{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", 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. 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:HE cdkn1a +/ ", "GSM7669025", "GSM7669025: PG HE 8mpf 1; Danio rerio; RNA Seq", "GSM7669025 r1", "GSM7669025", "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, "HE_PG_8mpf_1_S6_L003_R1_001.fastq.gz HE_PG_8mpf_1_S6_L003_R2_001.fastq.gz", "fastq fastq", 4587580737.0, 38590260.0, "GSM7669025 r1", "0:59.45 1:59.43", "A:1149031944;C:1121086335;G:1106925902;T:1203970839;N:6565717", 59, 59, null, null, 1149031944, 1121086335, 1106925902, 1203970839, 6565717, "SRX21195049", "SRS18453975", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.94032, 0.9437, 0.01481, 0.01462, 0.77682, 0.77774, 0.45843, 0.4699, 58, 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"], [24585, "SRR25462253", "SRX21195048", "SRS18453974", "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 8mpf 3", "GSM7669024", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing", "PG WT 8mpf 3", "Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. 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However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.", null, null, null, "PG WT 8mpf 2", "GSM7669023", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing", "PG WT 8mpf 2", "Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. 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However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.", null, null, null, "PG WT 8mpf 1", "GSM7669022", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing", "PG WT 8mpf 1", "Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file", "follicle", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+", "GSM7669022", "GSM7669022: PG WT 8mpf 1; Danio rerio; RNA Seq", "GSM7669022 r1", "GSM7669022", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452270", null, null, "WT_PG_8mpf_1_S9_L003_R1_001.fastq.gz WT_PG_8mpf_1_S9_L003_R2_001.fastq.gz", "fastq fastq", 3375380667.0, 28408784.0, "GSM7669022 r1", "0:59.42 1:59.40", "A:842316103;C:825987175;G:818715765;T:881225528;N:7136096", 59, 59, null, null, 842316103, 825987175, 818715765, 881225528, 7136096, "SRX21195046", "SRS18453972", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.94039, 0.9444, 0.0162, 0.01617, 0.7697, 0.76986, 0.47132, 0.46938, 60, 60, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Adult", "Adult", "Gonad", "Reproductive System"], [24588, "SRR25462256", "SRX21195045", "SRS18453971", "SRP452270", "PRJNA1000445", "CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption", "GSE239622", "Transcriptome Analysis", "CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.", null, null, null, "PG HE 50dpf 3", "GSM7669021", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing", "PG HE 50dpf 3", "Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file", "follicle", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ ", "GSM7669021", "GSM7669021: PG HE 50dpf 3; Danio rerio; RNA Seq", "GSM7669021 r1", "GSM7669021", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452270", null, null, "PG_HE_3_S26_L003_R1_001.fastq.gz PG_HE_3_S26_L003_R2_001.fastq.gz", "fastq fastq", 4520051001.0, 22984712.0, "GSM7669021 r1", "0:98.32 1:98.33", "A:1134815259;C:1102592573;G:1104475707;T:1160918938;N:17248524", 98, 98, null, null, 1134815259, 1102592573, 1104475707, 1160918938, 17248524, "SRX21195045", "SRS18453971", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.93438, 0.93937, 0.01237, 0.01252, 0.78208, 0.78192, 0.48454, 0.49474, 99, 99, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [24589, "SRR25462257", "SRX21195044", "SRS18453970", "SRP452270", "PRJNA1000445", "CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption", "GSE239622", "Transcriptome Analysis", "CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.", null, null, null, "PG HE 50dpf 2", "GSM7669020", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing", "PG HE 50dpf 2", "Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file", "follicle", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ ", "GSM7669020", "GSM7669020: PG HE 50dpf 2; Danio rerio; RNA Seq", "GSM7669020 r1", "GSM7669020", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452270", null, null, "PG_HE_2_S25_L003_R2_001.fastq.gz PG_HE_2_S25_L003_R1_001.fastq.gz", "fastq fastq", 3915471868.0, 19847479.0, "GSM7669020 r1", "0:98.64 1:98.64", "A:982714666;C:957212118;G:961590362;T:1003408448;N:10546274", 98, 98, null, null, 982714666, 957212118, 961590362, 1003408448, 10546274, "SRX21195044", "SRS18453970", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.93184, 0.93552, 0.01275, 0.01275, 0.78356, 0.7835, 0.49472, 0.48841, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [24590, "SRR25462258", "SRX21195043", "SRS18453969", "SRP452270", "PRJNA1000445", "CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption", "GSE239622", "Transcriptome Analysis", "CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.", null, null, null, "PG HE 50dpf 1", "GSM7669019", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing", "PG HE 50dpf 1", "Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file", "follicle", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ ", "GSM7669019", "GSM7669019: PG HE 50dpf 1; Danio rerio; RNA Seq", "GSM7669019 r1", "GSM7669019", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452270", null, null, "PG_HE_1_S24_L003_R1_001.fastq.gz PG_HE_1_S24_L003_R2_001.fastq.gz", "fastq fastq", 4764998144.0, 24264412.0, "GSM7669019 r1", "0:98.18 1:98.20", "A:1194676445;C:1161648051;G:1165061360;T:1221860864;N:21751424", 98, 98, null, null, 1194676445, 1161648051, 1165061360, 1221860864, 21751424, "SRX21195043", "SRS18453969", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.91864, 0.92247, 0.01213, 0.01245, 0.7949, 0.79584, 0.50422, 0.50318, 100, 98, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [24591, "SRR25462259", "SRX21195042", "SRS18453968", "SRP452270", "PRJNA1000445", "CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption", "GSE239622", "Transcriptome Analysis", "CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.", null, null, null, "PG WT 50dpf 3", "GSM7669018", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing", "PG WT 50dpf 3", "Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file", "follicle", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+", "GSM7669018", "GSM7669018: PG WT 50dpf 3; Danio rerio; RNA Seq", "GSM7669018 r1", "GSM7669018", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452270", null, null, "PG_WT_3_S23_L003_R1_001.fastq.gz PG_WT_3_S23_L003_R2_001.fastq.gz", "fastq fastq", 6204452412.0, 31480139.0, "GSM7669018 r1", "0:98.55 1:98.54", "A:1567898375;C:1505755791;G:1512895523;T:1599284546;N:18618177", 98, 98, null, null, 1567898375, 1505755791, 1512895523, 1599284546, 18618177, "SRX21195042", "SRS18453968", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.9312, 0.93599, 0.01692, 0.01686, 0.76426, 0.76439, 0.46519, 0.47751, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [24592, "SRR25462260", "SRX21195041", "SRS18453967", "SRP452270", "PRJNA1000445", "CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption", "GSE239622", "Transcriptome Analysis", "CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.", null, null, null, "PG WT 50dpf 2", "GSM7669017", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing", "PG WT 50dpf 2", "Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file", "follicle", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+", "GSM7669017", "GSM7669017: PG WT 50dpf 2; Danio rerio; RNA Seq", "GSM7669017 r1", "GSM7669017", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452270", null, null, "PG_WT_2_S22_L003_R1_001.fastq.gz PG_WT_2_S22_L003_R2_001.fastq.gz", "fastq fastq", 3907759829.0, 19906505.0, "GSM7669017 r1", "0:98.15 1:98.15", "A:991973983;C:940499355;G:946342572;T:1011476708;N:17467211", 98, 98, null, null, 991973983, 940499355, 946342572, 1011476708, 17467211, "SRX21195041", "SRS18453967", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.91435, 0.9186, 0.02035, 0.02032, 0.764, 0.76321, 0.48743, 0.48644, 97, 99, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [24593, "SRR25462261", "SRX21195040", "SRS18453966", "SRP452270", "PRJNA1000445", "CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption", "GSE239622", "Transcriptome Analysis", "CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.", null, null, null, "PG WT 50dpf 1", "GSM7669016", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing", "PG WT 50dpf 1", "Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file", "follicle", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+", "GSM7669016", "GSM7669016: PG WT 50dpf 1; Danio rerio; RNA Seq", "GSM7669016 r1", "GSM7669016", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452270", null, null, "PG_WT_1_S21_L003_R2_001.fastq.gz PG_WT_1_S21_L003_R1_001.fastq.gz", "fastq fastq", 7395136401.0, 37752582.0, "GSM7669016 r1", "0:97.94 1:97.94", "A:1865709287;C:1789949400;G:1796311820;T:1908470411;N:34695483", 97, 97, null, null, 1865709287, 1789949400, 1796311820, 1908470411, 34695483, "SRX21195040", "SRS18453966", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.9216, 0.92737, 0.01817, 0.01802, 0.76601, 0.76593, 0.48894, 0.4975, 100, 99, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [24594, "SRR25462243", "SRX21195038", "SRS18453964", "SRP452269", "PRJNA1000446", "Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish", "GSE239623", "Transcriptome Analysis", "Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study  we created an ybx1 mutant with CRISPR/Cas9  and showed that the folliculogenesis in the mutant ovary ybx1 /  was blocked at pre vitellogenic PV to early vitellogenic EV transition  leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 /  and the control ybx1+/  including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/   however  follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly  partial loss of p21 in heterozygous cdkn1a+/  could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/  females with normal follicle activation  in contrast to the PV EV blockade in ybx1 /  mutant. Interestingly  the follicle cells from the ybx1 /  mutant follicles displayed a poor proliferative activity in vitro; however  the cells from the ybx1 / p21+/  follicles resumed normal proliferation compared to that from the wildtype fish. In summary  we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a  a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade  we further isolated PV follicles from both WT ybx1+/+ and  ybx1 /  zebrafish. post RNA isolation  we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.", null, null, null, "PV  M3", "GSM7669033", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing", "PV  M3", "Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file", "follicle", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / ", "GSM7669033", "GSM7669033: PV  M3; Danio rerio; RNA Seq", "GSM7669033 r1", "GSM7669033", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452269", null, null, "PV_M3_R1.fastq.gz PV_M3_R2.fastq.gz", "fastq fastq", 4644457090.0, 23465750.0, "GSM7669033 r1", "0:98.98 1:98.94", "A:1196567358;C:1114203322;G:1109379777;T:1223156356;N:1150277", 98, 98, null, null, 1196567358, 1114203322, 1109379777, 1223156356, 1150277, "SRX21195038", "SRS18453964", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.94849, 0.95248, 0.02727, 0.02708, 0.73602, 0.73718, 0.48396, 0.4855, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [24595, "SRR25462244", "SRX21195037", "SRS18453963", "SRP452269", "PRJNA1000446", "Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish", "GSE239623", "Transcriptome Analysis", "Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study  we created an ybx1 mutant with CRISPR/Cas9  and showed that the folliculogenesis in the mutant ovary ybx1 /  was blocked at pre vitellogenic PV to early vitellogenic EV transition  leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 /  and the control ybx1+/  