{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Juvenile\" and technology = \"bulk\"", "rows": [[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. 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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 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. 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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 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. 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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 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. 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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 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. 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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 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"], [26487, "SRR26034371", "SRX21751586", "SRS18859093", "SRP459779", "PRJNA1015242", "Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.", "GSE242897", "Transcriptome Analysis", "Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals  3 individual tp53 mutant and ptch1 crispant animals  and 3 individual tp53 heterozygous and ptch1 crispant animals.", null, "pubmed:39078737", null, "19521X6 tp53het tumor", "GSM7774462", null, "source name:brain|tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous|geo loc name:missing|collection date:missing", "19521X6 tp53het tumor", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts.", "brain", "Brains were frozen at  80C in RNA stabilization solution QIAGEN.", "Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous", "GSM7774462", "GSM7774462: 19521X6 tp53het tumor; Danio rerio; RNA Seq", "GSM7774462 r1", "GSM7774462", "1", "Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459779", null, "loader:fastq load.py", "19521X6_220211_A00421_0418_AHGVTMDSX3_S177_L003_R1_001.fastq.gz 19521X6_220211_A00421_0418_AHGVTMDSX3_S177_L003_R2_001.fastq.gz", "fastq fastq", 13856710696.0, 45883148.0, "GSM7774462 r1", "0:151 1:151", "A:3910050404;C:3019565763;G:3183961340;T:3742992264;N:140925", 151, 151, null, null, 3910050404, 3019565763, 3183961340, 3742992264, 140925, "SRX21751586", "SRS18859093", "SRA1710210", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.8794, 0.87909, 0.38495, 0.38479, 0.69753, 0.70005, 0.49322, 0.49442, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-09-11", "Juvenile", "Juvenile", "Brain", "Nervous System"], [26488, "SRR26034372", "SRX21751585", "SRS18859092", "SRP459779", "PRJNA1015242", "Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.", "GSE242897", "Transcriptome Analysis", "Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals  3 individual tp53 mutant and ptch1 crispant animals  and 3 individual tp53 heterozygous and ptch1 crispant animals.", null, "pubmed:39078737", null, "19521X5 tp53het tumor", "GSM7774461", null, "source name:brain|tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous|geo loc name:missing|collection date:missing", "19521X5 tp53het tumor", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts.", "brain", "Brains were frozen at  80C in RNA stabilization solution QIAGEN.", "Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous", "GSM7774461", "GSM7774461: 19521X5 tp53het tumor; Danio rerio; RNA Seq", "GSM7774461 r1", "GSM7774461", "1", "Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459779", null, "loader:fastq load.py", "19521X5_220211_A00421_0418_AHGVTMDSX3_S176_L003_R1_001.fastq.gz 19521X5_220211_A00421_0418_AHGVTMDSX3_S176_L003_R2_001.fastq.gz", "fastq fastq", 18644081740.0, 61735370.0, "GSM7774461 r1", "0:151 1:151", "A:5198614433;C:4108657498;G:4307546758;T:5029072002;N:191049", 151, 151, null, null, 5198614433, 4108657498, 4307546758, 5029072002, 191049, "SRX21751585", "SRS18859092", "SRA1710210", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.88544, 0.88842, 0.35896, 0.35863, 0.69193, 0.69248, 0.49682, 0.50274, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-09-11", "Juvenile", "Juvenile", "Brain", "Nervous System"], [26489, "SRR26034373", "SRX21751584", "SRS18859091", "SRP459779", "PRJNA1015242", "Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.", "GSE242897", "Transcriptome Analysis", "Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals  3 individual tp53 mutant and ptch1 crispant animals  and 3 individual tp53 heterozygous and ptch1 crispant animals.", null, "pubmed:39078737", null, "19521X4 tp53het tumor", "GSM7774460", null, "source name:brain|tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous|geo loc name:missing|collection date:missing", "19521X4 tp53het tumor", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts.", "brain", "Brains were frozen at  80C in RNA stabilization solution QIAGEN.", "Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous", "GSM7774460", "GSM7774460: 19521X4 tp53het tumor; Danio rerio; RNA Seq", "GSM7774460 r1", "GSM7774460", "1", "Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459779", null, "loader:fastq load.py", "19521X4_220211_A00421_0418_AHGVTMDSX3_S175_L003_R1_001.fastq.gz 19521X4_220211_A00421_0418_AHGVTMDSX3_S175_L003_R2_001.fastq.gz", "fastq fastq", 14417628886.0, 47740493.0, "GSM7774460 r1", "0:151 1:151", "A:4016299076;C:3183962020;G:3341158152;T:3876059438;N:150200", 151, 151, null, null, 4016299076, 3183962020, 3341158152, 3876059438, 150200, "SRX21751584", "SRS18859091", "SRA1710210", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.89118, 0.89184, 0.33812, 0.33641, 0.68947, 0.68954, 0.49867, 0.50026, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-09-11", "Juvenile", "Juvenile", "Brain", "Nervous System"], [26491, "SRR26034375", "SRX21751582", "SRS18859089", "SRP459779", "PRJNA1015242", "Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.", "GSE242897", "Transcriptome Analysis", "Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals  3 individual tp53 mutant and ptch1 crispant animals  and 3 individual tp53 heterozygous and ptch1 crispant animals.", null, "pubmed:39078737", null, "19521X2 tp53mut tumor", "GSM7774458", null, "source name:brain|tissue:brain|tumor status:tumor|age:8 wpf|genotype:tp53 mutant|geo loc name:missing|collection date:missing", "19521X2 tp53mut tumor", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts.", "brain", "Brains were frozen at  80C in RNA stabilization solution QIAGEN.", "Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "tissue:brain|tumor status:tumor|age:8 wpf|genotype:tp53 mutant", "GSM7774458", "GSM7774458: 19521X2 tp53mut tumor; Danio rerio; RNA Seq", "GSM7774458 r1", "GSM7774458", "1", "Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459779", null, "loader:fastq load.py", "19521X2_220211_A00421_0418_AHGVTMDSX3_S173_L003_R1_001.fastq.gz 