{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\" and experiment.library_selection = \"size fractionation\"", "rows": [[10403, "ERR8527374", "ERX8137561", "ERS10539829", "ERP135430", "PRJEB50826", "scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish", "E-MTAB-11079_2", "Transcriptome Analysis", "Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted  from pooled kidneys of ren+/+ or ren /  zebrafish  which carried ren:RFP and acta2:EGFP reporter genes  allowing the isolation of renin expressing cells and smooth muscle cells.", "ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10", null, "Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA  specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.", "ZF2", "SAMEA12941033", "University Of Edinburgh", "ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941033|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF2|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP; ren / |individual:9 12 kidneys pooled|inferred cell type:recruited RLC|organism part:kidney|phenotype:ren knockout|sample name:E MTAB 11079 2:ZF2|sex:mixed|strain:WIK", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish", "E MTAB 11079 2:ZF2 p", "ZF2 p", "scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish", "Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively.  Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA   specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.", "Experimental Factor: phenotype:ren knockout", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "size fractionation", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP135430", "NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish", "ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10", "ZF2_S2_L002_I1_001.fastq.gz ZF2_S2_L002_R1_001.fastq.gz ZF2_S2_L002_R2_001.fastq.gz", "fastq fastq fastq", 38557081640.0, 125185330.0, "E MTAB 11079 2:ZF2 S2 L002", "0:8 1:150 2:150", "A:13781315856;C:6436030786;G:6578059630;T:10759631611;N:561117", 8, 150, 150, null, 13781315856, 6436030786, 6578059630, 10759631611, 561117, "ERX8137561", "ERS10539829", "ERA9016154", "University Of Edinburgh|European Nucleotide Archive", "University Of Edinburgh|European Nucleotide Archive", 2, 0.0, 0.84449, 0.0, 0.09657, 1.0, 0.8242, null, 0.52635, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2022-06-10", "Adult", "Adult", "Multi-tissue", "Multi-system"], [10404, "ERR8527377", "ERX8137561", "ERS10539829", "ERP135430", "PRJEB50826", "scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish", "E-MTAB-11079_2", "Transcriptome Analysis", "Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted  from pooled kidneys of ren+/+ or ren /  zebrafish  which carried ren:RFP and acta2:EGFP reporter genes  allowing the isolation of renin expressing cells and smooth muscle cells.", "ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10", null, "Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA  specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.", "ZF2", "SAMEA12941033", "University Of Edinburgh", "ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941033|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF2|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP; ren / |individual:9 12 kidneys pooled|inferred cell type:recruited RLC|organism part:kidney|phenotype:ren knockout|sample name:E MTAB 11079 2:ZF2|sex:mixed|strain:WIK", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish", "E MTAB 11079 2:ZF2 p", "ZF2 p", "scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish", "Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively.  Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA   specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.", "Experimental Factor: phenotype:ren knockout", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "size fractionation", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP135430", "NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish", "ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10", "ZF2_S2_L001_I1_001.fastq.gz ZF2_S2_L001_R1_001.fastq.gz ZF2_S2_L001_R2_001.fastq.gz", "fastq fastq fastq", 38872269128.0, 126208666.0, "E MTAB 11079 2:ZF2 S2 L001", "0:8 1:150 2:150", "A:15151865400;C:6355030057;G:6591732598;T:9763441371;N:530374", 8, 150, 150, null, 15151865400, 6355030057, 6591732598, 9763441371, 530374, "ERX8137561", "ERS10539829", "ERA9016154", "University Of Edinburgh|European Nucleotide Archive", "University Of Edinburgh|European Nucleotide Archive", 2, 0.0, 0.84526, 0.0, 0.09779, 1.0, 0.82609, null, 0.54388, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2022-06-10", "Adult", "Adult", "Multi-tissue", "Multi-system"], [10405, "ERR8527376", "ERX8137560", "ERS10539828", "ERP135430", "PRJEB50826", "scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish", "E-MTAB-11079_2", "Transcriptome Analysis", "Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted  from pooled kidneys of ren+/+ or ren /  zebrafish  which carried ren:RFP and acta2:EGFP reporter genes  allowing the isolation of renin expressing cells and smooth muscle cells.", "ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10", null, "Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA  specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.", "ZF1", "SAMEA12941032", "University Of Edinburgh", "ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941032|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF1|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP|individual:9 12 kidneys pooled|inferred cell type:juxtaglomerular cell|organism part:kidney|phenotype:wild type|sample name:E MTAB 11079 2:ZF1|sex:mixed|strain:WIK", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish", "E MTAB 11079 2:ZF1 p", "ZF1 p", "scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish", "Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively.  Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA   specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.", "Experimental Factor: phenotype:wild type", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "size fractionation", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP135430", "NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish", "ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10", "ZF1_S1_L002_I1_001.fastq.gz ZF1_S1_L002_R1_001.fastq.gz ZF1_S1_L002_R2_001.fastq.gz", "fastq fastq fastq", 39415722500.0, 127973125.0, "E MTAB 11079 2:ZF1 S1 L002", "0:8 1:150 2:150", "A:14261012964;C:6339158428;G:6467430919;T:11323758989;N:576200", 8, 150, 150, null, 14261012964, 6339158428, 6467430919, 11323758989, 576200, "ERX8137560", "ERS10539828", "ERA9016154", "University Of Edinburgh|European Nucleotide Archive", "University Of Edinburgh|European Nucleotide Archive", 2, 0.0, 0.81065, 0.0, 0.08289, 1.0, 0.82434, null, 0.52903, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2022-06-10", "Adult", "Adult", "Multi-tissue", "Multi-system"], [10406, "ERR8527375", "ERX8137560", "ERS10539828", "ERP135430", "PRJEB50826", "scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish", "E-MTAB-11079_2", "Transcriptome Analysis", "Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted  from pooled kidneys of ren+/+ or ren /  zebrafish  which carried ren:RFP and acta2:EGFP reporter genes  allowing the isolation of renin expressing cells and smooth muscle cells.", "ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10", null, "Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA  specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.", "ZF1", "SAMEA12941032", "University Of Edinburgh", "ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941032|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF1|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP|individual:9 12 kidneys pooled|inferred cell type:juxtaglomerular cell|organism part:kidney|phenotype:wild type|sample name:E MTAB 11079 2:ZF1|sex:mixed|strain:WIK", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish", "E MTAB 11079 2:ZF1 p", "ZF1 p", "scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish", "Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively.  Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA   specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.", "Experimental Factor: phenotype:wild type", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "size fractionation", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP135430", "NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish", "ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10", "ZF1_S1_L001_I1_001.fastq.gz ZF1_S1_L001_R1_001.fastq.gz ZF1_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 39744721324.0, 129041303.0, "E MTAB 11079 2:ZF1 S1 L001", "0:8 1:150 2:150", "A:15670316830;C:6278039908;G:6505806971;T:10257683184;N:544007", 8, 150, 150, null, 15670316830, 6278039908, 6505806971, 10257683184, 544007, "ERX8137560", "ERS10539828", "ERA9016154", "University Of Edinburgh|European Nucleotide Archive", "University Of Edinburgh|European Nucleotide Archive", 2, 0.0, 0.81031, 0.0, 0.08495, 1.0, 0.82169, null, 0.51724, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2022-06-10", "Adult", "Adult", "Multi-tissue", "Multi-system"], [11130, "ERR9979395", "ERX9520370", "ERS12499848", "ERP139765", "PRJEB54901", "Single cell RNA sequencing of germ free zebrafish embryos", "E-MTAB-11984", "Transcriptome Analysis", "The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish.  Here  we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22", null, "Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Sample 2 WT GO+BA", "SAMEA110401656", "Institute of Environmental Medicine, Karolinska Institutet", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401656|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 2 WT GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 2 WT GO+BA|sex:not available|stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos", "E MTAB 11984:Sample 2 WT GO+BA p", "Sample 2 WT GO+BA p", "Single cell RNA sequencing of germ free zebrafish embryos", "The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed.  The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Experimental Factor: stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM", "AMPLICON", "TRANSCRIPTOMIC SINGLE CELL", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP139765", "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22", "P22202_7002_S2_L002_R1_001.fastq.gz P22202_7002_S2_L002_R2_001.fastq.gz", "fastq fastq", 18144406998.0, 153766161.0, "E MTAB 11984:P22202 7002 S2 L002", "0:28 1:90", "A:5277424121;C:3880928155;G:4118706097;T:4866649878;N:698747", 28, 90, null, null, 5277424121, 3880928155, 4118706097, 4866649878, 698747, "ERX9520370", "ERS12499848", "ERA16483151", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", 2, 0.0109, 0.90145, 0.0053, 0.21373, 0.98746, 0.79423, 0.41198, 0.54447, 28, 90, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "full_length", "size_fractionation", "trueseq", "sc", "single_cell_droplet", "10x", null, "Sweden", "2022-07-22", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [11131, "ERR9979394", "ERX9520370", "ERS12499848", "ERP139765", "PRJEB54901", "Single cell RNA sequencing of germ free zebrafish embryos", "E-MTAB-11984", "Transcriptome Analysis", "The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish.  Here  we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22", null, "Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Sample 2 WT GO+BA", "SAMEA110401656", "Institute of Environmental Medicine, Karolinska Institutet", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401656|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 2 WT GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 2 WT GO+BA|sex:not available|stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos", "E MTAB 11984:Sample 2 WT GO+BA p", "Sample 2 WT GO+BA p", "Single cell RNA sequencing of germ free zebrafish embryos", "The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed.  The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Experimental Factor: stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM", "AMPLICON", "TRANSCRIPTOMIC SINGLE CELL", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP139765", "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22", "P22202_7002_S2_L001_R1_001.fastq.gz P22202_7002_S2_L001_R2_001.fastq.gz", "fastq fastq", 18458951574.0, 156431793.0, "E MTAB 11984:P22202 7002 S2 L001", "0:28 1:90", "A:5372920926;C:3946687814;G:4185647697;T:4953205454;N:489683", 28, 90, null, null, 5372920926, 3946687814, 4185647697, 4953205454, 489683, "ERX9520370", "ERS12499848", "ERA16483151", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", 2, 0.01037, 0.90168, 0.0048, 0.21246, 0.98752, 0.79297, 0.42601, 0.54996, 28, 90, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "full_length", "size_fractionation", "trueseq", "sc", "single_cell_droplet", "10x", null, "Sweden", "2022-07-22", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [11132, "ERR9979392", "ERX9520369", "ERS12499847", "ERP139765", "PRJEB54901", "Single cell RNA sequencing of germ free zebrafish embryos", "E-MTAB-11984", "Transcriptome Analysis", "The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish.  Here  we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22", null, "Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Sample 1 WT control", "SAMEA110401655", "Institute of Environmental Medicine, Karolinska Institutet", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401655|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 1 WT control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 1 WT control|sex:not available|stimulus:n1|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos", "E MTAB 11984:Sample 1 WT control p", "Sample 1 WT control p", "Single cell RNA sequencing of germ free zebrafish embryos", "The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed.  