{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"cDNA\", technology = \"bulk\" and tissue_curation_coarse = \"Reproductive System\"", "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"], [30755, "SRR28348921", "SRX23954975", "SRS20755396", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage IV  rep2", "GSM8147872", null, "source name:Oocyte|tissue:Oocyte|developmental stage:Stage IV|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Oocyte  Stage IV  rep2", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Oocyte", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Oocyte|developmental stage:Stage IV|genotype:AB  TF and TLF", "GSM8147872", "GSM8147872: Zebrafish Oocyte  Stage IV  rep2; Danio rerio; RNA Seq", "GSM8147872 r1", "GSM8147872", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "Z_oocyte_stage_4_2_Pa.fastq", "fastq", 2456514332.0, 32322557.0, "GSM8147872 r1", "0:76", "A:588246161;C:609187233;G:593122683;T:665837765;N:120490", 76, null, null, null, 588246161, 609187233, 593122683, 665837765, 120490, "SRX23954975", "SRS20755396", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [30756, "SRR28348922", "SRX23954974", "SRS20755395", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage IV  rep1", "GSM8147871", null, "source name:Oocyte|tissue:Oocyte|developmental stage:Stage IV|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Oocyte  Stage IV  rep1", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Oocyte", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Oocyte|developmental stage:Stage IV|genotype:AB  TF and TLF", "GSM8147871", "GSM8147871: Zebrafish Oocyte  Stage IV  rep1; Danio rerio; RNA Seq", "GSM8147871 r1", "GSM8147871", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "Z_oocyte_stage_4_1_Pa.fastq", "fastq", 2650784696.0, 34878746.0, "GSM8147871 r1", "0:76", "A:649971632;C:640667370;G:632570967;T:727447552;N:127175", 76, null, null, null, 649971632, 640667370, 632570967, 727447552, 127175, "SRX23954974", "SRS20755395", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [30757, "SRR28348923", "SRX23954973", "SRS20755394", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage III  rep2", "GSM8147870", null, "source name:Oocyte|tissue:Oocyte|developmental stage:Stage III|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Oocyte  Stage III  rep2", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Oocyte", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Oocyte|developmental stage:Stage III|genotype:AB  TF and TLF", "GSM8147870", "GSM8147870: Zebrafish Oocyte  Stage III  rep2; Danio rerio; RNA Seq", "GSM8147870 r1", "GSM8147870", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "Z_oocyte_stage_3_2_Pa.fastq", "fastq", 2809957956.0, 36973131.0, "GSM8147870 r1", "0:76", "A:679041537;C:690924547;G:702857353;T:736996218;N:138301", 76, null, null, null, 679041537, 690924547, 702857353, 736996218, 138301, "SRX23954973", "SRS20755394", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [30758, "SRR28348924", "SRX23954972", "SRS20755393", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage III  rep1", "GSM8147869", null, "source name:Oocyte|tissue:Oocyte|developmental stage:Stage III|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Oocyte  Stage III  rep1", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Oocyte", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Oocyte|developmental stage:Stage III|genotype:AB  TF and TLF", "GSM8147869", "GSM8147869: Zebrafish Oocyte  Stage III  rep1; Danio rerio; RNA Seq", "GSM8147869 r1", "GSM8147869", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "Z_oocyte_stage_3_1_Pa.fastq", "fastq", 2828372376.0, 37215426.0, "GSM8147869 r1", "0:76", "A:701751055;C:680571938;G:664212213;T:781698241;N:138929", 76, null, null, null, 701751055, 680571938, 664212213, 781698241, 138929, "SRX23954972", "SRS20755393", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [30759, "SRR28348925", "SRX23954971", "SRS20755392", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage II  rep2", "GSM8147868", null, "source name:Oocyte|tissue:Oocyte|developmental stage:Stage II|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Oocyte  Stage II  rep2", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Oocyte", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Oocyte|developmental stage:Stage II|genotype:AB  TF and TLF", "GSM8147868", "GSM8147868: Zebrafish Oocyte  Stage II  rep2; Danio rerio; RNA Seq", "GSM8147868 r1", "GSM8147868", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "Z_oocyte_stage_2_2_Pa.fastq", "fastq", 2837652432.0, 37337532.0, "GSM8147868 r1", "0:76", "A:698931608;C:681467909;G:683751172;T:773364392;N:137351", 76, null, null, null, 698931608, 681467909, 683751172, 773364392, 137351, "SRX23954971", "SRS20755392", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [30760, "SRR28348926", "SRX23954970", "SRS20755391", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage II  rep1", "GSM8147867", null, "source name:Oocyte|tissue:Oocyte|developmental stage:Stage II|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Oocyte  Stage II  rep1", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Oocyte", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Oocyte|developmental stage:Stage II|genotype:AB  TF and TLF", "GSM8147867", "GSM8147867: Zebrafish Oocyte  Stage II  rep1; Danio rerio; RNA Seq", "GSM8147867 r1", "GSM8147867", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "Z_oocyte_stage_2_1_Pa.fastq", "fastq", 3360126820.0, 44212195.0, "GSM8147867 r1", "0:76", "A:829333798;C:802089215;G:804982077;T:923557236;N:164494", 76, null, null, null, 829333798, 802089215, 804982077, 923557236, 164494, "SRX23954970", "SRS20755391", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [30761, "SRR28348927", "SRX23954969", "SRS20755390", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage I  rep2", "GSM8147866", null, "source name:Oocyte|tissue:Oocyte|developmental stage:Stage I|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Oocyte  Stage I  rep2", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Oocyte", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Oocyte|developmental stage:Stage I|genotype:AB  TF and TLF", "GSM8147866", "GSM8147866: Zebrafish Oocyte  Stage I  rep2; Danio rerio; RNA Seq", "GSM8147866 r1", "GSM8147866", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "Z_oocyte_stage_1_2_Pa.fastq", "fastq", 2739674220.0, 36048345.0, "GSM8147866 r1", "0:76", "A:653441701;C:681445567;G:663740568;T:740918288;N:128096", 76, null, null, null, 653441701, 681445567, 663740568, 740918288, 128096, "SRX23954969", "SRS20755390", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [30762, "SRR28348928", "SRX23954968", "SRS20755389", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage I  rep1", "GSM8147865", null, "source name:Oocyte|tissue:Oocyte|developmental stage:Stage I|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Oocyte  Stage I  rep1", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Oocyte", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Oocyte|developmental stage:Stage I|genotype:AB  TF and TLF", "GSM8147865", "GSM8147865: Zebrafish Oocyte  Stage I  rep1; Danio rerio; RNA Seq", "GSM8147865 r1", "GSM8147865", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "Z_oocyte_stage_1_1_Pa.fastq", "fastq", 3348831852.0, 44063577.0, "GSM8147865 r1", "0:76", "A:815134657;C:817210346;G:809175239;T:907149915;N:161695", 76, null, null, null, 815134657, 817210346, 809175239, 907149915, 161695, "SRX23954968", "SRS20755389", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [34094, "SRR31050909", "SRX26435351", "SRS22952031", "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 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. 