19521X2_220211_A00421_0418_AHGVTMDSX3_S173_L003_R2_001.fastq.gz", "fastq fastq", 14064076580.0, 46569790.0, "GSM7774458 r1", "0:151 1:151", "A:3935649548;C:3089754695;G:3257286821;T:3781242542;N:142974", 151, 151, null, null, 3935649548, 3089754695, 3257286821, 3781242542, 142974, "SRX21751582", "SRS18859089", "SRA1710210", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.89595, 0.89655, 0.35454, 0.35431, 0.68927, 0.69077, 0.47888, 0.47831, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-09-11", "Juvenile", "Juvenile", "Brain", "Nervous System"], [26492, "SRR26034376", "SRX21751581", "SRS18859088", "SRP459779", "PRJNA1015242", "Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.", "GSE242897", "Transcriptome Analysis", "Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals  3 individual tp53 mutant and ptch1 crispant animals  and 3 individual tp53 heterozygous and ptch1 crispant animals.", null, "pubmed:39078737", null, "19521X1 tp53mut tumor", "GSM7774457", null, "source name:brain|tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 mutant|geo loc name:missing|collection date:missing", "19521X1 tp53mut tumor", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts.", "brain", "Brains were frozen at  80C in RNA stabilization solution QIAGEN.", "Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 mutant", "GSM7774457", "GSM7774457: 19521X1 tp53mut tumor; Danio rerio; RNA Seq", "GSM7774457 r1", "GSM7774457", "1", "Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459779", null, "loader:fastq load.py", "19521X1_220211_A00421_0418_AHGVTMDSX3_S172_L003_R1_001.fastq.gz 19521X1_220211_A00421_0418_AHGVTMDSX3_S172_L003_R2_001.fastq.gz", "fastq fastq", 16911500190.0, 55998345.0, "GSM7774457 r1", "0:151 1:151", "A:4750241986;C:3698380612;G:3890633834;T:4572071732;N:172026", 151, 151, null, null, 4750241986, 3698380612, 3890633834, 4572071732, 172026, "SRX21751581", "SRS18859088", "SRA1710210", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.89695, 0.89831, 0.3562, 0.35542, 0.68392, 0.68369, 0.48172, 0.48641, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-09-11", "Juvenile", "Juvenile", "Brain", "Nervous System"], [53495, "SRR9886611", "SRX6639067", "SRS5209782", "SRP217245", "PRJNA558074", "Transcriptomic analysis of dj 1 /  zebrafish brains compared to wild type siblings", "GSE135271", "Transcriptome Analysis", "RNA Seq comparing transcript expression in the brains of 3 dj 1 /  mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1  /  zebrafish were generated by deep sequencing  in triplicate  using Illumina HiSeq 3000", null, "pubmed:32859696", null, "GH6", "GSM4002525", null, "source name:Brain|strain:LWT|tissue:Brain|age:12 wpf dj 1  / ", "GH6", "A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript  hypertext markup language document including read counts per sample", "Brain", null, "Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", null, "strain:LWT|tissue:Brain|age:12 wpf dj 1  / ", "GSM4002525", "GSM4002525: GH6; Danio rerio; RNA Seq", "GSM4002525", null, "1", "Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", "GEO Accession:GSM4002525", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP217245", null, null, "GH6_S41_L004_R1_001.fastq-004.gz GH6_S41_L004_R2_001.fastq-009.gz", "fastq fastq", 16197223984.0, 53633192.0, "GSM4002525 r1", "0:151 1:151", "A:4524520245;C:3580881754;G:3728671047;T:4362276906;N:874032", 151, 151, null, null, 4524520245, 3580881754, 3728671047, 4362276906, 874032, "SRX6639067", "SRS5209782", "SRA931013", "GEO", "Biology, University of York", 2, 0.91745, 0.9163, 0.15171, 0.14974, 0.69826, 0.70161, 0.49509, 0.48979, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United Kingdom", "2019-08-01", "Juvenile", "Juvenile", "Brain", "Nervous System"], [53496, "SRR9886610", "SRX6639066", "SRS5209781", "SRP217245", "PRJNA558074", "Transcriptomic analysis of dj 1 /  zebrafish brains compared to wild type siblings", "GSE135271", "Transcriptome Analysis", "RNA Seq comparing transcript expression in the brains of 3 dj 1 /  mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1  /  zebrafish were generated by deep sequencing  in triplicate  using Illumina HiSeq 3000", null, "pubmed:32859696", null, "GH5", "GSM4002524", null, "source name:Brain|strain:LWT|tissue:Brain|age:12 wpf dj 1  / ", "GH5", "A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript  hypertext markup language document including read counts per sample", "Brain", null, "Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", null, "strain:LWT|tissue:Brain|age:12 wpf dj 1  / ", "GSM4002524", "GSM4002524: GH5; Danio rerio; RNA Seq", "GSM4002524", null, "1", "Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", "GEO Accession:GSM4002524", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP217245", null, null, "GH5_S40_L004_R1_001.fastq-001.gz GH5_S40_L004_R2_001.fastq-003.gz", "fastq fastq", 14762621304.0, 48882852.0, "GSM4002524 r1", "0:151 1:151", "A:4134788753;C:3245817056;G:3388258601;T:3992937107;N:819787", 151, 151, null, null, 4134788753, 3245817056, 3388258601, 3992937107, 819787, "SRX6639066", "SRS5209781", "SRA931013", "GEO", "Biology, University of York", 2, 0.91356, 0.91354, 0.15637, 0.15448, 0.69755, 0.70177, 0.48873, 0.49642, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United Kingdom", "2019-08-01", "Juvenile", "Juvenile", "Brain", "Nervous System"], [53497, "SRR9886609", "SRX6639065", "SRS5209780", "SRP217245", "PRJNA558074", "Transcriptomic analysis of dj 1 /  zebrafish brains compared to wild type siblings", "GSE135271", "Transcriptome Analysis", "RNA Seq comparing transcript expression in the brains of 3 dj 1 /  mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1  /  zebrafish were generated by deep sequencing  in triplicate  using Illumina HiSeq 3000", null, "pubmed:32859696", null, "GH4", "GSM4002523", null, "source name:Brain|strain:LWT|tissue:Brain|age:12 wpf dj 1  / ", "GH4", "A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript  hypertext markup language document including read counts per sample", "Brain", null, "Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", null, "strain:LWT|tissue:Brain|age:12 wpf dj 1  / ", "GSM4002523", "GSM4002523: GH4; Danio rerio; RNA Seq", "GSM4002523", null, "1", "Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", "GEO Accession:GSM4002523", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP217245", null, null, "GH4_S39_L004_R1_001.fastq-008.gz GH4_S39_L004_R2_001.fastq-011.gz", "fastq fastq", 17232418376.0, 57060988.0, "GSM4002523 r1", "0:151 1:151", "A:4798343141;C:3812370940;G:3947002545;T:4673748329;N:953421", 151, 151, null, null, 4798343141, 3812370940, 3947002545, 4673748329, 953421, "SRX6639065", "SRS5209780", "SRA931013", "GEO", "Biology, University of York", 2, 0.91359, 0.91289, 0.15791, 0.15599, 0.70128, 