The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Experimental Factor: stimulus:n1", "AMPLICON", "TRANSCRIPTOMIC SINGLE CELL", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP139765", "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22", "P22202_7001_S1_L001_R1_001.fastq.gz P22202_7001_S1_L001_R2_001.fastq.gz", "fastq fastq", 19396994226.0, 164381307.0, "E MTAB 11984:P22202 7001 S1 L001", "0:28 1:90", "A:5665199484;C:4091196594;G:4415211076;T:5224866754;N:520318", 28, 90, null, null, 5665199484, 4091196594, 4415211076, 5224866754, 520318, "ERX9520369", "ERS12499847", "ERA16483151", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", 2, 0.01093, 0.89238, 0.00557, 0.232, 0.98764, 0.79444, 0.40806, 0.54781, 28, 90, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "full_length", "size_fractionation", "trueseq", "sc", "single_cell_droplet", "10x", null, "Sweden", "2022-07-22", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [11133, "ERR9979393", "ERX9520369", "ERS12499847", "ERP139765", "PRJEB54901", "Single cell RNA sequencing of germ free zebrafish embryos", "E-MTAB-11984", "Transcriptome Analysis", "The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish.  Here  we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22", null, "Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Sample 1 WT control", "SAMEA110401655", "Institute of Environmental Medicine, Karolinska Institutet", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401655|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 1 WT control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 1 WT control|sex:not available|stimulus:n1|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos", "E MTAB 11984:Sample 1 WT control p", "Sample 1 WT control p", "Single cell RNA sequencing of germ free zebrafish embryos", "The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed.  The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Experimental Factor: stimulus:n1", "AMPLICON", "TRANSCRIPTOMIC SINGLE CELL", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP139765", "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22", "P22202_7001_S1_L002_R1_001.fastq.gz P22202_7001_S1_L002_R2_001.fastq.gz", "fastq fastq", 19063958224.0, 161558968.0, "E MTAB 11984:P22202 7001 S1 L002", "0:28 1:90", "A:5563588848;C:4022930643;G:4344549562;T:5132136743;N:752428", 28, 90, null, null, 5563588848, 4022930643, 4344549562, 5132136743, 752428, "ERX9520369", "ERS12499847", "ERA16483151", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", 2, 0.01118, 0.89308, 0.00573, 0.23128, 0.98737, 0.79354, 0.39264, 0.54552, 28, 90, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "full_length", "size_fractionation", "trueseq", "sc", "single_cell_droplet", "10x", null, "Sweden", "2022-07-22", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [11134, "ERR9981089", "ERX9522049", "ERS12503451", "ERP139797", "PRJEB54930", "Single cell RNA sequencing of lck GFP transgenic zebrafish", "E-MTAB-11991", "Transcriptome Analysis", "The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23", null, "Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Sample 1 lck control", "SAMEA110406305", "Institute of Environmental Medicine, Karolinska Institutet", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406305|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 1 lck control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 1 lck control|strain:Tglck:GFP", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish", "E MTAB 11991:Sample 1 lck control p", "Sample 1 lck control p", "Single cell RNA sequencing of lck GFP transgenic zebrafish", "The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0", "Experimental Factor: stimulus:n1", "AMPLICON", "TRANSCRIPTOMIC SINGLE CELL", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP139797", "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23", "P25452_2002_S2_L001_R1_001.fastq.gz P25452_2002_S2_L001_R2_001.fastq.gz", "fastq fastq", 60177283876.0, 509976982.0, "E MTAB 11991:P25452 2002 S2 L001", "0:28 1:90", "A:17254566438;C:13547211711;G:14188233429;T:15185192817;N:2079481", 28, 90, null, null, 17254566438, 13547211711, 14188233429, 15185192817, 2079481, "ERX9522049", "ERS12503451", "ERA16488297", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", 2, 0.00671, 0.93031, 0.00231, 0.11028, 0.9932, 0.82227, 0.30887, 0.58272, 28, 90, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "full_length", "size_fractionation", "trueseq", "sc", "single_cell_droplet", "10x", null, "Sweden", "2022-07-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [11135, "ERR9981090", "ERX9522049", "ERS12503451", "ERP139797", "PRJEB54930", "Single cell RNA sequencing of lck GFP transgenic zebrafish", "E-MTAB-11991", "Transcriptome Analysis", "The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23", null, "Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Sample 1 lck control", "SAMEA110406305", "Institute of Environmental Medicine, Karolinska Institutet", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406305|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 1 lck control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 1 lck control|strain:Tglck:GFP", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish", "E MTAB 11991:Sample 1 lck control p", "Sample 1 lck control p", "Single cell RNA sequencing of lck GFP transgenic zebrafish", "The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0", "Experimental Factor: stimulus:n1", "AMPLICON", "TRANSCRIPTOMIC SINGLE CELL", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP139797", "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23", "P25452_2002_S2_L002_R1_001.fastq.gz P25452_2002_S2_L002_R2_001.fastq.gz", "fastq fastq", 60597886144.0, 513541408.0, "E MTAB 11991:P25452 2002 S2 L002", "0:28 1:90", "A:17368154358;C:13649089056;G:14296037620;T:15282869484;N:1735626", 28, 90, null, null, 17368154358, 13649089056, 14296037620, 15282869484, 1735626, "ERX9522049", "ERS12503451", "ERA16488297", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", 2, 0.00656, 0.92899, 0.00211, 0.11059, 0.99334, 0.82335, 0.32311, 0.57644, 28, 90, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "full_length", "size_fractionation", "trueseq", "sc", "single_cell_droplet", "10x", null, "Sweden", "2022-07-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [11136, "ERR9981087", "ERX9522048", "ERS12503450", "ERP139797", "PRJEB54930", "Single cell RNA sequencing of lck GFP transgenic zebrafish", "E-MTAB-11991", "Transcriptome Analysis", "The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23", null, "Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Sample 2 lck GO+BA", "SAMEA110406304", "Institute of Environmental Medicine, Karolinska Institutet", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406304|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 2 lck GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 2 lck GO+BA|strain:Tglck:GFP", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish", "E MTAB 11991:Sample 2 lck GO+BA p", "Sample 2 lck GO+BA p", "Single cell RNA sequencing of lck GFP transgenic zebrafish", "The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Experimental Factor: stimulus:graphene oxide  30 microgram per milliliter|Experimental Factor: compound:butyrate|Experimental Factor: dose:2.5", "AMPLICON", "TRANSCRIPTOMIC SINGLE CELL", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP139797", "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23", "P25452_2001_S1_L001_R1_001.fastq.gz P25452_2001_S1_L001_R2_001.fastq.gz", "fastq fastq", 20866120186.0, 176831527.0, "E MTAB 11991:P25452 2001 S1 L001", "0:28 1:90", "A:5933525376;C:4737179804;G:5025711080;T:5168983880;N:720046", 28, 90, null, null, 5933525376, 4737179804, 5025711080, 5168983880, 720046, "ERX9522048", "ERS12503450", "ERA16488297", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", 2, 0.00805, 0.92622, 0.00259, 0.11842, 0.99302, 0.83027, 0.2729, 0.57699, 28, 90, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "full_length", "size_fractionation", "trueseq", "sc", "single_cell_droplet", "10x", null, "Sweden", "2022-07-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [11137, "ERR9981088", "ERX9522048", "ERS12503450", "ERP139797", "PRJEB54930", "Single cell RNA sequencing of lck GFP transgenic zebrafish", "E-MTAB-11991", "Transcriptome Analysis", "The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23", null, "Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Sample 2 lck GO+BA", "SAMEA110406304", "Institute of Environmental Medicine, Karolinska Institutet", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406304|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 2 lck GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 2 lck GO+BA|strain:Tglck:GFP", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish", "E MTAB 11991:Sample 2 lck GO+BA p", "Sample 2 lck GO+BA p", "Single cell RNA sequencing of lck GFP transgenic zebrafish", "The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Experimental Factor: stimulus:graphene oxide  30 microgram per milliliter|Experimental Factor: compound:butyrate|Experimental Factor: dose:2.5", "AMPLICON", "TRANSCRIPTOMIC SINGLE CELL", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP139797", "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23", "P25452_2001_S1_L002_R1_001.fastq.gz P25452_2001_S1_L002_R2_001.fastq.gz", "fastq fastq", 21068682172.0, 178548154.0, "E MTAB 11991:P25452 2001 S1 L002", "0:28 1:90", "A:5987758267;C:4786100132;G:5078292970;T:5215926275;N:604528", 28, 90, null, null, 5987758267, 4786100132, 5078292970, 5215926275, 604528, "ERX9522048", "ERS12503450", "ERA16488297", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", 2, 0.00813, 0.92702, 0.00264, 0.11874, 0.99283, 0.82737, 0.30228, 0.56929, 28, 90, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "full_length", "size_fractionation", "trueseq", "sc", "single_cell_droplet", "10x", null, "Sweden", "2022-07-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28490, "SRR26319601", "SRX22027740", "SRS19100857", "SRP465070", "PRJNA1025141", "Danio rerio Raw sequence reads", "PRJNA1025141", "Other", "Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.", null, null, "Treatment", "CX3 for transcriptome 3", "CX3", null, "strain:AB|cultivar:WT|ecotype:China: Jiangsu|age:7 dpf|dev stage:Larvae|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.67 E|treatment:Treatment Group|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "ALST3 for transcriptome 3", "CX3 for transcriptome 3", "CX3 for transcriptome 3", "CX3 for transcriptome 3", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP465070", null, null, "Unknown_AY803-03T0006_good_1.fq.gz Unknown_AY803-03T0006_good_2.fq.gz", "fastq fastq", 6255596356.0, 20929531.0, "Unknown AY803 03T0006 good 1.fq.gz", "0:149.44 1:149.44", "A:1657365560;C:1463722268;G:1467057724;T:1667269298;N:181506", 149, 149, null, null, 1657365560, 1463722268, 1467057724, 1667269298, 181506, "SRX22027740", "SRS19100857", "SRA1727563", "Soochow University|School of biology &amp; basic medical sciences", "Soochow University", 2, 0.89228, 0.91654, 0.09286, 0.09714, 0.6588, 0.65604, 0.4631, 0.45773, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-10-11", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28491, "SRR26319602", "SRX22027739", "SRS19100854", "SRP465070", "PRJNA1025141", "Danio rerio Raw sequence reads", "PRJNA1025141", "Other", "Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.", null, null, "Treatment", "CX2 for transcriptome 2", "CX2", null, "strain:AB|cultivar:WT|ecotype:China: Jiangsu|age:7 dpf|dev stage:Larvae|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.66 E|treatment:Treatment Group|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "ALST2 for transcriptome 2", "CX2 for transcriptome 2", "CX2 for transcriptome 2", "CX2 for transcriptome 2", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP465070", null, null, "Unknown_AY803-03T0005_good_1.fq.gz Unknown_AY803-03T0005_good_2.fq.gz", "fastq fastq", 6598066464.0, 22061446.0, "Unknown AY803 03T0005 good 1.fq.gz", "0:149.54 1:149.54", "A:1747291499;C:1543289262;G:1549193118;T:1758088368;N:204217", 149, 149, null, null, 1747291499, 1543289262, 1549193118, 1758088368, 204217, "SRX22027739", "SRS19100854", "SRA1727563", "Soochow University|School of biology &amp; basic medical sciences", "Soochow University", 2, 0.88949, 0.92148, 0.08893, 0.0947, 0.65596, 0.65228, 0.46045, 0.47087, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-10-11", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28492, "SRR26319603", "SRX22027738", "SRS19100853", "SRP465070", "PRJNA1025141", "Danio rerio Raw sequence reads", "PRJNA1025141", "Other", "Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.", null, null, "Treatment", "CX1 for transcriptome 1", "CX1", null, "strain:AB|cultivar:WT|ecotype:China: Jiangsu|age:7 dpf|dev stage:Larvae|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.65 E|treatment:Treatment Group|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "ALST1 for transcriptome 1", "CX1 for transcriptome 1", "CX1 for transcriptome 1", "CX1 for transcriptome 1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP465070", null, null, "Unknown_AY803-03T0004_good_1.fq.gz Unknown_AY803-03T0004_good_2.fq.gz", "fastq fastq", 6478923586.0, 21662443.0, "Unknown AY803 03T0004 good 1.fq.gz", "0:149.54 1:149.54", "A:1712718473;C:1518937459;G:1523570227;T:1723510437;N:186990", 149, 149, null, null, 1712718473, 1518937459, 1523570227, 1723510437, 186990, "SRX22027738", "SRS19100853", "SRA1727563", "Soochow