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", "GSM8583344", "GSM8583344: Zebrafish  Testicle  Plastic  Replicate 3  Animal 3; Danio rerio; RNA Seq", "GSM8583344 r1", "GSM8583344", "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_A3_EKRN230074904-1A_HWT7HDSX7_L3_1.fq M6_C2_R3_A3_EKRN230074904-1A_HWT7HDSX7_L3_2.fq", "fastq fastq", 24813339000.0, 82711130.0, "GSM8583344 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX26435351", "SRS22952031", "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"], [34095, "SRR31050910", "SRX26435350", "SRS22952030", "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 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"], [63340, "SRR13729837", "SRX10117846", "SRS8272547", "SRP306811", "PRJNA702290", "RNA Seq analysis of localization along animal vegetal axis of Danio rerio", "GSE166917", "Transcriptome Analysis", "Asymmetrical localization of biomolecules inside the egg  results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs  of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However  our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models  Xenopus laevis  Danio rerio  Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly  we revealed RNAs that code for many known important genes such as germ layer determinants  germ plasm factors and members of key signalling pathways  are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis  section A first animal to section E last vegetal  followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000  Thermo Scientific  and the quality of RNA was assessed using a Fragment Analyzer AATI  High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.", null, "pubmed:35752299", null, "Oocyte  4E Danio", "GSM5088021", null, "tissue:Oocyte  4E|segment:E last vegetal|cell type:Oocyte|oocyte id:4", "Oocyte  4E Danio", "Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al  2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.", "Oocyte  4E", null, "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", null, "segment:E last vegetal|cell type:Oocyte|oocyte id:4", "GSM5088021", "GSM5088021: Oocyte  4E Danio; Danio rerio; RNA Seq", "GSM5088021", null, "1", "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", "GEO Accession:GSM5088021", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP306811", null, null, "4B5_1_sequence.fastq.gz 4B5_2_sequence.fastq.gz", "fastq fastq", 4152498238.0, 26122638.0, "GSM5088021 r1", "0:79.49 1:79.47", "A:1027163417;C:1014220497;G:1089779374;T:1018004142;N:3330808", 79, 79, null, null, 1027163417, 1014220497, 1089779374, 1018004142, 3330808, "SRX10117846", "SRS8272547", "SRA1197056", "GEO", "Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.", 2, 0.91753, 0.91112, 0.02745, 0.02398, 0.80996, 0.81292, 0.50181, 0.50039, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "lexogen", "bulk", "bulk", "bulk", null, "Czech Republic", "2021-02-17", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [63341, "SRR13729836", "SRX10117845", "SRS8272546", "SRP306811", "PRJNA702290", "RNA Seq analysis of localization along animal vegetal axis of Danio rerio", "GSE166917", "Transcriptome Analysis", "Asymmetrical localization of biomolecules inside the egg  results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs  of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However  our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models  Xenopus laevis  Danio rerio  Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly  we revealed RNAs that code for many known important genes such as germ layer determinants  germ plasm factors and members of key signalling pathways  are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis  section A first animal to section E last vegetal  followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000  Thermo Scientific  and the quality of RNA was assessed using a Fragment Analyzer AATI  High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.", null, "pubmed:35752299", null, "Oocyte  4C Danio", "GSM5088020", null, "tissue:Oocyte  4C|segment:C|cell type:Oocyte|oocyte id:4", "Oocyte  4C Danio", "Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al  2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.", "Oocyte  4C", null, "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", null, "segment:C|cell type:Oocyte|oocyte id:4", "GSM5088020", "GSM5088020: Oocyte  4C Danio; Danio rerio; RNA Seq", "GSM5088020", null, "1", "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", "GEO Accession:GSM5088020", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP306811", null, null, "4B3_1_sequence.fastq.gz 4B3_2_sequence.fastq.gz", "fastq fastq", 4303501885.0, 27073674.0, "GSM5088020 r1", "0:79.48 1:79.47", "A:1081539300;C:1029641993;G:1108664145;T:1080227921;N:3428526", 79, 79, null, null, 1081539300, 1029641993, 1108664145, 1080227921, 3428526, "SRX10117845", "SRS8272546", "SRA1197056", "GEO", "Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.", 2, 0.93052, 0.92329, 0.0289, 0.02632, 0.80728, 0.8086, 0.48613, 0.49318, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "lexogen", "bulk", "bulk", "bulk", null, "Czech Republic", "2021-02-17", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [63342, "SRR13729835", "SRX10117844", "SRS8272545", "SRP306811", "PRJNA702290", "RNA Seq analysis of localization along animal vegetal axis of Danio rerio", "GSE166917", "Transcriptome Analysis", "Asymmetrical localization of biomolecules inside the egg  results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs  of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However  our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models  Xenopus laevis  Danio rerio  Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly  we revealed RNAs that code for many known important genes such as germ layer determinants  germ plasm factors and members of key signalling pathways  are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis  section A first animal to section E last vegetal  followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000  Thermo Scientific  and the quality of RNA was assessed using a Fragment Analyzer AATI  High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.", null, "pubmed:35752299", null, "Oocyte  4B Danio", "GSM5088019", null, "tissue:Oocyte  4B|segment:B|cell type:Oocyte|oocyte id:4", "Oocyte  4B Danio", "Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al  2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.", "Oocyte  4B", null, "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", null, "segment:B|cell type:Oocyte|oocyte id:4", "GSM5088019", "GSM5088019: Oocyte  4B Danio; Danio rerio; RNA Seq", "GSM5088019", null, "1", "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", "GEO Accession:GSM5088019", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP306811", null, null, "4B2_1_sequence.fastq.gz 4B2_2_sequence.fastq.gz", "fastq fastq", 4568445606.0, 28740891.0, "GSM5088019 r1", "0:79.48 1:79.47", "A:1129548614;C:1110728719;G:1196533300;T:1127950040;N:3684933", 79, 79, null, null, 1129548614, 1110728719, 1196533300, 1127950040, 3684933, "SRX10117844", "SRS8272545", "SRA1197056", "GEO", "Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.", 2, 0.93047, 0.91851, 0.03423, 0.02988, 0.809, 0.81117, 0.49528, 0.49857, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "lexogen", "bulk", "bulk", "bulk", null, "Czech Republic", "2021-02-17", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [63343, "SRR13729834", "SRX10117843", "SRS8272544", "SRP306811", "PRJNA702290", "RNA Seq analysis of localization along animal vegetal axis of Danio rerio", "GSE166917", "Transcriptome Analysis", "Asymmetrical localization of biomolecules inside the egg  results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs  of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However  our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models  