001.fastq.gz", "fastq fastq", 7938136500.0, 26460455.0, "adad1 Mut C R1 001.fastq.gz", "0:150 1:150", "A:2011717685;C:1935444799;G:2053481206;T:1937375239;N:117571", 150, 150, null, null, 2011717685, 1935444799, 2053481206, 1937375239, 117571, "SRX20608287", "SRS17908181", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.92456, 0.92396, 0.08714, 0.08738, 0.70575, 0.70826, 0.5441, 0.52561, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76371, "SRR24844115", "SRX20608286", "SRS17908180", "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.", null, null, null, "adad1 mutant A", "adad1 Mut A", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:MutantA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 mutant: male testes", "adad1 Mut A", "adad1 Mut A", "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "adad1-Mut-A_R1_001.fastq.gz adad1-Mut-A_R2_001.fastq.gz", "fastq fastq", 7254148200.0, 24180494.0, "adad1 Mut A R1 001.fastq.gz", "0:150 1:150", "A:1849587944;C:1771248935;G:1861148471;T:1772049096;N:113754", 150, 150, null, null, 1849587944, 1771248935, 1861148471, 1772049096, 113754, "SRX20608286", "SRS17908180", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.93069, 0.93108, 0.10454, 0.10422, 0.69899, 0.70088, 0.53698, 0.55029, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"]], "truncated": false, "filtered_table_rows_count": 68, "expanded_columns": [], "expandable_columns": [], "columns": ["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", 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[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], 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