University|School of biology &amp; basic medical sciences", "Soochow University", 2, 0.89423, 0.9176, 0.08944, 0.09254, 0.6575, 0.65458, 0.4693, 0.46842, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-10-11", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28493, "SRR26319604", "SRX22027737", "SRS19100856", "SRP465070", "PRJNA1025141", "Danio rerio Raw sequence reads", "PRJNA1025141", "Other", "Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.", null, null, "Control", "con3 for transcriptome 3", "con3", null, "strain:AB|cultivar:Wild type|ecotype:China: Jiangsu suzhou|age:7 dpf|dev stage:Larvae phase|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.64 E|treatment:Control Group|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "con3 for transcriptome 3", "con3 for transcriptome 3", "con3 for transcriptome 3", "con3 for transcriptome 3", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP465070", null, null, "Unknown_AY803-03T0003_good_2.fq.gz Unknown_AY803-03T0003_good_1.fq.gz", "fastq fastq", 6341537566.0, 21218597.0, "Unknown AY803 03T0003 good 1.fq.gz", "0:149.43 1:149.43", "A:1679811754;C:1483631833;G:1489430825;T:1688482904;N:180250", 149, 149, null, null, 1679811754, 1483631833, 1489430825, 1688482904, 180250, "SRX22027737", "SRS19100856", "SRA1727563", "Soochow University|School of biology &amp; basic medical sciences", "Soochow University", 2, 0.88245, 0.91856, 0.09069, 0.09654, 0.66253, 0.65817, 0.46245, 0.46336, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-10-11", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28494, "SRR26319605", "SRX22027736", "SRS19100855", "SRP465070", "PRJNA1025141", "Danio rerio Raw sequence reads", "PRJNA1025141", "Other", "Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.", null, null, "Control", "con2 for transcriptome 2", "con2", null, "strain:AB|cultivar:Wild type|ecotype:China: Jiangsu suzhou|age:7 dpf|dev stage:Larvae phase|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.63 E|treatment:Control Group|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "con2 for transcriptome 2", "con2 for transcriptome 2", "con2 for transcriptome 2", "con2 for transcriptome 2", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP465070", null, null, "Unknown_AY803-03T0002_good_2.fq.gz Unknown_AY803-03T0002_good_1.fq.gz", "fastq fastq", 5709771178.0, 19100144.0, "Unknown AY803 03T0002 good 1.fq.gz", "0:149.47 1:149.47", "A:1505730979;C:1342843084;G:1346105868;T:1514941964;N:149283", 149, 149, null, null, 1505730979, 1342843084, 1346105868, 1514941964, 149283, "SRX22027736", "SRS19100855", "SRA1727563", "Soochow University|School of biology &amp; basic medical sciences", "Soochow University", 2, 0.8924, 0.91903, 0.09155, 0.09604, 0.65902, 0.65593, 0.4634, 0.46028, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-10-11", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28495, "SRR26319606", "SRX22027735", "SRS19100852", "SRP465070", "PRJNA1025141", "Danio rerio Raw sequence reads", "PRJNA1025141", "Other", "Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.", null, null, "Control", "con1 for transcriptome 1", "con1", null, "strain:AB|cultivar:Wild type|ecotype:China: Jiangsu suzhou|age:7 dpf|dev stage:Larvae phase|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.62 E|treatment:Control Group|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "con1 for transcriptome 1", "con1 for transcriptome 1", "con1 for transcriptome 1", "con1 for transcriptome 1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP465070", null, null, "Unknown_AY803-03T0001_good_1.fq.gz Unknown_AY803-03T0001_good_2.fq.gz", "fastq fastq", 6544586118.0, 21872265.0, "Unknown AY803 03T0001 good 1.fq.gz", "0:149.61 1:149.61", "A:1731179229;C:1528367346;G:1541103688;T:1743735521;N:200334", 149, 149, null, null, 1731179229, 1528367346, 1541103688, 1743735521, 200334, "SRX22027735", "SRS19100852", "SRA1727563", "Soochow University|School of biology &amp; basic medical sciences", "Soochow University", 2, 0.87588, 0.92739, 0.08683, 0.09494, 0.65711, 0.6504, 0.46774, 0.47072, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-10-11", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [29746, "SRR27467679", "SRX23139227", "SRS20090270", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "ovary BS R2", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:BS|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: ovary  BS  rep2", "EV02003", "EV02003", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV02003.R1.fastq.gz EV02003.R2.fastq.gz", "fastq fastq", 1031891720.0, 3416860.0, "EV02003.R1.fastq.gz", "0:151 1:151", "A:264464363;C:153440613;G:408557241;T:205367487;N:62016", 151, 151, null, null, 264464363, 153440613, 408557241, 205367487, 62016, "SRX23139227", "SRS20090270", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 2, 0.0, 0.00019, 0.0, 0.00015, 1.0, 0.99993, null, 1.0, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Adult", "Adult", "Gonad", "Reproductive System"], [29755, "SRR27467688", "SRX23139218", "SRS20090261", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "ovary DM R2", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:DM|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: ovary  DM  rep2", "EV02002", "EV02002", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV02002.R1.fastq.gz EV02002.R2.fastq.gz", "fastq fastq", 861320308.0, 2852054.0, "EV02002.R1.fastq.gz", "0:151 1:151", "A:205625519;C:162178974;G:334206312;T:159256900;N:52603", 151, 151, null, null, 205625519, 162178974, 334206312, 159256900, 52603, "SRX23139218", "SRS20090261", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 2, 2e-05, 0.00049, 0.0, 0.00027, 1.0, 0.99947, null, 0.44444, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Adult", "Adult", "Gonad", "Reproductive System"], [29756, "SRR27467689", "SRX23139217", "SRS20090260", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "ovary mock R2", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:mock|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: ovary  mock  rep2", "EV02001", "EV02001", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV02001.R1.fastq.gz EV02001.R2.fastq.gz", "fastq fastq", 520371066.0, 1723083.0, "EV02001.R1.fastq.gz", "0:151 1:151", "A:116107273;C:90896560;G:218652568;T:94682244;N:32421", 151, 151, null, null, 116107273, 90896560, 218652568, 94682244, 32421, "SRX23139217", "SRS20090260", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 2, 2e-05, 0.00086, 0.0, 0.00078, 0.99995, 0.99981, 0.0, 0.61538, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Adult", "Adult", "Gonad", "Reproductive System"], [31514, "SRR28435337", "SRX24039257", "SRS20832031", "SRP497569", "PRJNA1090643", "Danio rerio Raw sequence reads", "PRJNA1090643", "Other", "The transcriptome of WT and cry dash /  mutant are tested at CT 4 and CT 16.", null, null, "cry dash /  group 2 at CT 16", "Cryd CT16G2", "Unknown BA023 04T0008.fq.gz", null, "isolate:The second group of cry dash /  fish collected at CT 16.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:cry dash / |health state:Health|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: larvae", "Unknown BA023 04T0008.fq.gz", "Unknown BA023 04T0008.fq.gz", "CT16 cry dash group2", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "HiSeq X Five", null, "SRP497569", null, null, "Unknown_BA023-04T0008_good_2.fq.gz Unknown_BA023-04T0008_good_1.fq.gz", "fastq fastq", 6928082472.0, 23162452.0, "Unknown BA023 04T0008 good 1.fq.gz", "0:149.55 1:149.55", "A:1783381005;C:1671764458;G:1686432861;T:1786331460;N:172688", 149, 149, null, null, 1783381005, 1671764458, 1686432861, 1786331460, 172688, "SRX24039257", "SRS20832031", "SRA1832685", "Soochow University|School of Biology &amp; 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RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "F2g_R2.fq.gz F2g_R1.fq.gz", "fastq fastq", 9101949000.0, 30339830.0, "F2g R1.fq.gz", "0:150 1:150", "A:2052853923;C:2394247721;G:2773304460;T:1881440199;N:102697", 150, 150, null, null, 2052853923, 2394247721, 2773304460, 1881440199, 102697, "SRX25008885", "SRS21709104", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.65449, 0.37434, 0.04313, 0.12258, 0.99519, 0.99527, 0.61425, 0.56139, 150, 150, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Gut", "Digestive System"], [32924, "SRR29498568", "SRX25008884", "SRS21709103", "SRP515416", "PRJNA1127032", "Zebrafish Tissue Mid Range RNA Sequencing", "PRJNA1127032", "Other", "This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.", null, null, null, null, "F1g", null, "strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:gut|identifier:F1g|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "midRNA seq Danio rerio", "09", "09", "Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "F1g_R1.fq.gz F1g_R2.fq.gz", "fastq fastq", 8132653500.0, 27108845.0, "F1g R1.fq.gz", "0:150 1:150", "A:1811779602;C:2095863397;G:2529881799;T:1695036688;N:92014", 150, 150, null, null, 1811779602, 2095863397, 2529881799, 1695036688, 92014, "SRX25008884", "SRS21709103", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.53909, 0.24181, 0.01966, 0.04797, 0.99598, 0.99624, 0.59302, 0.62038, 150, 150, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Gut", "Digestive System"], [32925, "SRR29498569", "SRX25008883", "SRS21709102", "SRP515416", "PRJNA1127032", "Zebrafish Tissue Mid Range RNA Sequencing", "PRJNA1127032", "Other", "This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.", null, null, null, null, "M2l", null, "strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:liver|identifier:M2l|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "midRNA seq Danio rerio", "08", "08", "Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "M2l_R1.fq.gz M2l_R2.fq.gz", "fastq fastq", 7733826600.0, 25779422.0, "M2l R1.fq.gz", "0:150 1:150", "A:1754773283;C:2022716836;G:2330439864;T:1625790112;N:106505", 150, 150, null, null, 1754773283, 2022716836, 2330439864, 1625790112, 106505, "SRX25008883", "SRS21709102", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.60941, 0.31539, 0.0377, 0.09053, 0.995, 0.99478, 0.50937, 0.57123, 150, 150, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Liver", "Liver and Biliary System"], [32926, "SRR29498570", "SRX25008882", "SRS21709101", "SRP515416", "PRJNA1127032", "Zebrafish Tissue Mid Range RNA Sequencing", "PRJNA1127032", "Other", "This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.", null, null, null, null, "M2b", null, "strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:brain|identifier:M2b|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "midRNA seq Danio rerio", "07", "07", "Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "M2b_R1.fq.gz M2b_R2.fq.gz", "fastq fastq", 9324874800.0, 31082916.0, "M2b R1.fq.gz", "0:150 1:150", "A:2073617286;C:2382074775;G:2948687855;T:1920389281;N:105603", 150, 150, null, null, 2073617286, 2382074775, 2948687855, 1920389281, 105603, "SRX25008882", "SRS21709101", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.57388, 0.29571, 0.04187, 0.10168, 0.99506, 0.99513, 0.61677, 0.60641, 150, 150, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Brain", "Nervous System"], [32927, "SRR29498571", "SRX25008881", "SRS21709100", "SRP515416", "PRJNA1127032", "Zebrafish Tissue Mid Range RNA Sequencing", "PRJNA1127032", "Other", "This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.", null, null, null, null, "M1l", null, "strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:liver|identifier:M1l|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "midRNA seq Danio rerio", "06", "06", "Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "M1l_R2.fq.gz M1l_R1.fq.gz", "fastq fastq", 8301268800.0, 27670896.0, "M1l R1.fq.gz", "0:150 1:150", "A:1856070257;C:2266693166;G:2413641098;T:1764769457;N:94822", 150, 150, null, null, 1856070257, 2266693166, 2413641098, 1764769457, 94822, "SRX25008881", "SRS21709100", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.8289, 0.73852, 0.21964, 0.50932, 0.99648, 0.99701, 0.57332, 0.51129, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Liver", "Liver and Biliary System"], [32928, "SRR29498572", "SRX25008880", "SRS21709099", "SRP515416", "PRJNA1127032", "Zebrafish Tissue Mid Range RNA Sequencing", "PRJNA1127032", "Other", "This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.", null, null, null, null, "M1b", null, "strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:brain|identifier:M1b|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "midRNA seq Danio rerio", "05", "05", "Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "M1b_R1.fq.gz M1b_R2.fq.gz", "fastq fastq", 7947472800.0, 26491576.0, "M1b R1.fq.gz", "0:150 1:150", "A:1764190500;C:1937842699;G:2595509352;T:1649839967;N:90282", 150, 150, null, null, 1764190500, 1937842699, 2595509352, 1649839967, 90282, "SRX25008880", "SRS21709099", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.96542, 0.21476, 0.17288, 0.05982, 0.97289, 0.99711, 0.57845, 0.611, 150, 150, "B", "T", "mate2 technical by mapping diff", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Brain", "Nervous System"], [32929, "SRR29498573", "SRX25008879", "SRS21709098", "SRP515416", "PRJNA1127032", "Zebrafish Tissue Mid Range RNA Sequencing", "PRJNA1127032", "Other", "This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.", null, null, null, null, "F2l", null, "strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:liver|identifier:F2l|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "midRNA seq Danio rerio", "04", "04", "Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "F2l_R1.fq.gz F2l_R2.fq.gz", "fastq fastq", 8701893900.0, 29006313.0, "F2l R1.fq.gz", "0:150 1:150", "A:1977580339;C:2299061131;G:2585058451;T:1840095650;N:98329", 150, 150, null, null, 1977580339, 2299061131, 