0.70585, 0.48423, 0.48897, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United Kingdom", "2019-08-01", "Juvenile", "Juvenile", "Brain", "Nervous System"], [53498, "SRR9886608", "SRX6639064", "SRS5209779", "SRP217245", "PRJNA558074", "Transcriptomic analysis of dj 1 /  zebrafish brains compared to wild type siblings", "GSE135271", "Transcriptome Analysis", "RNA Seq comparing transcript expression in the brains of 3 dj 1 /  mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1  /  zebrafish were generated by deep sequencing  in triplicate  using Illumina HiSeq 3000", null, "pubmed:32859696", null, "GH3", "GSM4002522", null, "source name:Brain|strain:LWT|tissue:Brain|age:12 wpf type", "GH3", "A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript  hypertext markup language document including read counts per sample", "Brain", null, "Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", null, "strain:LWT|tissue:Brain|age:12 wpf type", "GSM4002522", "GSM4002522: GH3; Danio rerio; RNA Seq", "GSM4002522", null, "1", "Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", "GEO Accession:GSM4002522", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP217245", null, null, "GH3_S38_L004_R1_001.fastq-002.gz GH3_S38_L004_R2_001.fastq-005.gz", "fastq fastq", 15880659430.0, 52584965.0, "GSM4002522 r1", "0:151 1:151", "A:4428460730;C:3500855291;G:3647161094;T:4303300463;N:881852", 151, 151, null, null, 4428460730, 3500855291, 3647161094, 4303300463, 881852, "SRX6639064", "SRS5209779", "SRA931013", "GEO", "Biology, University of York", 2, 0.91311, 0.91404, 0.15734, 0.15592, 0.69621, 0.70092, 0.4936, 0.48217, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United Kingdom", "2019-08-01", "Juvenile", "Juvenile", "Brain", "Nervous System"], [53499, "SRR9886607", "SRX6639063", "SRS5209778", "SRP217245", "PRJNA558074", "Transcriptomic analysis of dj 1 /  zebrafish brains compared to wild type siblings", "GSE135271", "Transcriptome Analysis", "RNA Seq comparing transcript expression in the brains of 3 dj 1 /  mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1  /  zebrafish were generated by deep sequencing  in triplicate  using Illumina HiSeq 3000", null, "pubmed:32859696", null, "GH2", "GSM4002521", null, "source name:Brain|strain:LWT|tissue:Brain|age:12 wpf type", "GH2", "A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript  hypertext markup language document including read counts per sample", "Brain", null, "Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", null, "strain:LWT|tissue:Brain|age:12 wpf type", "GSM4002521", "GSM4002521: GH2; Danio rerio; RNA Seq", "GSM4002521", null, "1", "Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", "GEO Accession:GSM4002521", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP217245", null, null, "GH2_S37_L004_R1_001.fastq-006.gz GH2_S37_L004_R2_001.fastq-012.gz", "fastq fastq", 17721573816.0, 58680708.0, "GSM4002521 r1", "0:151 1:151", "A:4948184152;C:3901958410;G:4066182263;T:4804260891;N:988100", 151, 151, null, null, 4948184152, 3901958410, 4066182263, 4804260891, 988100, "SRX6639063", "SRS5209778", "SRA931013", "GEO", "Biology, University of York", 2, 0.90975, 0.90966, 0.16242, 0.16044, 0.69934, 0.70339, 0.48497, 0.49335, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United Kingdom", "2019-08-01", "Juvenile", "Juvenile", "Brain", "Nervous System"], [53500, "SRR9886606", "SRX6639062", "SRS5209777", "SRP217245", "PRJNA558074", "Transcriptomic analysis of dj 1 /  zebrafish brains compared to wild type siblings", "GSE135271", "Transcriptome Analysis", "RNA Seq comparing transcript expression in the brains of 3 dj 1 /  mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1  /  zebrafish were generated by deep sequencing  in triplicate  using Illumina HiSeq 3000", null, "pubmed:32859696", null, "GH1", "GSM4002520", null, "source name:Brain|strain:LWT|tissue:Brain|age:12 wpf type", "GH1", "A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript  hypertext markup language document including read counts per sample", "Brain", null, "Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", null, "strain:LWT|tissue:Brain|age:12 wpf type", "GSM4002520", "GSM4002520: GH1; Danio rerio; RNA Seq", "GSM4002520", null, "1", "Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", "GEO Accession:GSM4002520", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP217245", null, null, "GH1_S36_L004_R1_001.fastq-007.gz GH1_S36_L004_R2_001.fastq-010.gz", "fastq fastq", 16852076254.0, 55801577.0, "GSM4002520 r1", "0:151 1:151", "A:4697089825;C:3744087924;G:3878965083;T:4531030410;N:903012", 151, 151, null, null, 4697089825, 3744087924, 3878965083, 4531030410, 903012, "SRX6639062", "SRS5209777", "SRA931013", "GEO", "Biology, University of York", 2, 0.91719, 0.91765, 0.15136, 0.15011, 0.69998, 0.70455, 0.48284, 0.48335, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United Kingdom", "2019-08-01", "Juvenile", "Juvenile", "Brain", "Nervous System"], [60916, "SRR12658664", "SRX9139722", "SRS7381388", "SRP282671", "PRJNA663959", "Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development", "GSE158098", "Transcriptome Analysis", "Here we used RNA sequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNA seq was performed on surgically dissected kidneys from wild type and runx1 /  siblings 2.5 mpf  pool of 3 kidneys/replicate  n= 3 for each genotype.", "parent bioproject:PRJNA663961", "pubmed:34492681", null, "runx1 /  kidney3", "GSM4792207", null, "source name:adult kidney|strain:EK|genotype/variation:runx1 /  del25  hg97|age:2.5 month|tissue:kidney", "runx1 /  kidney3", "RNA seq reads were aligned to the zebrafish genome reference GRCz10 and transcript reference GRCz10.87 using STAR v2.5.26. We used RSEM to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz10 Supplementary files format and content: *.count.txt: Gene expression count matrix.", "adult kidney", null, "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", null, "strain:EK|genotype/variation:runx1 /  del25  hg97|age:2.5 month|tissue:kidney", "GSM4792207", "GSM4792207: runx1 /  kidney3; Danio rerio; RNA Seq", "GSM4792207", null, "1", "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", "GEO Accession:GSM4792207", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP282671", null, null, "runx1_del25_null_6.1.cln.fq.gz runx1_del25_null_6.2.cln.fq.gz", "fastq fastq", 9833070492.0, 39020121.0, "GSM4792207 r1", "0:126 1:126", "A:2595482323;C:2237794410;G:2283114442;T:2716679317;N:0", 126, 126, null, null, 2595482323, 2237794410, 2283114442, 2716679317, 0, "SRX9139722", "SRS7381388", "SRA1126725", "GEO", "NHGRI", 2, 0.95072, 0.95176, 0.08254, 0.08278, 0.72565, 0.7265, 0.55513, 0.55433, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2020-09-16", "Juvenile", "Juvenile", "Kidney", "Renal