Xenopus laevis  Danio rerio  Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly  we revealed RNAs that code for many known important genes such as germ layer determinants  germ plasm factors and members of key signalling pathways  are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis  section A first animal to section E last vegetal  followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000  Thermo Scientific  and the quality of RNA was assessed using a Fragment Analyzer AATI  High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.", null, "pubmed:35752299", null, "Oocyte  4A Danio", "GSM5088018", null, "tissue:Oocyte  4A|segment:A first animal|cell type:Oocyte|oocyte id:4", "Oocyte  4A Danio", "Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al  2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.", "Oocyte  4A", null, "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", null, "segment:A first animal|cell type:Oocyte|oocyte id:4", "GSM5088018", "GSM5088018: Oocyte  4A Danio; Danio rerio; RNA Seq", "GSM5088018", null, "1", "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", "GEO Accession:GSM5088018", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP306811", null, null, "4B1_1_sequence.fastq.gz 4B1_2_sequence.fastq.gz", "fastq fastq", 3817977815.0, 24018320.0, "GSM5088018 r1", "0:79.49 1:79.47", "A:963219571;C:910978829;G:981236983;T:959479009;N:3063423", 79, 79, null, null, 963219571, 910978829, 981236983, 959479009, 3063423, "SRX10117843", "SRS8272544", "SRA1197056", "GEO", "Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.", 2, 0.91985, 0.91378, 0.02505, 0.02244, 0.82487, 0.82662, 0.49099, 0.48748, 79, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "lexogen", "bulk", "bulk", "bulk", null, "Czech Republic", "2021-02-17", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [63344, "SRR13729833", "SRX10117842", "SRS8272543", "SRP306811", "PRJNA702290", "RNA Seq analysis of localization along animal vegetal axis of Danio rerio", "GSE166917", "Transcriptome Analysis", "Asymmetrical localization of biomolecules inside the egg  results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs  of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However  our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models  Xenopus laevis  Danio rerio  Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly  we revealed RNAs that code for many known important genes such as germ layer determinants  germ plasm factors and members of key signalling pathways  are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis  section A first animal to section E last vegetal  followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000  Thermo Scientific  and the quality of RNA was assessed using a Fragment Analyzer AATI  High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.", null, "pubmed:35752299", null, "Oocyte  3E Danio", "GSM5088017", null, "tissue:Oocyte  3E|segment:E last vegetal|cell type:Oocyte|oocyte id:3", "Oocyte  3E Danio", "Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al  2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.", "Oocyte  3E", null, "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", null, "segment:E last vegetal|cell type:Oocyte|oocyte id:3", "GSM5088017", "GSM5088017: Oocyte  3E Danio; Danio rerio; RNA Seq", "GSM5088017", null, "1", "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", "GEO Accession:GSM5088017", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP306811", null, null, "3B5_1_sequence.fastq.gz 3B5_2_sequence.fastq.gz", "fastq fastq", 4473509143.0, 28141276.0, "GSM5088017 r1", "0:79.48 1:79.48", "A:1097552285;C:1100434019;G:1180150633;T:1091792820;N:3579386", 79, 79, null, null, 1097552285, 1100434019, 1180150633, 1091792820, 3579386, "SRX10117842", "SRS8272543", "SRA1197056", "GEO", "Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.", 2, 0.91717, 0.91194, 0.03477, 0.02973, 0.81714, 0.81789, 0.50164, 0.50948, 80, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "lexogen", "bulk", "bulk", "bulk", null, "Czech Republic", "2021-02-17", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [63345, "SRR13729832", "SRX10117841", "SRS8272542", "SRP306811", "PRJNA702290", "RNA Seq analysis of localization along animal vegetal axis of Danio rerio", "GSE166917", "Transcriptome Analysis", "Asymmetrical localization of biomolecules inside the egg  results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs  of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However  our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models  Xenopus laevis  Danio rerio  Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly  we revealed RNAs that code for many known important genes such as germ layer determinants  germ plasm factors and members of key signalling pathways  are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis  section A first animal to section E last vegetal  followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000  Thermo Scientific  and the quality of RNA was assessed using a Fragment Analyzer AATI  High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.", null, "pubmed:35752299", null, "Oocyte  3D Danio", "GSM5088016", null, "tissue:Oocyte  3D|segment:D|cell type:Oocyte|oocyte id:3", "Oocyte  3D Danio", "Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al  2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.", "Oocyte  3D", null, "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", null, "segment:D|cell type:Oocyte|oocyte id:3", "GSM5088016", "GSM5088016: Oocyte  3D Danio; Danio rerio; RNA Seq", "GSM5088016", null, "1", "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", "GEO Accession:GSM5088016", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP306811", null, null, "3B4_1_sequence.fastq.gz 3B4_2_sequence.fastq.gz", "fastq fastq", 3795326466.0, 23875658.0, "GSM5088016 r1", "0:79.48 1:79.48", "A:920554794;C:947025114;G:1013528010;T:911203644;N:3014904", 79, 79, null, null, 920554794, 947025114, 1013528010, 911203644, 3014904, "SRX10117841", "SRS8272542", "SRA1197056", "GEO", "Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.", 2, 0.91408, 0.91455, 0.037, 0.03125, 0.82166, 0.82426, 0.53064, 0.53695, 78, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "lexogen", "bulk", "bulk", "bulk", null, "Czech Republic", "2021-02-17", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [63346, "SRR13729831", "SRX10117840", "SRS8272541", "SRP306811", "PRJNA702290", "RNA Seq analysis of localization along animal vegetal axis of Danio rerio", "GSE166917", "Transcriptome Analysis", "Asymmetrical localization of biomolecules inside the egg  results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs  of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However  our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models  Xenopus laevis  Danio rerio  Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly  we revealed RNAs that code for many known important genes such as germ layer determinants  germ plasm factors and members of key signalling pathways  are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis  section A first animal to section E last vegetal  followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000  Thermo Scientific  and the quality of RNA was assessed using a Fragment Analyzer AATI  High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.", null, "pubmed:35752299", null, "Oocyte  3C Danio", "GSM5088015", null, "tissue:Oocyte  3C|segment:C|cell type:Oocyte|oocyte id:3", "Oocyte  3C Danio", "Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al  2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.", "Oocyte  3C", null, "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", null, "segment:C|cell type:Oocyte|oocyte id:3", "GSM5088015", "GSM5088015: Oocyte  3C Danio; Danio