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Sequencing technology was provided by UNIKAWA Biotechnology Co.Ltd Hangzhou  China.", null, "pubmed:38812038", null, "inh5", "GSM7775461", null, "source name:larvae fin|tissue:larvae fin|genotype:mtor inhibition|treatment:Rapamycin|geo loc name:missing|collection date:missing", "inh5", "Raw data quality control Reference genome alignment Transcript assembly Read count extration and normalization DEGs analysis Assembly: mm10", "larvae fin", null, "SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. cDNA was fragmented by dsDNA Fragmentase NEB  M0348S by incubate at 37\u00b0C for 30min. Library construction begins with fragmented cDNA. Blunt end DNA fragments are generated using a combination of fill in reactions and exonuclease activity  and size selection is performed with provided sample purification beads. An A base is then added to the blunt ends of each strand  indexed Y adapters are ligated to the fragments  and the ligated products are amplified with PCR.", null, "tissue:larvae fin|genotype:mtor inhibition|treatment:Rapamycin", "GSM7775461", "GSM7775461: inh5; Danio rerio; RNA Seq", "GSM7775461 r1", "GSM7775461", "1", "SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. cDNA was fragmented by dsDNA Fragmentase NEB  M0348S by incubate at 37\u00b0C for 30min. Library construction begins with fragmented cDNA. Blunt end DNA fragments are generated using a combination of fill in reactions and exonuclease activity  and size selection is performed with provided sample purification beads. An A base is then added to the blunt ends of each strand  indexed Y adapters are ligated to the fragments  and the ligated products are amplified with PCR.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459901", null, "loader:fastq load.py", "inh5_Clean_Data1.fq.gz inh5_Clean_Data2.fq.gz", "fastq fastq", 5310575587.0, 18136361.0, "GSM7775461 r1", "0:146.55 1:146.26", "A:1423902511;C:1238406241;G:1244410553;T:1403706639;N:149643", 146, 146, null, null, 1423902511, 1238406241, 1244410553, 1403706639, 149643, "SRX21755511", "SRS18862356", "SRA1710567", "Chongqing Medical University", "Chongqing Medical University", 2, 0.95015, 0.94801, 0.06797, 0.06821, 0.72837, 0.73028, 0.48734, 0.48305, 149, 149, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "China", "2023-09-12", "Larval", "Larval", "Fin", "Surface Structure"], [26507, "SRR26038416", "SRX21755510", "SRS18862353", "SRP459901", "PRJNA1015602", "mTOR promotes zebrafish larvae fin regeneration through regulating macrophages activation and CaM mTOR dnm1l axis", "GSE242949", "Transcriptome Analysis", "To investigate the functional and mechanistic roles of mTOR in zebrafish larvae fin regeneration  we firstly examined the spatiotemporal expression of mTOR in larvae fin and established a mTOR knockout mTOR KO  transgenic fish line using CRISPER / Cas9 gene editing technology. Moreover  mTOR was essential for the activation of macrophages  which is a key factor in maintaining the regenerative repair process. We also demonstrated that mTOR knockdown attenuated the proliferative capacity of bud embryo cell during the regenerative phase  while cell apoptosis was not affected. RNA sequence analysis showed changes in mitochondrial function and dnm1l was identified as the main regulatory factor during the fin regeneration stage. We further suggested that mTOR may promote mitochondrial fission to support bud embryo cell regeneration via CaM mTOR dnm1l axis. Overall design: Sequencing samples for the micro transcriptome were obtained from tail fin tissues regenerated for 24 h. Fifty regenerated tail fins were extracted for each sample from the control and experimental groups treated with 1 uM Rapamycin. Each group had 3 biological replicates and samples were lysed using Trizol. Sequencing technology was provided by UNIKAWA Biotechnology Co.Ltd Hangzhou  China.", null, "pubmed:38812038", null, "inh4", "GSM7775460", null, "source name:larvae fin|tissue:larvae fin|genotype:mtor inhibition|treatment:Rapamycin|geo loc name:missing|collection date:missing", "inh4", "Raw data quality control Reference genome alignment Transcript assembly Read count extration and normalization DEGs analysis Assembly: mm10", "larvae fin", null, "SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. cDNA was fragmented by dsDNA Fragmentase NEB  M0348S by incubate at 37\u00b0C for 30min. Library construction begins with fragmented cDNA. Blunt end DNA fragments are generated using a combination of fill in reactions and exonuclease activity  and size selection is performed with provided sample purification beads. An A base is then added to the blunt ends of each strand  indexed Y adapters are ligated to the fragments  and the ligated products are amplified with PCR.", null, "tissue:larvae fin|genotype:mtor inhibition|treatment:Rapamycin", "GSM7775460", "GSM7775460: inh4; Danio rerio; RNA Seq", "GSM7775460 r1", "GSM7775460", "1", "SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. cDNA was fragmented by dsDNA Fragmentase NEB  M0348S by incubate at 37\u00b0C for 30min. Library construction begins with fragmented cDNA. Blunt end DNA fragments are generated using a combination of fill in reactions and exonuclease activity  and size selection is performed with provided sample purification beads. An A base is then added to the blunt ends of each strand  indexed Y adapters are ligated to the fragments  and the ligated products are amplified with PCR.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459901", null, "loader:fastq load.py", "inh4_Clean_Data1.fq.gz inh4_Clean_Data2.fq.gz", "fastq fastq", 5197656995.0, 17730782.0, "GSM7775460 r1", "0:146.71 1:146.43", "A:1388735355;C:1217185681;G:1223043812;T:1368550802;N:141345", 146, 146, null, null, 1388735355, 1217185681, 1223043812, 1368550802, 141345, "SRX21755510", "SRS18862353", "SRA1710567", "Chongqing Medical University", "Chongqing Medical University", 2, 0.94482, 0.94389, 0.06919, 0.06901, 0.72849, 0.72868, 0.47769, 0.49, 149, 149, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "China", "2023-09-12", "Larval", "Larval", "Fin", "Surface Structure"], [26508, "SRR26038417", "SRX21755509", "SRS18862352", "SRP459901", "PRJNA1015602", "mTOR promotes zebrafish larvae fin regeneration through regulating macrophages activation and CaM mTOR dnm1l axis", "GSE242949", "Transcriptome Analysis", "To investigate the functional and mechanistic roles of mTOR in zebrafish larvae fin regeneration  we firstly examined the spatiotemporal expression of mTOR in larvae fin and established a mTOR knockout mTOR KO  transgenic fish line using CRISPER / Cas9 gene editing technology. Moreover  mTOR was essential for the activation of macrophages  which is a key factor in maintaining the regenerative repair process. We also demonstrated that mTOR knockdown attenuated the proliferative capacity of bud embryo cell during the regenerative phase  while cell apoptosis was not affected. RNA sequence analysis showed changes in mitochondrial function and dnm1l was identified as the main regulatory factor during the fin regeneration stage. We further suggested that mTOR may promote mitochondrial fission to support bud embryo cell regeneration via CaM mTOR dnm1l axis. Overall design: Sequencing samples for the micro transcriptome were obtained from tail fin tissues regenerated for 24 h. Fifty regenerated tail fins were extracted for each sample from the control and experimental groups treated with 1 uM Rapamycin. Each group had 3 biological replicates and samples were lysed using Trizol. Sequencing technology was provided by UNIKAWA Biotechnology Co.Ltd Hangzhou  China.", null, "pubmed:38812038", null, "ctrl3", "GSM7775459", null, "source name:larvae fin|tissue:larvae fin|genotype:WT|treatment:DMSO|geo loc name:missing|collection date:missing", "ctrl3", "Raw data quality control Reference genome alignment Transcript assembly Read count extration and normalization DEGs analysis Assembly: mm10", "larvae fin", null, "SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. cDNA was fragmented by dsDNA Fragmentase NEB  M0348S by incubate at 37\u00b0C for 30min. Library construction begins with fragmented cDNA. Blunt end DNA fragments are generated using a combination of fill in reactions and exonuclease activity  and size selection is performed with provided sample purification beads. An A base is then added to the blunt ends of each strand  indexed Y adapters are ligated to the fragments  and the ligated products are amplified with PCR.", null, "tissue:larvae fin|genotype:WT|treatment:DMSO", "GSM7775459", "GSM7775459: ctrl3; Danio rerio; RNA Seq", "GSM7775459 r1", "GSM7775459", "1", "SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. cDNA was fragmented by dsDNA Fragmentase NEB  M0348S by incubate at 37\u00b0C for 30min. Library construction begins with fragmented cDNA. Blunt end DNA fragments are generated using a combination of fill in reactions and exonuclease activity  and size selection is performed with provided sample purification beads. An A base is then added to the blunt ends of each strand  indexed Y adapters are ligated to the fragments  and the ligated products are amplified with PCR.