System"], [60917, "SRR12658663", "SRX9139721", "SRS7381387", "SRP282671", "PRJNA663959", "Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development", "GSE158098", "Transcriptome Analysis", "Here we used RNA sequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNA seq was performed on surgically dissected kidneys from wild type and runx1 /  siblings 2.5 mpf  pool of 3 kidneys/replicate  n= 3 for each genotype.", "parent bioproject:PRJNA663961", "pubmed:34492681", null, "runx1 /  kidney2", "GSM4792206", null, "source name:adult kidney|strain:EK|genotype/variation:runx1 /  del25  hg97|age:2.5 month|tissue:kidney", "runx1 /  kidney2", "RNA seq reads were aligned to the zebrafish genome reference GRCz10 and transcript reference GRCz10.87 using STAR v2.5.26. We used RSEM to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz10 Supplementary files format and content: *.count.txt: Gene expression count matrix.", "adult kidney", null, "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", null, "strain:EK|genotype/variation:runx1 /  del25  hg97|age:2.5 month|tissue:kidney", "GSM4792206", "GSM4792206: runx1 /  kidney2; Danio rerio; RNA Seq", "GSM4792206", null, "1", "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", "GEO Accession:GSM4792206", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP282671", null, null, "runx1_del25_null_5.1.cln.fq.gz runx1_del25_null_5.2.cln.fq.gz", "fastq fastq", 10411105572.0, 41313911.0, "GSM4792206 r1", "0:126 1:126", "A:2758731492;C:2362241256;G:2412281429;T:2877851395;N:0", 126, 126, null, null, 2758731492, 2362241256, 2412281429, 2877851395, 0, "SRX9139721", "SRS7381387", "SRA1126725", "GEO", "NHGRI", 2, 0.9462, 0.94718, 0.09575, 0.09572, 0.74282, 0.74391, 0.53729, 0.53866, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2020-09-16", "Juvenile", "Juvenile", "Kidney", "Renal System"], [60918, "SRR12658662", "SRX9139720", "SRS7381386", "SRP282671", "PRJNA663959", "Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development", "GSE158098", "Transcriptome Analysis", "Here we used RNA sequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNA seq was performed on surgically dissected kidneys from wild type and runx1 /  siblings 2.5 mpf  pool of 3 kidneys/replicate  n= 3 for each genotype.", "parent bioproject:PRJNA663961", "pubmed:34492681", null, "runx1 /  kidney1", "GSM4792205", null, "source name:adult kidney|strain:EK|genotype/variation:runx1 /  del25  hg97|age:2.5 month|tissue:kidney", "runx1 /  kidney1", "RNA seq reads were aligned to the zebrafish genome reference GRCz10 and transcript reference GRCz10.87 using STAR v2.5.26. We used RSEM to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz10 Supplementary files format and content: *.count.txt: Gene expression count matrix.", "adult kidney", null, "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", null, "strain:EK|genotype/variation:runx1 /  del25  hg97|age:2.5 month|tissue:kidney", "GSM4792205", "GSM4792205: runx1 /  kidney1; Danio rerio; RNA Seq", "GSM4792205", null, "1", "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", "GEO Accession:GSM4792205", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP282671", null, null, "runx1_del25_null_4.1.cln.fq.gz runx1_del25_null_4.2.cln.fq.gz", "fastq fastq", 6973886556.0, 27674153.0, "GSM4792205 r1", "0:126 1:126", "A:1932833306;C:1502732434;G:1534451974;T:2003868842;N:0", 126, 126, null, null, 1932833306, 1502732434, 1534451974, 2003868842, 0, "SRX9139720", "SRS7381386", "SRA1126725", "GEO", "NHGRI", 2, 0.93692, 0.93786, 0.11567, 0.11588, 0.74123, 0.74099, 0.56167, 0.56297, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2020-09-16", "Juvenile", "Juvenile", "Kidney", "Renal System"], [60919, "SRR12658661", "SRX9139719", "SRS7381385", "SRP282671", "PRJNA663959", "Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development", "GSE158098", "Transcriptome Analysis", "Here we used RNA sequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNA seq was performed on surgically dissected kidneys from wild type and runx1 /  siblings 2.5 mpf  pool of 3 kidneys/replicate  n= 3 for each genotype.", "parent bioproject:PRJNA663961", "pubmed:34492681", null, "WT kidney3", "GSM4792204", null, "source name:adult kidney|strain:EK|genotype/variation:WT|age:2.5 month|tissue:kidney", "WT kidney3", "RNA seq reads were aligned to the zebrafish genome reference GRCz10 and transcript reference GRCz10.87 using STAR v2.5.26. We used RSEM to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz10 Supplementary files format and content: *.count.txt: Gene expression count matrix.", "adult kidney", null, "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", null, "strain:EK|genotype/variation:WT|age:2.5 month|tissue:kidney", "GSM4792204", "GSM4792204: WT kidney3; Danio rerio; RNA Seq", "GSM4792204", null, "1", "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", "GEO Accession:GSM4792204", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP282671", null, null, "runx1_del25_WT_3.1.cln.fq.gz runx1_del25_WT_3.2.cln.fq.gz", "fastq fastq", 11183311944.0, 44378222.0, "GSM4792204 r1", "0:126 1:126", "A:2920698001;C:2577574528;G:2637485861;T:3047553554;N:0", 126, 126, null, null, 2920698001, 2577574528, 2637485861, 3047553554, 0, "SRX9139719", "SRS7381385", "SRA1126725", "GEO", "NHGRI", 2, 0.95338, 0.95426, 0.07656, 0.07667, 0.72693, 0.72782, 0.51199, 0.51082, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2020-09-16", "Juvenile", "Juvenile", "Kidney", "Renal System"], [60920, "SRR12658660", "SRX9139718", "SRS7381384", "SRP282671", "PRJNA663959", "Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development", "GSE158098", "Transcriptome Analysis", "Here we used RNA sequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNA seq was performed on surgically dissected kidneys from wild type and runx1 /  siblings 2.5 mpf  pool of 3 kidneys/replicate  n= 3 for each genotype.", "parent bioproject:PRJNA663961", "pubmed:34492681", null, "WT kidney2", "GSM4792203", null, "source name:adult kidney|strain:EK|genotype/variation:WT|age:2.5 month|tissue:kidney", "WT kidney2", "RNA seq reads were aligned to the zebrafish genome reference GRCz10 and transcript reference GRCz10.87 using STAR v2.5.26. We used RSEM to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz10 Supplementary files format and content: *.count.txt: Gene expression count matrix.", "adult kidney", null, "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", null, "strain:EK|genotype/variation:WT|age:2.5 month|tissue:kidney", "GSM4792203", "GSM4792203: WT kidney2; Danio rerio; RNA Seq", "GSM4792203", null, "1", "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", "GEO Accession:GSM4792203", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP282671", null, null, "runx1_del25_WT_2.1.cln.fq.gz runx1_del25_WT_2.2.cln.fq.gz", "fastq fastq", 9052361388.0, 35922069.0, "GSM4792203 