2585058451, 1840095650, 98329, "SRX25008879", "SRS21709098", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.72425, 0.57704, 0.15111, 0.37121, 0.99744, 0.99762, 0.61161, 0.55762, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Liver", "Liver and Biliary System"], [32930, "SRR29498574", "SRX25008878", "SRS21709097", "SRP515416", "PRJNA1127032", "Zebrafish Tissue Mid Range RNA Sequencing", "PRJNA1127032", "Other", "This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.", null, null, null, null, "F2b", null, "strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:brain|identifier:F2b|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "midRNA seq Danio rerio", "03", "03", "Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "F2b_R1.fq.gz F2b_R2.fq.gz", "fastq fastq", 9249410100.0, 30831367.0, "F2b R1.fq.gz", "0:150 1:150", "A:2101671138;C:2272479255;G:2931272789;T:1943881150;N:105768", 150, 150, null, null, 2101671138, 2272479255, 2931272789, 1943881150, 105768, "SRX25008878", "SRS21709097", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.96654, 0.19343, 0.23127, 0.08081, 0.95272, 0.99326, 0.63762, 0.64901, 150, 150, "B", "T", "mate2 technical by mapping diff", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Brain", "Nervous System"], [32931, "SRR29498575", "SRX25008877", "SRS21709096", "SRP515416", "PRJNA1127032", "Zebrafish Tissue Mid Range RNA Sequencing", "PRJNA1127032", "Other", "This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.", null, null, null, null, "M2g", null, "strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:gut|identifier:M2g|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "midRNA seq Danio rerio", "12", "12", "Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "M2g_R1.fq.gz M2g_R2.fq.gz", "fastq fastq", 7106243100.0, 23687477.0, "M2g R1.fq.gz", "0:150 1:150", "A:1567154123;C:1866065312;G:2213286944;T:1459656676;N:80045", 150, 150, null, null, 1567154123, 1866065312, 2213286944, 1459656676, 80045, "SRX25008877", "SRS21709096", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.56476, 0.25026, 0.02259, 0.04481, 0.99667, 0.99701, 0.63277, 0.65693, 150, 150, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Gut", "Digestive System"], [32932, "SRR29498576", "SRX25008876", "SRS21709095", "SRP515416", "PRJNA1127032", "Zebrafish Tissue Mid Range RNA Sequencing", "PRJNA1127032", "Other", "This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.", null, null, null, null, "M1g", null, "strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:gut|identifier:M1g|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "midRNA seq Danio rerio", "11", "11", "Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "M1g_R2.fq.gz M1g_R1.fq.gz", "fastq fastq", 7351182000.0, 24503940.0, "M1g R1.fq.gz", "0:150 1:150", "A:1623685246;C:1858847576;G:2315396486;T:1553169371;N:83321", 150, 150, null, null, 1623685246, 1858847576, 2315396486, 1553169371, 83321, "SRX25008876", "SRS21709095", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.96004, 0.21521, 0.16113, 0.04578, 0.92431, 0.99143, 0.61867, 0.63432, 150, 150, "B", "T", "mate2 technical by mapping diff", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Gut", "Digestive System"], [32933, "SRR29498577", "SRX25008875", "SRS21709094", "SRP515416", "PRJNA1127032", "Zebrafish Tissue Mid Range RNA Sequencing", "PRJNA1127032", "Other", "This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.", null, null, null, null, "F1l", null, "strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:liver|identifier:F1l|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "midRNA seq Danio rerio", "02", "02", "Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "F1l_R2.fq.gz F1l_R1.fq.gz", "fastq fastq", 4647564000.0, 15491880.0, "F1l R1.fq.gz", "0:150 1:150", "A:993332389;C:862184908;G:1814249126;T:977710185;N:87392", 150, 150, null, null, 993332389, 862184908, 1814249126, 977710185, 87392, "SRX25008875", "SRS21709094", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.88683, 0.14922, 0.24654, 0.08178, 0.9583, 0.99819, 0.70978, 0.20254, 150, 150, "B", "T", "mate2 technical by mapping diff", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Liver", "Liver and Biliary System"], [32934, "SRR29498578", "SRX25008874", "SRS21709093", "SRP515416", "PRJNA1127032", "Zebrafish Tissue Mid Range RNA Sequencing", "PRJNA1127032", "Other", "This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.", null, null, null, null, "F1b", null, "strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:brain|identifier:F1b|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "midRNA seq Danio rerio", "01", "01", "Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "F1b_R2.fq.gz F1b_R1.fq.gz", "fastq fastq", 7995852300.0, 26652841.0, "F1b R1.fq.gz", "0:150 1:150", "A:1744452113;C:2053788787;G:2580416325;T:1617104387;N:90688", 150, 150, null, null, 1744452113, 2053788787, 2580416325, 1617104387, 90688, "SRX25008874", "SRS21709093", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.96107, 0.17798, 0.16452, 0.02921, 0.96759, 0.99677, 0.66455, 0.62672, 150, 150, "B", "T", "mate2 technical by mapping diff", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Brain", "Nervous System"], [40707, "SRR3502888", "SRX1760541", "SRS1436386", "SRP072296", "PRJNA316313", "Codon optimality and mRNA decay in zebrafish and Xenopus", "PRJNA316313", "Other", "Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved \u201ccodon optimality code\u201d that shapes mRNA stability and translation efficiency across vertebrates.", null, null, null, "Zebrafish tRNA at 6hpf", "tRNA AB 6h", null, "strain:TUAB|age:6hpf|dev stage:Shield|sex:pooled male and female|tissue:Whole animal|collected by:Ariel Bazzini|genotype:WT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish tRNAs at 6hpf", "tRNA 6hpf zebrafish", "TGIRT tRNA Library", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP072296", null, null, "AB-tRNA_S9_R1_001.fastq.gz AB-tRNA_S9_R2_001.fastq.gz", "fastq fastq", 7860522000.0, 26201740.0, "tRNA zebrafish 6hpf", "0:150 1:150", "A:1945184302;C:2012637521;G:2171934357;T:1730625218;N:140602", 150, 150, null, null, 1945184302, 2012637521, 2171934357, 1730625218, 140602, "SRX1760541", "SRS1436386", "SRA395141", "Yale University|Giraldez Lab", "Yale University", 2, 0.04186, 0.04313, 0.00633, 0.00639, 0.96834, 0.96913, 0.53967, 0.5329, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-17", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [41348, "SRR4302022", "SRX2194190", "SRS1716514", "SRP090540", "PRJNA344550", "Danio rerio strain:AB Raw sequence reads", "PRJNA344550", "Whole Genome Sequencing", "Identification of circular RNAs in zebrafish", null, "pubmed:27878987", null, null, "Zebrafish circRNA", null, "strain:AB|age:Adult|sex:pooled male and female|tissue:brain  eyes  heart  liver  spleen  kidney  intestines  skin  muscle  gill  ovary  testis|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Identification of circular RNAs in zebrafish", "Zebrafish circRNAs", "Key Lab of Agricultural Animal Genetics", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP090540", null, null, "MIX_R1.fastq.gz MIX_R2.fastq.gz", "fastq fastq", 21319208400.0, 71064028.0, "Zebrafish circRNAs", "0:150 1:150", "A:4973737880;C:5734846860;G:5920594296;T:4689011877;N:1017487", 150, 150, null, null, 4973737880, 5734846860, 5920594296, 4689011877, 1017487, "SRX2194190", "SRS1716514", "SRA480645", "Huazhong Agricultural University|Key Lab of Agricultural Animal Genetics", "Huazhong Agricultural University", 2, 0.89959, 0.92292, 0.28429, 0.27588, 0.87207, 0.86866, 0.65238, 0.78485, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2016-11-28", "Adult", "Adult", "Multi-tissue", "Multi-system"], [42495, "SRR5666979", "SRX2902577", "SRS2269173", "SRP108989", "PRJNA390119", "HLX & Hematopoiesis", "PRJNA390119", "Other", "HLX &amp; Hematopoiesis", null, null, "rnaseq and atacseq", "hlx hematopoiesis", "hlx", null, "isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "kdrl GFP cells hlx1  MO rep2", "3", "kdrl GFP cells hlx1  MO rep2", "SMART SEQ ultra low RNA seq kit Clonetech", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP108989", null, "assembly:danRer10", "flk_gfp_hlx_8ng_48hrs_2_R1.fastq.gz flk_gfp_hlx_8ng_48hrs_2_R2.fastq.gz", "fastq fastq", 1887289200.0, 12581928.0, "flk gfp hlx 8ng 48hrs 2 R1.fastq.gz", "0:75 1:75", "A:493825524;C:448630716;G:436118597;T:508410442;N:303921", 75, 75, null, null, 493825524, 448630716, 436118597, 508410442, 303921, "SRX2902577", "SRS2269173", "SRA573518", "BRFAA|Molecular Biology", "BRFAA", 2, 0.9202, 0.9216, 0.09499, 0.09558, 0.73805, 0.73878, 0.48809, 0.48787, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Greece", "2017-06-13", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [42496, "SRR5666980", "SRX2902576", "SRS2269173", "SRP108989", "PRJNA390119", "HLX & Hematopoiesis", "PRJNA390119", "Other", "HLX &amp; Hematopoiesis", null, null, "rnaseq and atacseq", "hlx hematopoiesis", "hlx", null, "isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "kdrl GFP cells hlx1  MO rep1", "2", "kdrl GFP cells hlx1  MO rep1", "SMART SEQ ultra low RNA seq kit Clonetech", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP108989", null, "assembly:danRer10", "flk_gfp_hlx_8ng_48hrs_1_R1.fastq.gz flk_gfp_hlx_8ng_48hrs_1_R2.fastq.gz", "fastq fastq", 1561083900.0, 10407226.0, "flk gfp hlx 8ng 48hrs 1 R2.fastq.gz", "0:75 1:75", "A:412744284;C:366776465;G:356834742;T:424473871;N:254538", 75, 75, null, null, 412744284, 366776465, 356834742, 424473871, 254538, "SRX2902576", "SRS2269173", "SRA573518", "BRFAA|Molecular Biology", "BRFAA", 2, 0.9172, 0.91824, 0.09957, 0.09961, 0.73965, 0.73975, 0.48906, 0.48977, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Greece", "2017-06-13", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [42497, "SRR5666981", "SRX2902575", "SRS2269173", "SRP108989", "PRJNA390119", "HLX & Hematopoiesis", "PRJNA390119", "Other", "HLX &amp; Hematopoiesis", null, null, "rnaseq and atacseq", "hlx hematopoiesis", "hlx", null, "isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "kdrl GFP cells control 2", "1", "kdrl GFP cells control 2", "SMART SEQ ultra low RNA seq kit Clonetech", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application 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[42498, "SRR5666982", "SRX2902574", "SRS2269173", "SRP108989", "PRJNA390119", "HLX & Hematopoiesis", "PRJNA390119", "Other", "HLX &amp; Hematopoiesis", null, null, "rnaseq and atacseq", "hlx hematopoiesis", "hlx", null, "isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "kdrl GFP cells control 1", "0", "kdrl GFP cells control 1", "SMART SEQ ultra low RNA seq kit Clonetech", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP108989", null, "assembly:danRer10", "flk_gfp_48hrs_con1_R2.fastq.gz flk_gfp_48hrs_con1_R1.fastq.gz", "fastq fastq", 1678987200.0, 11193248.0, "flk gfp 48hrs con1 R2.fastq.gz", "0:75 1:75", "A:437283407;C:401234553;G:387947515;T:452257282;N:264443", 75, 75, null, null, 437283407, 401234553, 387947515, 452257282, 264443, "SRX2902574", "SRS2269173", "SRA573518", "BRFAA|Molecular Biology", "BRFAA", 2, 0.91593, 0.91737, 0.08937, 0.08988, 0.75607, 0.75696, 0.50103, 0.45539, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Greece", "2017-06-13", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [42499, "SRR5666985", "SRX2902571", "SRS2269173", "SRP108989", "PRJNA390119", "HLX & Hematopoiesis", "PRJNA390119", "Other", "HLX &amp; Hematopoiesis", null, null, "rnaseq and atacseq", "hlx hematopoiesis", "hlx", null, "isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "fli GFP cells hHLXOE rep 2", "5", "fli GFP cells hHLXOE rep 2", "SMART SEQ ultra low RNA seq kit Clonetech", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP108989", null, "assembly:danRer10", "fli_gal4_uas_hlx_endo_48h_s2_R2.fastq.gz fli_gal4_uas_hlx_endo_48h_s2_R1.fastq.gz", "fastq fastq", 4490898450.0, 29939323.0, "fli gal4 uas hlx endo 48h s2 R2.fastq.gz", "0:75 1:75", "A:870349076;C:1346136891;G:1401796534;T:869066463;N:3549486", 75, 75, null, null, 870349076, 1346136891, 1401796534, 869066463, 3549486, "SRX2902571", "SRS2269173", "SRA573518", "BRFAA|Molecular Biology", "BRFAA", 2, 0.5714, 0.57344, 0.27957, 0.28321, 0.85102, 0.85342, 0.53304, 0.53368, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Greece", "2017-06-13", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [42500, "SRR5666986", "SRX2902570", "SRS2269173", "SRP108989", "PRJNA390119", "HLX & Hematopoiesis", "PRJNA390119", "Other", "HLX &amp; Hematopoiesis", null, null, "rnaseq and atacseq", "hlx hematopoiesis", "hlx", null, "isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "fli GFP cells hHLXOE rep 1", "4", "fli GFP cells hHLXOE rep 1", "SMART SEQ ultra low RNA seq kit Clonetech", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP108989", null, "assembly:danRer10", "fli_gal4_uas_hlx_endo_48h_s1_R1.fastq.gz fli_gal4_uas_hlx_endo_48h_s1_R2.fastq.gz", "fastq fastq", 3459602100.0, 23064014.0, "fli gal4 uas hlx endo 48h s1 R1.fastq.gz", "0:75 1:75", "A:658343595;C:1050309687;G:1097759573;T:650443491;N:2745754", 75, 75, null, null, 658343595, 1050309687, 1097759573, 650443491, 2745754, "SRX2902570", "SRS2269173", "SRA573518", "BRFAA|Molecular Biology", "BRFAA", 2, 0.57077, 0.57481, 0.2173, 0.2185, 0.79553, 0.79762, 0.50405, 0.48708, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Greece", "2017-06-13", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [48625, "SRR7280652", "SRX4184230", "SRS3395609", "SRP149913", "PRJNA474911", "Origin and Evolution of Neural Microexons", "PRJNA474911", "Other", "Our study focuses on the origin of the neural microexon program.We discover that neural microexon programs are present in non vertebrate speciesand trace their origin to bilaterian ancestors