including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/   however  follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly  partial loss of p21 in heterozygous cdkn1a+/  could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/  females with normal follicle activation  in contrast to the PV EV blockade in ybx1 /  mutant. Interestingly  the follicle cells from the ybx1 /  mutant follicles displayed a poor proliferative activity in vitro; however  the cells from the ybx1 / p21+/  follicles resumed normal proliferation compared to that from the wildtype fish. In summary  we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a  a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade  we further isolated PV follicles from both WT ybx1+/+ and  ybx1 /  zebrafish. post RNA isolation  we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.", null, null, null, "PV  M2", "GSM7669032", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing", "PV  M2", "Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file", "follicle", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / ", "GSM7669032", "GSM7669032: PV  M2; Danio rerio; RNA Seq", "GSM7669032 r1", "GSM7669032", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452269", null, null, "PV_M2_R1.fastq.gz PV_M2_R2.fastq.gz", "fastq fastq", 2464506276.0, 12449948.0, "GSM7669032 r1", "0:98.99 1:98.96", "A:632587002;C:593372099;G:591579950;T:646214108;N:753117", 98, 98, null, null, 632587002, 593372099, 591579950, 646214108, 753117, "SRX21195037", "SRS18453963", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.94889, 0.9522, 0.02585, 0.02585, 0.73669, 0.73841, 0.48398, 0.48486, 100, 99, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [24596, "SRR25462245", "SRX21195036", "SRS18453962", "SRP452269", "PRJNA1000446", "Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish", "GSE239623", "Transcriptome Analysis", "Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study  we created an ybx1 mutant with CRISPR/Cas9  and showed that the folliculogenesis in the mutant ovary ybx1 /  was blocked at pre vitellogenic PV to early vitellogenic EV transition  leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 /  and the control ybx1+/  including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/   however  follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly  partial loss of p21 in heterozygous cdkn1a+/  could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/  females with normal follicle activation  in contrast to the PV EV blockade in ybx1 /  mutant. Interestingly  the follicle cells from the ybx1 /  mutant follicles displayed a poor proliferative activity in vitro; however  the cells from the ybx1 / p21+/  follicles resumed normal proliferation compared to that from the wildtype fish. In summary  we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a  a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade  we further isolated PV follicles from both WT ybx1+/+ and  ybx1 /  zebrafish. post RNA isolation  we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.", null, null, null, "PV  M1", "GSM7669031", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing", "PV  M1", "Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file", "follicle", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / ", "GSM7669031", "GSM7669031: PV  M1; Danio rerio; RNA Seq", "GSM7669031 r1", "GSM7669031", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452269", null, null, "PV_M1_R1.fastq.gz PV_M1_R2.fastq.gz", "fastq fastq", 3634173229.0, 18461903.0, "GSM7669031 r1", "0:98.44 1:98.41", "A:930322973;C:875929476;G:875710056;T:948595199;N:3615525", 98, 98, null, null, 930322973, 875929476, 875710056, 948595199, 3615525, "SRX21195036", "SRS18453962", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.94787, 0.95134, 0.02457, 0.02445, 0.73762, 0.73843, 0.48244, 0.48069, 100, 98, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [24597, "SRR25462246", "SRX21195035", "SRS18453961", "SRP452269", "PRJNA1000446", "Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish", "GSE239623", "Transcriptome Analysis", "Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study  we created an ybx1 mutant with CRISPR/Cas9  and showed that the folliculogenesis in the mutant ovary ybx1 /  was blocked at pre vitellogenic PV to early vitellogenic EV transition  leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 /  and the control ybx1+/  including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/   however  follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly  partial loss of p21 in heterozygous cdkn1a+/  could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/  females with normal follicle activation  in contrast to the PV EV blockade in ybx1 /  mutant. Interestingly  the follicle cells from the ybx1 /  mutant follicles displayed a poor proliferative activity in vitro; however  the cells from the ybx1 / p21+/  follicles resumed normal proliferation compared to that from the wildtype fish. In summary  we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a  a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade  we further isolated PV follicles from both WT ybx1+/+ and  ybx1 /  zebrafish. post RNA isolation  we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.", null, null, null, "PV  WT3", "GSM7669030", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing", "PV  WT3", "Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file", "follicle", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+", "GSM7669030", "GSM7669030: PV  WT3; Danio rerio; RNA Seq", "GSM7669030 r1", "GSM7669030", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452269", null, null, "PV_WT3_R2.fastq PV_WT3_R1.fastq", "fastq fastq", 2965772270.0, 14976621.0, "GSM7669030 r1", "0:99.03 1:98.99", "A:759343389;C:716154246;G:713466520;T:775995980;N:812135", 99, 98, null, null, 759343389, 716154246, 713466520, 775995980, 812135, "SRX21195035", "SRS18453961", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.95027, 0.95485, 0.02356, 0.02292, 0.74422, 0.74554, 0.47974, 0.48267, 100, 98, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [24598, "SRR25462247", "SRX21195034", "SRS18453960", "SRP452269", "PRJNA1000446", "Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish", "GSE239623", "Transcriptome Analysis", "Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study  we created an ybx1 mutant with CRISPR/Cas9  and showed that the folliculogenesis in the mutant ovary ybx1 /  was blocked at pre vitellogenic PV to early vitellogenic EV transition  leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 /  and the control ybx1+/  including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/   however  follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly  partial loss of p21 in heterozygous cdkn1a+/  could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/  females with normal follicle activation  in contrast to the PV EV blockade in ybx1 /  mutant. Interestingly  the follicle cells from the ybx1 /  mutant follicles displayed a poor proliferative activity in vitro; however  the cells from the ybx1 / p21+/  follicles resumed normal proliferation compared to that from the wildtype fish. In summary  we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a  a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade  we further isolated PV follicles from both WT ybx1+/+ and  ybx1 /  zebrafish. post RNA isolation  we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.", null, null, null, "PV  WT2", "GSM7669029", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing", "PV  WT2", "Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file", "follicle", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+", "GSM7669029", "GSM7669029: PV  WT2; Danio rerio; RNA Seq", "GSM7669029 r1", "GSM7669029", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452269", null, null, "PV_WT2_R2.fastq PV_WT2_R1.fastq", "fastq fastq", 2021387268.0, 10195384.0, "GSM7669029 r1", "0:99.15 1:99.12", "A:517788644;C:487363563;G:485168383;T:530550229;N:516449", 99, 99, null, null, 517788644, 487363563, 485168383, 530550229, 516449, "SRX21195034", "SRS18453960", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.95113, 0.9544, 0.02394, 0.02364, 0.74168, 0.74363, 0.47881, 0.47499, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [24599, "SRR25462248", "SRX21195033", "SRS18453959", "SRP452269", "PRJNA1000446", "Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish", "GSE239623", "Transcriptome Analysis", "Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study  we created an ybx1 mutant with CRISPR/Cas9  and showed that the folliculogenesis in the mutant ovary ybx1 /  was blocked at pre vitellogenic PV to early vitellogenic EV transition  leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 /  and the control ybx1+/  including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/   however  follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly  partial loss of p21 in heterozygous cdkn1a+/  could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/  females with normal follicle activation  in contrast to the PV EV blockade in ybx1 /  mutant. Interestingly  the follicle cells from the ybx1 /  mutant follicles displayed a poor proliferative activity in vitro; however  the cells from the ybx1 / p21+/  follicles resumed normal proliferation compared to that from the wildtype fish. In summary  we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a  a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade  we further isolated PV follicles from both WT ybx1+/+ and  ybx1 /  zebrafish. post RNA isolation  we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.", null, null, null, "PV  WT1", "GSM7669028", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing", "PV  WT1", "Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file", "follicle", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+", "GSM7669028", "GSM7669028: PV  WT1; Danio rerio; RNA Seq", "GSM7669028 r1", "GSM7669028", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452269", null, null, "PV_WT1_R1.fastq PV_WT1_R2.fastq", "fastq fastq", 3244660111.0, 16481925.0, "GSM7669028 r1", "0:98.44 1:98.42", "A:831426044;C:781489498;G:779991004;T:848549246;N:3204319", 98, 98, null, null, 831426044, 781489498, 779991004, 848549246, 3204319, "SRX21195033", "SRS18453959", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.94779, 0.95185, 0.02328, 0.02298, 0.74294, 0.74391, 0.48052, 0.47966, 95, 95, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [30556, "SRR27836071", "SRX23499420", "SRS20351177", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "Rbpms2 mApple crosslinked SR3", "GSM8059038", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing", "Rbpms2 mApple crosslinked SR3", "Basespace illumina platform was used and reads were mapped using tophate2 aligner. Estimation of reference genes and transcript was done using cufflinks and reads were mapped to the genome GRCz10. Reads were aligned with the TopHat Alignment App. GRCz10 CSV file that compiled includes tracking ids  gene loci  and FPKMs for each samples CSV files include tracking and gene id  gene short name  tss id  locus  and FPKM for each sample", "Gonad", null, "RNA was extracted with an Rneasy Mini Kit Qiagen  74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina  20020589", null, "tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype", "GSM8059038", "GSM8059038: Rbpms2 mApple crosslinked SR3; Danio rerio; RNA Seq", "GSM8059038 r1", "GSM8059038", "1", "RNA was extracted with an Rneasy Mini Kit Qiagen  74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina  20020589", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, null, "SR-3_S4_L001_R1_001.fastq.gz SR-3_S4_L001_R2_001.fastq.gz", "fastq fastq", 588252864.0, 3949222.0, "GSM8059038 r1", "0:74.42 1:74.53", "A:116383167;C:176622592;G:176850622;T:118306997;N:89486", 74, 74, null, null, 116383167, 176622592, 176850622, 118306997, 89486, "SRX23499420", "SRS20351177", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [30557, "SRR27836072", "SRX23499419", "SRS20351178", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "Rbpms2 