r1", "0:126 1:126", "A:2412816184;C:2041456610;G:2086024563;T:2512064031;N:0", 126, 126, null, null, 2412816184, 2041456610, 2086024563, 2512064031, 0, "SRX9139718", "SRS7381384", "SRA1126725", "GEO", "NHGRI", 2, 0.94726, 0.94854, 0.09295, 0.09312, 0.73198, 0.73206, 0.54429, 0.54313, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2020-09-16", "Juvenile", "Juvenile", "Kidney", "Renal System"], [60921, "SRR12658659", "SRX9139717", "SRS7381383", "SRP282671", "PRJNA663959", "Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development", "GSE158098", "Transcriptome Analysis", "Here we used RNA sequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNA seq was performed on surgically dissected kidneys from wild type and runx1 /  siblings 2.5 mpf  pool of 3 kidneys/replicate  n= 3 for each genotype.", "parent bioproject:PRJNA663961", "pubmed:34492681", null, "WT kidney1", "GSM4792202", null, "source name:adult kidney|strain:EK|genotype/variation:WT|age:2.5 month|tissue:kidney", "WT kidney1", "RNA seq reads were aligned to the zebrafish genome reference GRCz10 and transcript reference GRCz10.87 using STAR v2.5.26. We used RSEM to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz10 Supplementary files format and content: *.count.txt: Gene expression count matrix.", "adult kidney", null, "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", null, "strain:EK|genotype/variation:WT|age:2.5 month|tissue:kidney", "GSM4792202", "GSM4792202: WT kidney1; Danio rerio; RNA Seq", "GSM4792202", null, "1", "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", "GEO Accession:GSM4792202", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP282671", null, null, "runx1_del25_WT_1.1.cln.fq.gz runx1_del25_WT_1.2.cln.fq.gz", "fastq fastq", 10029561192.0, 39799846.0, "GSM4792202 r1", "0:126 1:126", "A:2618335131;C:2316817389;G:2358350895;T:2736057777;N:0", 126, 126, null, null, 2618335131, 2316817389, 2358350895, 2736057777, 0, "SRX9139717", "SRS7381383", "SRA1126725", "GEO", "NHGRI", 2, 0.95028, 0.95138, 0.08999, 0.09004, 0.77956, 0.78102, 0.54427, 0.5347, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2020-09-16", "Juvenile", "Juvenile", "Kidney", "Renal System"], [61643, "SRR12899696", "SRX9364743", "SRS7586958", "SRP288615", "PRJNA672100", "Nrl dependent and independent rod photoreceptor development in zebrafish [RNA Seq]", "GSE160138", "Transcriptome Analysis", "NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study  we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods  we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms  bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly  we found that rods exhibited noticeable heterogeneities in the gene expression patterns  and a part of rods in nrl knockout zebrafish misexpressed the green cone genes  reflecting a hybrid status of rod and green cone. Furthermore  we identified mafba as a novel regulator of rod genesis  which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species  and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: Two WT and two nrl KO samples two biological replicates were analyzed. Each sample represented a pool of RNAs from three zebrafish retinas at the age of 2 month. The differentially expressed genes between WT and nrl KO groups were identified.", "parent bioproject:PRJNA672094", "pubmed:35245286", null, "nrl R2", "GSM4861209", null, "source name:Retina|tissue:Retina|strain:AB|age:2 mpf KO", "nrl R2", "Quality control  mapping and expression analysis: Image analysis and base calling were conducted by the HiSeq Control Software HCS + OLB + GAPipeline 1.6 Illumina on the HiSeq instrument. The high quality clean data were generated by Trimmomatic v0.30 and aligned to the reference genome of zebrafish via software Hisat2 v2.0.1. Differential expression analysis: Gene and isoform expression levels were estimated by HTSeq v0.6.1. Differential expression analysis was performed by DESeq Bioconductor package. post adjusted by Benjamini and Hochberg\u2019s approach for controlling the false discovery rate  the threshold of p values was set to <0.05 to detect differentially expressed genes. GO and KEGG enrichment analysis: GO TermFinder was used identifying Gene Ontology GO terms that annotate a list of enriched genes with a significant p value less than 0.05. KEGG Kyoto Encyclopedia of Genes and Genomes is a collection of databases dealing with genomes  biological pathways  diseases  drugs  and chemical substances http://en.wikipedia.org/wiki/KEGG  which was used to enrich significant differential expression gene in KEGG pathways. Genome build: GRCz11 from Ensembl Supplementary files format and content: Tab delimited text files including the raw counts and FPKM values for each Sample Supplementary files format and content: Tab delimited text files showing the foldchanges and p values of the differentially expressed genes", "Retina", null, "For each RNA sample  three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara  Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN \u22659.5 and A260/280 \u22651.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer\u2019s protocol.", null, "tissue:Retina|strain:AB|age:2 mpf KO", "GSM4861209", "GSM4861209: nrl R2; Danio rerio; RNA Seq", "GSM4861209", null, "1", "For each RNA sample  three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara  Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN \u22659.5 and A260/280 \u22651.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer's protocol.", "GEO Accession:GSM4861209", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP288615", null, null, "nrl-R2_combined_R1.fastq.gz nrl-R2_combined_R2.fastq.gz", "fastq fastq", 7231497600.0, 24104992.0, "GSM4861209 r1", "0:150 1:150", "A:1995457626;C:1613822880;G:1630032692;T:1991951852;N:232550", 150, 150, null, null, 1995457626, 1613822880, 1630032692, 1991951852, 232550, "SRX9364743", "SRS7586958", "SRA1147909", "GEO", "College of Life Science and Technology, Huazhong University of Science and Technology", 2, 0.91539, 0.91383, 0.13441, 0.13499, 0.69296, 0.70021, 0.5139, 0.50426, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "sc_generic", "bulk", "bulk", null, "China", "2020-10-26", "Juvenile", "Juvenile", "Eye", "Sensory System"], [61644, "SRR12899695", "SRX9364742", "SRS7586957", "SRP288615", "PRJNA672100", "Nrl dependent and independent rod photoreceptor development in zebrafish [RNA Seq]", "GSE160138", "Transcriptome Analysis", "NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study  we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods  we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms  bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly  we found that rods exhibited noticeable heterogeneities in the gene expression patterns  and a part of rods in nrl knockout zebrafish misexpressed the green