rerio; RNA Seq", "GSM5088015", null, "1", "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", "GEO Accession:GSM5088015", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP306811", null, null, "3B3_1_sequence.fastq.gz 3B3_2_sequence.fastq.gz", "fastq fastq", 4384361494.0, 27581768.0, "GSM5088015 r1", "0:79.49 1:79.47", "A:1098383452;C:1051673687;G:1134807000;T:1095992230;N:3505125", 79, 79, null, null, 1098383452, 1051673687, 1134807000, 1095992230, 3505125, "SRX10117840", "SRS8272541", "SRA1197056", "GEO", "Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.", 2, 0.92005, 0.91267, 0.02325, 0.02051, 0.84593, 0.84652, 0.47588, 0.47964, 80, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "lexogen", "bulk", "bulk", "bulk", null, "Czech Republic", "2021-02-17", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [63347, "SRR13729830", "SRX10117839", "SRS8272540", "SRP306811", "PRJNA702290", "RNA Seq analysis of localization along animal vegetal axis of Danio rerio", "GSE166917", "Transcriptome Analysis", "Asymmetrical localization of biomolecules inside the egg  results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs  of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However  our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models  Xenopus laevis  Danio rerio  Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly  we revealed RNAs that code for many known important genes such as germ layer determinants  germ plasm factors and members of key signalling pathways  are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis  section A first animal to section E last vegetal  followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000  Thermo Scientific  and the quality of RNA was assessed using a Fragment Analyzer AATI  High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.", null, "pubmed:35752299", null, "Oocyte  3A Danio", "GSM5088014", null, "tissue:Oocyte  3A|segment:A first animal|cell type:Oocyte|oocyte id:3", "Oocyte  3A Danio", "Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al  2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.", "Oocyte  3A", null, "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", null, "segment:A first animal|cell type:Oocyte|oocyte id:3", "GSM5088014", "GSM5088014: Oocyte  3A Danio; Danio rerio; RNA Seq", "GSM5088014", null, "1", "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", "GEO Accession:GSM5088014", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP306811", null, null, "3B1_1_sequence.fastq.gz 3B1_2_sequence.fastq.gz", "fastq fastq", 3411652124.0, 21461889.0, "GSM5088014 r1", "0:79.49 1:79.47", "A:845211429;C:831298444;G:892682122;T:839715401;N:2744728", 79, 79, null, null, 845211429, 831298444, 892682122, 839715401, 2744728, "SRX10117839", "SRS8272540", "SRA1197056", "GEO", "Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.", 2, 0.91312, 0.90785, 0.03043, 0.03046, 0.81227, 0.81412, 0.47591, 0.48217, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "lexogen", "bulk", "bulk", "bulk", null, "Czech Republic", "2021-02-17", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [63348, "SRR13729829", "SRX10117838", "SRS8272539", "SRP306811", "PRJNA702290", "RNA Seq analysis of localization along animal vegetal axis of Danio rerio", "GSE166917", "Transcriptome Analysis", "Asymmetrical localization of biomolecules inside the egg  results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs  of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However  our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models  Xenopus laevis  Danio rerio  Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly  we revealed RNAs that code for many known important genes such as germ layer determinants  germ plasm factors and members of key signalling pathways  are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis  section A first animal to section E last vegetal  followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000  Thermo Scientific  and the quality of RNA was assessed using a Fragment Analyzer AATI  High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.", null, "pubmed:35752299", null, "Oocyte  2D Danio", "GSM5088013", null, "tissue:Oocyte  2D|segment:D|cell type:Oocyte|oocyte id:2", "Oocyte  2D Danio", "Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al  2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.", "Oocyte  2D", null, "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", null, "segment:D|cell type:Oocyte|oocyte id:2", "GSM5088013", "GSM5088013: Oocyte  2D Danio; Danio rerio; RNA Seq", "GSM5088013", null, "1", "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", "GEO Accession:GSM5088013", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP306811", null, null, "2B4_1_sequence.fastq.gz 2B4_2_sequence.fastq.gz", "fastq fastq", 4315673164.0, 27151788.0, "GSM5088013 r1", "0:79.48 1:79.47", "A:1054372456;C:1069138368;G:1139564933;T:1049164939;N:3432468", 79, 79, null, null, 1054372456, 1069138368, 1139564933, 1049164939, 3432468, "SRX10117838", "SRS8272539", "SRA1197056", "GEO", "Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.", 2, 0.92682, 0.91833, 0.0285, 0.02736, 0.83128, 0.83386, 0.49243, 0.48841, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "lexogen", "bulk", "bulk", "bulk", null, "Czech Republic", "2021-02-17", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [63349, "SRR13729828", "SRX10117837", "SRS8272538", "SRP306811", "PRJNA702290", "RNA Seq analysis of localization along animal vegetal axis of Danio rerio", "GSE166917", "Transcriptome Analysis", "Asymmetrical localization of biomolecules inside the egg  results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs  of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However  our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models  Xenopus laevis  Danio rerio  Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly  we revealed RNAs that code for many known important genes such as germ layer determinants  germ plasm factors and members of key signalling pathways  are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis  section A first animal to section E last vegetal  followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000  Thermo Scientific  and the quality of RNA was assessed using a Fragment Analyzer AATI  High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.", null, "pubmed:35752299", null, "Oocyte  2C Danio", "GSM5088012", null, "tissue:Oocyte  2C|segment:C|cell type:Oocyte|oocyte id:2", "Oocyte  2C Danio", "Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al  2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.", "Oocyte  2C", null, "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", null, "segment:C|cell type:Oocyte|oocyte id:2", "GSM5088012", "GSM5088012: Oocyte  2C Danio; Danio rerio; RNA Seq", "GSM5088012", null, "1", "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", "GEO Accession:GSM5088012", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP306811", null, null, "2B3_1_sequence.fastq.gz 2B3_2_sequence.fastq.gz", "fastq fastq", 2940179416.0, 18498584.0, "GSM5088012 r1", "0:79.48 1:79.46", "A:706640732;C:738153613;G:787676271;T:705356358;N:2352442", 79, 79, null, null, 706640732, 738153613, 787676271, 705356358, 2352442, "SRX10117837", "SRS8272538", "SRA1197056", "GEO", "Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.", 2, 0.91412, 0.90752, 0.03266, 0.03078, 0.81294, 0.81544, 0.48861, 0.50372, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "lexogen", "bulk", "bulk", "bulk", null, "Czech Republic", "2021-02-17", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [63350, "SRR13729827", "SRX10117836", "SRS8272537", "SRP306811", "PRJNA702290", "RNA Seq analysis of localization along animal vegetal axis of Danio rerio", "GSE166917", "Transcriptome Analysis", "Asymmetrical