mApple uncrosslinked SR2", "GSM8059037", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing", "Rbpms2 mApple uncrosslinked SR2", "Basespace illumina platform was used and reads were mapped using tophate2 aligner. Estimation of reference genes and transcript was done using cufflinks and reads were mapped to the genome GRCz10. Reads were aligned with the TopHat Alignment App. GRCz10 CSV file that compiled includes tracking ids  gene loci  and FPKMs for each samples CSV files include tracking and gene id  gene short name  tss id  locus  and FPKM for each sample", "Gonad", null, "RNA was extracted with an Rneasy Mini Kit Qiagen  74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina  20020589", null, "tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype", "GSM8059037", "GSM8059037: Rbpms2 mApple uncrosslinked SR2; Danio rerio; RNA Seq", "GSM8059037 r1", "GSM8059037", "1", "RNA was extracted with an Rneasy Mini Kit Qiagen  74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina  20020589", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, null, "SR-2_S3_L001_R1_001.fastq.gz SR-2_S3_L001_R2_001.fastq.gz", "fastq fastq", 547329260.0, 3670350.0, "GSM8059037 r1", "0:74.51 1:74.61", "A:109193152;C:163365002;G:162344228;T:112378069;N:48809", 74, 74, null, null, 109193152, 163365002, 162344228, 112378069, 48809, "SRX23499419", "SRS20351178", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [30558, "SRR27836073", "SRX23499418", "SRS20351176", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "mApple control crosslinked SR8", "GSM8059036", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing", "mApple control crosslinked SR8", "Basespace illumina platform was used and reads were mapped using tophate2 aligner. Estimation of reference genes and transcript was done using cufflinks and reads were mapped to the genome GRCz10. Reads were aligned with the TopHat Alignment App. GRCz10 CSV file that compiled includes tracking ids  gene loci  and FPKMs for each samples CSV files include tracking and gene id  gene short name  tss id  locus  and FPKM for each sample", "Gonad", null, "RNA was extracted with an Rneasy Mini Kit Qiagen  74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina  20020589", null, "tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype", "GSM8059036", "GSM8059036: mApple control crosslinked SR8; Danio rerio; RNA Seq", "GSM8059036 r1", "GSM8059036", "1", "RNA was extracted with an Rneasy Mini Kit Qiagen  74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina  20020589", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, null, "SR-8_S6_L001_R1_001.fastq.gz SR-8_S6_L001_R2_001.fastq.gz", "fastq fastq", 474378287.0, 3180744.0, "GSM8059036 r1", "0:74.52 1:74.62", "A:90310344;C:145884340;G:146185172;T:91942086;N:56345", 74, 74, null, null, 90310344, 145884340, 146185172, 91942086, 56345, "SRX23499418", "SRS20351176", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [30559, "SRR27836074", "SRX23499417", "SRS20351175", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "mApple control uncrosslinked SR6", "GSM8059035", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing", "mApple control uncrosslinked SR6", "Basespace illumina platform was used and reads were mapped using tophate2 aligner. Estimation of reference genes and transcript was done using cufflinks and reads were mapped to the genome GRCz10. Reads were aligned with the TopHat Alignment App. GRCz10 CSV file that compiled includes tracking ids  gene loci  and FPKMs for each samples CSV files include tracking and gene id  gene short name  tss id  locus  and FPKM for each sample", "Gonad", null, "RNA was extracted with an Rneasy Mini Kit Qiagen  74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina  20020589", null, "tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype", "GSM8059035", "GSM8059035: mApple control uncrosslinked SR6; Danio rerio; RNA Seq", "GSM8059035 r1", "GSM8059035", "1", "RNA was extracted with an Rneasy Mini Kit Qiagen  74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina  20020589", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, null, "SR-6_S5_L001_R1_001.fastq.gz SR-6_S5_L001_R2_001.fastq.gz", "fastq fastq", 1667210566.0, 11187841.0, "GSM8059035 r1", "0:74.46 1:74.56", "A:348153529;C:480420209;G:474792496;T:363567978;N:276354", 74, 74, null, null, 348153529, 480420209, 474792496, 363567978, 276354, "SRX23499417", "SRS20351175", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [30560, "SRR27836075", "SRX23499416", "SRS20351174", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 mutant 4  21 dpf", "GSM8059034", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing", "rbpms2 mutant 4  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM", "GSM8059034", "GSM8059034: rbpms2 mutant 4  21 dpf; Danio rerio; RNA Seq", "GSM8059034 r1", "GSM8059034", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-DM_4_S8_L001_R1_001.fastq.gz rbpms2-d21-DM_4_S8_L001_R2_001.fastq.gz", "fastq fastq", 2533252722.0, 24835811.0, "GSM8059034 r1", "0:51 1:51", "A:767895104;C:496128064;G:502250517;T:766951391;N:27646", 51, 51, null, null, 767895104, 496128064, 502250517, 766951391, 27646, "SRX23499416", "SRS20351174", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [30561, "SRR27836076", "SRX23499416", "SRS20351174", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 mutant 4  21 dpf", "GSM8059034", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing", "rbpms2 mutant 4  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM", "GSM8059034", "GSM8059034: rbpms2 mutant 4  21 dpf; Danio rerio; RNA Seq", "GSM8059034 r1", "GSM8059034", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-DM_4_S8_L002_R1_001.fastq.gz rbpms2-d21-DM_4_S8_L002_R2_001.fastq.gz", "fastq fastq", 2500214514.0, 24511907.0, "GSM8059034 r2", "0:51 1:51", "A:757980090;C:489633622;G:495839519;T:756737989;N:23294", 51, 51, null, null, 757980090, 489633622, 495839519, 756737989, 23294, "SRX23499416", "SRS20351174", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [30562, "SRR27836077", "SRX23499415", "SRS20351173", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 mutant 3  21 dpf", "GSM8059033", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing", "rbpms2 mutant 3  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM", "GSM8059033", "GSM8059033: rbpms2 mutant 3  21 dpf; Danio rerio; RNA Seq", "GSM8059033 r1", "GSM8059033", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-DM_3_S7_L001_R1_001.fastq.gz rbpms2-d21-DM_3_S7_L001_R2_001.fastq.gz", "fastq fastq", 2383569354.0, 23368327.0, "GSM8059033 r1", "0:51 1:51", "A:705650487;C:468856307;G:473479720;T:735556568;N:26272", 51, 51, null, null, 705650487, 468856307, 473479720, 735556568, 26272, "SRX23499415", "SRS20351173", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [30563, "SRR27836078", "SRX23499415", "SRS20351173", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 mutant 3  21 dpf", "GSM8059033", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing", "rbpms2 mutant 3  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM", "GSM8059033", "GSM8059033: rbpms2 mutant 3  21 dpf; Danio rerio; RNA Seq", "GSM8059033 r1", "GSM8059033", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-DM_3_S7_L002_R1_001.fastq.gz rbpms2-d21-DM_3_S7_L002_R2_001.fastq.gz", "fastq fastq", 2324856114.0, 22792707.0, "GSM8059033 r2", "0:51 1:51", "A:688232198;C:457346277;G:462034541;T:717221485;N:21613", 51, 51, null, null, 688232198, 457346277, 462034541, 717221485, 21613, "SRX23499415", "SRS20351173", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [30564, "SRR27836079", "SRX23499414", "SRS20351172", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 mutant 1  21 dpf", "GSM8059032", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing", "rbpms2 mutant 1  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM", "GSM8059032", "GSM8059032: rbpms2 mutant 1  21 dpf; Danio rerio; RNA Seq", "GSM8059032 r1", "GSM8059032", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-DM_1_S5_L001_R1_001.fastq.gz rbpms2-d21-DM_1_S5_L001_R2_001.fastq.gz", "fastq fastq", 2412458100.0, 23651550.0, "GSM8059032 r1", "0:51 1:51", "A:726246267;C:465733066;G:465377798;T:755071663;N:29306", 51, 51, null, null, 726246267, 465733066, 465377798, 755071663, 29306, "SRX23499414", "SRS20351172", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [30565, "SRR27836080", "SRX23499414", "SRS20351172", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 mutant 1  21 dpf", "GSM8059032", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing", "rbpms2 mutant 1  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM", "GSM8059032", "GSM8059032: rbpms2 mutant 1  21 dpf; Danio rerio; RNA Seq", "GSM8059032 r1", "GSM8059032", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-DM_1_S5_L002_R1_001.fastq.gz rbpms2-d21-DM_1_S5_L002_R2_001.fastq.gz", "fastq fastq", 2363898144.0, 23175472.0, "GSM8059032 r2", "0:51 1:51", "A:711756208;C:456236364;G:456088591;T:739792903;N:24078", 51, 51, null, null, 711756208, 456236364, 456088591, 739792903, 24078, "SRX23499414", "SRS20351172", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [30566, "SRR27836081", "SRX23499413", "SRS20351171", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 wildtype 3  21 dpf", "GSM8059031", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing", "rbpms2 wildtype 3  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype", "GSM8059031", "GSM8059031: rbpms2 wildtype 3  21 dpf; Danio rerio; RNA Seq", "GSM8059031 r1", "GSM8059031", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-WT_3_S3_L001_R1_001.fastq.gz rbpms2-d21-WT_3_S3_L001_R2_001.fastq.gz", "fastq fastq", 2048418162.0, 20082531.0, "GSM8059031 r1", "0:51 1:51", "A:612611264;C:409068349;G:413909657;T:612805097;N:23795", 51, 51, null, null, 612611264, 409068349, 413909657, 612805097, 23795, "SRX23499413", "SRS20351171", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [30567, "SRR27836082", "SRX23499413", "SRS20351171", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 wildtype 3  21 dpf", "GSM8059031", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing", "rbpms2 wildtype 3  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype", "GSM8059031", "GSM8059031: rbpms2 wildtype 3  21 dpf; Danio rerio; RNA Seq", "GSM8059031 r1", "GSM8059031", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-WT_3_S3_L002_R1_001.fastq.gz rbpms2-d21-WT_3_S3_L002_R2_001.fastq.gz", "fastq fastq", 2018915070.0, 19793285.0, "GSM8059031 r2", "0:51 1:51", "A:603776465;C:403221066;G:408169193;T:603728354;N:19992", 51, 51, null, null, 603776465, 403221066, 408169193, 603728354, 19992, "SRX23499413", "SRS20351171", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [30568, "SRR27836083", "SRX23499412", "SRS20351179", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 wildtype 2  21 dpf", "GSM8059030", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing", "rbpms2 wildtype 2  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype", "GSM8059030", "GSM8059030: rbpms2 wildtype 2  21 dpf; Danio rerio; RNA Seq", "GSM8059030 r1", "GSM8059030", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-WT_2_S2_L001_R1_001.fastq.gz rbpms2-d21-WT_2_S2_L001_R2_001.fastq.gz", "fastq fastq", 1927777866.0, 18899783.0, "GSM8059030 r1", "0:51 1:51", "A:589122616;C:372230241;G:374787285;T:591617780;N:19944", 51, 51, null, null, 589122616, 372230241, 374787285, 591617780, 19944, "SRX23499412", "SRS20351179", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [30569, "SRR27836084", "SRX23499412", "SRS20351179", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 wildtype 2  21 dpf", "GSM8059030", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing", "rbpms2 wildtype 2  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype", "GSM8059030", "GSM8059030: rbpms2 wildtype 2  21 dpf; Danio rerio; RNA Seq", "GSM8059030 r1", "GSM8059030", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-WT_2_S2_L002_R1_001.fastq.gz rbpms2-d21-WT_2_S2_L002_R2_001.fastq.gz", "fastq fastq", 1901436570.0, 18641535.0, "GSM8059030 r2", "0:51 