cone genes  reflecting a hybrid status of rod and green cone. Furthermore  we identified mafba as a novel regulator of rod genesis  which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species  and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: Two WT and two nrl KO samples two biological replicates were analyzed. Each sample represented a pool of RNAs from three zebrafish retinas at the age of 2 month. The differentially expressed genes between WT and nrl KO groups were identified.", "parent bioproject:PRJNA672094", "pubmed:35245286", null, "nrl R1", "GSM4861208", null, "source name:Retina|tissue:Retina|strain:AB|age:2 mpf KO", "nrl R1", "Quality control  mapping and expression analysis: Image analysis and base calling were conducted by the HiSeq Control Software HCS + OLB + GAPipeline 1.6 Illumina on the HiSeq instrument. The high quality clean data were generated by Trimmomatic v0.30 and aligned to the reference genome of zebrafish via software Hisat2 v2.0.1. Differential expression analysis: Gene and isoform expression levels were estimated by HTSeq v0.6.1. Differential expression analysis was performed by DESeq Bioconductor package. post adjusted by Benjamini and Hochberg\u2019s approach for controlling the false discovery rate  the threshold of p values was set to <0.05 to detect differentially expressed genes. GO and KEGG enrichment analysis: GO TermFinder was used identifying Gene Ontology GO terms that annotate a list of enriched genes with a significant p value less than 0.05. KEGG Kyoto Encyclopedia of Genes and Genomes is a collection of databases dealing with genomes  biological pathways  diseases  drugs  and chemical substances http://en.wikipedia.org/wiki/KEGG  which was used to enrich significant differential expression gene in KEGG pathways. Genome build: GRCz11 from Ensembl Supplementary files format and content: Tab delimited text files including the raw counts and FPKM values for each Sample Supplementary files format and content: Tab delimited text files showing the foldchanges and p values of the differentially expressed genes", "Retina", null, "For each RNA sample  three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara  Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN \u22659.5 and A260/280 \u22651.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer\u2019s protocol.", null, "tissue:Retina|strain:AB|age:2 mpf KO", "GSM4861208", "GSM4861208: nrl R1; Danio rerio; RNA Seq", "GSM4861208", null, "1", "For each RNA sample  three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara  Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN \u22659.5 and A260/280 \u22651.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer's protocol.", "GEO Accession:GSM4861208", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP288615", null, null, "nrl-R1_combined_R1.fastq.gz nrl-R1_combined_R2.fastq.gz", "fastq fastq", 6989998200.0, 23299994.0, "GSM4861208 r1", "0:150 1:150", "A:1947895730;C:1539849390;G:1551787456;T:1950215842;N:249782", 150, 150, null, null, 1947895730, 1539849390, 1551787456, 1950215842, 249782, "SRX9364742", "SRS7586957", "SRA1147909", "GEO", "College of Life Science and Technology, Huazhong University of Science and Technology", 2, 0.90616, 0.9059, 0.15209, 0.15341, 0.68998, 0.69885, 0.49879, 0.49931, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "sc_generic", "bulk", "bulk", null, "China", "2020-10-26", "Juvenile", "Juvenile", "Eye", "Sensory System"], [61645, "SRR12899694", "SRX9364741", "SRS7586956", "SRP288615", "PRJNA672100", "Nrl dependent and independent rod photoreceptor development in zebrafish [RNA Seq]", "GSE160138", "Transcriptome Analysis", "NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study  we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods  we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms  bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly  we found that rods exhibited noticeable heterogeneities in the gene expression patterns  and a part of rods in nrl knockout zebrafish misexpressed the green cone genes  reflecting a hybrid status of rod and green cone. Furthermore  we identified mafba as a novel regulator of rod genesis  which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species  and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: Two WT and two nrl KO samples two biological replicates were analyzed. Each sample represented a pool of RNAs from three zebrafish retinas at the age of 2 month. The differentially expressed genes between WT and nrl KO groups were identified.", "parent bioproject:PRJNA672094", "pubmed:35245286", null, "WT R2", "GSM4861207", null, "source name:Retina|tissue:Retina|strain:AB|age:2 mpf type", "WT R2", "Quality control  mapping and expression analysis: Image analysis and base calling were conducted by the HiSeq Control Software HCS + OLB + GAPipeline 1.6 Illumina on the HiSeq instrument. The high quality clean data were generated by Trimmomatic v0.30 and aligned to the reference genome of zebrafish via software Hisat2 v2.0.1. Differential expression analysis: Gene and isoform expression levels were estimated by HTSeq v0.6.1. Differential expression analysis was performed by DESeq Bioconductor package. post adjusted by Benjamini and Hochberg\u2019s approach for controlling the false discovery rate  the threshold of p values was set to <0.05 to detect differentially expressed genes. GO and KEGG enrichment analysis: GO TermFinder was used identifying Gene Ontology GO terms that annotate a list of enriched genes with a significant p value less than 0.05. KEGG Kyoto Encyclopedia of Genes and Genomes is a collection of databases dealing with genomes  biological pathways  diseases  drugs  and chemical substances http://en.wikipedia.org/wiki/KEGG  which was used to enrich significant differential expression gene in KEGG pathways. Genome build: GRCz11 from Ensembl Supplementary files format and content: Tab delimited text files including the raw counts and FPKM values for each Sample Supplementary files format and content: Tab delimited text files showing the foldchanges and p values of the differentially expressed genes", "Retina", null, "For each RNA sample  three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara  Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN \u22659.5 and A260/280 \u22651.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer\u2019s protocol.", null, "tissue:Retina|strain:AB|age:2 mpf type", "GSM4861207", "GSM4861207: WT R2; Danio rerio; RNA Seq", "GSM4861207", null, "1", "For each RNA sample  three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara  Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN \u22659.5 and A260/280 \u22651.