through the emergenceof a previously uncharacterized \"enhancer of microexon\" eMIC protein domain", null, null, null, "Telencephalon", "Brain Telenc", null, "strain:AB|age:adult|sex:pooled male and female|tissue:Telencephalon|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: telencephalon", "Brain Telenc", "Brain Telenc", "RNA from dissociated telencephalons of males and females", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP149913", null, null, "Brain_Telenc_R1-125.fq.gz Brain_Telenc_R2-125.fq.gz", "fastq fastq", 71366993000.0, 285467972.0, "Brain Telenc R1 125.fq.gz", "0:125 1:125", "A:19965884492;C:15794543428;G:15865015134;T:19703234174;N:38315772", 125, 125, null, null, 19965884492, 15794543428, 15865015134, 19703234174, 38315772, "SRX4184230", "SRS3395609", "SRA717220", "Centre for Genomic Regulation|Systems Biology Department", "Centre for Genomic Regulation", 2, 0.94146, 0.94273, 0.14194, 0.14162, 0.70167, 0.70396, 0.52125, 0.51616, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2019-01-22", "Adult", "Adult", "Brain", "Nervous System"], [48626, "SRR7280653", "SRX4184229", "SRS3395610", "SRP149913", "PRJNA474911", "Origin and Evolution of Neural Microexons", "PRJNA474911", "Other", "Our study focuses on the origin of the neural microexon program.We discover that neural microexon programs are present in non vertebrate speciesand trace their origin to bilaterian ancestors through the emergenceof a previously uncharacterized \"enhancer of microexon\" eMIC protein domain", null, null, null, "Cerebellum", "Cerebellum", null, "strain:AB|age:adult|sex:pooled male and female|tissue:Cerebellum|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: cerebellum", "Cerebellum", "Cerebellum", "RNA from dissociated cerebellum from males and females", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP149913", null, null, "Cerebellum_R1-125.fq.gz Cerebellum_R2-125.fq.gz", "fastq fastq", 34135866750.0, 136543467.0, "Cerebellum R2 125.fq.gz", "0:125 1:125", "A:9659073468;C:7434102293;G:7478952142;T:9549216912;N:14521935", 125, 125, null, null, 9659073468, 7434102293, 7478952142, 9549216912, 14521935, "SRX4184229", "SRS3395610", "SRA717220", "Centre for Genomic Regulation|Systems Biology Department", "Centre for Genomic Regulation", 2, 0.93517, 0.93417, 0.16496, 0.16457, 0.73695, 0.73476, 0.47363, 0.48287, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2019-01-22", "Adult", "Adult", "Brain", "Nervous System"], [48627, "SRR7280654", "SRX4184228", "SRS3395608", "SRP149913", "PRJNA474911", "Origin and Evolution of Neural Microexons", "PRJNA474911", "Other", "Our study focuses on the origin of the neural microexon program.We discover that neural microexon programs are present in non vertebrate speciesand trace their origin to bilaterian ancestors through the emergenceof a previously uncharacterized \"enhancer of microexon\" eMIC protein domain", null, null, "Pool of one hundred 2hpf embryos", "2hpf embryos", "Embr 2hpf", null, "strain:AB|dev stage:2hpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: 2hpf embryos", "Embr 2hpf", "Embr 2hpf", "RNA extracted from a pool of one hundred embryos", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP149913", null, null, "Embr_2hpf_R2-125.fq.gz Embr_2hpf_R1-125.fq.gz", "fastq fastq", 17109578000.0, 68438312.0, "Embr 2hpf R1 125.fq.gz", "0:125 1:125", "A:4536550134;C:4009266695;G:4076560218;T:4484964079;N:2236874", 125, 125, null, null, 4536550134, 4009266695, 4076560218, 4484964079, 2236874, "SRX4184228", "SRS3395608", "SRA717220", "Centre for Genomic Regulation|Systems Biology Department", "Centre for Genomic Regulation", 2, 0.96221, 0.96458, 0.02765, 0.02716, 0.77116, 0.77325, 0.48649, 0.4853, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2019-01-22", "Cleavage", "Embryo", "Trunk", "Surface Structure"], [48628, "SRR7280655", "SRX4184227", "SRS3395607", "SRP149913", "PRJNA474911", "Origin and Evolution of Neural Microexons", "PRJNA474911", "Other", "Our study focuses on the origin of the neural microexon program.We discover that neural microexon programs are present in non vertebrate speciesand trace their origin to bilaterian ancestors through the emergenceof a previously uncharacterized \"enhancer of microexon\" eMIC protein domain", null, null, "Pool of one hundred 8hpf embryos", "8hpf embryos", "Embr 8hpf", null, "strain:AB|dev stage:8hpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: 8hpf embryos", "Embr 8hpf", "Embr 8hpf", "RNA extracted from a pool of one hundred embryos", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP149913", null, null, "Embr_8hpf_R1-125.fq.gz Embr_8hpf_R2-125.fq.gz", "fastq fastq", 20486524750.0, 81946099.0, "Embr 8hpf R2 125.fq.gz", "0:125 1:125", "A:5437735333;C:4808439456;G:4859422420;T:5377132981;N:3794560", 125, 125, null, null, 5437735333, 4808439456, 4859422420, 5377132981, 3794560, "SRX4184227", "SRS3395607", "SRA717220", "Centre for Genomic Regulation|Systems Biology Department", "Centre for Genomic Regulation", 2, 0.96373, 0.95763, 0.07096, 0.0702, 0.75937, 0.75866, 0.48455, 0.484, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2019-01-22", "Gastrula", "Embryo", "Trunk", "Surface Structure"], [48629, "SRR7280656", "SRX4184226", "SRS3395606", "SRP149913", "PRJNA474911", "Origin and Evolution of Neural Microexons", "PRJNA474911", "Other", "Our study focuses on the origin of the neural microexon program.We discover that neural microexon programs are present in non vertebrate speciesand trace their origin to bilaterian ancestors through the emergenceof a previously uncharacterized \"enhancer of microexon\" eMIC protein domain", null, null, "Pool of one hundred 12hpf embryos", "12hpf embryos", "Embr 12hpf", null, "strain:AB|dev stage:12hpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: 12hpf embryos", "Embr 12hpf", "Embr 12hpf", "RNA extracted from a pool of one hundred embryos", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP149913", null, null, "Embr_12hpf_R2-125.fq.gz Embr_12hpf_R1-125.fq.gz", "fastq fastq", 22366284500.0, 89465138.0, "Embr 12hpf R1 125.fq.gz", "0:125 1:125", "A:5886492098;C:5284016845;G:5382041408;T:5809628253;N:4105896", 125, 125, null, null, 5886492098, 5284016845, 5382041408, 5809628253, 4105896, "SRX4184226", "SRS3395606", "SRA717220", "Centre for Genomic Regulation|Systems Biology Department", "Centre for Genomic Regulation", 2, 0.96226, 0.96763, 0.06393, 0.06451, 0.74355, 0.74472, 0.48233, 0.48387, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2019-01-22", "Segmentation", "Embryo", "Trunk", "Surface Structure"], [49091, "SRR7666344", "SRX4527573", "SRS3645455", "SRP157045", "PRJNA485433", "Diurnal transcriptome of adult zebrafish eye", "PRJNA485433", "Other", "Circadian rhythms orchestrate organism physiology to rhythmic changes in the environment  with the daily day and night cycle being the most prominent cyclic change occurring. In this regard  retina being a light responsive organ shows its vital physiological processes to be regulated by the clock. Here we report the diurnal transcriptome of zebrafish retina at Zt4day and Zt16night. We found 39% and 31% of the known genes to be expressed in retina at Zt4 and Zt16 respectively Reference genome Zv9. Also  by applying stringent cutoff of 5FPKM we identified 123 transcripts to be expressed differentially between the two time points  which contains few novel transcripts. In future  this study will contribute to the understanding of organ and species specific regulation of circadian rhythms and will also provide novel genes involved in the circadian regulation of retina.", null, null, null, null, "ZT4", null, "strain:Assam wild type|age:>3 month|dev stage:adult|sex:pooled male and female|tissue:eye|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "diurnal trancriptome of retina", "ZT4 101nt", "ZT4 101nt", "total transcriptome with Truseq stranded library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP157045", null, null, "ZF_Eye_CT4_gt50_R1_P.fastq ZF_Eye_CT4_gt50_R2_P.fastq", "fastq fastq", 4550334348.0, 22527137.0, "ZF Eye CT4 gt50 R1 P.fastq", "0:101.00 1:101.00", "A:1196463938;C:1068045211;G:1064853438;T:1220233324;N:738437", 101, 101, null, null, 1196463938, 1068045211, 1064853438, 1220233324, 738437, "SRX4527573", "SRS3645455", "SRA756783", "CSIR Insitute of Genomics and Integrative Biology|Functional Genomics", "CSIR Insitute of Genomics and Integrative Biology", 2, 0.92663, 0.92909, 0.33125, 0.32333, 0.70197, 0.7013, 0.55991, 0.52684, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "India", "2018-12-27", "Adult", "Adult", "Eye", "Sensory System"], [49092, "SRR7666345", "SRX4527572", "SRS3645456", "SRP157045", "PRJNA485433", "Diurnal transcriptome of adult zebrafish eye", "PRJNA485433", "Other", "Circadian rhythms orchestrate organism physiology to rhythmic changes in the environment  with the daily day and night cycle being the most prominent cyclic change occurring. In this regard  retina being a light responsive organ shows its vital physiological processes to be regulated by the clock. Here we report the diurnal transcriptome of zebrafish retina at Zt4day and Zt16night. We found 39% and 31% of the known genes to be expressed in retina at Zt4 and Zt16 respectively Reference genome Zv9. Also  by applying stringent cutoff of 5FPKM we identified 123 transcripts to be expressed differentially between the two time points  which contains few novel transcripts. In future  this study will contribute to the understanding of organ and species specific regulation of circadian rhythms and will also provide novel genes involved in the circadian regulation of retina.", null, null, null, null, "ZT16", null, "strain:Assam wild type|age:>3months|dev stage:adult|sex:pooled male and female|tissue:eye|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "diurnal transcriptome of retina", "ZT16 101nt", "ZT16 101nt", "total transcriptome with Truseq stranded library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP157045", null, null, "ZF_Eye_CT016_gt50_R1_P.fastq ZF_Eye_CT016_gt50_R2_P.fastq", "fastq fastq", 14656436974.0, 72560331.0, "ZF Eye CT016 gt50 R1 P.fastq", "0:100.99 1:100.99", "A:3573626926;C:3724443056;G:3714836422;T:3641178568;N:2352002", 100, 100, null, null, 3573626926, 3724443056, 3714836422, 3641178568, 2352002, "SRX4527572", "SRS3645456", "SRA756783", "CSIR Insitute of Genomics and Integrative Biology|Functional Genomics", "CSIR Insitute of Genomics and Integrative Biology", 2, 0.917, 0.91899, 0.27178, 0.261, 0.72135, 0.72082, 0.63885, 0.63571, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "India", "2018-08-10", "Adult", "Adult", "Eye", "Sensory System"], [49332, "SRR7888761", "SRX4726390", "SRS3810123", "SRP162319", "PRJNA492406", "Profiles analysis reveals circRNAs involving zebrafish physiological development", "GSE120289", "Transcriptome Analysis", "Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins  modulation of transcription and interference with splicing  and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development  further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period  gastrula period  segmentation period  throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes  then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways  cardiovascular system development  retinal ganglion cell axon guidance and so on. Moreover  circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b  miR 124 and so on  some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points  suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula  gastrula  segmentation  throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500.", null, null, null, "72h", "GSM3397729", null, "source name:Embryo|tissue:Embryo|age:72 hpf|developmental stage:incubation|strain:Tubingenz|genotype:WT", "72h", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters \"mem  T 19\". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs  raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC \u22652 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample.", "Embryo", "Zebrafish were reared at 28\u00b11\u2103 in a water circulatory system that osmotic pressure stability  UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5\u00b10.5\u2103. Morphological features were used to judge the stage of embryonic development.", "Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer\u2019s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer\u2019s instructions Illumina", null, "tissue:Embryo|age:72 hpf|developmental stage:incubation|strain:Tubingenz|genotype:WT", "GSM3397729", "GSM3397729: 72h; Danio rerio; ncRNA Seq", "GSM3397729", null, "1", "Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina", "GEO Accession:GSM3397729", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162319", null, null, "72h_1.fq.gz 72h_2.fq.gz", "fastq fastq", 12097159200.0, 40323864.0, "GSM3397729 r1", "0:150 1:150", "A:2809307023;C:3169515166;G:3184429517;T:2931448896;N:2458598", 150, 150, null, null, 2809307023, 3169515166, 3184429517, 2931448896, 2458598, "SRX4726390", "SRS3810123", "SRA781248", "GEO", "Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital", 2, 0.90426, 0.90717, 0.27165, 0.26439, 0.70739, 0.72397, 0.60155, 0.60561, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-09-21", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [49333, "SRR7888760", "SRX4726389", "SRS3810122", "SRP162319", "PRJNA492406", "Profiles analysis reveals circRNAs involving zebrafish physiological development", "GSE120289", "Transcriptome Analysis", "Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins  modulation of transcription and interference with splicing  and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development  further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period  gastrula period  segmentation period  throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes  then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways  cardiovascular system development  retinal ganglion cell axon guidance and so on. Moreover  circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b  miR 124 and so on  some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points  suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula  gastrula  segmentation  throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500.", null, null, null, "48h", "GSM3397728", null, "source name:Embryo|tissue:Embryo|age:48 hpf|developmental stage:throat|strain:Tubingenz|genotype:WT", "48h", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters \"mem  T 19\". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs  raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC \u22652 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample.", "Embryo", "Zebrafish were reared at 28\u00b11\u2103 in a water circulatory system that osmotic pressure stability  UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5\u00b10.5\u2103. Morphological features were used to judge the stage of embryonic development.", "Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer\u2019s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer\u2019s instructions Illumina", null, "tissue:Embryo|age:48 hpf|developmental stage:throat|strain:Tubingenz|genotype:WT", "GSM3397728", "GSM3397728: 48h; Danio rerio; ncRNA Seq", "GSM3397728", null, "1", "Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina", "GEO Accession:GSM3397728", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162319", null, null, "48h_2.fq.gz 48h_1.fq.gz", "fastq fastq", 13525174500.0, 45083915.0, "GSM3397728 r1", "0:150 1:150", "A:2352542664;C:4312268007;G:4256218842;T:2601416951;N:2728036", 150, 150, null, null, 2352542664, 4312268007, 4256218842, 2601416951, 2728036, "SRX4726389", "SRS3810122", "SRA781248", "GEO", "Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital", 2, 0.91614, 0.91412, 0.12891, 0.12218, 0.76751, 0.77948, 0.71008, 0.73648, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-09-21", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [49334, "SRR7888759", "SRX4726388", "SRS3810120", "SRP162319", "PRJNA492406", "Profiles analysis reveals circRNAs involving zebrafish physiological development", "GSE120289", "Transcriptome Analysis", "Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins  modulation of transcription and interference with splicing  and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development  further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period  gastrula period  segmentation period  throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes  then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways  cardiovascular system development  retinal ganglion cell axon guidance and so on. Moreover  circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b  miR 124 and so on  some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points  suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula  gastrula  segmentation  throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500.", null, null, null, "24h", "GSM3397727", null, "source name:Embryo|tissue:Embryo|age:24 hpf|developmental stage:segmentation|strain:Tubingenz|genotype:WT", "24h", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters \"mem  T 19\". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs  raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC \u22652 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample.", "Embryo", "Zebrafish were reared at 28\u00b11\u2103 in a water circulatory system that osmotic pressure stability  UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5\u00b10.5\u2103. Morphological features were used to judge the stage of embryonic development.", "Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer\u2019s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer\u2019s instructions Illumina", null, "tissue:Embryo|age:24 hpf|developmental stage:segmentation|strain:Tubingenz|genotype:WT", "GSM3397727", "GSM3397727: 24h; Danio rerio; ncRNA Seq", "GSM3397727", null, "1", "Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina", "GEO Accession:GSM3397727", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162319", null, null, "24h_1.fq.gz 24h_2.fq.gz", "fastq fastq", 14333175000.0, 47777250.0, "GSM3397727 r1", "0:150 1:150", "A:2728754113;C:4276840070;G:4344116037;T:2980570245;N:2894535", 150, 150, null, null, 2728754113, 4276840070, 4344116037, 2980570245, 2894535, "SRX4726388", "SRS3810120", "SRA781248", "GEO", "Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital", 2, 0.89719, 0.89478, 0.18044, 0.18119, 0.76942, 0.7876, 0.75758, 0.75366, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-09-21", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [49335, "SRR7888758", "SRX4726387", "SRS3810121", "SRP162319", "PRJNA492406", "Profiles analysis reveals circRNAs involving zebrafish physiological development", "GSE120289", "Transcriptome Analysis", "Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins  modulation of transcription and interference with splicing  and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development  further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period  gastrula period  segmentation period  throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes  then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways  cardiovascular system development  retinal ganglion cell axon guidance and so on. Moreover  circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b  miR 124 and so on  some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points  suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula  gastrula  segmentation  throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500.", null, null, null, "8h", "GSM3397726", null, "source name:Embryo|tissue:Embryo|age:8 hpf|developmental stage:gastrula|strain:Tubingenz|genotype:WT", "8h", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters \"mem  T 19\". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs  raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC \u22652 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample.", "Embryo", "Zebrafish were reared at 28\u00b11\u2103 in a water circulatory system that osmotic pressure stability  UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5\u00b10.5\u2103. Morphological features were used to judge the stage of embryonic development.", "Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer\u2019s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer\u2019s instructions Illumina", null, "tissue:Embryo|age:8 hpf|developmental stage:gastrula|strain:Tubingenz|genotype:WT", "GSM3397726", "GSM3397726: 8h; Danio rerio; ncRNA Seq", "GSM3397726", null, "1", "Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina", "GEO Accession:GSM3397726", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162319", null, null, "8h_2.fq.gz 8h_1.fq.gz", "fastq fastq", 15434085600.0, 51446952.0, "GSM3397726 r1", "0:150 1:150", "A:2318158791;C:5134519748;G:5292209580;T:2686084369;N:3113112", 150, 150, null, null, 2318158791, 5134519748, 5292209580, 2686084369, 3113112, "SRX4726387", "SRS3810121", "SRA781248", "GEO", "Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital", 2, 0.95788, 0.95584, 0.07233, 0.07686, 0.81889, 0.82946, 0.81383, 0.80143, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-09-21", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [49336, "SRR7888757", "SRX4726386", "SRS3810119", "SRP162319", "PRJNA492406", "Profiles analysis reveals circRNAs involving zebrafish physiological development", "GSE120289", "Transcriptome Analysis", "Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins  modulation of transcription and interference with splicing  and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development  further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period  gastrula period  segmentation period  throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes  then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways  cardiovascular system development  retinal ganglion cell axon guidance and so on. Moreover  circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b  miR 124 and so on  some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points  suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula  gastrula  segmentation  throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500.", null, null, null, "4.5h", "GSM3397725", null, "source name:Embryo|tissue:Embryo|age:4.5 hpf|developmental stage:blastula|strain:Tubingenz|genotype:WT", "4.5h", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters \"mem  T 19\". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs  raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC \u22652 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample.", "Embryo", "Zebrafish were reared at 28\u00b11\u2103 in a water circulatory system that osmotic pressure stability  UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5\u00b10.5\u2103. Morphological features were used to judge the stage of embryonic development.", "Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer\u2019s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer\u2019s instructions Illumina", null, "tissue:Embryo|age:4.5 hpf|developmental stage:blastula|strain:Tubingenz|genotype:WT", "GSM3397725", "GSM3397725: 4.5h; Danio rerio; ncRNA Seq", "GSM3397725", null, "1", "Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina", "GEO Accession:GSM3397725", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162319", null, null, "4_5h_2.fq.gz 4_5h_1.fq.gz", "fastq fastq", 12988242600.0, 43294142.0, "GSM3397725 r1", "0:150 1:150", "A:2232301074;C:3998769528;G:4233380689;T:2521224783;N:2566526", 150, 150, null, null, 2232301074, 3998769528, 4233380689, 2521224783, 2566526, "SRX4726386", "SRS3810119", "SRA781248", "GEO", "Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital", 2, 0.96961, 0.96817, 0.05627, 0.05463, 0.77068, 0.78198, 0.74899, 0.75759, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-09-21", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [53507, "SRR9899207", "SRX6651058", "SRS5212730", "SRP217299", "PRJNA558506", "Bmpr2b mutant zebrafish sequencing", "PRJNA558506", "Other", "In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.", null, null, null, null, "zebrafish bmpr2b mutant", null, "strain:AB zebrafish|isolate:mutant|breed:zebrafish|cultivar:zebrafish|ecotype:Wuhan  China|age:15 days|dev stage:larval fish|sex:unknown|tissue:skeleton  muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of mutant fish", "mutant1", "mutant1", "Total RNA was isolated from the 15 dpf dpf bmpr2b mutant larval fishes using RNAiso Plus Reagent TaKaRa  China according to the manufacturers protocol. post RNA quality and quantity control  the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP217299", null, null, "m1_1.fq.gz m1_2.fq.gz", "fastq fastq", 8332769700.0, 27775899.0, "m1 1.fq.gz", "0:150 1:150", "A:2157086519;C:2009631895;G:2036110721;T:2129846686;N:93879", 150, 150, null, null, 2157086519, 2009631895, 2036110721, 2129846686, 93879, "SRX6651058", "SRS5212730", "SRA932406", "Huazhong Agricultural University|College of Fisheries, Key Lab of Freshwater Animal", "Huazhong Agricultural University", 2, 0.95476, 0.95486, 0.06414, 0.06413, 0.66115, 0.66156, 0.47619, 0.47307, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "China", "2019-08-03", "Larval", "Larval", "Muscle", "Muscular System"], [53508, "SRR9899208", "SRX6651057", "SRS5212731", "SRP217299", "PRJNA558506", "Bmpr2b mutant zebrafish sequencing", "PRJNA558506", "Other", "In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.", null, null, null, null, "zebrafish wild", null, "strain:AB zebrafish|isolate:wild fish|breed:zebrafish|cultivar:zebrafish|ecotype:Wuhan  China|age:15 days|dev stage:larval fish|sex:unknown|tissue:skeleton  muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of wild fish", "wild3", "wild3", "Total RNA was isolated from the 15 dpf dpf wild larval fishes using RNAiso Plus Reagent TaKaRa  China according to the manufacturers protocol. post RNA quality and quantity control  the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP217299", null, null, "w3_1.fq.gz w3_2.fq.gz", "fastq fastq", 8715170100.0, 29050567.0, "w3 1.fq.gz", "0:150 1:150", "A:2265881414;C:2090871457;G:2123814411;T:2234503490;N:99328", 150, 150, null, null, 2265881414, 2090871457, 2123814411, 2234503490, 99328, "SRX6651057", "SRS5212731", "SRA932406", "Huazhong Agricultural University|College of Fisheries, Key Lab of Freshwater Animal", "Huazhong Agricultural University", 2, 0.95085, 0.95146, 0.06684, 0.0667, 0.65886, 0.6588, 0.47356, 0.48005, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "China", "2019-08-03", "Larval", "Larval", "Muscle", "Muscular System"], [53509, "SRR9899209", "SRX6651056", "SRS5212731", "SRP217299", "PRJNA558506", "Bmpr2b mutant zebrafish sequencing", "PRJNA558506", "Other", "In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.", null, null, null, null, "zebrafish wild", null, "strain:AB zebrafish|isolate:wild fish|breed:zebrafish|cultivar:zebrafish|ecotype:Wuhan  China|age:15 days|dev stage:larval fish|sex:unknown|tissue:skeleton  muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of wild fish", "wild2", "wild2", "Total RNA was isolated from the 15 dpf dpf wild larval fishes using RNAiso Plus Reagent TaKaRa  China according to the manufacturers protocol. post RNA quality and quantity control  the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP217299", null, null, "w2_1.fq.gz w2_2.fq.gz", "fastq fastq", 9346269600.0, 31154232.0, "w2 1.fq.gz", "0:150 