localization of biomolecules inside the egg  results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs  of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However  our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models  Xenopus laevis  Danio rerio  Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly  we revealed RNAs that code for many known important genes such as germ layer determinants  germ plasm factors and members of key signalling pathways  are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis  section A first animal to section E last vegetal  followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000  Thermo Scientific  and the quality of RNA was assessed using a Fragment Analyzer AATI  High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.", null, "pubmed:35752299", null, "Oocyte  2B Danio", "GSM5088011", null, "tissue:Oocyte  2B|segment:B|cell type:Oocyte|oocyte id:2", "Oocyte  2B Danio", "Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al  2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.", "Oocyte  2B", null, "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", null, "segment:B|cell type:Oocyte|oocyte id:2", "GSM5088011", "GSM5088011: Oocyte  2B Danio; Danio rerio; RNA Seq", "GSM5088011", null, "1", "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", "GEO Accession:GSM5088011", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP306811", null, null, "2B2_1_sequence.fastq.gz 2B2_2_sequence.fastq.gz", "fastq fastq", 4697262619.0, 29554887.0, "GSM5088011 r1", "0:79.47 1:79.46", "A:1144577689;C:1159225165;G:1242203382;T:1147513885;N:3742498", 79, 79, null, null, 1144577689, 1159225165, 1242203382, 1147513885, 3742498, "SRX10117836", "SRS8272537", "SRA1197056", "GEO", "Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.", 2, 0.92868, 0.92039, 0.03005, 0.02833, 0.83043, 0.83201, 0.48282, 0.4842, 80, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "lexogen", "bulk", "bulk", "bulk", null, "Czech Republic", "2021-02-17", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [63351, "SRR13729826", "SRX10117835", "SRS8272536", "SRP306811", "PRJNA702290", "RNA Seq analysis of localization along animal vegetal axis of Danio rerio", "GSE166917", "Transcriptome Analysis", "Asymmetrical localization of biomolecules inside the egg  results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs  of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However  our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models  Xenopus laevis  Danio rerio  Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly  we revealed RNAs that code for many known important genes such as germ layer determinants  germ plasm factors and members of key signalling pathways  are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis  section A first animal to section E last vegetal  followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000  Thermo Scientific  and the quality of RNA was assessed using a Fragment Analyzer AATI  High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.", null, "pubmed:35752299", null, "Oocyte  2A Danio", "GSM5088010", null, "tissue:Oocyte  2A|segment:A first animal|cell type:Oocyte|oocyte id:2", "Oocyte  2A Danio", "Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al  2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.", "Oocyte  2A", null, "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", null, "segment:A first animal|cell type:Oocyte|oocyte id:2", "GSM5088010", "GSM5088010: Oocyte  2A Danio; Danio rerio; RNA Seq", "GSM5088010", null, "1", "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", "GEO Accession:GSM5088010", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP306811", null, null, "2B1_1_sequence.fastq.gz 2B1_2_sequence.fastq.gz", "fastq fastq", 4258170980.0, 26788207.0, "GSM5088010 r1", "0:79.49 1:79.47", "A:1030159627;C:1059437908;G:1140549602;T:1024611576;N:3412267", 79, 79, null, null, 1030159627, 1059437908, 1140549602, 1024611576, 3412267, "SRX10117835", "SRS8272536", "SRA1197056", "GEO", "Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.", 2, 0.90756, 0.90301, 0.03357, 0.03114, 0.82246, 0.82353, 0.48748, 0.48875, 78, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "lexogen", "bulk", "bulk", "bulk", null, "Czech Republic", "2021-02-17", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [63352, "SRR13729825", "SRX10117834", "SRS8272535", "SRP306811", "PRJNA702290", "RNA Seq analysis of localization along animal vegetal axis of Danio rerio", "GSE166917", "Transcriptome Analysis", "Asymmetrical localization of biomolecules inside the egg  results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs  of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However  our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models  Xenopus laevis  Danio rerio  Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly  we revealed RNAs that code for many known important genes such as germ layer determinants  germ plasm factors and members of key signalling pathways  are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis  section A first animal to section E last vegetal  followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000  Thermo Scientific  and the quality of RNA was assessed using a Fragment Analyzer AATI  High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.", null, "pubmed:35752299", null, "Oocyte  1E Danio", "GSM5088009", null, "tissue:Oocyte  1E|segment:E last vegetal|cell type:Oocyte|oocyte id:1", "Oocyte  1E Danio", "Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al  2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.", "Oocyte  1E", null, "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", null, "segment:E last vegetal|cell type:Oocyte|oocyte id:1", "GSM5088009", "GSM5088009: Oocyte  1E Danio; Danio rerio; RNA Seq", "GSM5088009", null, "1", "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", "GEO Accession:GSM5088009", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP306811", null, null, "1B5_1_sequence.fastq.gz 1B5_2_sequence.fastq.gz", "fastq fastq", 1540315534.0, 9689873.0, "GSM5088009 r1", "0:79.49 1:79.47", "A:379857715;C:379231426;G:406324313;T:373666639;N:1235441", 79, 79, null, null, 379857715, 379231426, 406324313, 373666639, 1235441, "SRX10117834", "SRS8272535", "SRA1197056", "GEO", "Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.", 2, 0.90259, 0.90038, 0.02393, 0.02279, 0.82538, 0.828, 0.50474, 0.50554, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "lexogen", "bulk", "bulk", "bulk", null, "Czech Republic", "2021-02-17", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [63353, "SRR13729824", "SRX10117833", "SRS8272534", "SRP306811", "PRJNA702290", "RNA Seq analysis of localization along animal vegetal axis of Danio rerio", "GSE166917", "Transcriptome Analysis", "Asymmetrical localization of biomolecules inside the egg  results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs  of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However  our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models  Xenopus laevis  Danio rerio  Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly  we revealed RNAs that code for many known important genes such as germ layer determinants  germ plasm factors and members of key signalling pathways  are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis  section A first animal to section E last vegetal  followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000  Thermo Scientific  and the quality of RNA was assessed using a Fragment Analyzer AATI  High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.", null, "pubmed:35752299", null, "Oocyte  1D Danio", "GSM5088008", null, "tissue:Oocyte  1D|segment:D|cell type:Oocyte|oocyte id:1", "Oocyte  1D Danio", "Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al  