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459901", null, "loader:fastq load.py", "ctrl3_Clean_Data1.fq.gz ctrl3_Clean_Data2.fq.gz", "fastq fastq", 4713279144.0, 16083894.0, "GSM7775459 r1", "0:146.67 1:146.37", "A:1259944484;C:1102611255;G:1109604596;T:1240990931;N:127878", 146, 146, null, null, 1259944484, 1102611255, 1109604596, 1240990931, 127878, "SRX21755509", "SRS18862352", "SRA1710567", "Chongqing Medical University", "Chongqing Medical University", 2, 0.95066, 0.94853, 0.04942, 0.04977, 0.74142, 0.74276, 0.46137, 0.4689, 149, 124, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "China", "2023-09-12", "Larval", "Larval", "Fin", "Surface Structure"], [26509, "SRR26038418", "SRX21755508", "SRS18862355", "SRP459901", "PRJNA1015602", "mTOR promotes zebrafish larvae fin regeneration through regulating macrophages activation and CaM mTOR dnm1l axis", "GSE242949", "Transcriptome Analysis", "To investigate the functional and mechanistic roles of mTOR in zebrafish larvae fin regeneration  we firstly examined the spatiotemporal expression of mTOR in larvae fin and established a mTOR knockout mTOR KO  transgenic fish line using CRISPER / Cas9 gene editing technology. Moreover  mTOR was essential for the activation of macrophages  which is a key factor in maintaining the regenerative repair process. We also demonstrated that mTOR knockdown attenuated the proliferative capacity of bud embryo cell during the regenerative phase  while cell apoptosis was not affected. RNA sequence analysis showed changes in mitochondrial function and dnm1l was identified as the main regulatory factor during the fin regeneration stage. We further suggested that mTOR may promote mitochondrial fission to support bud embryo cell regeneration via CaM mTOR dnm1l axis. Overall design: Sequencing samples for the micro transcriptome were obtained from tail fin tissues regenerated for 24 h. Fifty regenerated tail fins were extracted for each sample from the control and experimental groups treated with 1 uM Rapamycin. Each group had 3 biological replicates and samples were lysed using Trizol. Sequencing technology was provided by UNIKAWA Biotechnology Co.Ltd Hangzhou  China.", null, "pubmed:38812038", null, "ctrl2", "GSM7775458", null, "source name:larvae fin|tissue:larvae fin|genotype:WT|treatment:DMSO|geo loc name:missing|collection date:missing", "ctrl2", "Raw data quality control Reference genome alignment Transcript assembly Read count extration and normalization DEGs analysis Assembly: mm10", "larvae fin", null, "SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. cDNA was fragmented by dsDNA Fragmentase NEB  M0348S by incubate at 37\u00b0C for 30min. Library construction begins with fragmented cDNA. Blunt end DNA fragments are generated using a combination of fill in reactions and exonuclease activity  and size selection is performed with provided sample purification beads. An A base is then added to the blunt ends of each strand  indexed Y adapters are ligated to the fragments  and the ligated products are amplified with PCR.", null, "tissue:larvae fin|genotype:WT|treatment:DMSO", "GSM7775458", "GSM7775458: ctrl2; Danio rerio; RNA Seq", "GSM7775458 r1", "GSM7775458", "1", "SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. cDNA was fragmented by dsDNA Fragmentase NEB  M0348S by incubate at 37\u00b0C for 30min. Library construction begins with fragmented cDNA. Blunt end DNA fragments are generated using a combination of fill in reactions and exonuclease activity  and size selection is performed with provided sample purification beads. An A base is then added to the blunt ends of each strand  indexed Y adapters are ligated to the fragments  and the ligated products are amplified with PCR.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459901", null, "loader:fastq load.py", "ctrl2_Clean_Data1.fq.gz ctrl2_Clean_Data2.fq.gz", "fastq fastq", 5227164341.0, 17870214.0, "GSM7775458 r1", "0:146.39 1:146.12", "A:1415008178;C:1206338951;G:1214004481;T:1391669432;N:143299", 146, 146, null, null, 1415008178, 1206338951, 1214004481, 1391669432, 143299, "SRX21755508", "SRS18862355", "SRA1710567", "Chongqing Medical University", "Chongqing Medical University", 2, 0.95212, 0.95021, 0.06542, 0.06559, 0.7288, 0.7292, 0.47726, 0.48188, 149, 149, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "China", "2023-09-12", "Larval", "Larval", "Fin", "Surface Structure"], [26510, "SRR26038419", "SRX21755507", "SRS18862354", "SRP459901", "PRJNA1015602", "mTOR promotes zebrafish larvae fin regeneration through regulating macrophages activation and CaM mTOR dnm1l axis", "GSE242949", "Transcriptome Analysis", "To investigate the functional and mechanistic roles of mTOR in zebrafish larvae fin regeneration  we firstly examined the spatiotemporal expression of mTOR in larvae fin and established a mTOR knockout mTOR KO  transgenic fish line using CRISPER / Cas9 gene editing technology. Moreover  mTOR was essential for the activation of macrophages  which is a key factor in maintaining the regenerative repair process. We also demonstrated that mTOR knockdown attenuated the proliferative capacity of bud embryo cell during the regenerative phase  while cell apoptosis was not affected. RNA sequence analysis showed changes in mitochondrial function and dnm1l was identified as the main regulatory factor during the fin regeneration stage. We further suggested that mTOR may promote mitochondrial fission to support bud embryo cell regeneration via CaM mTOR dnm1l axis. Overall design: Sequencing samples for the micro transcriptome were obtained from tail fin tissues regenerated for 24 h. Fifty regenerated tail fins were extracted for each sample from the control and experimental groups treated with 1 uM Rapamycin. Each group had 3 biological replicates and samples were lysed using Trizol. Sequencing technology was provided by UNIKAWA Biotechnology Co.Ltd Hangzhou  China.", null, "pubmed:38812038", null, "ctrl1", "GSM7775457", null, "source name:larvae fin|tissue:larvae fin|genotype:WT|treatment:DMSO|geo loc name:missing|collection date:missing", "ctrl1", "Raw data quality control Reference genome alignment Transcript assembly Read count extration and normalization DEGs analysis Assembly: mm10", "larvae fin", null, "SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. cDNA was fragmented by dsDNA Fragmentase NEB  M0348S by incubate at 37\u00b0C for 30min. Library construction begins with fragmented cDNA. Blunt end DNA fragments are generated using a combination of fill in reactions and exonuclease activity  and size selection is performed with provided sample purification beads. An A base is then added to the blunt ends of each strand  indexed Y adapters are ligated to the fragments  and the ligated products are amplified with PCR.", null, "tissue:larvae fin|genotype:WT|treatment:DMSO", "GSM7775457", "GSM7775457: ctrl1; Danio rerio; RNA Seq", "GSM7775457 r1", "GSM7775457", "1", "SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. cDNA was fragmented by dsDNA Fragmentase NEB  M0348S by incubate at 37\u00b0C for 30min. Library construction begins with fragmented cDNA. Blunt end DNA fragments are generated using a combination of fill in reactions and exonuclease activity  and size selection is performed with provided sample purification beads. An A base is then added to the blunt ends of each strand  indexed Y adapters are ligated to the fragments  and the ligated products are amplified with PCR.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459901", null, "loader:fastq load.py", "ctrl1_Clean_Data1.fq.gz ctrl1_Clean_Data2.fq.gz", "fastq fastq", 5342798577.0, 18260213.0, "GSM7775457 r1", "0:146.40 1:146.19", "A:1434645762;C:1243936102;G:1249988331;T:1414082855;N:145527", 146, 146, null, null, 1434645762, 1243936102, 1249988331, 1414082855, 145527, "SRX21755507", "SRS18862354", "SRA1710567", "Chongqing Medical University", "Chongqing Medical University", 2, 0.95229, 0.95004, 0.06613, 0.06596, 0.71086, 0.71303, 0.47912, 0.47827, 149, 149, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "China", "2023-09-12", "Larval", "Larval", "Fin", "Surface Structure"], [48892, "SRR7444117", "SRX4314656", "SRS3474417", "SRP151493", "PRJNA478247", "Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome [ssRNA seq]", "GSE116358", "Transcriptome Analysis", "The goal of this study was to investigate DNA methylation and gene expression changes in a zebrafish model of ICF Syndrome which were generated by mutation of ICF gene zbtb24. Comparison of gene expression changes between wildtype and zbtb24 homozygous mutants revealed upregulation of interferon response genes following zbtb24 deletion. Upregulation of interferon response genes was blocked by mutation of the dsRNA helicase Mda5. Overall design: For RNA seq  gene expression was compared in whole two wpf zebrafish larvae that were wildtype or homozygous for the zbtb24mk22 mutant allele. We further performed RNA Seq analysis in three wpf zebrafish larvae that were WT  mda5mk29/mk29   zbtb24mk22/mk22  and mda5mk29/mk29 ;zbtb24mk22/mk22. Three samples consisting of pools of 10 larvae were examined for each genotype.  For ERRBS  DNA was separately isolated from the fins of three wildtype and three zbtb24mk22 homozygous mutant adults.", "parent bioproject:PRJNA478246", "pubmed:30484769", null, "Mut3", "GSM3229933", null, "tissue:Fin|development stage:Larvae|genotype/variation:Mutant", "Mut3", "Reads were mapped to the Zebrafish genome danRer7 using the rnaStar aligner v2.5.0a. We used the 2 pass mapping method outlined in Engstro\u0308m et.al Nat. Meth. 2013. The first mapping pass used a list of known annotated junctions from Ensemble. Novel junctions found in the first pass were then added to the known junctions and a second mapping pass was done on the second pass the RemoveNoncanoncial flag was used.