1:51", "A:581077435;C:367152917;G:369822980;T:583366137;N:17101", 51, 51, null, null, 581077435, 367152917, 369822980, 583366137, 17101, "SRX23499412", "SRS20351179", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [30570, "SRR27836085", "SRX23499411", "SRS20351170", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 wildtype 1  21 dpf", "GSM8059029", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing", "rbpms2 wildtype 1  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype", "GSM8059029", "GSM8059029: rbpms2 wildtype 1  21 dpf; Danio rerio; RNA Seq", "GSM8059029 r1", "GSM8059029", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-WT_1_S1_L001_R1_001.fastq.gz rbpms2-d21-WT_1_S1_L001_R2_001.fastq.gz", "fastq fastq", 1878693222.0, 18418561.0, "GSM8059029 r1", "0:51 1:51", "A:581058368;C:356028122;G:360378733;T:581204723;N:23276", 51, 51, null, null, 581058368, 356028122, 360378733, 581204723, 23276, "SRX23499411", "SRS20351170", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [30571, "SRR27836086", "SRX23499411", "SRS20351170", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 wildtype 1  21 dpf", "GSM8059029", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing", "rbpms2 wildtype 1  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype", "GSM8059029", "GSM8059029: rbpms2 wildtype 1  21 dpf; Danio rerio; RNA Seq", "GSM8059029 r1", "GSM8059029", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-WT_1_S1_L002_R1_001.fastq.gz rbpms2-d21-WT_1_S1_L002_R2_001.fastq.gz", "fastq fastq", 1861916160.0, 18254080.0, "GSM8059029 r2", "0:51 1:51", "A:575859972;C:352771580;G:357641601;T:575624138;N:18869", 51, 51, null, null, 575859972, 352771580, 357641601, 575624138, 18869, "SRX23499411", "SRS20351170", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"], [32476, "SRR29270149", "SRX24787634", "SRS21505104", "SRP511487", "PRJNA1119569", "RNA seq of zebrafish foxl2l mutant", "PRJNA1119569", "Other", "Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.", null, null, null, null, "foxl2l Mut 20 1", null, "strain:AB|age:20|collection date:2023 06 10|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "foxl2l Mut 20 1", "E10", "E10", "50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme  NR604 01", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP511487", null, null, "foxl2l_Mut-20-1_S162_R1.fastq.gz foxl2l_Mut-20-1_S162_R2.fastq.gz", "fastq fastq", 8940963680.0, 29605840.0, "foxl2l Mut 20 1 S162 R1.fastq.gz", "0:151 1:151", "A:2232167098;C:2229744850;G:2271326718;T:2207692629;N:32385", 151, 151, null, null, 2232167098, 2229744850, 2271326718, 2207692629, 32385, "SRX24787634", "SRS21505104", "SRA1887976", "Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology", "Institute of Hydrobiology, Chinese Academy of Sciences", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "China", "2024-06-03", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [32477, "SRR29270150", "SRX24787633", "SRS21505103", "SRP511487", "PRJNA1119569", "RNA seq of zebrafish foxl2l mutant", "PRJNA1119569", "Other", "Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. 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This is particularly salient in aquatic ecosystems  where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end  zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that  in males  nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction  resulting in viable spermatozoa but with reduced motility. Moreover  in females we observed an alteration in oocyte stages frequencies during oogenesis  possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure  meiosis and DNA double strand break formation and repair progression  and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall  our results demonstrate that acute exposure to NPs can compromise reproductive fitness  underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples", null, "pubmed:39556913", null, "Zebrafish  Testicle  Plastic  Replicate 3  Animal 3", "GSM8583344", null, "source name:testicles|tissue:testicles|cell line:germline|genotype:WT|treatment:Plastic|geo loc name:missing|collection date:missing", "Zebrafish  Testicle  Plastic  Replicate 3  Animal 3", "Anaconda The sequencing quality was checked before performing the assembly. 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This is particularly salient in aquatic ecosystems  where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end  zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that  in males  nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction  resulting in viable spermatozoa but with reduced motility. Moreover  in females we observed an alteration in oocyte stages frequencies during oogenesis  possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure  meiosis and DNA double strand break formation and repair progression  and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall  our results demonstrate that acute exposure to NPs can compromise reproductive fitness  underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples", null, "pubmed:39556913", null, "Zebrafish  Testicle  Plastic  Replicate 3  Animal 1", "GSM8583343", null, "source name:testicles|tissue:testicles|cell line:germline|genotype:WT|treatment:Plastic|geo loc name:missing|collection date:missing", "Zebrafish  Testicle  Plastic  Replicate 3  Animal 1", "Anaconda The sequencing quality was checked before performing the assembly. STAR bioconda was used for the assembly smartools bioconda was used to generate the intermediate files Sam and Bam Counts were obtained from the bam intermediate file Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample", "testicles", "Half of the fish were exposed to polystyrene nanoplastics each 24 hours added in the water during 96 hours accute exposure. The rest were used as controls  so no plastics were added in the water.", "Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment", "Adult zebrafish were maintained at the animal house under standard conditions", "tissue:testicles|cell line:germline|genotype:WT|treatment:Plastic", "GSM8583343", "GSM8583343: Zebrafish  Testicle  Plastic  Replicate 3  Animal 1; Danio rerio; RNA Seq", "GSM8583343 r1", "GSM8583343", "1", "Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP539687", null, null, "M6_C2_R3_A1_EKRN230074902-1A_HWT7HDSX7_L3_1.fq M6_C2_R3_A1_EKRN230074902-1A_HWT7HDSX7_L3_2.fq", "fastq fastq", 21334650000.0, 71115500.0, "GSM8583343 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX26435350", "SRS22952030", "SRA1994234", "UAB (Universidad Aut\u00f3noma de Barcelona)", "UAB (Universidad Aut\u00f3noma de Barcelona)", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Spain", "2024-10-20", "Adult", "Adult", "Gonad", "Reproductive System"], [34096, "SRR31050911", "SRX26435349", "SRS22952029", "SRP539687", "PRJNA1175381", "Short term polystyrene nanoplastic exposure alters zebrafish male and female germline and reproductive outcomes  unveiling pollutant impacted molecular pathways", "GSE279916", "Transcriptome Analysis", "Nanoplastics pollution is a rising environmental concern whose impacts on biodiversity and human health are far from being understood. This is particularly salient in aquatic ecosystems  where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end  zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that  in males  nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction  resulting in viable spermatozoa but with reduced motility. Moreover  in females we observed an alteration in oocyte stages frequencies during oogenesis  possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure  meiosis and DNA double strand break formation and repair progression  and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall  our results demonstrate that acute exposure to NPs can compromise reproductive fitness  underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples", null, "pubmed:39556913", null, "Zebrafish  Testicle  Plastic  Replicate 2  Animal 2", "GSM8583342", null, "source name:testicles|tissue:testicles|cell line:germline|genotype:WT|treatment:Plastic|geo loc name:missing|collection date:missing", "Zebrafish  Testicle  Plastic  Replicate 2  Animal 2", "Anaconda The sequencing quality was checked before performing the assembly. STAR bioconda was used for the assembly smartools bioconda was used to generate the intermediate files Sam and Bam Counts were obtained from the bam intermediate file Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample", "testicles", "Half of the fish were exposed to polystyrene nanoplastics each 24 hours added in the water during 96 hours accute exposure. The rest were used as controls  so no plastics were added in the water.", "Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment", "Adult zebrafish were maintained at the animal house under standard conditions", "tissue:testicles|cell line:germline|genotype:WT|treatment:Plastic", "GSM8583342", "GSM8583342: Zebrafish  Testicle  Plastic  Replicate 2  Animal 2; Danio rerio; RNA Seq", "GSM8583342 r1", "GSM8583342", "1", "Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP539687", null, null, "M6_C2_R2_A2_EKRN230074901-1A_HWT7HDSX7_L2_1.fq M6_C2_R2_A2_EKRN230074901-1A_HWT7HDSX7_L2_2.fq", "fastq fastq", 23956812900.0, 79856043.0, "GSM8583342 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX26435349", "SRS22952029", "SRA1994234", "UAB (Universidad Aut\u00f3noma de Barcelona)", "UAB (Universidad Aut\u00f3noma de Barcelona)", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Spain", "2024-10-20", "Adult", "Adult", "Gonad", "Reproductive System"], [34097, "SRR31050912", "SRX26435348", "SRS22952028", "SRP539687", "PRJNA1175381", "Short term polystyrene nanoplastic exposure alters zebrafish male and female germline and reproductive outcomes  unveiling pollutant impacted molecular pathways", "GSE279916", "Transcriptome Analysis", "Nanoplastics pollution is a rising environmental concern whose impacts on biodiversity and human health are far from being understood. This is particularly salient in aquatic ecosystems  where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end  zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that  in males  nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction  resulting in viable spermatozoa but with reduced motility. Moreover  in females we observed an alteration in oocyte stages frequencies during oogenesis  possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure  meiosis and DNA double strand break formation and repair progression  and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall  our results demonstrate that acute exposure to NPs can compromise reproductive fitness  underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples", null, "pubmed:39556913", null, "Zebrafish  Testicle  Control  Replicate 3  Animal 1", "GSM8583341", null, "source name:testicles|tissue:testicles|cell line:germline|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing", "Zebrafish  Testicle  Control  Replicate 3  Animal 1", "Anaconda The sequencing quality was checked before performing the assembly. STAR bioconda was used for the assembly smartools bioconda was used to generate the intermediate files Sam and Bam Counts were obtained from the bam intermediate file Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample", "testicles", "Half of the fish were exposed to polystyrene nanoplastics each 24 hours added in the water during 96 hours accute exposure. The rest were used as controls  so no plastics were added in the water.", "Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment", "Adult zebrafish were maintained at the animal house under standard conditions", "tissue:testicles|cell line:germline|genotype:WT|treatment:Control", "GSM8583341", "GSM8583341: Zebrafish  Testicle  Control  Replicate 3  Animal 1; Danio rerio; RNA Seq", "GSM8583341 r1", "GSM8583341", "1", "Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP539687", null, null, "M6_C1_R3_A1_EKRN230074898-1A_HWT7HDSX7_L2_1.fq M6_C1_R3_A1_EKRN230074898-1A_HWT7HDSX7_L2_2.fq", "fastq fastq", 17143802100.0, 57146007.0, "GSM8583341 r1", "0:150 