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer's protocol.", "GEO Accession:GSM4861207", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP288615", null, null, "WT-R2_combined_R1.fastq.gz WT-R2_combined_R2.fastq.gz", "fastq fastq", 7066558200.0, 23555194.0, "GSM4861207 r1", "0:150 1:150", "A:1911018201;C:1615965707;G:1630234641;T:1909071420;N:268231", 150, 150, null, null, 1911018201, 1615965707, 1630234641, 1909071420, 268231, "SRX9364741", "SRS7586956", "SRA1147909", "GEO", "College of Life Science and Technology, Huazhong University of Science and Technology", 2, 0.91673, 0.91647, 0.11542, 0.11684, 0.68781, 0.69637, 0.48784, 0.49134, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "sc_generic", "bulk", "bulk", null, "China", "2020-10-26", "Juvenile", "Juvenile", "Eye", "Sensory System"], [61646, "SRR12899693", "SRX9364740", "SRS7586955", "SRP288615", "PRJNA672100", "Nrl dependent and independent rod photoreceptor development in zebrafish [RNA Seq]", "GSE160138", "Transcriptome Analysis", "NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study  we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods  we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms  bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly  we found that rods exhibited noticeable heterogeneities in the gene expression patterns  and a part of rods in nrl knockout zebrafish misexpressed the green cone genes  reflecting a hybrid status of rod and green cone. Furthermore  we identified mafba as a novel regulator of rod genesis  which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species  and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: Two WT and two nrl KO samples two biological replicates were analyzed. Each sample represented a pool of RNAs from three zebrafish retinas at the age of 2 month. The differentially expressed genes between WT and nrl KO groups were identified.", "parent bioproject:PRJNA672094", "pubmed:35245286", null, "WT R1", "GSM4861206", null, "source name:Retina|tissue:Retina|strain:AB|age:2 mpf type", "WT R1", "Quality control  mapping and expression analysis: Image analysis and base calling were conducted by the HiSeq Control Software HCS + OLB + GAPipeline 1.6 Illumina on the HiSeq instrument. The high quality clean data were generated by Trimmomatic v0.30 and aligned to the reference genome of zebrafish via software Hisat2 v2.0.1. Differential expression analysis: Gene and isoform expression levels were estimated by HTSeq v0.6.1. Differential expression analysis was performed by DESeq Bioconductor package. post adjusted by Benjamini and Hochberg\u2019s approach for controlling the false discovery rate  the threshold of p values was set to <0.05 to detect differentially expressed genes. GO and KEGG enrichment analysis: GO TermFinder was used identifying Gene Ontology GO terms that annotate a list of enriched genes with a significant p value less than 0.05. KEGG Kyoto Encyclopedia of Genes and Genomes is a collection of databases dealing with genomes  biological pathways  diseases  drugs  and chemical substances http://en.wikipedia.org/wiki/KEGG  which was used to enrich significant differential expression gene in KEGG pathways. Genome build: GRCz11 from Ensembl Supplementary files format and content: Tab delimited text files including the raw counts and FPKM values for each Sample Supplementary files format and content: Tab delimited text files showing the foldchanges and p values of the differentially expressed genes", "Retina", null, "For each RNA sample  three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara  Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN \u22659.5 and A260/280 \u22651.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer\u2019s protocol.", null, "tissue:Retina|strain:AB|age:2 mpf type", "GSM4861206", "GSM4861206: WT R1; Danio rerio; RNA Seq", "GSM4861206", null, "1", "For each RNA sample  three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara  Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN \u22659.5 and A260/280 \u22651.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer's protocol.", "GEO Accession:GSM4861206", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP288615", null, null, "WT-R1_combined_R1.fastq.gz WT-R1_combined_R2.fastq.gz", "fastq fastq", 6933407700.0, 23111359.0, "GSM4861206 r1", "0:150 1:150", "A:1917552178;C:1542500715;G:1553125711;T:1919988847;N:240249", 150, 150, null, null, 1917552178, 1542500715, 1553125711, 1919988847, 240249, "SRX9364740", "SRS7586955", "SRA1147909", "GEO", "College of Life Science and Technology, Huazhong University of Science and Technology", 2, 0.90701, 0.90456, 0.14405, 0.14325, 0.68335, 0.69221, 0.49207, 0.4926, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "sc_generic", "bulk", "bulk", null, "China", "2020-10-26", "Juvenile", "Juvenile", "Eye", "Sensory System"], [64385, "SRR14679147", "SRX11017528", "SRS9089834", "SRP321802", "PRJNA733247", "Danio rerio breed:Danio Raw sequence reads", "PRJNA733247", "Whole Genome Sequencing", "zebrafish muscle tissue for scRNA seq and bulk RNA seq", null, null, null, "Model organism or animal sample from Danio rerio", "zebrafish", null, "breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "bulk RNA seq", "runx2b+/+ 2 bulk RNA seq", "runx2b+/+ 2 bulk RNA seq", "tail muscle with intermuscular bone", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP321802", null, null, "WT_2_60dpf.R1.fq.gz WT_2_60dpf.R2.fq.gz", "fastq fastq", 7007750400.0, 23359168.0, "WT 2 60dpf.R1.fq.gz", "0:150 1:150", "A:1714498514;C:1702913716;G:1897215939;T:1693105532;N:16699", 150, 150, null, null, 1714498514, 1702913716, 1897215939, 1693105532, 16699, "SRX11017528", "SRS9089834", "SRA1238123", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.93184, 0.92606, 0.01222, 0.01169, 0.84762, 0.85033, 0.67174, 0.64259, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2021-05-28", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [64386, "SRR14679148", "SRX11017527", "SRS9089834", "SRP321802", "PRJNA733247", "Danio rerio breed:Danio Raw sequence reads", "PRJNA733247", "Whole Genome Sequencing", "zebrafish muscle tissue for scRNA seq and bulk RNA seq", null, null, null, "Model organism or animal sample from Danio rerio", "zebrafish", null, "breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "bulk RNA seq", "runx2b+/+ 1 bulk RNA seq", "runx2b+/+ 1 bulk RNA seq", "tail muscle with intermuscular bone", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP321802", null, null, "WT_1_60dpf.R1.fq.gz WT_1_60dpf.R2.fq.gz", "fastq fastq", 6785203800.0, 22617346.0, "WT 1 60dpf.R1.fq.gz", "0:150 1:150", "A:1660992152;C:1637869425;G:1843210897;T:1643114944;N:16382", 150, 150, null, null, 1660992152, 1637869425, 1843210897, 1643114944, 16382, "SRX11017527", "SRS9089834", "SRA1238123", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.92764, 0.92197, 0.00968, 0.00947, 0.84323, 0.84577, 0.65455, 