\u00a0Expression counts were computed from the mapped reads using HTSeq v0.5.3 and Ensemble D.rerio v79 gene annotations. Normalization and differential expression was performed using DESeq. Genome build: danRer7 Supplementary files format and content: Tab delimited normalized RNA seq counts per million for each sample.", "Fin", null, "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", null, "development stage:Larvae|genotype/variation:Mutant", "GSM3229933", "GSM3229933: Mut3; Danio rerio; RNA Seq", "GSM3229933", null, "1", "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", "GEO Accession:GSM3229933", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP151493", null, null, "zbtb24DelMut_3_IGO_06387_6_S68_L008_R2_001.fastq.gz zbtb24DelMut_3_IGO_06387_6_S68_L008_R1_001.fastq.gz", "fastq fastq", 3719967400.0, 37199674.0, "GSM3229933 r1", "0:50 1:50", "A:986918955;C:862641737;G:855857408;T:1004343769;N:10205531", 50, 50, null, null, 986918955, 862641737, 855857408, 1004343769, 10205531, "SRX4314656", "SRS3474417", "SRA729908", "GEO", "Center for Pharmacogenomics, Washington University School of Medicine", 2, 0.95873, 0.95994, 0.09834, 0.09744, 0.66312, 0.66567, 0.49102, 0.49442, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-06-27", "Larval", "Larval", "Fin", "Surface Structure"], [48893, "SRR7444116", "SRX4314655", "SRS3474415", "SRP151493", "PRJNA478247", "Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome [ssRNA seq]", "GSE116358", "Transcriptome Analysis", "The goal of this study was to investigate DNA methylation and gene expression changes in a zebrafish model of ICF Syndrome which were generated by mutation of ICF gene zbtb24. Comparison of gene expression changes between wildtype and zbtb24 homozygous mutants revealed upregulation of interferon response genes following zbtb24 deletion. Upregulation of interferon response genes was blocked by mutation of the dsRNA helicase Mda5. Overall design: For RNA seq  gene expression was compared in whole two wpf zebrafish larvae that were wildtype or homozygous for the zbtb24mk22 mutant allele. We further performed RNA Seq analysis in three wpf zebrafish larvae that were WT  mda5mk29/mk29   zbtb24mk22/mk22  and mda5mk29/mk29 ;zbtb24mk22/mk22. Three samples consisting of pools of 10 larvae were examined for each genotype.  For ERRBS  DNA was separately isolated from the fins of three wildtype and three zbtb24mk22 homozygous mutant adults.", "parent bioproject:PRJNA478246", "pubmed:30484769", null, "Mut2", "GSM3229932", null, "tissue:Fin|development stage:Larvae|genotype/variation:Mutant", "Mut2", "Reads were mapped to the Zebrafish genome danRer7 using the rnaStar aligner v2.5.0a. We used the 2 pass mapping method outlined in Engstro\u0308m et.al Nat. Meth. 2013. The first mapping pass used a list of known annotated junctions from Ensemble. Novel junctions found in the first pass were then added to the known junctions and a second mapping pass was done on the second pass the RemoveNoncanoncial flag was used.\u00a0Expression counts were computed from the mapped reads using HTSeq v0.5.3 and Ensemble D.rerio v79 gene annotations. Normalization and differential expression was performed using DESeq. Genome build: danRer7 Supplementary files format and content: Tab delimited normalized RNA seq counts per million for each sample.", "Fin", null, "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", null, "development stage:Larvae|genotype/variation:Mutant", "GSM3229932", "GSM3229932: Mut2; Danio rerio; RNA Seq", "GSM3229932", null, "1", "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", "GEO Accession:GSM3229932", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP151493", null, null, "zbtb24DelMut_2_IGO_06387_5_S67_L008_R1_001.fastq.gz zbtb24DelMut_2_IGO_06387_5_S67_L008_R2_001.fastq.gz", "fastq fastq", 3472742800.0, 34727428.0, "GSM3229932 r1", "0:50 1:50", "A:926610880;C:802153731;G:789000796;T:945257086;N:9720307", 50, 50, null, null, 926610880, 802153731, 789000796, 945257086, 9720307, "SRX4314655", "SRS3474415", "SRA729908", "GEO", "Center for Pharmacogenomics, Washington University School of Medicine", 2, 0.95852, 0.96008, 0.09702, 0.09659, 0.66119, 0.66281, 0.49124, 0.49331, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-06-27", "Larval", "Larval", "Fin", "Surface Structure"], [48894, "SRR7444115", "SRX4314654", "SRS3474414", "SRP151493", "PRJNA478247", "Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome [ssRNA seq]", "GSE116358", "Transcriptome Analysis", "The goal of this study was to investigate DNA methylation and gene expression changes in a zebrafish model of ICF Syndrome which were generated by mutation of ICF gene zbtb24. Comparison of gene expression changes between wildtype and zbtb24 homozygous mutants revealed upregulation of interferon response genes following zbtb24 deletion. Upregulation of interferon response genes was blocked by mutation of the dsRNA helicase Mda5. Overall design: For RNA seq  gene expression was compared in whole two wpf zebrafish larvae that were wildtype or homozygous for the zbtb24mk22 mutant allele. We further performed RNA Seq analysis in three wpf zebrafish larvae that were WT  mda5mk29/mk29   zbtb24mk22/mk22  and mda5mk29/mk29 ;zbtb24mk22/mk22. Three samples consisting of pools of 10 larvae were examined for each genotype.  For ERRBS  DNA was separately isolated from the fins of three wildtype and three zbtb24mk22 homozygous mutant adults.", "parent bioproject:PRJNA478246", "pubmed:30484769", null, "Mut1", "GSM3229931", null, "tissue:Fin|development stage:Larvae|genotype/variation:Mutant", "Mut1", "Reads were mapped to the Zebrafish genome danRer7 using the rnaStar aligner v2.5.0a. We used the 2 pass mapping method outlined in Engstro\u0308m et.al Nat. Meth. 2013. The first mapping pass used a list of known annotated junctions from Ensemble. Novel junctions found in the first pass were then added to the known junctions and a second mapping pass was done on the second pass the RemoveNoncanoncial flag was used.\u00a0Expression counts were computed from the mapped reads using HTSeq v0.5.3 and Ensemble D.rerio v79 gene annotations. Normalization and differential expression was performed using DESeq. Genome build: danRer7 Supplementary files format and content: Tab delimited normalized RNA seq counts per million for each sample.", "Fin", null, "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", null, "development stage:Larvae|genotype/variation:Mutant", "GSM3229931", "GSM3229931: Mut1; Danio rerio; RNA Seq", "GSM3229931", null, "1", "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", "GEO Accession:GSM3229931", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP151493", null, null, "zbtb24DelMut_1_IGO_06387_4_S69_L008_R2_001.fastq.gz zbtb24DelMut_1_IGO_06387_4_S69_L008_R1_001.fastq.gz", "fastq fastq", 3794382600.0, 37943826.0, "GSM3229931 r1", "0:50 1:50", "A:995335879;C:890930546;G:885930890;T:1011869099;N:10316186", 50, 50, null, null, 995335879, 890930546, 885930890, 1011869099, 10316186, "SRX4314654", "SRS3474414", "SRA729908", "GEO", "Center for Pharmacogenomics, Washington University School of Medicine", 2, 0.96049, 0.96131, 0.09447, 0.09422, 0.66022, 0.66314, 0.48621, 0.494, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-06-27", "Larval", "Larval", "Fin", "Surface Structure"], [48895, "SRR7444114", "SRX4314653", "SRS3474413", "SRP151493", "PRJNA478247", "Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome [ssRNA seq]", "GSE116358", "Transcriptome Analysis", "The goal of this study was to investigate DNA methylation and gene expression changes in a zebrafish model of ICF Syndrome which were generated by mutation of ICF gene zbtb24. Comparison of gene expression changes between wildtype and zbtb24 homozygous mutants revealed upregulation of interferon response genes following zbtb24 deletion. Upregulation of interferon response genes was blocked by mutation of the dsRNA helicase Mda5. Overall design: For RNA seq  gene expression was compared in whole two wpf zebrafish larvae that were wildtype or homozygous for the zbtb24mk22 mutant allele. We further performed RNA Seq analysis in three wpf zebrafish larvae that were WT  mda5mk29/mk29   zbtb24mk22/mk22  and mda5mk29/mk29 ;zbtb24mk22/mk22. Three samples consisting of pools of 10 larvae were examined for each genotype.  For ERRBS  DNA was separately isolated from the fins of three wildtype and three zbtb24mk22 homozygous mutant adults.", "parent bioproject:PRJNA478246", "pubmed:30484769", null, "WT2A", "GSM3229930", null, "tissue:Fin|development stage:Larvae|genotype/variation:WT", "WT2A", "Reads were mapped to the Zebrafish genome danRer7 using the rnaStar aligner v2.5.0a. We used the 2 pass mapping method outlined in Engstro\u0308m et.al Nat. Meth. 2013. The first mapping pass used a list of known annotated junctions from Ensemble. Novel junctions found in the first pass were then added to the known junctions and a second mapping pass was done on the second pass the RemoveNoncanoncial flag was used.\u00a0Expression counts were computed from the mapped reads using HTSeq v0.5.3 and Ensemble D.rerio v79 gene annotations. Normalization and differential expression was performed using DESeq. Genome build: danRer7 Supplementary files format and content: Tab delimited normalized RNA seq counts per million for each sample.", "Fin", null, "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", null, "development stage:Larvae|genotype/variation:WT", "GSM3229930", "GSM3229930: WT2A; Danio rerio; RNA Seq", "GSM3229930", null, "1", "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", "GEO Accession:GSM3229930", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP151493", null, null, "WT_2A_IGO_06387_3_S71_L008_R1_001.fastq.gz WT_2A_IGO_06387_3_S71_L008_R2_001.fastq.gz", "fastq fastq", 3402949100.0, 34029491.0, "GSM3229930 r1", "0:50 1:50", "A:891664443;C:800386138;G:792288516;T:909424992;N:9185011", 50, 50, null, null, 891664443, 800386138, 792288516, 909424992, 9185011, "SRX4314653", "SRS3474413", "SRA729908", "GEO", "Center for Pharmacogenomics, Washington University School of Medicine", 2, 0.95927, 0.96093, 0.10072, 0.10101, 0.65717, 0.6604, 0.48926, 0.49224, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-06-27", "Larval", "Larval", "Fin", "Surface Structure"], [48896, "SRR7444113", "SRX4314652", "SRS3474416", "SRP151493", "PRJNA478247", "Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome [ssRNA seq]", "GSE116358", "Transcriptome Analysis", "The goal of this study was to investigate DNA methylation and gene expression changes in a zebrafish model of ICF Syndrome which were generated by mutation of ICF gene zbtb24. Comparison of gene expression changes between wildtype and zbtb24 homozygous mutants revealed upregulation of interferon response genes following zbtb24 deletion. Upregulation of interferon response genes was blocked by mutation of the dsRNA helicase Mda5. Overall design: For RNA seq  gene expression was compared in whole two wpf zebrafish larvae that were wildtype or homozygous for the zbtb24mk22 mutant allele. We further performed RNA Seq analysis in three wpf zebrafish larvae that were WT  mda5mk29/mk29   zbtb24mk22/mk22  and mda5mk29/mk29 ;zbtb24mk22/mk22. Three samples consisting of pools of 10 larvae were examined for each genotype.  