1:150", "A:4588084574;C:4015807096;G:4039433882;T:4500279277;N:197271", 150, 150, null, null, 4588084574, 4015807096, 4039433882, 4500279277, 197271, "SRX26435348", "SRS22952028", "SRA1994234", "UAB (Universidad Aut\u00f3noma de Barcelona)", "UAB (Universidad Aut\u00f3noma de Barcelona)", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Spain", "2024-10-20", "Adult", "Adult", "Gonad", "Reproductive System"], [34098, "SRR31050913", "SRX26435347", "SRS22952027", "SRP539687", "PRJNA1175381", "Short term polystyrene nanoplastic exposure alters zebrafish male and female germline and reproductive outcomes  unveiling pollutant impacted molecular pathways", "GSE279916", "Transcriptome Analysis", "Nanoplastics pollution is a rising environmental concern whose impacts on biodiversity and human health are far from being understood. This is particularly salient in aquatic ecosystems  where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end  zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that  in males  nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction  resulting in viable spermatozoa but with reduced motility. Moreover  in females we observed an alteration in oocyte stages frequencies during oogenesis  possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure  meiosis and DNA double strand break formation and repair progression  and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall  our results demonstrate that acute exposure to NPs can compromise reproductive fitness  underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples", null, "pubmed:39556913", null, "Zebrafish  Testicle  Control  Replicate 2  Animal 2", "GSM8583340", null, "source name:testicles|tissue:testicles|cell line:germline|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing", "Zebrafish  Testicle  Control  Replicate 2  Animal 2", "Anaconda The sequencing quality was checked before performing the assembly. STAR bioconda was used for the assembly smartools bioconda was used to generate the intermediate files Sam and Bam Counts were obtained from the bam intermediate file Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample", "testicles", "Half of the fish were exposed to polystyrene nanoplastics each 24 hours added in the water during 96 hours accute exposure. The rest were used as controls  so no plastics were added in the water.", "Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment", "Adult zebrafish were maintained at the animal house under standard conditions", "tissue:testicles|cell line:germline|genotype:WT|treatment:Control", "GSM8583340", "GSM8583340: Zebrafish  Testicle  Control  Replicate 2  Animal 2; Danio rerio; RNA Seq", "GSM8583340 r1", "GSM8583340", "1", "Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP539687", null, null, "M6_C1_R2_A2_1.fq M6_C1_R2_A2_2.fq", "fastq fastq", 17289440100.0, 57631467.0, "GSM8583340 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX26435347", "SRS22952027", "SRA1994234", "UAB (Universidad Aut\u00f3noma de Barcelona)", "UAB (Universidad Aut\u00f3noma de Barcelona)", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Spain", "2024-10-20", "Adult", "Adult", "Gonad", "Reproductive System"], [34099, "SRR31050914", "SRX26435346", "SRS22952026", "SRP539687", "PRJNA1175381", "Short term polystyrene nanoplastic exposure alters zebrafish male and female germline and reproductive outcomes  unveiling pollutant impacted molecular pathways", "GSE279916", "Transcriptome Analysis", "Nanoplastics pollution is a rising environmental concern whose impacts on biodiversity and human health are far from being understood. This is particularly salient in aquatic ecosystems  where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end  zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that  in males  nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction  resulting in viable spermatozoa but with reduced motility. Moreover  in females we observed an alteration in oocyte stages frequencies during oogenesis  possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure  meiosis and DNA double strand break formation and repair progression  and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall  our results demonstrate that acute exposure to NPs can compromise reproductive fitness  underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples", null, "pubmed:39556913", null, "Zebrafish  Testicle  Control  Replicate 1  Animal 2", "GSM8583339", null, "source name:testicles|tissue:testicles|cell line:germline|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing", "Zebrafish  Testicle  Control  Replicate 1  Animal 2", "Anaconda The sequencing quality was checked before performing the assembly. STAR bioconda was used for the assembly smartools bioconda was used to generate the intermediate files Sam and Bam Counts were obtained from the bam intermediate file Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample", "testicles", "Half of the fish were exposed to polystyrene nanoplastics each 24 hours added in the water during 96 hours accute exposure. The rest were used as controls  so no plastics were added in the water.", "Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment", "Adult zebrafish were maintained at the animal house under standard conditions", "tissue:testicles|cell line:germline|genotype:WT|treatment:Control", "GSM8583339", "GSM8583339: Zebrafish  Testicle  Control  Replicate 1  Animal 2; Danio rerio; RNA Seq", "GSM8583339 r1", "GSM8583339", "1", "Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP539687", null, null, "M6_C1_R1_A2_EKRN230074896-1A_HWT7HDSX7_L2_1.fq M6_C1_R1_A2_EKRN230074896-1A_HWT7HDSX7_L2_2.fq", "fastq fastq", 19275937200.0, 64253124.0, "GSM8583339 r1", "0:150 1:150", "A:5148413409;C:4525316389;G:4541110001;T:5060873310;N:224091", 150, 150, null, null, 5148413409, 4525316389, 4541110001, 5060873310, 224091, "SRX26435346", "SRS22952026", "SRA1994234", "UAB (Universidad Aut\u00f3noma de Barcelona)", "UAB (Universidad Aut\u00f3noma de Barcelona)", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Spain", "2024-10-20", "Adult", "Adult", "Gonad", "Reproductive System"], [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"], [66194, "SRR16096233", "SRX12382357", "SRS10353019", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 1cell Rep5", "GSM5599725", null, "tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 1cell Rep5", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 1cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599725", "GSM5599725: ZF zygote IP 1cell Rep5; Danio rerio; RIP Seq", "GSM5599725", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599725", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_1cell_Rep5_R1.fastq.gz ZF_zygote_IP_1cell_Rep5_R2.fastq.gz", "fastq fastq", 3660517860.0, 35887430.0, "GSM5599725 r1", "0:51 1:51", "A:858138600;C:924733544;G:1002150083;T:875349961;N:145672", 51, 51, null, null, 858138600, 924733544, 1002150083, 875349961, 145672, "SRX12382357", "SRS10353019", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.83384, 0.82667, 0.09687, 0.11892, 0.79076, 0.79326, 0.63739, 0.60941, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66195, "SRR16096232", "SRX12382356", "SRS10353018", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 1cell Rep4", "GSM5599724", null, "tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 1cell Rep4", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 1cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599724", "GSM5599724: ZF zygote IP 1cell Rep4; Danio rerio; RIP Seq", "GSM5599724", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599724", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_1cell_Rep4_R1.fastq.gz ZF_zygote_IP_1cell_Rep4_R2.fastq.gz", "fastq fastq", 3660205842.0, 35884371.0, "GSM5599724 r1", "0:51 1:51", "A:895738659;C:880838836;G:971118499;T:912364119;N:145729", 51, 51, null, null, 895738659, 880838836, 971118499, 912364119, 145729, "SRX12382356", "SRS10353018", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.87258, 0.86932, 0.06573, 0.07958, 0.78044, 0.78374, 0.55531, 0.5462, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66196, "SRR16096231", "SRX12382355", "SRS10353016", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 1cell Rep3", "GSM5599723", null, "tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 1cell Rep3", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 1cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599723", "GSM5599723: ZF zygote IP 1cell Rep3; Danio rerio; RIP Seq", "GSM5599723", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599723", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_1cell_Rep3_R1.fastq.gz ZF_zygote_IP_1cell_Rep3_R2.fastq.gz", "fastq fastq", 2732409048.0, 26788324.0, "GSM5599723 r1", "0:51 1:51", "A:669345195;C:656715671;G:724415204;T:681825149;N:107829", 51, 51, null, null, 669345195, 656715671, 724415204, 681825149, 107829, "SRX12382355", "SRS10353016", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.85204, 0.83607, 0.06526, 0.08046, 0.78535, 0.78748, 0.60467, 0.50165, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66197, "SRR16096230", "SRX12382354", "SRS10353017", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 1cell Rep2", "GSM5599722", null, "tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 1cell Rep2", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 1cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599722", "GSM5599722: ZF zygote IP 1cell Rep2; Danio rerio; RIP Seq", "GSM5599722", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599722", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_1cell_Rep2_R1.fastq.gz ZF_zygote_IP_1cell_Rep2_R2.fastq.gz", "fastq fastq", 2235668028.0, 21918314.0, "GSM5599722 r1", "0:51 1:51", "A:552522700;C:535947981;G:588168855;T:558939713;N:88779", 51, 51, null, null, 552522700, 535947981, 588168855, 558939713, 88779, "SRX12382354", "SRS10353017", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.85597, 0.85298, 0.06663, 0.07927, 0.79058, 0.79237, 0.57626, 0.56525, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66198, "SRR16096229", "SRX12382353", "SRS10353015", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 1cell Rep1", "GSM5599721", null, "tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 1cell Rep1", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 1cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599721", "GSM5599721: ZF zygote IP 1cell Rep1; Danio rerio; RIP Seq", "GSM5599721", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599721", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_1cell_Rep1_R1.fastq.gz ZF_zygote_IP_1cell_Rep1_R2.fastq.gz", "fastq fastq", 1785761736.0, 17507468.0, "GSM5599721 r1", "0:51 1:51", "A:429081683;C:435813601;G:481376346;T:439419714;N:70392", 51, 51, null, null, 429081683, 435813601, 481376346, 439419714, 70392, "SRX12382353", "SRS10353015", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.75314, 0.75693, 0.0543, 0.06639, 0.79482, 0.79594, 0.57979, 0.56522, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66199, "SRR16096228", "SRX12382352", "SRS10353014", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 5cell Rep3", "GSM5599720", null, "tissue:ZF zygote IP 5cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 5cell Rep3", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 5cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599720", "GSM5599720: ZF zygote IP 5cell Rep3; Danio rerio; RIP Seq", "GSM5599720", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599720", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_5cell_Rep3_R1.fastq.gz ZF_zygote_IP_5cell_Rep3_R2.fastq.gz", "fastq fastq", 2179659420.0, 21369210.0, "GSM5599720 r1", "0:51 1:51", "A:539092949;C:513857324;G:569620218;T:556940661;N:148268", 51, 51, null, null, 539092949, 513857324, 569620218, 556940661, 148268, "SRX12382352", "SRS10353014", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.92028, 0.90706, 0.03967, 0.05572, 0.78431, 0.78886, 0.49727, 0.48541, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66200, "SRR16096227", "SRX12382351", "SRS10353012", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 