2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.", "Oocyte  1D", null, "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", null, "segment:D|cell type:Oocyte|oocyte id:1", "GSM5088008", "GSM5088008: Oocyte  1D Danio; Danio rerio; RNA Seq", "GSM5088008", null, "1", "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", "GEO Accession:GSM5088008", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP306811", null, null, "1B4_1_sequence.fastq.gz 1B4_2_sequence.fastq.gz", "fastq fastq", 962876607.0, 6058091.0, "GSM5088008 r1", "0:79.47 1:79.47", "A:229221564;C:244601669;G:261639054;T:226646308;N:768012", 79, 79, null, null, 229221564, 244601669, 261639054, 226646308, 768012, "SRX10117833", "SRS8272534", "SRA1197056", "GEO", "Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.", 2, 0.90756, 0.90342, 0.03356, 0.03192, 0.81418, 0.81588, 0.53647, 0.53381, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "lexogen", "bulk", "bulk", "bulk", null, "Czech Republic", "2021-02-17", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [63354, "SRR13729823", "SRX10117832", "SRS8272532", "SRP306811", "PRJNA702290", "RNA Seq analysis of localization along animal vegetal axis of Danio rerio", "GSE166917", "Transcriptome Analysis", "Asymmetrical localization of biomolecules inside the egg  results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs  of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However  our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models  Xenopus laevis  Danio rerio  Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly  we revealed RNAs that code for many known important genes such as germ layer determinants  germ plasm factors and members of key signalling pathways  are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis  section A first animal to section E last vegetal  followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000  Thermo Scientific  and the quality of RNA was assessed using a Fragment Analyzer AATI  High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.", null, "pubmed:35752299", null, "Oocyte  1C Danio", "GSM5088007", null, "tissue:Oocyte  1C|segment:C|cell type:Oocyte|oocyte id:1", "Oocyte  1C Danio", "Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al  2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.", "Oocyte  1C", null, "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", null, "segment:C|cell type:Oocyte|oocyte id:1", "GSM5088007", "GSM5088007: Oocyte  1C Danio; Danio rerio; RNA Seq", "GSM5088007", null, "1", "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", "GEO Accession:GSM5088007", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP306811", null, null, "1B3_1_sequence.fastq.gz 1B3_2_sequence.fastq.gz", "fastq fastq", 1582022971.0, 9951749.0, "GSM5088007 r1", "0:79.49 1:79.48", "A:396538041;C:379495578;G:410865933;T:393855027;N:1268392", 79, 79, null, null, 396538041, 379495578, 410865933, 393855027, 1268392, "SRX10117832", "SRS8272532", "SRA1197056", "GEO", "Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.", 2, 0.93154, 0.91852, 0.03066, 0.02748, 0.81874, 0.82037, 0.50484, 0.50755, 80, 78, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "lexogen", "bulk", "bulk", "bulk", null, "Czech Republic", "2021-02-17", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [63355, "SRR13729822", "SRX10117831", "SRS8272533", "SRP306811", "PRJNA702290", "RNA Seq analysis of localization along animal vegetal axis of Danio rerio", "GSE166917", "Transcriptome Analysis", "Asymmetrical localization of biomolecules inside the egg  results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs  of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However  our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models  Xenopus laevis  Danio rerio  Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly  we revealed RNAs that code for many known important genes such as germ layer determinants  germ plasm factors and members of key signalling pathways  are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis  section A first animal to section E last vegetal  followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000  Thermo Scientific  and the quality of RNA was assessed using a Fragment Analyzer AATI  High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.", null, "pubmed:35752299", null, "Oocyte  1B Danio", "GSM5088006", null, "tissue:Oocyte  1B|segment:B|cell type:Oocyte|oocyte id:1", "Oocyte  1B Danio", "Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al  2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.", "Oocyte  1B", null, "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", null, "segment:B|cell type:Oocyte|oocyte id:1", "GSM5088006", "GSM5088006: Oocyte  1B Danio; Danio rerio; RNA Seq", "GSM5088006", null, "1", "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", "GEO Accession:GSM5088006", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP306811", null, null, "1B2_1_sequence.fastq.gz 1B2_2_sequence.fastq.gz", "fastq fastq", 1673988669.0, 10530092.0, "GSM5088006 r1", "0:79.49 1:79.48", "A:422626348;C:401664830;G:430984922;T:417384157;N:1328412", 79, 79, null, null, 422626348, 401664830, 430984922, 417384157, 1328412, "SRX10117831", "SRS8272533", "SRA1197056", "GEO", "Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.", 2, 0.92018, 0.91786, 0.03334, 0.02831, 0.82217, 0.82359, 0.49692, 0.49869, 79, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "lexogen", "bulk", "bulk", "bulk", null, "Czech Republic", "2021-02-17", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [63356, "SRR13729821", "SRX10117830", "SRS8272531", "SRP306811", "PRJNA702290", "RNA Seq analysis of localization along animal vegetal axis of Danio rerio", "GSE166917", "Transcriptome Analysis", "Asymmetrical localization of biomolecules inside the egg  results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs  of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However  our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models  Xenopus laevis  Danio rerio  Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly  we revealed RNAs that code for many known important genes such as germ layer determinants  germ plasm factors and members of key signalling pathways  are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis  section A first animal to section E last vegetal  followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000  Thermo Scientific  and the quality of RNA was assessed using a Fragment Analyzer AATI  High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.", null, "pubmed:35752299", null, "Oocyte  1A Danio", "GSM5088005", null, "tissue:Oocyte  1A|segment:A first animal|cell type:Oocyte|oocyte id:1", "Oocyte  1A Danio", "Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al  2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.", "Oocyte  1A", null, "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", null, "segment:A first animal|cell type:Oocyte|oocyte id:1", "GSM5088005", "GSM5088005: Oocyte  1A Danio; Danio rerio; RNA Seq", "GSM5088005", null, "1", "Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.", "GEO Accession:GSM5088005", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP306811", null, null, "1B1_1_sequence.fastq.gz 1B1_2_sequence.fastq.gz", "fastq fastq", 2267520035.0, 14263997.0, "GSM5088005 r1", "0:79.47 1:79.49", "A:545496147;C:565118612;G:611364916;T:543726981;N:1813379", 79, 79, null, null, 545496147, 565118612, 611364916, 543726981, 1813379, "SRX10117830", "SRS8272531", "SRA1197056", "GEO", "Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.", 2, 0.93336, 0.92007, 0.06438, 0.05136, 0.82349, 0.82483, 0.54418, 0.55879, 78, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "lexogen", "bulk", "bulk", "bulk", null, "Czech