For ERRBS  DNA was separately isolated from the fins of three wildtype and three zbtb24mk22 homozygous mutant adults.", "parent bioproject:PRJNA478246", "pubmed:30484769", null, "WT1A", "GSM3229929", null, "tissue:Fin|development stage:Larvae|genotype/variation:WT", "WT1A", "Reads were mapped to the Zebrafish genome danRer7 using the rnaStar aligner v2.5.0a. We used the 2 pass mapping method outlined in Engstro\u0308m et.al Nat. Meth. 2013. The first mapping pass used a list of known annotated junctions from Ensemble. Novel junctions found in the first pass were then added to the known junctions and a second mapping pass was done on the second pass the RemoveNoncanoncial flag was used.\u00a0Expression counts were computed from the mapped reads using HTSeq v0.5.3 and Ensemble D.rerio v79 gene annotations. Normalization and differential expression was performed using DESeq. Genome build: danRer7 Supplementary files format and content: Tab delimited normalized RNA seq counts per million for each sample.", "Fin", null, "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", null, "development stage:Larvae|genotype/variation:WT", "GSM3229929", "GSM3229929: WT1A; Danio rerio; RNA Seq", "GSM3229929", null, "1", "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", "GEO Accession:GSM3229929", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP151493", null, null, "WT_1A_IGO_06387_2_S70_L008_R1_001.fastq.gz WT_1A_IGO_06387_2_S70_L008_R2_001.fastq.gz", "fastq fastq", 4153998900.0, 41539989.0, "GSM3229929 r1", "0:50 1:50", "A:1096533750;C:967821783;G:961567594;T:1116538303;N:11537470", 50, 50, null, null, 1096533750, 967821783, 961567594, 1116538303, 11537470, "SRX4314652", "SRS3474416", "SRA729908", "GEO", "Center for Pharmacogenomics, Washington University School of Medicine", 2, 0.95805, 0.96007, 0.10692, 0.10729, 0.65395, 0.65598, 0.47849, 0.48749, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-06-27", "Larval", "Larval", "Fin", "Surface Structure"], [48897, "SRR7444130", "SRX4314669", "SRS3474635", "SRP151494", "PRJNA478248", "Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome [dsRNA seq]", "GSE116359", "Transcriptome Analysis", "The goal of this study was to investigate DNA methylation and gene expression changes in a zebrafish model of ICF Syndrome which were generated by mutation of ICF gene zbtb24. Comparison of gene expression changes between wildtype and zbtb24 homozygous mutants revealed upregulation of interferon response genes following zbtb24 deletion. Upregulation of interferon response genes was blocked by mutation of the dsRNA helicase Mda5. Overall design: For RNA seq  gene expression was compared in whole two wpf zebrafish larvae that were wildtype or homozygous for the zbtb24mk22 mutant allele. We further performed RNA Seq analysis in three wpf zebrafish larvae that were WT  mda5mk29/mk29   zbtb24mk22/mk22  and mda5mk29/mk29 ;zbtb24mk22/mk22. Three samples consisting of pools of 10 larvae were examined for each genotype.  For ERRBS  DNA was separately isolated from the fins of three wildtype and three zbtb24mk22 homozygous mutant adults.", "parent bioproject:PRJNA478246", "pubmed:30484769", null, "ifih1WT z24WT 3", "GSM3229946", null, "tissue:Fin|development stage:Larvae|genotype/variation:ifih1 WT|tag:zbtb24 WT", "ifih1WT z24WT 3", "Raw RNA seq FASTQ reads were trimmed for adapters and preprocessed to remove low quality reads using Trimmomatic v0.33 arguments: LEADING:3 TRAILING:3 MINLEN:36 Bolger et al.  2014 prior to mapping to the Danio rerio GRCz10 reference genome assembly. Reads were mapped using TopHat v2.1.1 Kim et al.  2013 supplied with a reference General Features File GFF to the Danio rerioGRCz10 reference genome assembly  and with the following arguments:  i 10  I 5000   library type fr firststrand. Gene expression was estimated using Cuffquant a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand.  Expression level were normalized in FPKM units by Cuffnorm a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand. Genome build: GRCz10 Supplementary files format and content: Tab delimited normalized RNA seq FPKM for each sample.", "Fin", null, "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", null, "development stage:Larvae|genotype/variation:ifih1 WT|tag:zbtb24 WT", "GSM3229946", "GSM3229946: ifih1WT z24WT 3; Danio rerio; RNA Seq", "GSM3229946", null, "1", "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", "GEO Accession:GSM3229946", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP151494", null, null, "ifih1WT_z24WT_3_IGO_07828_3_S27_R1_001.fastq.gz ifih1WT_z24WT_3_IGO_07828_3_S27_R2_001.fastq.gz", "fastq fastq", 4987025820.0, 48892410.0, "GSM3229946 r1", "0:51 1:51", "A:1265790796;C:1221257508;G:1185306048;T:1305753966;N:8917502", 51, 51, null, null, 1265790796, 1221257508, 1185306048, 1305753966, 8917502, "SRX4314669", "SRS3474635", "SRA729909", "GEO", "Center for Pharmacogenomics, Washington University School of Medicine", 2, 0.96538, 0.9703, 0.06941, 0.06967, 0.68615, 0.68852, 0.46863, 0.47315, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-06-27", "Larval", "Larval", "Fin", "Surface Structure"], [48898, "SRR7444129", "SRX4314668", "SRS3474634", "SRP151494", "PRJNA478248", "Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome [dsRNA seq]", "GSE116359", "Transcriptome Analysis", "The goal of this study was to investigate DNA methylation and gene expression changes in a zebrafish model of ICF Syndrome which were generated by mutation of ICF gene zbtb24. Comparison of gene expression changes between wildtype and zbtb24 homozygous mutants revealed upregulation of interferon response genes following zbtb24 deletion. Upregulation of interferon response genes was blocked by mutation of the dsRNA helicase Mda5. Overall design: For RNA seq  gene expression was compared in whole two wpf zebrafish larvae that were wildtype or homozygous for the zbtb24mk22 mutant allele. We further performed RNA Seq analysis in three wpf zebrafish larvae that were WT  mda5mk29/mk29   zbtb24mk22/mk22  and mda5mk29/mk29 ;zbtb24mk22/mk22. Three samples consisting of pools of 10 larvae were examined for each genotype.  For ERRBS  DNA was separately isolated from the fins of three wildtype and three zbtb24mk22 homozygous mutant adults.", "parent bioproject:PRJNA478246", "pubmed:30484769", null, "ifih1WT z24WT 2", "GSM3229945", null, "tissue:Fin|development stage:Larvae|genotype/variation:ifih1 WT|tag:zbtb24 WT", "ifih1WT z24WT 2", "Raw RNA seq FASTQ reads were trimmed for adapters and preprocessed to remove low quality reads using Trimmomatic v0.33 arguments: LEADING:3 TRAILING:3 MINLEN:36 Bolger et al.  2014 prior to mapping to the Danio rerio GRCz10 reference genome assembly. Reads were mapped using TopHat v2.1.1 Kim et al.  2013 supplied with a reference General Features File GFF to the Danio rerioGRCz10 reference genome assembly  and with the following arguments:  i 10  I 5000   library type fr firststrand. Gene expression was estimated using Cuffquant a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand.  Expression level were normalized in FPKM units by Cuffnorm a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand. Genome build: GRCz10 Supplementary files format and content: Tab delimited normalized RNA seq FPKM for each sample.", "Fin", null, "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", null, "development stage:Larvae|genotype/variation:ifih1 WT|tag:zbtb24 WT", "GSM3229945", "GSM3229945: ifih1WT z24WT 2; Danio rerio; RNA Seq", "GSM3229945", null, "1", "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", "GEO Accession:GSM3229945", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP151494", null, null, "ifih1WT_z24WT_2_IGO_07828_2_S26_R2_001.fastq.gz ifih1WT_z24WT_2_IGO_07828_2_S26_R1_001.fastq.gz", "fastq fastq", 4640240712.0, 45492556.0, "GSM3229945 r1", "0:51 1:51", "A:1182933694;C:1132199918;G:1096661504;T:1219941706;N:8503890", 51, 51, null, null, 1182933694, 1132199918, 1096661504, 1219941706, 8503890, "SRX4314668", "SRS3474634", "SRA729909", "GEO", "Center for Pharmacogenomics, Washington University School of Medicine", 2, 0.96376, 0.9675, 0.08469, 0.0844, 0.67166, 0.67525, 0.46471, 0.47131, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-06-27", "Larval", "Larval", "Fin", "Surface Structure"], [48899, "SRR7444128", "SRX4314667", "SRS3474633", "SRP151494", "PRJNA478248", "Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome [dsRNA seq]", "GSE116359", "Transcriptome Analysis", "The goal of this study was to investigate DNA methylation and gene expression changes in a zebrafish model of ICF Syndrome which were generated by mutation of ICF gene zbtb24. Comparison of gene expression changes between wildtype and zbtb24 homozygous mutants revealed upregulation of interferon response genes following zbtb24 deletion. Upregulation of interferon response genes was blocked by mutation of the dsRNA helicase Mda5. Overall design: For RNA seq  gene expression was compared in whole two wpf zebrafish larvae that were wildtype or homozygous for the zbtb24mk22 mutant allele. We further performed RNA Seq analysis in three wpf zebrafish larvae that were WT  mda5mk29/mk29   zbtb24mk22/mk22  and mda5mk29/mk29 ;zbtb24mk22/mk22. Three samples consisting of pools of 10 larvae were examined for each genotype.  