5cell Rep2", "GSM5599719", null, "tissue:ZF zygote IP 5cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 5cell Rep2", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 5cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599719", "GSM5599719: ZF zygote IP 5cell Rep2; Danio rerio; RIP Seq", "GSM5599719", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599719", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_5cell_Rep2_R1.fastq.gz ZF_zygote_IP_5cell_Rep2_R2.fastq.gz", "fastq fastq", 2527184538.0, 24776319.0, "GSM5599719 r1", "0:51 1:51", "A:628307375;C:594702688;G:657847712;T:646151885;N:174878", 51, 51, null, null, 628307375, 594702688, 657847712, 646151885, 174878, "SRX12382351", "SRS10353012", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91811, 0.90487, 0.03919, 0.05376, 0.78315, 0.78729, 0.49414, 0.48564, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66201, "SRR16096226", "SRX12382350", "SRS10353011", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 5cell Rep1", "GSM5599718", null, "tissue:ZF zygote IP 5cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 5cell Rep1", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 5cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599718", "GSM5599718: ZF zygote IP 5cell Rep1; Danio rerio; RIP Seq", "GSM5599718", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599718", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_5cell_Rep1_R1.fastq.gz ZF_zygote_IP_5cell_Rep1_R2.fastq.gz", "fastq fastq", 3481342518.0, 34130809.0, "GSM5599718 r1", "0:51 1:51", "A:865680250;C:823420389;G:907146965;T:884854199;N:240715", 51, 51, null, null, 865680250, 823420389, 907146965, 884854199, 240715, "SRX12382350", "SRS10353011", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91893, 0.90939, 0.04544, 0.06005, 0.78025, 0.78348, 0.50569, 0.49155, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66202, "SRR16096225", "SRX12382349", "SRS10353013", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 10cell Rep3", "GSM5599717", null, "tissue:ZF zygote IP 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 10cell Rep3", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 10cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599717", "GSM5599717: ZF zygote IP 10cell Rep3; Danio rerio; RIP Seq", "GSM5599717", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599717", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_10cell_Rep3_R1.fastq.gz ZF_zygote_IP_10cell_Rep3_R2.fastq.gz", "fastq fastq", 2172362850.0, 21297675.0, "GSM5599717 r1", "0:51 1:51", "A:536043605;C:513512883;G:568368414;T:554284996;N:152952", 51, 51, null, null, 536043605, 513512883, 568368414, 554284996, 152952, "SRX12382349", "SRS10353013", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91859, 0.90522, 0.03736, 0.05214, 0.78715, 0.79129, 0.49736, 0.48681, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66203, "SRR16096224", "SRX12382348", "SRS10353010", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 10cell Rep2", "GSM5599716", null, "tissue:ZF zygote IP 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 10cell Rep2", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 10cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599716", "GSM5599716: ZF zygote IP 10cell Rep2; Danio rerio; RIP Seq", "GSM5599716", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599716", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_10cell_Rep2_R1.fastq.gz ZF_zygote_IP_10cell_Rep2_R2.fastq.gz", "fastq fastq", 1840839492.0, 18047446.0, "GSM5599716 r1", "0:51 1:51", "A:454385290;C:437082102;G:482351138;T:466893642;N:127320", 51, 51, null, null, 454385290, 437082102, 482351138, 466893642, 127320, "SRX12382348", "SRS10353010", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.92217, 0.90956, 0.04012, 0.05483, 0.78819, 0.79318, 0.49756, 0.48256, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66204, "SRR16096223", "SRX12382347", "SRS10353009", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 10cell Rep1", "GSM5599715", null, "tissue:ZF zygote IP 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 10cell Rep1", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 10cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599715", "GSM5599715: ZF zygote IP 10cell Rep1; Danio rerio; RIP Seq", "GSM5599715", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599715", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_10cell_Rep1_R1.fastq.gz ZF_zygote_IP_10cell_Rep1_R2.fastq.gz", "fastq fastq", 2400553680.0, 23534840.0, "GSM5599715 r1", "0:51 1:51", "A:594878203;C:567573525;G:625488388;T:612448386;N:165178", 51, 51, null, null, 594878203, 567573525, 625488388, 612448386, 165178, "SRX12382347", "SRS10353009", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91641, 0.908, 0.03979, 0.05394, 0.78455, 0.7892, 0.48862, 0.47478, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66205, "SRR16096222", "SRX12382346", "SRS10353008", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote Input 10cell Rep2", "GSM5599714", null, "tissue:ZF zygote Input 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote Input 10cell Rep2", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote Input 10cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599714", "GSM5599714: ZF zygote Input 10cell Rep2; Danio rerio; RIP Seq", "GSM5599714", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599714", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_Input_10cell_Rep2_R1.fastq.gz ZF_zygote_Input_10cell_Rep2_R2.fastq.gz", "fastq fastq", 3842772582.0, 37674241.0, "GSM5599714 r1", "0:51 1:51", "A:843564828;C:1054412690;G:1130769812;T:813758353;N:266899", 51, 51, null, null, 843564828, 1054412690, 1130769812, 813758353, 266899, "SRX12382346", "SRS10353008", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91511, 0.90868, 0.32791, 0.38048, 0.89457, 0.89441, 0.81532, 0.75274, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66206, "SRR16096221", "SRX12382345", "SRS10353007", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote Input 10cell Rep1", "GSM5599713", null, "tissue:ZF zygote Input 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote Input 10cell Rep1", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote Input 10cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599713", "GSM5599713: ZF zygote Input 10cell Rep1; Danio rerio; RIP Seq", "GSM5599713", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599713", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_Input_10cell_Rep1_R1.fastq.gz ZF_zygote_Input_10cell_Rep1_R2.fastq.gz", "fastq fastq", 4029368016.0, 39503608.0, "GSM5599713 r1", "0:51 1:51", "A:893562237;C:1096986475;G:1180690796;T:857849967;N:278541", 51, 51, null, null, 893562237, 1096986475, 1180690796, 857849967, 278541, "SRX12382345", "SRS10353007", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91491, 0.90807, 0.32799, 0.37836, 0.89292, 0.89282, 0.81006, 0.73354, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [76356, "SRR24844103", "SRX20608301", "SRS17908187", "SRP441411", "PRJNA980839", "Adad1 knockout and misense mutant RNAseq", "PRJNA980839", "Other", "The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice  Adad1 is necessary for sperm differentiation  however its function outside of mammals has not been investigated. Here  through an N ethyl N nitrosourea ENU based forward genetic screen  we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish  however germ cells populated the gonad  proliferated  and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes  the spermatocytes failed to progress beyond the zygotene stage. Thus  Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay  and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings  suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1  we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification  pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.", null, null, null, "LB023 mutant B", "LB023 Mut B", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense MutantB|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 missense mutant: male testes", "LB023 Mut B", "LB023 Mut B", "Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age  5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences  NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "LB023-Mut-B_R1_001.fastq.gz LB023-Mut-B_R2_001.fastq.gz", "fastq fastq", 5532352200.0, 18441174.0, "LB023 Mut B R1 001.fastq.gz", "0:150 1:150", "A:1408144772;C:1348146392;G:1440174663;T:1335799503;N:86870", 150, 150, null, null, 1408144772, 1348146392, 1440174663, 1335799503, 86870, "SRX20608301", "SRS17908187", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.93072, 0.9289, 0.0921, 0.09129, 0.73129, 0.73143, 0.55139, 0.54723, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76357, "SRR24844100", "SRX20608300", "SRS17908192", "SRP441411", "PRJNA980839", "Adad1 knockout and misense mutant RNAseq", "PRJNA980839", "Other", "The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice  Adad1 is necessary for sperm differentiation  however its function outside of mammals has not been investigated. Here  through an N ethyl N nitrosourea ENU based forward genetic screen  we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish  however germ cells populated the gonad  proliferated  and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes  the spermatocytes failed to progress beyond the zygotene stage. Thus  Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay  and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings  suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1  we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification  pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.", null, null, null, "LB023 mutant C", "LB023 Mut C", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense MutantC|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 missense mutant: male testes", "LB023 Mut C", "LB023 Mut C", "Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age  5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences  NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "LB023-Mut-C_R2_001.fastq.gz LB023-Mut-C_R1_001.fastq.gz", "fastq fastq", 6159317100.0, 20531057.0, "LB023 Mut C R1 001.fastq.gz", "0:150 1:150", "A:1639865405;C:1424690953;G:1522945570;T:1571725037;N:90135", 150, 150, null, null, 1639865405, 1424690953, 1522945570, 1571725037, 90135, "SRX20608300", "SRS17908192", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.92565, 0.92502, 0.07339, 0.0724, 0.70832, 0.70924, 0.50224, 0.49923, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76358, "SRR24844101", "SRX20608299", "SRS17908193", "SRP441411", "PRJNA980839", "Adad1 knockout and misense mutant RNAseq", "PRJNA980839", "Other", "The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice  Adad1 is necessary for sperm differentiation  however its function outside of mammals has not been investigated. Here  through an N ethyl N nitrosourea ENU based forward genetic screen  we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish  however germ cells populated the gonad  proliferated  and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes  the spermatocytes failed to progress beyond the zygotene stage. Thus  Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay  and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings  suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1  we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification  pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.", null, null, null, "LB023 wildtype sibling control D", "LB023 WT D", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense WildtypeD|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 missense wildtype sibling: male testes", "LB023 WT D", "LB023 WT D", "Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age  5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences  NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "LB023-WT-D_R2_001.fastq.gz LB023-WT-D_R1_001.fastq.gz", "fastq fastq", 5436242700.0, 18120809.0, "LB023 WT D R1 001.fastq.gz", "0:150 