Republic", "2021-02-17", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [67554, "SRR17210893", "SRX13390812", "SRS11294344", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 10nM Rep6", "GSM5730194", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "RNAseq PCB126 10nM Rep6", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "GSM5730194", "GSM5730194: RNAseq PCB126 10nM Rep6; Danio rerio; RNA Seq", "GSM5730194", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730194", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T24_S18_R1_001.fastq.gz", "fastq", 1912515249.0, 37500299.0, "GSM5730194 r1", "0:51 1:0", "A:477251176;C:466929755;G:439380761;T:528825431;N:128126", 51, 0, null, null, 477251176, 466929755, 439380761, 528825431, 128126, "SRX13390812", "SRS11294344", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95015, null, 0.10454, null, 0.64922, null, 0.53267, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67555, "SRR17210892", "SRX13390811", "SRS11294345", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 10nM Rep5", "GSM5730193", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "RNAseq PCB126 10nM Rep5", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "GSM5730193", "GSM5730193: RNAseq PCB126 10nM Rep5; Danio rerio; RNA Seq", "GSM5730193", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730193", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T23_S17_R1_001.fastq.gz", "fastq", 1344965778.0, 26371878.0, "GSM5730193 r1", "0:51 1:0", "A:347349418;C:318051347;G:301879882;T:377595413;N:89718", 51, 0, null, null, 347349418, 318051347, 301879882, 377595413, 89718, "SRX13390811", "SRS11294345", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.94726, null, 0.10386, null, 0.64948, null, 0.5434, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67556, "SRR17210891", "SRX13390810", "SRS11294343", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 10nM Rep4", "GSM5730192", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "RNAseq PCB126 10nM Rep4", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "GSM5730192", "GSM5730192: RNAseq PCB126 10nM Rep4; Danio rerio; RNA Seq", "GSM5730192", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730192", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T21_S16_R1_001.fastq.gz", "fastq", 2077575474.0, 40736774.0, "GSM5730192 r1", "0:51 1:0", "A:507322408;C:503941476;G:510925051;T:555250063;N:136476", 51, 0, null, null, 507322408, 503941476, 510925051, 555250063, 136476, "SRX13390810", "SRS11294343", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95021, null, 0.06976, null, 0.6464, null, 0.50296, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67557, "SRR17210890", "SRX13390809", "SRS11294342", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 10nM Rep3", "GSM5730191", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "RNAseq PCB126 10nM Rep3", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "GSM5730191", "GSM5730191: RNAseq PCB126 10nM Rep3; Danio rerio; RNA Seq", "GSM5730191", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730191", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T19_S15_R1_001.fastq.gz", "fastq", 1514204127.0, 29690277.0, "GSM5730191 r1", "0:51 1:0", "A:362659383;C:370554761;G:356314539;T:424574865;N:100579", 51, 0, null, null, 362659383, 370554761, 356314539, 424574865, 100579, "SRX13390809", "SRS11294342", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95191, null, 0.07368, null, 0.62509, null, 0.48965, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67558, "SRR17210889", "SRX13390808", "SRS11294341", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 10nM Rep2", "GSM5730190", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "RNAseq PCB126 10nM Rep2", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "GSM5730190", "GSM5730190: RNAseq PCB126 10nM Rep2; Danio rerio; RNA Seq", "GSM5730190", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730190", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T18_S14_R1_001.fastq.gz", "fastq", 1381687155.0, 27091905.0, "GSM5730190 r1", "0:51 1:0", "A:333912162;C:335458932;G:326378401;T:385845588;N:92072", 51, 0, null, null, 333912162, 335458932, 326378401, 385845588, 92072, "SRX13390808", "SRS11294341", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95313, null, 0.07433, null, 0.63177, null, 0.50475, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67559, "SRR17210888", "SRX13390807", "SRS11294340", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 10nM Rep1", "GSM5730189", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "RNAseq PCB126 10nM Rep1", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "GSM5730189", "GSM5730189: RNAseq PCB126 10nM Rep1; Danio rerio; RNA Seq", "GSM5730189", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730189", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T17_S13_R1_001.fastq.gz", "fastq", 1508524920.0, 29578920.0, "GSM5730189 r1", "0:51 1:0", "A:393426431;C:349348415;G:337538750;T:428110887;N:100437", 51, 0, null, null, 393426431, 349348415, 337538750, 428110887, 100437, "SRX13390807", "SRS11294340", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.94765, null, 0.0935, null, 0.64743, null, 0.53646, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67560, "SRR17210887", "SRX13390806", "SRS11294338", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 3nM Rep6", "GSM5730188", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "RNAseq PCB126 3nM Rep6", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "GSM5730188", "GSM5730188: RNAseq PCB126 3nM Rep6; Danio rerio; RNA Seq", "GSM5730188", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730188", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T16_S12_R1_001.fastq.gz", "fastq", 1840726935.0, 36092685.0, "GSM5730188 r1", "0:51 1:0", "A:466997928;C:437493060;G:421124744;T:514986449;N:124754", 51, 0, null, null, 466997928, 437493060, 421124744, 514986449, 124754, "SRX13390806", "SRS11294338", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.9474, null, 0.0984, null, 0.64165, null, 0.51348, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67561, "SRR17210886", "SRX13390805", "SRS11294339", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 3nM Rep5", "GSM5730187", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "RNAseq PCB126 3nM Rep5", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "GSM5730187", "GSM5730187: RNAseq PCB126 3nM Rep5; Danio rerio; RNA Seq", "GSM5730187", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730187", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T15_S11_R1_001.fastq.gz", "fastq", 1384282545.0, 27142795.0, "GSM5730187 r1", "0:51 1:0", "A:325552702;C:343473865;G:329054590;T:386110707;N:90681", 51, 0, null, null, 325552702, 343473865, 329054590, 386110707, 90681, "SRX13390805", "SRS11294339", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95623, null, 0.06621, null, 0.63345, null, 0.49688, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67562, "SRR17210885", "SRX13390804", "SRS11294337", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 3nM Rep4", "GSM5730186", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "RNAseq PCB126 3nM Rep4", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "GSM5730186", "GSM5730186: RNAseq PCB126 3nM Rep4; Danio rerio; RNA Seq", "GSM5730186", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730186", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T14_S10_R1_001.fastq.gz", "fastq", 2099071260.0, 41158260.0, "GSM5730186 r1", "0:51 1:0", "A:525168723;C:513155313;G:482406202;T:578202593;N:138429", 51, 0, null, null, 525168723, 513155313, 482406202, 578202593, 138429, "SRX13390804", "SRS11294337", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.94639, null, 0.10285, null, 0.64942, null, 0.50757, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67563, "SRR17210884", "SRX13390803", "SRS11294336", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 