For ERRBS  DNA was separately isolated from the fins of three wildtype and three zbtb24mk22 homozygous mutant adults.", "parent bioproject:PRJNA478246", "pubmed:30484769", null, "ifih1WT z24WT 1", "GSM3229944", null, "tissue:Fin|development stage:Larvae|genotype/variation:ifih1 WT|tag:zbtb24 WT", "ifih1WT z24WT 1", "Raw RNA seq FASTQ reads were trimmed for adapters and preprocessed to remove low quality reads using Trimmomatic v0.33 arguments: LEADING:3 TRAILING:3 MINLEN:36 Bolger et al.  2014 prior to mapping to the Danio rerio GRCz10 reference genome assembly. Reads were mapped using TopHat v2.1.1 Kim et al.  2013 supplied with a reference General Features File GFF to the Danio rerioGRCz10 reference genome assembly  and with the following arguments:  i 10  I 5000   library type fr firststrand. Gene expression was estimated using Cuffquant a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand.  Expression level were normalized in FPKM units by Cuffnorm a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand. Genome build: GRCz10 Supplementary files format and content: Tab delimited normalized RNA seq FPKM for each sample.", "Fin", null, "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", null, "development stage:Larvae|genotype/variation:ifih1 WT|tag:zbtb24 WT", "GSM3229944", "GSM3229944: ifih1WT z24WT 1; Danio rerio; RNA Seq", "GSM3229944", null, "1", "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", "GEO Accession:GSM3229944", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP151494", null, null, "ifih1WT_z24WT_1_IGO_07828_1_S25_R1_001.fastq.gz ifih1WT_z24WT_1_IGO_07828_1_S25_R2_001.fastq.gz", "fastq fastq", 4549184088.0, 44599844.0, "GSM3229944 r1", "0:51 1:51", "A:1159412637;C:1111795159;G:1072779961;T:1197013276;N:8183055", 51, 51, null, null, 1159412637, 1111795159, 1072779961, 1197013276, 8183055, "SRX4314667", "SRS3474633", "SRA729909", "GEO", "Center for Pharmacogenomics, Washington University School of Medicine", 2, 0.96479, 0.96887, 0.07633, 0.07643, 0.68087, 0.68347, 0.46851, 0.47658, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-06-27", "Larval", "Larval", "Fin", "Surface Structure"], [48900, "SRR7444127", "SRX4314666", "SRS3474632", "SRP151494", "PRJNA478248", "Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome [dsRNA seq]", "GSE116359", "Transcriptome Analysis", "The goal of this study was to investigate DNA methylation and gene expression changes in a zebrafish model of ICF Syndrome which were generated by mutation of ICF gene zbtb24. Comparison of gene expression changes between wildtype and zbtb24 homozygous mutants revealed upregulation of interferon response genes following zbtb24 deletion. Upregulation of interferon response genes was blocked by mutation of the dsRNA helicase Mda5. Overall design: For RNA seq  gene expression was compared in whole two wpf zebrafish larvae that were wildtype or homozygous for the zbtb24mk22 mutant allele. We further performed RNA Seq analysis in three wpf zebrafish larvae that were WT  mda5mk29/mk29   zbtb24mk22/mk22  and mda5mk29/mk29 ;zbtb24mk22/mk22. Three samples consisting of pools of 10 larvae were examined for each genotype.  For ERRBS  DNA was separately isolated from the fins of three wildtype and three zbtb24mk22 homozygous mutant adults.", "parent bioproject:PRJNA478246", "pubmed:30484769", null, "ifih1WT z24Mu 3", "GSM3229943", null, "tissue:Fin|development stage:Larvae|genotype/variation:ifih1 WT|tag:zbtb24 Mutant", "ifih1WT z24Mu 3", "Raw RNA seq FASTQ reads were trimmed for adapters and preprocessed to remove low quality reads using Trimmomatic v0.33 arguments: LEADING:3 TRAILING:3 MINLEN:36 Bolger et al.  2014 prior to mapping to the Danio rerio GRCz10 reference genome assembly. Reads were mapped using TopHat v2.1.1 Kim et al.  2013 supplied with a reference General Features File GFF to the Danio rerioGRCz10 reference genome assembly  and with the following arguments:  i 10  I 5000   library type fr firststrand. Gene expression was estimated using Cuffquant a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand.  Expression level were normalized in FPKM units by Cuffnorm a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand. Genome build: GRCz10 Supplementary files format and content: Tab delimited normalized RNA seq FPKM for each sample.", "Fin", null, "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", null, "development stage:Larvae|genotype/variation:ifih1 WT|tag:zbtb24 Mutant", "GSM3229943", "GSM3229943: ifih1WT z24Mu 3; Danio rerio; RNA Seq", "GSM3229943", null, "1", "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", "GEO Accession:GSM3229943", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP151494", null, null, "ifih1WT_z24Mu_3_IGO_07828_9_S33_R1_001.fastq.gz ifih1WT_z24Mu_3_IGO_07828_9_S33_R2_001.fastq.gz", "fastq fastq", 5276089638.0, 51726369.0, "GSM3229943 r1", "0:51 1:51", "A:1351805083;C:1278775837;G:1240624382;T:1395247014;N:9637322", 51, 51, null, null, 1351805083, 1278775837, 1240624382, 1395247014, 9637322, "SRX4314666", "SRS3474632", "SRA729909", "GEO", "Center for Pharmacogenomics, Washington University School of Medicine", 2, 0.96006, 0.96326, 0.09783, 0.09794, 0.66685, 0.67073, 0.47385, 0.48651, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-06-27", "Larval", "Larval", "Fin", "Surface Structure"], [48901, "SRR7444126", "SRX4314665", "SRS3474631", "SRP151494", "PRJNA478248", "Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome [dsRNA seq]", "GSE116359", "Transcriptome Analysis", "The goal of this study was to investigate DNA methylation and gene expression changes in a zebrafish model of ICF Syndrome which were generated by mutation of ICF gene zbtb24. Comparison of gene expression changes between wildtype and zbtb24 homozygous mutants revealed upregulation of interferon response genes following zbtb24 deletion. Upregulation of interferon response genes was blocked by mutation of the dsRNA helicase Mda5. Overall design: For RNA seq  gene expression was compared in whole two wpf zebrafish larvae that were wildtype or homozygous for the zbtb24mk22 mutant allele. We further performed RNA Seq analysis in three wpf zebrafish larvae that were WT  mda5mk29/mk29   zbtb24mk22/mk22  and mda5mk29/mk29 ;zbtb24mk22/mk22. Three samples consisting of pools of 10 larvae were examined for each genotype.  For ERRBS  DNA was separately isolated from the fins of three wildtype and three zbtb24mk22 homozygous mutant adults.", "parent bioproject:PRJNA478246", "pubmed:30484769", null, "ifih1WT z24Mu 2", "GSM3229942", null, "tissue:Fin|development stage:Larvae|genotype/variation:ifih1 WT|tag:zbtb24 Mutant", "ifih1WT z24Mu 2", "Raw RNA seq FASTQ reads were trimmed for adapters and preprocessed to remove low quality reads using Trimmomatic v0.33 arguments: LEADING:3 TRAILING:3 MINLEN:36 Bolger et al.  2014 prior to mapping to the Danio rerio GRCz10 reference genome assembly. Reads were mapped using TopHat v2.1.1 Kim et al.  2013 supplied with a reference General Features File GFF to the Danio rerioGRCz10 reference genome assembly  and with the following arguments:  i 10  I 5000   library type fr firststrand. Gene expression was estimated using Cuffquant a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand.  Expression level were normalized in FPKM units by Cuffnorm a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand. Genome build: GRCz10 Supplementary files format and content: Tab delimited normalized RNA seq FPKM for each sample.", "Fin", null, "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", null, "development stage:Larvae|genotype/variation:ifih1 WT|tag:zbtb24 Mutant", "GSM3229942", "GSM3229942: ifih1WT z24Mu 2; Danio rerio; RNA Seq", "GSM3229942", null, "1", "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", "GEO Accession:GSM3229942", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP151494", null, null, "ifih1WT_z24Mu_2_IGO_07828_8_S32_R2_001.fastq.gz ifih1WT_z24Mu_2_IGO_07828_8_S32_R1_001.fastq.gz", "fastq fastq", 5674442988.0, 55631794.0, "GSM3229942 r1", "0:51 1:51", "A:1452597651;C:1378531446;G:1336131468;T:1496960264;N:10222159", 51, 51, null, null, 1452597651, 1378531446, 1336131468, 1496960264, 10222159, "SRX4314665", "SRS3474631", "SRA729909", "GEO", "Center for Pharmacogenomics, Washington University School of Medicine", 2, 0.96194, 0.96563, 0.0908, 0.09181, 0.67253, 0.67505, 0.46626, 0.47096, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-06-27", "Larval", "Larval", "Fin", "Surface Structure"], [48902, "SRR7444125", "SRX4314664", "SRS3474630", "SRP151494", "PRJNA478248", "Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome [dsRNA seq]", "GSE116359", "Transcriptome Analysis", "The goal of this study was to investigate DNA methylation and gene expression changes in a zebrafish model of ICF Syndrome which were generated by mutation of ICF gene zbtb24. Comparison of gene expression changes between wildtype and zbtb24 homozygous mutants revealed upregulation of interferon response genes following zbtb24 deletion. Upregulation of interferon response genes was blocked by mutation of the dsRNA helicase Mda5. Overall design: For RNA seq  gene expression was compared in whole two wpf zebrafish larvae that were wildtype or homozygous for the zbtb24mk22 mutant allele. We further performed RNA Seq analysis in three wpf zebrafish larvae that were WT  mda5mk29/mk29   zbtb24mk22/mk22  and mda5mk29/mk29 ;zbtb24mk22/mk22. Three samples consisting of pools of 10 larvae were examined for each genotype.  