1:150", "A:1448689171;C:1252673824;G:1358298822;T:1376497051;N:83832", 150, 150, null, null, 1448689171, 1252673824, 1358298822, 1376497051, 83832, "SRX20608299", "SRS17908193", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.91802, 0.91762, 0.09407, 0.09394, 0.70916, 0.7108, 0.54977, 0.55217, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76359, "SRR24844102", "SRX20608298", "SRS17908191", "SRP441411", "PRJNA980839", "Adad1 knockout and misense mutant RNAseq", "PRJNA980839", "Other", "The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice  Adad1 is necessary for sperm differentiation  however its function outside of mammals has not been investigated. Here  through an N ethyl N nitrosourea ENU based forward genetic screen  we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish  however germ cells populated the gonad  proliferated  and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes  the spermatocytes failed to progress beyond the zygotene stage. Thus  Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay  and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings  suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1  we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification  pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.", null, null, null, "adad1 mutant E", "adad1 Mut E", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:MutantE|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 mutant: male testes", "adad1 Mut E", "adad1 Mut E", "Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age  5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences  NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "adad1-Mut-E_R2_001.fastq.gz adad1-Mut-E_R1_001.fastq.gz", "fastq fastq", 4958837100.0, 16529457.0, "adad1 Mut E R1 001.fastq.gz", "0:150 1:150", "A:1311870356;C:1151609197;G:1254712533;T:1240567756;N:77258", 150, 150, null, null, 1311870356, 1151609197, 1254712533, 1240567756, 77258, "SRX20608298", "SRS17908191", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.901, 0.90124, 0.11096, 0.11139, 0.71851, 0.71967, 0.5526, 0.57121, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76360, "SRR24844104", "SRX20608297", "SRS17908190", "SRP441411", "PRJNA980839", "Adad1 knockout and misense mutant RNAseq", "PRJNA980839", "Other", "The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice  Adad1 is necessary for sperm differentiation  however its function outside of mammals has not been investigated. Here  through an N ethyl N nitrosourea ENU based forward genetic screen  we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish  however germ cells populated the gonad  proliferated  and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes  the spermatocytes failed to progress beyond the zygotene stage. Thus  Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay  and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings  suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1  we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification  pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.", null, null, null, "adad1 mutant F", "adad1 Mut F", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:MutantF|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 mutant: male testes", "adad1 Mut F", "adad1 Mut F", "Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age  5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences  NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "adad1-Mut-F_R1_001.fastq.gz adad1-Mut-F_R2_001.fastq.gz", "fastq fastq", 5780694600.0, 19268982.0, "adad1 Mut F R1 001.fastq.gz", "0:150 1:150", "A:1502665613;C:1371103253;G:1490414769;T:1416422204;N:88761", 150, 150, null, null, 1502665613, 1371103253, 1490414769, 1416422204, 88761, "SRX20608297", "SRS17908190", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.89657, 0.89588, 0.10966, 0.10896, 0.72671, 0.72728, 0.57267, 0.55033, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76361, "SRR24844105", "SRX20608296", "SRS17908189", "SRP441411", "PRJNA980839", "Adad1 knockout and misense mutant RNAseq", "PRJNA980839", "Other", "The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice  Adad1 is necessary for sperm differentiation  however its function outside of mammals has not been investigated. Here  through an N ethyl N nitrosourea ENU based forward genetic screen  we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish  however germ cells populated the gonad  proliferated  and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes  the spermatocytes failed to progress beyond the zygotene stage. Thus  Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay  and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings  suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1  we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification  pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.", null, null, null, "adad1 wildtype sibling control A", "adad1 WT A", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:WildtypeA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 wildtype sibling: male testes", "adad1 WT A", "adad1 WT A", "Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age  5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences  NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "adad1-WT-A_R1_001.fastq.gz adad1-WT-A_R2_001.fastq.gz", "fastq fastq", 8011954200.0, 26706514.0, "adad1 WT A R1 001.fastq.gz", "0:150 1:150", "A:2090202005;C:1898897650;G:2026356221;T:1996371474;N:126850", 150, 150, null, null, 2090202005, 1898897650, 2026356221, 1996371474, 126850, "SRX20608296", "SRS17908189", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.91189, 0.91021, 0.06102, 0.06139, 0.68525, 0.68718, 0.50676, 0.50889, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76362, "SRR24844106", "SRX20608295", "SRS17908186", "SRP441411", "PRJNA980839", "Adad1 knockout and misense mutant RNAseq", "PRJNA980839", "Other", "The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice  Adad1 is necessary for sperm differentiation  however its function outside of mammals has not been investigated. Here  through an N ethyl N nitrosourea ENU based forward genetic screen  we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish  however germ cells populated the gonad  proliferated  and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes  the spermatocytes failed to progress beyond the zygotene stage. Thus  Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay  and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings  suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1  we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification  pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.", null, null, null, "adad1 wildtype sibling control B", "adad1 WT B", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:WildtypeB|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 wildtype sibling: male testes", "adad1 WT B", "adad1 WT B", "Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age  5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences  NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "adad1-WT-B_R1_001.fastq.gz adad1-WT-B_R2_001.fastq.gz", "fastq fastq", 7492292100.0, 24974307.0, "adad1 WT B R1 001.fastq.gz", "0:150 1:150", "A:1943185783;C:1771813934;G:1904551325;T:1872624369;N:116689", 150, 150, null, null, 1943185783, 1771813934, 1904551325, 1872624369, 116689, "SRX20608295", "SRS17908186", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.90916, 0.90763, 0.11162, 0.11123, 0.67399, 0.6743, 0.52068, 0.52927, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76363, "SRR24844107", "SRX20608294", "SRS17908185", "SRP441411", "PRJNA980839", "Adad1 knockout and misense mutant RNAseq", "PRJNA980839", "Other", "The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice  Adad1 is necessary for sperm differentiation  however its function outside of mammals has not been investigated. Here  through an N ethyl N nitrosourea ENU based forward genetic screen  we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish  however germ cells populated the gonad  proliferated  and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes  the spermatocytes failed to progress beyond the zygotene stage. Thus  Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay  and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings  suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1  we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification  pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.", null, null, null, "adad1 wildtype sibling control C", "adad1 WT C", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:WildtypeC|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 wildtype sibling: male testes", "adad1 WT C", "adad1 WT C", "Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age  5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences  NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "adad1-WT-C_R2_001.fastq.gz adad1-WT-C_R1_001.fastq.gz", "fastq fastq", 7521501900.0, 25071673.0, "adad1 WT C R1 001.fastq.gz", "0:150 1:150", "A:1804312038;C:1905161135;G:2076680572;T:1735230886;N:117269", 150, 150, null, null, 1804312038, 1905161135, 2076680572, 1735230886, 117269, "SRX20608294", "SRS17908185", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.91415, 0.91424, 0.1126, 0.11157, 0.72861, 0.72924, 0.60581, 0.59123, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76364, "SRR24844111", "SRX20608293", "SRS17908188", "SRP441411", "PRJNA980839", "Adad1 knockout and misense mutant RNAseq", "PRJNA980839", "Other", "The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice  Adad1 is necessary for sperm differentiation  however its function outside of mammals has not been investigated. Here  through an N ethyl N nitrosourea ENU based forward genetic screen  we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish  however germ cells populated the gonad  proliferated  and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes  the spermatocytes failed to progress beyond the zygotene stage. Thus  Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay  and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings  suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1  we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification  pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.", null, null, null, "adad1 wildtype sibling control D", "adad1 WT D", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:WildtypeD|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 wildtype sibling: male testes", "adad1 WT D", "adad1 WT D", "Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age  5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences  NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "adad1-WT-D_R2_001.fastq.gz adad1-WT-D_R1_001.fastq.gz", "fastq fastq", 6723661500.0, 22412205.0, "adad1 WT D R1 001.fastq.gz", "0:150 1:150", "A:1762783841;C:1577461245;G:1700257202;T:1683053935;N:105277", 150, 150, null, null, 1762783841, 1577461245, 1700257202, 1683053935, 105277, "SRX20608293", "SRS17908188", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.90669, 0.90515, 0.1057, 0.1054, 0.7055, 0.70648, 0.53378, 0.53859, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76365, "SRR24844108", "SRX20608292", "SRS17908183", "SRP441411", "PRJNA980839", "Adad1 knockout and misense mutant RNAseq", "PRJNA980839", "Other", "The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice  Adad1 is necessary for sperm differentiation  however its function outside of mammals has not been investigated. Here  through an N ethyl N nitrosourea ENU based forward genetic screen  we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish  however germ cells populated the gonad  proliferated  and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes  the spermatocytes failed to progress beyond the zygotene stage. Thus  Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay  and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings  suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1  we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification  pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.", null, null, null, "LB023 wildtype sibling control C", "LB023 WT C", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense WildtypeC|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 missense wildtype sibling: male testes", "LB023 WT C", "LB023 WT C", "Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age  5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences  NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "LB023-WT-C_R1_001.fastq.gz LB023-WT-C_R2_001.fastq.gz", "fastq fastq", 6931350600.0, 23104502.0, "LB023 WT C R1 001.fastq.gz", "0:150 1:150", "A:1738105921;C:1615563430;G:1915220365;T:1662351851;N:109033", 150, 150, null, null, 1738105921, 1615563430, 1915220365, 1662351851, 109033, "SRX20608292", "SRS17908183", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.85918, 0.86008, 0.0973, 0.0972, 0.75621, 0.75617, 0.51414, 0.52127, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76366, "SRR24844109", "SRX20608291", "SRS17908182", "SRP441411", "PRJNA980839", "Adad1 knockout and misense mutant RNAseq", "PRJNA980839", "Other", "The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice  Adad1 is necessary for sperm differentiation  however its function outside of mammals has not been investigated. Here  through an N ethyl N nitrosourea ENU based forward genetic screen  we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish  however germ cells populated the gonad  proliferated  and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes  the spermatocytes failed to progress beyond the zygotene stage. Thus  Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay  and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings  suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1  we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification  pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.", null, null, null, "LB023 wildtype sibling control B", "LB023 WT B", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense WildtypeB|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 missense wildtype sibling: male testes", "LB023 WT B", "LB023 WT B", "Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age  5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences  NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "LB023-WT-B_R1_001.fastq.gz LB023-WT-B_R2_001.fastq.gz", "fastq fastq", 6486567300.0, 21621891.0, "LB023 WT B R1 001.fastq.gz", "0:150 1:150", "A:1659315544;C:1565803285;G:1669608945;T:1591739895;N:99631", 150, 150, null, null, 1659315544, 1565803285, 1669608945, 1591739895, 99631, "SRX20608291", "SRS17908182", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.92214, 0.92196, 0.09064, 0.09079, 0.70092, 0.70207, 0.54638, 0.55145, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76367, "SRR24844110", "SRX20608290", "SRS17908184", "SRP441411", "PRJNA980839", "Adad1 knockout and misense mutant RNAseq", "PRJNA980839", "Other", "The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice  Adad1 is necessary for sperm differentiation  however its function outside of mammals has not been investigated. Here  through an N ethyl N nitrosourea ENU based forward genetic screen  we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish  however germ cells populated the gonad  proliferated  and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes  the spermatocytes failed to progress beyond the zygotene stage. Thus  Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay  and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings  suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1  we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification  pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.", null, null, null, "LB023 wildtype sibling control A", "LB023 WT A", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense WildtypeA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 missense wildtype sibling: male testes", "LB023 WT A", "LB023 WT A", "Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age  5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences  NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "LB023-WT-A_R1_001.fastq.gz LB023-WT-A_R2_001.fastq.gz", "fastq fastq", 7085531700.0, 23618439.0, "LB023 WT A R1 001.fastq.gz", "0:150 1:150", "A:1870324648;C:1666204540;G:1769576825;T:1779314498;N:111189", 150, 150, null, null, 1870324648, 1666204540, 1769576825, 1779314498, 111189, "SRX20608290", "SRS17908184", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.91831, 0.91753, 0.06037, 0.06044, 0.70307, 0.70368, 0.51531, 0.51099, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76368, "SRR24844112", "SRX20608289", "SRS17908179", "SRP441411", "PRJNA980839", "Adad1 knockout and misense mutant RNAseq", "PRJNA980839", "Other", "The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice  Adad1 is necessary for sperm differentiation  however its function outside of mammals has not been investigated. Here  through an N ethyl N nitrosourea ENU based forward genetic screen  we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish  however germ cells populated the gonad  proliferated  and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes  the spermatocytes failed to progress beyond the zygotene stage. Thus  Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay  and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings  suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1  we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification  pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.", null, null, null, "LB023 mutant F", "LB023 Mut F", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense MutantF|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 missense mutant: male testes", "LB023 Mut F", "LB023 Mut F", "Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age  5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences  NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "LB023-Mut-F_R1_001.fastq.gz LB023-Mut-F_R2_001.fastq.gz", "fastq fastq", 7753356600.0, 25844522.0, "LB023 Mut F R1 001.fastq.gz", "0:150 1:150", "A:2031483621;C:1809017944;G:1970064517;T:1942669709;N:120809", 150, 150, null, null, 2031483621, 1809017944, 1970064517, 1942669709, 120809, "SRX20608289", "SRS17908179", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.87475, 0.87314, 0.09092, 0.09089, 0.75373, 0.75434, 0.5602, 0.56521, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76369, "SRR24844113", "SRX20608288", "SRS17908178", "SRP441411", "PRJNA980839", "Adad1 knockout and misense mutant RNAseq", "PRJNA980839", "Other", "The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice  Adad1 is necessary for sperm differentiation  however its function outside of mammals has not been investigated. Here  through an N ethyl N nitrosourea ENU based forward genetic screen  we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish  however germ cells populated the gonad  proliferated  and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes  the spermatocytes failed to progress beyond the zygotene stage. Thus  Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay  and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings  suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1  we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification  pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.", null, null, null, "LB023 mutant E", "LB023 Mut E", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense MutantE|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 missense mutant: male testes", "LB023 Mut E", "LB023 Mut E", "Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age  5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences  NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "LB023-Mut-E_R1_001.fastq.gz LB023-Mut-E_R2_001.fastq.gz", "fastq fastq", 4532652000.0, 15108840.0, "LB023 Mut E R1 001.fastq.gz", "0:150 1:150", "A:1199854650;C:1037858889;G:1150707006;T:1144159494;N:71961", 150, 150, null, null, 1199854650, 1037858889, 1150707006, 1144159494, 71961, "SRX20608288", "SRS17908178", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.87501, 0.87504, 0.08393, 0.08384, 0.76021, 0.76055, 0.54045, 0.54351, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76370, "SRR24844114", "SRX20608287", "SRS17908181", "SRP441411", "PRJNA980839", "Adad1 knockout and misense mutant RNAseq", "PRJNA980839", "Other", "The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice  Adad1 is necessary for sperm differentiation  however its function outside of mammals has not been investigated. Here  through an N ethyl N nitrosourea ENU based forward genetic screen  we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish  however germ cells populated the gonad  proliferated  and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes  the spermatocytes failed to progress beyond the zygotene stage. Thus  Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay  and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings  suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1  we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification  pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.", null, null, null, "adad1 mutant C", "adad1 Mut C", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:MutantC|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 mutant: male testes", "adad1 Mut C", "adad1 Mut C", "Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age  5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences  NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "adad1-Mut-C_R1_001.fastq.gz adad1-Mut-C_R2_001.fastq.gz", "fastq fastq", 7938136500.0, 26460455.0, "adad1 Mut C R1 001.fastq.gz", "0:150 1:150", "A:2011717685;C:1935444799;G:2053481206;T:1937375239;N:117571", 150, 150, null, null, 2011717685, 1935444799, 2053481206, 1937375239, 117571, "SRX20608287", "SRS17908181", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.92456, 0.92396, 0.08714, 0.08738, 0.70575, 0.70826, 0.5441, 0.52561, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [76371, "SRR24844115", "SRX20608286", "SRS17908180", "SRP441411", "PRJNA980839", "Adad1 knockout and misense mutant RNAseq", "PRJNA980839", "Other", "The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice  Adad1 is necessary for sperm differentiation  however its function outside of mammals has not been investigated. Here  through an N ethyl N nitrosourea ENU based forward genetic screen  we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish  however germ cells populated the gonad  proliferated  and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes  the spermatocytes failed to progress beyond the zygotene stage. Thus  Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay  and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings  suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1  we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification  pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.", null, null, null, "adad1 mutant A", "adad1 Mut A", null, "strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:MutantA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio adad1 mutant: male testes", "adad1 Mut A", "adad1 Mut A", "Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age  5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences  NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP441411", null, null, "adad1-Mut-A_R1_001.fastq.gz adad1-Mut-A_R2_001.fastq.gz", "fastq fastq", 7254148200.0, 24180494.0, "adad1 Mut A R1 001.fastq.gz", "0:150 1:150", "A:1849587944;C:1771248935;G:1861148471;T:1772049096;N:113754", 150, 150, null, null, 1849587944, 1771248935, 1861148471, 1772049096, 113754, "SRX20608286", "SRS17908180", "SRA1650047", "University of Massachusetts Boston|Biology", "University of Massachusetts Boston", 2, 0.93069, 0.93108, 0.10454, 0.10422, 0.69899, 0.70088, 0.53698, 0.55029, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-07", "Juvenile", "Juvenile", 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