1:150", "A:2421899244;C:2254190061;G:2283375277;T:2386698720;N:106298", 150, 150, null, null, 2421899244, 2254190061, 2283375277, 2386698720, 106298, "SRX6651056", "SRS5212731", "SRA932406", "Huazhong Agricultural University|College of Fisheries, Key Lab of Freshwater Animal", "Huazhong Agricultural University", 2, 0.95445, 0.95603, 0.06361, 0.06276, 0.6616, 0.66121, 0.47635, 0.47716, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "China", "2019-08-03", "Larval", "Larval", "Muscle", "Muscular System"], [53510, "SRR9899210", "SRX6651055", "SRS5212731", "SRP217299", "PRJNA558506", "Bmpr2b mutant zebrafish sequencing", "PRJNA558506", "Other", "In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.", null, null, null, null, "zebrafish wild", null, "strain:AB zebrafish|isolate:wild fish|breed:zebrafish|cultivar:zebrafish|ecotype:Wuhan  China|age:15 days|dev stage:larval fish|sex:unknown|tissue:skeleton  muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of wild fish", "wild1", "wild1", "Total RNA was isolated from the 15 dpf dpf wild larval fishes using RNAiso Plus Reagent TaKaRa  China according to the manufacturers protocol. post RNA quality and quantity control  the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP217299", null, null, "w1_1.fq.gz w1_2.fq.gz", "fastq fastq", 8756101500.0, 29187005.0, "w1 1.fq.gz", "0:150 1:150", "A:2274557262;C:2102935324;G:2133197715;T:2245310628;N:100571", 150, 150, null, null, 2274557262, 2102935324, 2133197715, 2245310628, 100571, "SRX6651055", "SRS5212731", "SRA932406", "Huazhong Agricultural University|College of Fisheries, Key Lab of Freshwater Animal", "Huazhong Agricultural University", 2, 0.95161, 0.95225, 0.06682, 0.06678, 0.65831, 0.65993, 0.47144, 0.47166, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "China", "2019-08-03", "Larval", "Larval", "Muscle", "Muscular System"], [53511, "SRR9899211", "SRX6651054", "SRS5212730", "SRP217299", "PRJNA558506", "Bmpr2b mutant zebrafish sequencing", "PRJNA558506", "Other", "In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.", null, null, null, null, "zebrafish bmpr2b mutant", null, "strain:AB zebrafish|isolate:mutant|breed:zebrafish|cultivar:zebrafish|ecotype:Wuhan  China|age:15 days|dev stage:larval fish|sex:unknown|tissue:skeleton  muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of mutant fish", "mutant3", "mutant3", "Total RNA was isolated from the 15 dpf dpf bmpr2b mutant larval fishes using RNAiso Plus Reagent TaKaRa  China according to the manufacturers protocol. post RNA quality and quantity control  the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP217299", null, null, "m3_1.fq.gz m3_2.fq.gz", "fastq fastq", 8385335400.0, 27951118.0, "m3 1.fq.gz", "0:150 1:150", "A:2179183324;C:2013493686;G:2044351918;T:2148211353;N:95119", 150, 150, null, null, 2179183324, 2013493686, 2044351918, 2148211353, 95119, "SRX6651054", "SRS5212730", "SRA932406", "Huazhong Agricultural University|College of Fisheries, Key Lab of Freshwater Animal", "Huazhong Agricultural University", 2, 0.94884, 0.94904, 0.0643, 0.06403, 0.66145, 0.66316, 0.46951, 0.4767, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "China", "2019-08-03", "Larval", "Larval", "Muscle", "Muscular System"], [53512, "SRR9899212", "SRX6651053", "SRS5212730", "SRP217299", "PRJNA558506", "Bmpr2b mutant zebrafish sequencing", "PRJNA558506", "Other", "In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.", null, null, null, null, "zebrafish bmpr2b mutant", null, "strain:AB zebrafish|isolate:mutant|breed:zebrafish|cultivar:zebrafish|ecotype:Wuhan  China|age:15 days|dev stage:larval fish|sex:unknown|tissue:skeleton  muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of mutant fish", "mutant2", "mutant2", "Total RNA was isolated from the 15 dpf dpf bmpr2b mutant larval fishes using RNAiso Plus Reagent TaKaRa  China according to the manufacturers protocol. post RNA quality and quantity control  the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP217299", null, null, "m2_1.fq.gz m2_2.fq.gz", "fastq fastq", 8728240500.0, 29094135.0, "m2 1.fq.gz", "0:150 1:150", "A:2262292258;C:2101600854;G:2129980194;T:2234266968;N:100226", 150, 150, null, null, 2262292258, 2101600854, 2129980194, 2234266968, 100226, "SRX6651053", "SRS5212730", "SRA932406", "Huazhong Agricultural University|College of Fisheries, Key Lab of Freshwater Animal", "Huazhong Agricultural University", 2, 0.95297, 0.95358, 0.06449, 0.06417, 0.65965, 0.65918, 0.47932, 0.4645, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "China", "2019-08-03", "Larval", "Larval", "Muscle", "Muscular System"], [55379, "SRR10323881", "SRX7034716", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2", "10", "10", "NEBNext Low Input RNA Library Prep Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz", "fastq fastq", 3356658750.0, 22377725.0, "RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz", "0:75 1:75", "A:875300673;C:782517555;G:796855605;T:901672776;N:312141", 75, 75, null, null, 875300673, 782517555, 796855605, 901672776, 312141, "SRX7034716", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.68437, 0.73326, 0.04743, 0.05194, 0.80241, 0.80517, 0.51875, 0.52196, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55380, "SRR10323882", "SRX7034715", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1", "9", "9", "NEBNext Low Input RNA Library Prep Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz", "fastq fastq", 3459242400.0, 23061616.0, "RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz", "0:75 1:75", "A:924400584;C:762078140;G:779330250;T:993109509;N:323917", 75, 75, null, null, 924400584, 762078140, 779330250, 993109509, 323917, "SRX7034715", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.67032, 0.73764, 0.07629, 0.08303, 0.80856, 0.80748, 0.52094, 0.52695, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55381, "SRR10323883", "SRX7034714", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq  mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2", "8", "8", "NEBNext Low Input RNA Library Prep Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz", "fastq fastq", 3238312500.0, 21588750.0, "RNA seq mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz", "0:75 1:75", "A:881635390;C:656958401;G:673596788;T:1025824968;N:296953", 75, 75, null, null, 881635390, 656958401, 673596788, 1025824968, 296953, "SRX7034714", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.59623, 0.72377, 0.07781, 0.08944, 0.80608, 0.8016, 0.53277, 0.53095, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55382, "SRR10323884", "SRX7034713", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq  mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1", "7", "7", "NEBNext Low Input RNA Library Prep Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz", "fastq fastq", 3255021150.0, 21700141.0, "RNA seq mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz", "0:75 1:75", "A:858912760;C:733048670;G:750496371;T:912263495;N:299854", 75, 75, null, null, 858912760, 733048670, 750496371, 912263495, 299854, "SRX7034713", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.65481, 0.71883, 0.05477, 0.05995, 0.7903, 0.7921, 0.51367, 0.51188, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55383, "SRR10323885", "SRX7034712", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. 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We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. 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We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. 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We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq  decitabine treatment in hemogenic endothelial cell 26hpf replicate 2", "24", "24", "NEBNext Low Input RNA Library Prep Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz", "fastq fastq", 5849571450.0, 38997143.0, "RNA seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz", "0:75 1:75", "A:1574421853;C:1316832574;G:1315527058;T:1642305644;N:484321", 75, 75, null, null, 1574421853, 1316832574, 1315527058, 1642305644, 484321, "SRX7034699", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.78221, 0.84034, 0.0684, 0.07089, 0.76607, 0.77025, 0.50712, 0.50772, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55387, "SRR10323899", "SRX7034698", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1", "23", "23", "NEBNext Low Input RNA Library Prep Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz", "fastq fastq", 5656815000.0, 37712100.0, "RNA seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz", "0:75 1:75", "A:1487198866;C:1332723090;G:1275197163;T:1514410765;N:47285116", 75, 75, null, null, 1487198866, 1332723090, 1275197163, 1514410765, 47285116, "SRX7034698", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.86399, 0.76012, 0.0587, 0.05779, 0.76461, 0.9105, 0.49754, 0.51037, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55388, "SRR10323900", "SRX7034697", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq  VPA treatment in hemogenic endothelial cell 26hpf replicate 2", "22", "22", "NEBNext Low Input RNA Library Prep Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq VPA treatment in hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq VPA treatment in hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz", "fastq fastq", 5978780250.0, 39858535.0, "RNA seq VPA treatment in hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz", "0:75 1:75", "A:1580804547;C:1404640964;G:1399714637;T:1593586843;N:33259", 75, 75, null, null, 1580804547, 1404640964, 1399714637, 1593586843, 33259, "SRX7034697", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.92216, 0.92477, 0.04155, 0.04126, 0.74537, 0.7512, 0.48148, 0.49049, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55389, "SRR10323901", "SRX7034696", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. 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Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq control for VPA treatment in hemogenic endothelial cell 26hpf replicate 1", "19", "19", "NEBNext Low Input RNA Library Prep Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq control for VPA_or_decitabine treatment in hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq control for VPA_or_decitabine treatment in hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz", "fastq fastq", 8021297850.0, 53475319.0, "RNA seq control for VPA or decitabine treatment in hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz", "0:75 1:75", "A:2121666298;C:1880005094;G:1872358379;T:2147221627;N:46452", 75, 75, null, null, 2121666298, 1880005094, 1872358379, 2147221627, 46452, "SRX7034693", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.91273, 0.91897, 0.0437, 0.04345, 0.75485, 0.76037, 0.46259, 0.47199, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55393, "SRR10323905", "SRX7034692", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2", "18", "18", "TruSeq stranded mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz", "fastq fastq", 4925792850.0, 32838619.0, "RNA seq mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz", "0:75 1:75", "A:1327496924;C:1143172265;G:1121827107;T:1332765205;N:531349", 75, 75, null, null, 1327496924, 1143172265, 1121827107, 1332765205, 531349, "SRX7034692", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.9235, 0.923, 0.07189, 0.07157, 0.74576, 0.7486, 0.46424, 0.46997, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55394, "SRR10323906", "SRX7034691", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq  mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1", "17", "17", "TruSeq stranded mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz", "fastq fastq", 4481194200.0, 29874628.0, "RNA seq mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz", "0:75 1:75", "A:1207561849;C:1040055195;G:1022613796;T:1210492037;N:471323", 75, 75, null, null, 1207561849, 1040055195, 1022613796, 1210492037, 471323, "SRX7034691", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.92094, 0.92157, 0.07292, 0.07281, 0.74704, 0.75067, 0.47205, 0.47416, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55395, "SRR10323907", "SRX7034690", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq  rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2", "16", "16", "TruSeq stranded mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz", "fastq fastq", 2071385250.0, 13809235.0, "RNA seq rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz", "0:75 1:75", "A:497024628;C:535934066;G:538798491;T:499539772;N:88293", 75, 75, null, null, 497024628, 535934066, 538798491, 499539772, 88293, "SRX7034690", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.92507, 0.92563, 0.0745, 0.07106, 0.74148, 0.74186, 0.5137, 0.52923, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55396, "SRR10323908", "SRX7034689", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq  rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1", "15", "15", "TruSeq stranded mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz", "fastq fastq", 1708336800.0, 11388912.0, "RNA seq rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz", "0:75 1:75", "A:413739883;C:438115098;G:440441368;T:415968029;N:72422", 75, 75, null, null, 413739883, 438115098, 440441368, 415968029, 72422, "SRX7034689", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.92948, 0.93123, 0.08112, 0.07757, 0.7472, 0.74921, 0.49384, 0.502, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55397, "SRR10323909", "SRX7034688", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 2", "14", "14", "TruSeq stranded mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz", "fastq fastq", 2742841800.0, 18285612.0, "RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz", "0:75 1:75", "A:771268784;C:600759252;G:605972112;T:764554978;N:286674", 