For ERRBS  DNA was separately isolated from the fins of three wildtype and three zbtb24mk22 homozygous mutant adults.", "parent bioproject:PRJNA478246", "pubmed:30484769", null, "ifih1WT z24Mu 1", "GSM3229941", null, "tissue:Fin|development stage:Larvae|genotype/variation:ifih1 WT|tag:zbtb24 Mutant", "ifih1WT z24Mu 1", "Raw RNA seq FASTQ reads were trimmed for adapters and preprocessed to remove low quality reads using Trimmomatic v0.33 arguments: LEADING:3 TRAILING:3 MINLEN:36 Bolger et al.  2014 prior to mapping to the Danio rerio GRCz10 reference genome assembly. Reads were mapped using TopHat v2.1.1 Kim et al.  2013 supplied with a reference General Features File GFF to the Danio rerioGRCz10 reference genome assembly  and with the following arguments:  i 10  I 5000   library type fr firststrand. Gene expression was estimated using Cuffquant a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand.  Expression level were normalized in FPKM units by Cuffnorm a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand. Genome build: GRCz10 Supplementary files format and content: Tab delimited normalized RNA seq FPKM for each sample.", "Fin", null, "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", null, "development stage:Larvae|genotype/variation:ifih1 WT|tag:zbtb24 Mutant", "GSM3229941", "GSM3229941: ifih1WT z24Mu 1; Danio rerio; RNA Seq", "GSM3229941", null, "1", "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", "GEO Accession:GSM3229941", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP151494", null, null, "ifih1WT_z24Mu_1_IGO_07828_7_S31_R2_001.fastq.gz ifih1WT_z24Mu_1_IGO_07828_7_S31_R1_001.fastq.gz", "fastq fastq", 5332447392.0, 52278896.0, "GSM3229941 r1", "0:51 1:51", "A:1364811486;C:1294095984;G:1255513596;T:1408377876;N:9648450", 51, 51, null, null, 1364811486, 1294095984, 1255513596, 1408377876, 9648450, "SRX4314664", "SRS3474630", "SRA729909", "GEO", "Center for Pharmacogenomics, Washington University School of Medicine", 2, 0.96196, 0.9654, 0.08911, 0.0894, 0.66856, 0.67203, 0.47158, 0.46941, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-06-27", "Larval", "Larval", "Fin", "Surface Structure"], [48903, "SRR7444124", "SRX4314663", "SRS3474629", "SRP151494", "PRJNA478248", "Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome [dsRNA seq]", "GSE116359", "Transcriptome Analysis", "The goal of this study was to investigate DNA methylation and gene expression changes in a zebrafish model of ICF Syndrome which were generated by mutation of ICF gene zbtb24. Comparison of gene expression changes between wildtype and zbtb24 homozygous mutants revealed upregulation of interferon response genes following zbtb24 deletion. Upregulation of interferon response genes was blocked by mutation of the dsRNA helicase Mda5. Overall design: For RNA seq  gene expression was compared in whole two wpf zebrafish larvae that were wildtype or homozygous for the zbtb24mk22 mutant allele. We further performed RNA Seq analysis in three wpf zebrafish larvae that were WT  mda5mk29/mk29   zbtb24mk22/mk22  and mda5mk29/mk29 ;zbtb24mk22/mk22. Three samples consisting of pools of 10 larvae were examined for each genotype.  For ERRBS  DNA was separately isolated from the fins of three wildtype and three zbtb24mk22 homozygous mutant adults.", "parent bioproject:PRJNA478246", "pubmed:30484769", null, "ifih1Mu z24WT 3", "GSM3229940", null, "tissue:Fin|development stage:Larvae|genotype/variation:ifih1 Mutant|tag:zbtb24 WT", "ifih1Mu z24WT 3", "Raw RNA seq FASTQ reads were trimmed for adapters and preprocessed to remove low quality reads using Trimmomatic v0.33 arguments: LEADING:3 TRAILING:3 MINLEN:36 Bolger et al.  2014 prior to mapping to the Danio rerio GRCz10 reference genome assembly. Reads were mapped using TopHat v2.1.1 Kim et al.  2013 supplied with a reference General Features File GFF to the Danio rerioGRCz10 reference genome assembly  and with the following arguments:  i 10  I 5000   library type fr firststrand. Gene expression was estimated using Cuffquant a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand.  Expression level were normalized in FPKM units by Cuffnorm a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand. Genome build: GRCz10 Supplementary files format and content: Tab delimited normalized RNA seq FPKM for each sample.", "Fin", null, "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", null, "development stage:Larvae|genotype/variation:ifih1 Mutant|tag:zbtb24 WT", "GSM3229940", "GSM3229940: ifih1Mu z24WT 3; Danio rerio; RNA Seq", "GSM3229940", null, "1", "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", "GEO Accession:GSM3229940", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP151494", null, null, "ifih1Mu_z24WT_3_IGO_07828_6_S30_R2_001.fastq.gz ifih1Mu_z24WT_3_IGO_07828_6_S30_R1_001.fastq.gz", "fastq fastq", 5346424146.0, 52415923.0, "GSM3229940 r1", "0:51 1:51", "A:1368795461;C:1298768841;G:1258299909;T:1411056305;N:9503630", 51, 51, null, null, 1368795461, 1298768841, 1258299909, 1411056305, 9503630, "SRX4314663", "SRS3474629", "SRA729909", "GEO", "Center for Pharmacogenomics, Washington University School of Medicine", 2, 0.96023, 0.96414, 0.09211, 0.09257, 0.66541, 0.66837, 0.46891, 0.45854, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-06-27", "Larval", "Larval", "Fin", "Surface Structure"], [48904, "SRR7444123", "SRX4314662", "SRS3474628", "SRP151494", "PRJNA478248", "Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome [dsRNA seq]", "GSE116359", "Transcriptome Analysis", "The goal of this study was to investigate DNA methylation and gene expression changes in a zebrafish model of ICF Syndrome which were generated by mutation of ICF gene zbtb24. Comparison of gene expression changes between wildtype and zbtb24 homozygous mutants revealed upregulation of interferon response genes following zbtb24 deletion. Upregulation of interferon response genes was blocked by mutation of the dsRNA helicase Mda5. Overall design: For RNA seq  gene expression was compared in whole two wpf zebrafish larvae that were wildtype or homozygous for the zbtb24mk22 mutant allele. We further performed RNA Seq analysis in three wpf zebrafish larvae that were WT  mda5mk29/mk29   zbtb24mk22/mk22  and mda5mk29/mk29 ;zbtb24mk22/mk22. Three samples consisting of pools of 10 larvae were examined for each genotype.  For ERRBS  DNA was separately isolated from the fins of three wildtype and three zbtb24mk22 homozygous mutant adults.", "parent bioproject:PRJNA478246", "pubmed:30484769", null, "ifih1Mu z24WT 2", "GSM3229939", null, "tissue:Fin|development stage:Larvae|genotype/variation:ifih1 Mutant|tag:zbtb24 WT", "ifih1Mu z24WT 2", "Raw RNA seq FASTQ reads were trimmed for adapters and preprocessed to remove low quality reads using Trimmomatic v0.33 arguments: LEADING:3 TRAILING:3 MINLEN:36 Bolger et al.  2014 prior to mapping to the Danio rerio GRCz10 reference genome assembly. Reads were mapped using TopHat v2.1.1 Kim et al.  2013 supplied with a reference General Features File GFF to the Danio rerioGRCz10 reference genome assembly  and with the following arguments:  i 10  I 5000   library type fr firststrand. Gene expression was estimated using Cuffquant a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand.  Expression level were normalized in FPKM units by Cuffnorm a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand. Genome build: GRCz10 Supplementary files format and content: Tab delimited normalized RNA seq FPKM for each sample.", "Fin", null, "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", null, "development stage:Larvae|genotype/variation:ifih1 Mutant|tag:zbtb24 WT", "GSM3229939", "GSM3229939: ifih1Mu z24WT 2; Danio rerio; RNA Seq", "GSM3229939", null, "1", "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", "GEO Accession:GSM3229939", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP151494", null, null, "ifih1Mu_z24WT_2_IGO_07828_5_S29_R1_001.fastq.gz ifih1Mu_z24WT_2_IGO_07828_5_S29_R2_001.fastq.gz", "fastq fastq", 5944176684.0, 58276242.0, "GSM3229939 r1", "0:51 1:51", "A:1530558421;C:1435721293;G:1386779917;T:1580241707;N:10875346", 51, 51, null, null, 1530558421, 1435721293, 1386779917, 1580241707, 10875346, "SRX4314662", "SRS3474628", "SRA729909", "GEO", "Center for Pharmacogenomics, Washington University School of Medicine", 2, 0.96031, 0.96443, 0.09096, 0.09097, 0.66929, 0.67241, 0.46155, 0.4794, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-06-27", "Larval", "Larval", "Fin", "Surface Structure"], [48905, "SRR7444122", "SRX4314661", "SRS3474627", "SRP151494", "PRJNA478248", "Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome [dsRNA seq]", "GSE116359", "Transcriptome Analysis", "The goal of this study was to investigate DNA methylation and gene expression changes in a zebrafish model of ICF Syndrome which were generated by mutation of ICF gene zbtb24. Comparison of gene expression changes between wildtype and zbtb24 homozygous mutants revealed upregulation of interferon response genes following zbtb24 deletion. Upregulation of interferon response genes was blocked by mutation of the dsRNA helicase Mda5. Overall design: For RNA seq  gene expression was compared in whole two wpf zebrafish larvae that were wildtype or homozygous for the zbtb24mk22 mutant allele. We further performed RNA Seq analysis in three wpf zebrafish larvae that were WT  mda5mk29/mk29   zbtb24mk22/mk22  and mda5mk29/mk29 ;zbtb24mk22/mk22. Three samples consisting of pools of 10 larvae were examined for each genotype.  For ERRBS  DNA was separately isolated from the fins of three wildtype and three zbtb24mk22 homozygous mutant adults.", "parent bioproject:PRJNA478246", "pubmed:30484769", null, "ifih1Mu z24WT 1", "GSM3229938", null, "tissue:Fin|development stage:Larvae|genotype/variation:ifih1 Mutant|tag:zbtb24 WT", "ifih1Mu z24WT 1", "Raw RNA seq FASTQ reads were trimmed for adapters and preprocessed to remove low quality reads using Trimmomatic v0.33 arguments: LEADING:3 TRAILING:3 MINLEN:36 Bolger et al.  2014 prior to mapping to the Danio rerio GRCz10 reference genome assembly. Reads were mapped using TopHat v2.1.1 Kim et al.  2013 supplied with a reference General Features File GFF to the Danio rerioGRCz10 reference genome assembly  and with the following arguments:  i 10  I 5000   library type fr firststrand. Gene expression was estimated using Cuffquant a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand.  