3nM Rep3", "GSM5730185", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "RNAseq PCB126 3nM Rep3", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "GSM5730185", "GSM5730185: RNAseq PCB126 3nM Rep3; Danio rerio; RNA Seq", "GSM5730185", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730185", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T13_S9_R1_001.fastq.gz", "fastq", 1877300055.0, 36809805.0, "GSM5730185 r1", "0:51 1:0", "A:447373671;C:463401185;G:439915337;T:526483226;N:126636", 51, 0, null, null, 447373671, 463401185, 439915337, 526483226, 126636, "SRX13390803", "SRS11294336", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95301, null, 0.06979, null, 0.64319, null, 0.49994, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67564, "SRR17210883", "SRX13390802", "SRS11294335", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 3nM Rep2", "GSM5730184", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "RNAseq PCB126 3nM Rep2", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "GSM5730184", "GSM5730184: RNAseq PCB126 3nM Rep2; Danio rerio; RNA Seq", "GSM5730184", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730184", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T11_S8_R1_001.fastq.gz", "fastq", 1788165621.0, 35062071.0, "GSM5730184 r1", "0:51 1:0", "A:420221044;C:445407082;G:423493165;T:498924231;N:120099", 51, 0, null, null, 420221044, 445407082, 423493165, 498924231, 120099, "SRX13390802", "SRS11294335", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95488, null, 0.06451, null, 0.63126, null, 0.49662, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67565, "SRR17210882", "SRX13390801", "SRS11294334", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 3nM Rep1", "GSM5730183", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "RNAseq PCB126 3nM Rep1", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "GSM5730183", "GSM5730183: RNAseq PCB126 3nM Rep1; Danio rerio; RNA Seq", "GSM5730183", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730183", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T9_S7_R1_001.fastq.gz", "fastq", 1855410702.0, 36380602.0, "GSM5730183 r1", "0:51 1:0", "A:459292963;C:465999847;G:421852734;T:508143917;N:121241", 51, 0, null, null, 459292963, 465999847, 421852734, 508143917, 121241, "SRX13390801", "SRS11294334", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95181, null, 0.07794, null, 0.65141, null, 0.51342, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67566, "SRR17210881", "SRX13390800", "SRS11294333", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq DMSO Rep6", "GSM5730182", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:DMSO", "RNAseq DMSO Rep6", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:DMSO", "GSM5730182", "GSM5730182: RNAseq DMSO Rep6; Danio rerio; RNA Seq", "GSM5730182", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730182", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T8_S6_R1_001.fastq.gz", "fastq", 1923223464.0, 37710264.0, "GSM5730182 r1", "0:51 1:0", "A:451684628;C:481126641;G:454781274;T:535502647;N:128274", 51, 0, null, null, 451684628, 481126641, 454781274, 535502647, 128274, "SRX13390800", "SRS11294333", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95508, null, 0.07375, null, 0.63183, null, 0.49887, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67567, "SRR17210880", "SRX13390799", "SRS11294332", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq DMSO Rep5", "GSM5730181", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:DMSO", "RNAseq DMSO Rep5", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:DMSO", "GSM5730181", "GSM5730181: RNAseq DMSO Rep5; Danio rerio; RNA Seq", "GSM5730181", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730181", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T6_S5_R1_001.fastq.gz", "fastq", 1752584247.0, 34364397.0, "GSM5730181 r1", "0:51 1:0", "A:413763719;C:434326065;G:412787803;T:491589762;N:116898", 51, 0, null, null, 413763719, 434326065, 412787803, 491589762, 116898, "SRX13390799", "SRS11294332", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95515, null, 0.06656, null, 0.63859, null, 0.49877, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67568, "SRR17210879", "SRX13390798", "SRS11294331", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq DMSO Rep4", "GSM5730180", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:DMSO", "RNAseq DMSO Rep4", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:DMSO", "GSM5730180", "GSM5730180: RNAseq DMSO Rep4; Danio rerio; RNA Seq", "GSM5730180", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730180", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T5_S4_R1_001.fastq.gz", "fastq", 1783559199.0, 34971749.0, "GSM5730180 r1", "0:51 1:0", "A:426389805;C:442827488;G:416807133;T:497417118;N:117655", 51, 0, null, null, 426389805, 442827488, 416807133, 497417118, 117655, "SRX13390798", "SRS11294331", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95322, null, 0.0736, null, 0.6354, null, 0.49805, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67569, "SRR17210878", "SRX13390797", "SRS11294329", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq DMSO Rep3", "GSM5730179", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:DMSO", "RNAseq DMSO Rep3", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:DMSO", "GSM5730179", "GSM5730179: RNAseq DMSO Rep3; Danio rerio; RNA Seq", "GSM5730179", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730179", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T4_S3_R1_001.fastq.gz", "fastq", 1907367207.0, 37399357.0, "GSM5730179 r1", "0:51 1:0", "A:508707164;C:436434670;G:414734236;T:547363631;N:127506", 51, 0, null, null, 508707164, 436434670, 414734236, 547363631, 127506, "SRX13390797", "SRS11294329", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.50915, null, 0.03593, null, 0.70147, null, 0.49838, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67570, "SRR17210877", "SRX13390796", "SRS11294330", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq DMSO Rep2", "GSM5730178", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:DMSO", "RNAseq DMSO Rep2", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:DMSO", "GSM5730178", "GSM5730178: RNAseq DMSO Rep2; Danio rerio; RNA Seq", "GSM5730178", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730178", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T3_S2_R1_001.fastq.gz", "fastq", 1756085856.0, 34433056.0, "GSM5730178 r1", "0:51 1:0", "A:409690032;C:438746739;G:419437935;T:488094432;N:116718", 51, 0, null, null, 409690032, 438746739, 419437935, 488094432, 116718, "SRX13390796", "SRS11294330", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95577, null, 0.06639, null, 0.64076, null, 0.49674, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67571, "SRR17210876", "SRX13390795", "SRS11294328", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq DMSO Rep1", "GSM5730177", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:DMSO", "RNAseq DMSO Rep1", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:DMSO", "GSM5730177", "GSM5730177: RNAseq DMSO Rep1; Danio rerio; RNA Seq", "GSM5730177", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730177", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T1_S1_R1_001.fastq.gz", "fastq", 1791620310.0, 35129810.0, "GSM5730177 r1", "0:51 1:0", "A:422311870;C:442811083;G:428686648;T:497691822;N:118887", 51, 0, null, null, 422311870, 442811083, 428686648, 497691822, 118887, "SRX13390795", "SRS11294328", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95683, null, 0.06919, null, 0.6495, null, 0.49403, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"]], "truncated": false, "filtered_table_rows_count": 83, "expanded_columns": 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