75, 75, null, null, 771268784, 600759252, 605972112, 764554978, 286674, "SRX7034688", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.91195, 0.91276, 0.15552, 0.15531, 0.7191, 0.7247, 0.487, 0.47379, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55398, "SRR10323910", "SRX7034687", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 1", "13", "13", "TruSeq stranded mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz", "fastq fastq", 1909021350.0, 12726809.0, "RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz", "0:75 1:75", "A:536542827;C:420010389;G:423642042;T:528630203;N:195889", 75, 75, null, null, 536542827, 420010389, 423642042, 528630203, 195889, "SRX7034687", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.91535, 0.91534, 0.11578, 0.11457, 0.73705, 0.74373, 0.47609, 0.47115, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55399, "SRR10323911", "SRX7034686", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq  lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2", "12", "12", "NEBNext Low Input RNA Library Prep Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz", "fastq fastq", 5135290500.0, 34235270.0, "RNA seq lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz", "0:75 1:75", "A:1339180940;C:1202946694;G:1230552771;T:1362120185;N:489910", 75, 75, null, null, 1339180940, 1202946694, 1230552771, 1362120185, 489910, "SRX7034686", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.66031, 0.70687, 0.04575, 0.04896, 0.81075, 0.81195, 0.50951, 0.47552, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55400, "SRR10323912", "SRX7034685", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq  lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1", "11", "11", "NEBNext Low Input RNA Library Prep Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz", "fastq fastq", 3890046300.0, 25933642.0, "RNA seq lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz", "0:75 1:75", "A:1020376762;C:903218301;G:916043426;T:1050047618;N:360193", 75, 75, null, null, 1020376762, 903218301, 916043426, 1050047618, 360193, "SRX7034685", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.70733, 0.75223, 0.05929, 0.06271, 0.80807, 0.81071, 0.48475, 0.49323, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55401, "SRR10323913", "SRX7034684", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2", "2", "2", "NEBNext Low Input RNA Library Prep Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz", "fastq fastq", 2547796350.0, 16985309.0, "RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz", "0:75 1:75", "A:686259539;C:560800822;G:567842650;T:732652800;N:240539", 75, 75, null, null, 686259539, 560800822, 567842650, 732652800, 240539, "SRX7034684", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.70188, 0.75886, 0.08072, 0.08833, 0.8034, 0.80649, 0.51507, 0.5194, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55402, "SRR10323914", "SRX7034683", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1", "1", "1", "NEBNext Low Input RNA Library Prep Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz", "fastq fastq", 2438070600.0, 16253804.0, "RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz", "0:75 1:75", "A:654282012;C:534555119;G:543878428;T:705130425;N:224616", 75, 75, null, null, 654282012, 534555119, 543878428, 705130425, 224616, "SRX7034683", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.69336, 0.75626, 0.09168, 0.09896, 0.80166, 0.80253, 0.51795, 0.52538, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [67823, "SRR17335719", "SRX13511115", "SRS11405356", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CPF3", "GSM5754470", null, "source name:Brain tissue|tissue:Brain|treatment:CPF toxication|geo loc name:missing|collection date:missing", "CPF3", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CPF toxication", "GSM5754470", "GSM5754470: CPF3; Danio rerio; ncRNA Seq", "GSM5754470 r1", "GSM5754470", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CPF3_1.fq.gz CPF3_2.fq.gz", "fastq fastq", 12726241500.0, 42420805.0, "GSM5754470 r1", "0:150 1:150", "A:3447613023;C:2896153797;G:2922038320;T:3459698412;N:737948", 150, 150, null, null, 3447613023, 2896153797, 2922038320, 3459698412, 737948, "SRX13511115", "SRS11405356", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.89399, 0.89612, 0.38172, 0.37657, 0.66628, 0.66799, 0.53056, 0.53213, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67824, "SRR17335720", "SRX13511114", "SRS11405355", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CPF2", "GSM5754469", null, "source name:Brain tissue|tissue:Brain|treatment:CPF toxication|geo loc name:missing|collection date:missing", "CPF2", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CPF toxication", "GSM5754469", "GSM5754469: CPF2; Danio rerio; ncRNA Seq", "GSM5754469 r1", "GSM5754469", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CPF2_1.fq.gz CPF2_2.fq.gz", "fastq fastq", 14881715100.0, 49605717.0, "GSM5754469 r1", "0:150 1:150", "A:4214905088;C:3201163283;G:3225795074;T:4239665352;N:186303", 150, 150, null, null, 4214905088, 3201163283, 3225795074, 4239665352, 186303, "SRX13511114", "SRS11405355", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.87491, 0.87638, 0.40844, 0.40479, 0.67123, 0.67018, 0.49174, 0.48952, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67825, "SRR17335721", "SRX13511113", "SRS11405354", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CPF1", "GSM5754468", null, "source name:Brain tissue|tissue:Brain|treatment:CPF toxication|geo loc name:missing|collection date:missing", "CPF1", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CPF toxication", "GSM5754468", "GSM5754468: CPF1; Danio rerio; ncRNA Seq", "GSM5754468 r1", "GSM5754468", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CPF1_1.fq.gz CPF1_2.fq.gz", "fastq fastq", 16447798800.0, 54825996.0, "GSM5754468 r1", "0:150 1:150", "A:4454573413;C:3748270411;G:3776995203;T:4467442717;N:517056", 150, 150, null, null, 4454573413, 3748270411, 3776995203, 4467442717, 517056, "SRX13511113", "SRS11405354", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.89313, 0.8947, 0.35381, 0.35194, 0.64954, 0.64831, 0.51962, 0.52475, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67826, "SRR17335722", "SRX13511112", "SRS11405353", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CYP3", "GSM5754467", null, "source name:Brain tissue|tissue:Brain|treatment:CYP toxication|geo loc name:missing|collection date:missing", "CYP3", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CYP toxication", "GSM5754467", "GSM5754467: CYP3; Danio rerio; ncRNA Seq", "GSM5754467 r1", "GSM5754467", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CYP3_1.fq.gz CYP3_2.fq.gz", "fastq fastq", 13417868100.0, 44726227.0, "GSM5754467 r1", "0:150 1:150", "A:3645134270;C:3041754103;G:3084809543;T:3645750889;N:419295", 150, 150, null, null, 3645134270, 3041754103, 3084809543, 3645750889, 419295, "SRX13511112", "SRS11405353", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.86122, 0.8638, 0.4112, 0.40785, 0.68738, 0.68519, 0.54768, 0.44856, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67827, "SRR17335723", "SRX13511111", "SRS11405352", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CYP2", "GSM5754466", null, "source name:Brain tissue|tissue:Brain|treatment:CYP toxication|geo loc name:missing|collection date:missing", "CYP2", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CYP toxication", "GSM5754466", "GSM5754466: CYP2; Danio rerio; ncRNA Seq", "GSM5754466 r1", "GSM5754466", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CYP2_1.fq.gz CYP2_2.fq.gz", "fastq fastq", 13096007700.0, 43653359.0, "GSM5754466 r1", "0:150 1:150", "A:3638241155;C:2892284693;G:2925857490;T:3639296449;N:327913", 150, 150, null, null, 3638241155, 2892284693, 2925857490, 3639296449, 327913, "SRX13511111", "SRS11405352", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.85953, 0.86247, 0.41975, 0.41734, 0.68174, 0.67862, 0.52504, 0.5324, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67828, "SRR17335724", "SRX13511110", "SRS11405351", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CYP1", "GSM5754465", null, "source name:Brain tissue|tissue:Brain|treatment:CYP toxication|geo loc name:missing|collection date:missing", "CYP1", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CYP toxication", "GSM5754465", "GSM5754465: CYP1; Danio rerio; ncRNA Seq", "GSM5754465 r1", "GSM5754465", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CYP1_1.fq.gz CYP1_2.fq.gz", "fastq fastq", 16372872000.0, 54576240.0, "GSM5754465 r1", "0:150 1:150", "A:4747286217;C:3417115980;G:3453793026;T:4754530080;N:146697", 150, 150, null, null, 4747286217, 3417115980, 3453793026, 4754530080, 146697, "SRX13511110", "SRS11405351", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.85322, 0.85414, 0.46298, 0.45901, 0.68016, 0.67866, 0.47694, 0.47897, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67829, "SRR17335725", "SRX13511109", "SRS11405350", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "Cont3", "GSM5754464", null, "source name:Brain tissue|tissue:Brain|treatment:No toxication|geo loc name:missing|collection date:missing", "Cont3", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:No toxication", "GSM5754464", "GSM5754464: Cont3; Danio rerio; ncRNA Seq", "GSM5754464 r1", "GSM5754464", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "Cont3_1.fq.gz Cont3_2.fq.gz", "fastq fastq", 15202443900.0, 50674813.0, "GSM5754464 r1", "0:150 1:150", "A:4400470018;C:3173803928;G:3218623722;T:4409335756;N:210476", 150, 150, null, null, 4400470018, 3173803928, 3218623722, 4409335756, 210476, "SRX13511109", "SRS11405350", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.86129, 0.84677, 0.45657, 0.44799, 0.67884, 0.68083, 0.48291, 0.4763, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67830, "SRR17335726", "SRX13511108", "SRS11405349", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "Cont2", "GSM5754463", null, "source name:Brain tissue|tissue:Brain|treatment:No toxication|geo loc name:missing|collection date:missing", "Cont2", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:No toxication", "GSM5754463", "GSM5754463: Cont2; Danio rerio; ncRNA Seq", "GSM5754463 r1", "GSM5754463", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "Cont2_1.fq.gz Cont2_2.fq.gz", "fastq fastq", 12927267600.0, 43090892.0, "GSM5754463 r1", "0:150 1:150", "A:3474574877;C:2959326086;G:3006553706;T:3486600752;N:212179", 150, 150, null, null, 3474574877, 2959326086, 3006553706, 3486600752, 212179, "SRX13511108", "SRS11405349", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.87695, 0.87907, 0.41673, 0.41416, 0.69266, 0.69266, 0.53339, 0.58145, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67831, "SRR17335727", "SRX13511107", "SRS11405348", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "Cont1", "GSM5754462", null, "source name:Brain tissue|tissue:Brain|treatment:No toxication|geo loc name:missing|collection date:missing", "Cont1", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:No toxication", "GSM5754462", "GSM5754462: Cont1; Danio rerio; ncRNA Seq", "GSM5754462 r1", "GSM5754462", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "Cont1_1.fq.gz Cont1_2.fq.gz", "fastq fastq", 18395362500.0, 61317875.0, "GSM5754462 r1", "0:150 1:150", "A:5379624768;C:3792463355;G:3842313235;T:5380702187;N:258955", 150, 150, null, null, 5379624768, 3792463355, 3842313235, 5380702187, 258955, "SRX13511107", "SRS11405348", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.83439, 0.83446, 0.45703, 0.44894, 0.68828, 0.68578, 0.4957, 0.49639, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"]], "truncated": false, "filtered_table_rows_count": 108, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"experiment.library_layout\" = :p0 and \"experiment.library_selection\" = :p1 order by rowid limit 101", "params": {"p0": "PAIRED", "p1": "size fractionation"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": 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108, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation", "selected": true}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=size+fractionation", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 108, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=size+fractionation&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=size+fractionation", "results": [{"value": "Embryo", "label": "Embryo", "count": 36, "toggle_url": 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"truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=size+fractionation", "results": [{"value": "Larval", "label": "Larval", "count": 33, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=size+fractionation&devstage_curation=Larval", "selected": false}, {"value": "Adult", "label": "Adult", "count": 24, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=size+fractionation&devstage_curation=Adult", "selected": false}, {"value": "Pharyngula", "label": "Pharyngula", "count": 24, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=size+fractionation&devstage_curation=Pharyngula", 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"tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=size+fractionation", "results": [{"value": "Cardiovascular System", "label": "Cardiovascular System", "count": 30, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=size+fractionation&tissue_curation_coarse=Cardiovascular+System", "selected": false}, {"value": "All anatomical structures", "label": "All anatomical structures", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=size+fractionation&tissue_curation_coarse=All+anatomical+structures", "selected": false}, {"value": "Nervous System", "label": "Nervous System", "count": 15, "toggle_url": 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