Expression level were normalized in FPKM units by Cuffnorm a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand. Genome build: GRCz10 Supplementary files format and content: Tab delimited normalized RNA seq FPKM for each sample.", "Fin", null, "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", null, "development stage:Larvae|genotype/variation:ifih1 Mutant|tag:zbtb24 WT", "GSM3229938", "GSM3229938: ifih1Mu z24WT 1; Danio rerio; RNA Seq", "GSM3229938", null, "1", "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", "GEO Accession:GSM3229938", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP151494", null, null, "ifih1Mu_z24WT_1_IGO_07828_4_S28_R1_001.fastq.gz ifih1Mu_z24WT_1_IGO_07828_4_S28_R2_001.fastq.gz", "fastq fastq", 4335135150.0, 42501325.0, "GSM3229938 r1", "0:51 1:51", "A:1113133494;C:1048893773;G:1020239085;T:1145153354;N:7715444", 51, 51, null, null, 1113133494, 1048893773, 1020239085, 1145153354, 7715444, "SRX4314661", "SRS3474627", "SRA729909", "GEO", "Center for Pharmacogenomics, Washington University School of Medicine", 2, 0.96028, 0.96398, 0.08596, 0.08606, 0.6662, 0.66888, 0.46379, 0.47566, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-06-27", "Larval", "Larval", "Fin", "Surface Structure"], [48906, "SRR7444121", "SRX4314660", "SRS3474626", "SRP151494", "PRJNA478248", "Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome [dsRNA seq]", "GSE116359", "Transcriptome Analysis", "The goal of this study was to investigate DNA methylation and gene expression changes in a zebrafish model of ICF Syndrome which were generated by mutation of ICF gene zbtb24. Comparison of gene expression changes between wildtype and zbtb24 homozygous mutants revealed upregulation of interferon response genes following zbtb24 deletion. Upregulation of interferon response genes was blocked by mutation of the dsRNA helicase Mda5. Overall design: For RNA seq  gene expression was compared in whole two wpf zebrafish larvae that were wildtype or homozygous for the zbtb24mk22 mutant allele. We further performed RNA Seq analysis in three wpf zebrafish larvae that were WT  mda5mk29/mk29   zbtb24mk22/mk22  and mda5mk29/mk29 ;zbtb24mk22/mk22. Three samples consisting of pools of 10 larvae were examined for each genotype.  For ERRBS  DNA was separately isolated from the fins of three wildtype and three zbtb24mk22 homozygous mutant adults.", "parent bioproject:PRJNA478246", "pubmed:30484769", null, "ifih1Mu z24Mu 3", "GSM3229937", null, "tissue:Fin|development stage:Larvae|genotype/variation:ifih1 Mutant|tag:zbtb24 mutant", "ifih1Mu z24Mu 3", "Raw RNA seq FASTQ reads were trimmed for adapters and preprocessed to remove low quality reads using Trimmomatic v0.33 arguments: LEADING:3 TRAILING:3 MINLEN:36 Bolger et al.  2014 prior to mapping to the Danio rerio GRCz10 reference genome assembly. Reads were mapped using TopHat v2.1.1 Kim et al.  2013 supplied with a reference General Features File GFF to the Danio rerioGRCz10 reference genome assembly  and with the following arguments:  i 10  I 5000   library type fr firststrand. Gene expression was estimated using Cuffquant a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand.  Expression level were normalized in FPKM units by Cuffnorm a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand. Genome build: GRCz10 Supplementary files format and content: Tab delimited normalized RNA seq FPKM for each sample.", "Fin", null, "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", null, "development stage:Larvae|genotype/variation:ifih1 Mutant|tag:zbtb24 mutant", "GSM3229937", "GSM3229937: ifih1Mu z24Mu 3; Danio rerio; RNA Seq", "GSM3229937", null, "1", "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", "GEO Accession:GSM3229937", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP151494", null, null, "ifih1Mu_z24Mu_3_IGO_07828_12_S24_R1_001.fastq.gz ifih1Mu_z24Mu_3_IGO_07828_12_S24_R2_001.fastq.gz", "fastq fastq", 5227514280.0, 51250140.0, "GSM3229937 r1", "0:51 1:51", "A:1344879990;C:1261213568;G:1225325966;T:1386479002;N:9615754", 51, 51, null, null, 1344879990, 1261213568, 1225325966, 1386479002, 9615754, "SRX4314660", "SRS3474626", "SRA729909", "GEO", "Center for Pharmacogenomics, Washington University School of Medicine", 2, 0.96309, 0.96498, 0.08736, 0.08692, 0.67434, 0.6788, 0.47013, 0.47853, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-06-27", "Larval", "Larval", "Fin", "Surface Structure"], [48907, "SRR7444120", "SRX4314659", "SRS3474625", "SRP151494", "PRJNA478248", "Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome [dsRNA seq]", "GSE116359", "Transcriptome Analysis", "The goal of this study was to investigate DNA methylation and gene expression changes in a zebrafish model of ICF Syndrome which were generated by mutation of ICF gene zbtb24. Comparison of gene expression changes between wildtype and zbtb24 homozygous mutants revealed upregulation of interferon response genes following zbtb24 deletion. Upregulation of interferon response genes was blocked by mutation of the dsRNA helicase Mda5. Overall design: For RNA seq  gene expression was compared in whole two wpf zebrafish larvae that were wildtype or homozygous for the zbtb24mk22 mutant allele. We further performed RNA Seq analysis in three wpf zebrafish larvae that were WT  mda5mk29/mk29   zbtb24mk22/mk22  and mda5mk29/mk29 ;zbtb24mk22/mk22. Three samples consisting of pools of 10 larvae were examined for each genotype.  For ERRBS  DNA was separately isolated from the fins of three wildtype and three zbtb24mk22 homozygous mutant adults.", "parent bioproject:PRJNA478246", "pubmed:30484769", null, "ifih1Mu z24Mu 2", "GSM3229936", null, "tissue:Fin|development stage:Larvae|genotype/variation:ifih1 Mutant|tag:zbtb24 mutant", "ifih1Mu z24Mu 2", "Raw RNA seq FASTQ reads were trimmed for adapters and preprocessed to remove low quality reads using Trimmomatic v0.33 arguments: LEADING:3 TRAILING:3 MINLEN:36 Bolger et al.  2014 prior to mapping to the Danio rerio GRCz10 reference genome assembly. Reads were mapped using TopHat v2.1.1 Kim et al.  2013 supplied with a reference General Features File GFF to the Danio rerioGRCz10 reference genome assembly  and with the following arguments:  i 10  I 5000   library type fr firststrand. Gene expression was estimated using Cuffquant a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand.  Expression level were normalized in FPKM units by Cuffnorm a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand. Genome build: GRCz10 Supplementary files format and content: Tab delimited normalized RNA seq FPKM for each sample.", "Fin", null, "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", null, "development stage:Larvae|genotype/variation:ifih1 Mutant|tag:zbtb24 mutant", "GSM3229936", "GSM3229936: ifih1Mu z24Mu 2; Danio rerio; RNA Seq", "GSM3229936", null, "1", "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", "GEO Accession:GSM3229936", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP151494", null, null, "ifih1Mu_z24Mu_2_IGO_07828_11_S23_R1_001.fastq.gz ifih1Mu_z24Mu_2_IGO_07828_11_S23_R2_001.fastq.gz", "fastq fastq", 4920907176.0, 48244188.0, "GSM3229936 r1", "0:51 1:51", "A:1256352748;C:1195155437;G:1176053988;T:1284662400;N:8682603", 51, 51, null, null, 1256352748, 1195155437, 1176053988, 1284662400, 8682603, "SRX4314659", "SRS3474625", "SRA729909", "GEO", "Center for Pharmacogenomics, Washington University School of Medicine", 2, 0.96438, 0.96805, 0.07448, 0.07435, 0.68489, 0.68838, 0.45902, 0.47239, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-06-27", "Larval", "Larval", "Fin", "Surface Structure"], [48908, "SRR7444119", "SRX4314658", "SRS3474624", "SRP151494", "PRJNA478248", "Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome [dsRNA seq]", "GSE116359", "Transcriptome Analysis", "The goal of this study was to investigate DNA methylation and gene expression changes in a zebrafish model of ICF Syndrome which were generated by mutation of ICF gene zbtb24. Comparison of gene expression changes between wildtype and zbtb24 homozygous mutants revealed upregulation of interferon response genes following zbtb24 deletion. Upregulation of interferon response genes was blocked by mutation of the dsRNA helicase Mda5. Overall design: For RNA seq  gene expression was compared in whole two wpf zebrafish larvae that were wildtype or homozygous for the zbtb24mk22 mutant allele. We further performed RNA Seq analysis in three wpf zebrafish larvae that were WT  mda5mk29/mk29   zbtb24mk22/mk22  and mda5mk29/mk29 ;zbtb24mk22/mk22. Three samples consisting of pools of 10 larvae were examined for each genotype.  For ERRBS  DNA was separately isolated from the fins of three wildtype and three zbtb24mk22 homozygous mutant adults.", "parent bioproject:PRJNA478246", "pubmed:30484769", null, "ifih1Mu z24Mu 1", "GSM3229935", null, "tissue:Fin|development stage:Larvae|genotype/variation:ifih1 Mutant|tag:zbtb24 mutant", "ifih1Mu z24Mu 1", "Raw RNA seq FASTQ reads were trimmed for adapters and preprocessed to remove low quality reads using Trimmomatic v0.33 arguments: LEADING:3 TRAILING:3 MINLEN:36 Bolger et al.  2014 prior to mapping to the Danio rerio GRCz10 reference genome assembly. Reads were mapped using TopHat v2.1.1 Kim et al.  2013 supplied with a reference General Features File GFF to the Danio rerioGRCz10 reference genome assembly  and with the following arguments:  i 10  I 5000   library type fr firststrand. Gene expression was estimated using Cuffquant a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand.  