0.6592, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2021-05-28", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [64387, "SRR14679149", "SRX11017526", "SRS9089834", "SRP321802", "PRJNA733247", "Danio rerio breed:Danio Raw sequence reads", "PRJNA733247", "Whole Genome Sequencing", "zebrafish muscle tissue for scRNA seq and bulk RNA seq", null, null, null, "Model organism or animal sample from Danio rerio", "zebrafish", null, "breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq", "runx2b /  scRNA seq", "runx2b /  scRNA seq", "tail muscle without xxx bone", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP321802", null, null, "MU_S2_L003_R1_001.fastq.gz MU_S2_L003_R2_001.fastq.gz", "fastq fastq", 112565768100.0, 375219227.0, "MU S2 L003 R1 001.fastq.gz", "0:150 1:150", "A:34329910863;C:17430450121;G:18090145246;T:42713500460;N:1761410", 150, 150, null, null, 34329910863, 17430450121, 18090145246, 42713500460, 1761410, "SRX11017526", "SRS9089834", "SRA1238123", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.34692, 0.92476, 0.05138, 0.09375, 0.98543, 0.82371, 0.68433, 0.7376, 150, 150, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "bulk", "bulk", null, "China", "2021-05-29", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [64388, "SRR14679150", "SRX11017525", "SRS9089834", "SRP321802", "PRJNA733247", "Danio rerio breed:Danio Raw sequence reads", "PRJNA733247", "Whole Genome Sequencing", "zebrafish muscle tissue for scRNA seq and bulk RNA seq", null, null, null, "Model organism or animal sample from Danio rerio", "zebrafish", null, "breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq", "runx2b+/+ scRNA seq", "runx2b+/+ scRNA seq", "tail muscle with intermuscular bone", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP321802", null, null, "WT_S1_L003_R1_001.fastq.gz WT_S1_L003_R2_001.fastq.gz", "fastq fastq", 99838157100.0, 332793857.0, "WT S1 L003 R1 001.fastq.gz", "0:150 1:150", "A:30283010374;C:15529232903;G:16181518775;T:37842782328;N:1612720", 150, 150, null, null, 30283010374, 15529232903, 16181518775, 37842782328, 1612720, "SRX11017525", "SRS9089834", "SRA1238123", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.34302, 0.92611, 0.04637, 0.09453, 0.98701, 0.83658, 0.71917, 0.76074, 150, 150, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "bulk", "bulk", null, "China", "2021-05-29", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [64389, "SRR14679151", "SRX11017524", "SRS9089834", "SRP321802", "PRJNA733247", "Danio rerio breed:Danio Raw sequence reads", "PRJNA733247", "Whole Genome Sequencing", "zebrafish muscle tissue for scRNA seq and bulk RNA seq", null, null, null, "Model organism or animal sample from Danio rerio", "zebrafish", null, "breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "bulk RNA seq", "runx2b /  3 bulk RNA seq", "runx2b /  3 bulk RNA seq", "tail muscle without xxx bone", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP321802", null, null, "MUT_3_60dpf.R1.fq.gz MUT_3_60dpf.R2.fq.gz", "fastq fastq", 7358370600.0, 24527902.0, "MUT 3 60dpf.R1.fq.gz", "0:150 1:150", "A:1781646726;C:1790446433;G:2025455441;T:1760804227;N:17773", 150, 150, null, null, 1781646726, 1790446433, 2025455441, 1760804227, 17773, "SRX11017524", "SRS9089834", "SRA1238123", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.92552, 0.9218, 0.01223, 0.01223, 0.86222, 0.86348, 0.68246, 0.64029, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2021-05-28", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [64390, "SRR14679152", "SRX11017523", "SRS9089834", "SRP321802", "PRJNA733247", "Danio rerio breed:Danio Raw sequence reads", "PRJNA733247", "Whole Genome Sequencing", "zebrafish muscle tissue for scRNA seq and bulk RNA seq", null, null, null, "Model organism or animal sample from Danio rerio", "zebrafish", null, "breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "bulk RNA seq", "runx2b /  2 bulk RNA seq", "runx2b /  2 bulk RNA seq", "tail muscle without xxx bone", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP321802", null, null, "MUT_2_60dpf.R1.fq.gz MUT_2_60dpf.R2.fq.gz", "fastq fastq", 5983046100.0, 19943487.0, "MUT 2 60dpf.R1.fq.gz", "0:150 1:150", "A:1456794159;C:1460953692;G:1613536834;T:1451747111;N:14304", 150, 150, null, null, 1456794159, 1460953692, 1613536834, 1451747111, 14304, "SRX11017523", "SRS9089834", "SRA1238123", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.93491, 0.9294, 0.01148, 0.01117, 0.85474, 0.85667, 0.69448, 0.63383, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2021-05-28", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [64391, "SRR14679153", "SRX11017522", "SRS9089834", "SRP321802", "PRJNA733247", "Danio rerio breed:Danio Raw sequence reads", "PRJNA733247", "Whole Genome Sequencing", "zebrafish muscle tissue for scRNA seq and bulk RNA seq", null, null, null, "Model organism or animal sample from Danio rerio", "zebrafish", null, "breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "bulk RNA seq", "runx2b /  1 bulk RNA seq", "runx2b /  1 bulk RNA seq", "tail muscle without xxx bone", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP321802", null, null, "MUT_1_60dpf.R1.fq.gz MUT_1_60dpf.R2.fq.gz", "fastq fastq", 6876053100.0, 22920177.0, "MUT 1 60dpf.R1.fq.gz", "0:150 1:150", "A:1683687632;C:1665466650;G:1862910858;T:1663971371;N:16589", 150, 150, null, null, 1683687632, 1665466650, 1862910858, 1663971371, 16589, "SRX11017522", "SRS9089834", "SRA1238123", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.93272, 0.92802, 0.01179, 0.01133, 0.84861, 0.84993, 0.62206, 0.67726, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2021-05-28", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [64392, "SRR14679154", "SRX11017521", "SRS9089834", "SRP321802", "PRJNA733247", "Danio rerio breed:Danio Raw sequence reads", "PRJNA733247", "Whole Genome Sequencing", "zebrafish muscle tissue for scRNA seq and bulk RNA seq", null, null, null, "Model organism or animal sample from Danio rerio", "zebrafish", null, "breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "bulk RNA seq", "runx2b+/+ 3 bulk RNA seq", "runx2b+/+ 3 bulk RNA seq", "tail muscle with intermuscular bone", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP321802", null, null, "WT_3_60dpf.R1.fq.gz WT_3_60dpf.R2.fq.gz", "fastq fastq", 6834033900.0, 22780113.0, "WT 3 60dpf.R1.fq.gz", "0:150 1:150", "A:1665713519;C:1660512523;G:1864685424;T:1643106338;N:16096", 150, 150, null, null, 1665713519, 1660512523, 1864685424, 1643106338, 16096, "SRX11017521", "SRS9089834", "SRA1238123", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.92968, 0.92349, 0.01013, 0.01013, 0.85811, 0.85999, 0.62541, 0.6776, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2021-05-28", "Juvenile", "Juvenile", "Muscle", "Muscular 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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