Expression level were normalized in FPKM units by Cuffnorm a tool from Cufflinks v2.2.1  with following arguments   library type fr firststrand. Genome build: GRCz10 Supplementary files format and content: Tab delimited normalized RNA seq FPKM for each sample.", "Fin", null, "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", null, "development stage:Larvae|genotype/variation:ifih1 Mutant|tag:zbtb24 mutant", "GSM3229935", "GSM3229935: ifih1Mu z24Mu 1; Danio rerio; RNA Seq", "GSM3229935", null, "1", "Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer  500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit  with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run  using the TruSeq SBS v4 Kit Illumina.", "GEO Accession:GSM3229935", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP151494", null, null, "ifih1Mu_z24Mu_1_IGO_07828_10_S22_R1_001.fastq.gz ifih1Mu_z24Mu_1_IGO_07828_10_S22_R2_001.fastq.gz", "fastq fastq", 4804806900.0, 47105950.0, "GSM3229935 r1", "0:51 1:51", "A:1225079647;C:1170060925;G:1144916313;T:1256098833;N:8651182", 51, 51, null, null, 1225079647, 1170060925, 1144916313, 1256098833, 8651182, "SRX4314658", "SRS3474624", "SRA729909", "GEO", "Center for Pharmacogenomics, Washington University School of Medicine", 2, 0.96231, 0.96637, 0.08255, 0.08306, 0.68114, 0.68463, 0.48013, 0.47758, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-06-27", "Larval", "Larval", "Fin", "Surface Structure"], [49194, "SRR7789507", "SRX4644363", "SRS3742431", "SRP159668", "PRJNA489469", "The Lysosomal Transcription Factor TFEB regulates myelination downstream of the Rag Ragulator complex.", "GSE119332", "Transcriptome Analysis", "Purpose: To identify genes that are differentially expressed in oligodendrocytes between control and rraga mutant zebrafish  we performed RNA seq using the Illumina platform Overall design: Oligodendrocytes were isolated from control and rraga mutant zebrafish at 5 dpf using FACS sorting of Cldnk:GFP positive cells. RNA was extracted from these cells and sequenced using standard Illumina protocol.", null, "pubmed:30399334", null, "Cldnk GFP MUT", "GSM3370088", null, "tissue:Oligodendrocytes|strain:TL Tupfel long fin|developmental stage:5 dpf mutant", "Cldnk GFP MUT", "Trimmed  paired end reads from each sample were mapped to zebrafish reference genome using CLC Genomics Workbench 11.0 Danio rerio reference genome and transcriptome was downloaded from CLC Genomics workbench 11.0 Differential expression analysis was performed by comparing mapped control and rraga mutant reads using CLC Genomics Workbench 11.0 while controling for two independent experiments Gene ontology was performed using zebrafish annotations file v1.4 downloaded from Gene Ontology Consortium Genome build: GRCz11 Supplementary files format and content: Fold change", "Oligodendrocytes", null, "Cldnk:GFP cells were isolated from wildtype and rraga mutant samples by FACS sorting. Libraries were prepared using Illumina NextSeq Mid", null, "strain:TL Tupfel long fin|developmental stage:5 dpf mutant", "GSM3370088", "GSM3370088: Cldnk GFP MUT; Danio rerio; RNA Seq", "GSM3370088", null, "1", "Cldnk:GFP cells were isolated from wildtype and rraga mutant samples by FACS sorting. Libraries were prepared using Illumina NextSeq Mid", "GEO Accession:GSM3370088", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP159668", null, null, "cldnkGFP_MUT1.fastq.gz cldnkGFP_MUT2.fastq.gz", "fastq fastq", 7028935735.0, 49120946.0, "GSM3370088 r1", "0:71.46 1:71.63", "A:1941787078;C:1568186490;G:1573320845;T:1941675008;N:3966314", 71, 71, null, null, 1941787078, 1568186490, 1573320845, 1941675008, 3966314, "SRX4644363", "SRS3742431", "SRA767417", "GEO", "Talbot, Developmental Biology, Stanford University", 2, 0.93501, 0.93465, 0.06806, 0.06772, 0.77906, 0.78066, 0.52104, 0.52105, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-08-31", "Larval", "Larval", "Fin", "Surface Structure"], [49195, "SRR7789506", "SRX4644362", "SRS3742432", "SRP159668", "PRJNA489469", "The Lysosomal Transcription Factor TFEB regulates myelination downstream of the Rag Ragulator complex.", "GSE119332", "Transcriptome Analysis", "Purpose: To identify genes that are differentially expressed in oligodendrocytes between control and rraga mutant zebrafish  we performed RNA seq using the Illumina platform Overall design: Oligodendrocytes were isolated from control and rraga mutant zebrafish at 5 dpf using FACS sorting of Cldnk:GFP positive cells. RNA was extracted from these cells and sequenced using standard Illumina protocol.", null, "pubmed:30399334", null, "Cldnk GFP WT", "GSM3370087", null, "tissue:Oligodendrocytes|strain:TL Tupfel long fin|developmental stage:5 dpf type", "Cldnk GFP WT", "Trimmed  paired end reads from each sample were mapped to zebrafish reference genome using CLC Genomics Workbench 11.0 Danio rerio reference genome and transcriptome was downloaded from CLC Genomics workbench 11.0 Differential expression analysis was performed by comparing mapped control and rraga mutant reads using CLC Genomics Workbench 11.0 while controling for two independent experiments Gene ontology was performed using zebrafish annotations file v1.4 downloaded from Gene Ontology Consortium Genome build: GRCz11 Supplementary files format and content: Fold change", "Oligodendrocytes", null, "Cldnk:GFP cells were isolated from wildtype and rraga mutant samples by FACS sorting. Libraries were prepared using Illumina NextSeq Mid", null, "strain:TL Tupfel long fin|developmental stage:5 dpf type", "GSM3370087", "GSM3370087: Cldnk GFP WT; Danio rerio; RNA Seq", "GSM3370087", null, "1", "Cldnk:GFP cells were isolated from wildtype and rraga mutant samples by FACS sorting. Libraries were prepared using Illumina NextSeq Mid", "GEO Accession:GSM3370087", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP159668", null, null, "cldnkGFP_WT2.fastq.gz cldnkGFP_WT1.fastq.gz", "fastq fastq", 6674339658.0, 46733475.0, "GSM3370087 r1", "0:71.27 1:71.55", "A:1817040601;C:1501041809;G:1524935125;T:1827161188;N:4160935", 71, 71, null, null, 1817040601, 1501041809, 1524935125, 1827161188, 4160935, "SRX4644362", "SRS3742432", "SRA767417", "GEO", "Talbot, Developmental Biology, Stanford University", 2, 0.93563, 0.93694, 0.0541, 0.05296, 0.81339, 0.82572, 0.52248, 0.52293, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-08-31", "Larval", "Larval", "Fin", "Surface Structure"], [61429, "SRR12749699", "SRX9221655", "SRS7455356", "SRP285950", "PRJNA666695", "Single cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae", "GSE158851", "Transcriptome Analysis", "Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single cell RNA sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation.  Methods: 150 of regenerating caudal fin cut and intact caudal fine uncut samples were dissociated and loaded into the 10x Genomics Chromium Platform  and sequenced using Illumina NovaSeq 6000.  Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single molecule based sequencing technology for high throughput profiling of both intact uncut and regenerating caudal fin samples cut at 24hpA. We confirmed the presence of macrophage subsets  previously described by our group to govern zebrafish fin regeneration  and identified a novel blastemal cell population. Overall design: Cells from intact and regenerating caudal fin were used for single cell RNA sequencing 10xGenomics Chromium Platform  and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection UMAP.", null, "pubmed:34732706;pubmed:35664055", null, "Uncut caudal fin scRNA", "GSM4812244", null, "source name:caudal fin|tissue:caudal fin|developmental stage:larvae|treatment:uncut|time:24 hours post amputation", "Uncut caudal fin scRNA", "Image analyses and base calling were performed using the NovaSeq Control Software and Real Time Analysis component Illumina. Demultiplexing was performed using cellranger mkfastq v3.1.0. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV Sequencing Analysis Viewer. cellranger count v3.1.0 was used to align reads to the reference genome and generate the raw and filtered gene barcodes matrices. cellranger aggr v3.1.0 was used to combine the results of the two samples. Genome build: danRer11 Supplementary files format and content: MEX file format\u00a0: the matrix.mtx file contains the filtered gene barcode matrix total UMI count per cell and gene combination\u00a0; the .tsv files contain all annotated genes and cell barcodes represented in the mtx file. In the file Aggregation barcodes.tsv  barcodes appended with ' 1' represent the sample 'Cut' and barcodes appended with ' 2' represent the sample 'UnCut'.", "caudal fin", null, "Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/\u03bcl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer\u2019s instructions using Chromium\u2122 Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.", null, "tissue:caudal fin|developmental stage:larvae|treatment:uncut|time:24 hours post amputation", "GSM4812244", "GSM4812244: Uncut caudal fin scRNA; Danio rerio; RNA Seq", "GSM4812244", null, "1", "Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/\u03bcl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer's instructions using Chromium\u2122 Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.", "GEO Accession:GSM4812244", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP285950", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=Uncut S8 L001 R1 001.fastq.gz   read2PairFiles=Uncut S8 L001 R2 001.fastq.gz   read3PairFiles=Uncut S8 L001 I1 001.fastq.gz", "Uncut_S8_L001_I1_001.fastq.gz Uncut_S8_L001_R1_001.fastq.gz Uncut_S8_L001_R2_001.fastq.gz", "fastq fastq fastq", 18909629967.0, 153736829.0, "GSM4812244 r1", "0:28 1:87 2:8", "A:5220924848;C:4279280050;G:4788532540;T:4619612909;N:1279620", 28, 87, 8, null, 5220924848, 4279280050, 4788532540, 4619612909, 1279620, "SRX9221655", "SRS7455356", "SRA1136463", "GEO", "Institute for Regenerative Medecine and Biotherapy, University Hospital of Montpellier, Inserm", 1, 0.63376, null, 0.11724, null, 0.8393, null, 0.55679, null, 87, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "France", "2020-09-30", "Larval", "Larval", "Fin", "Surface Structure"], [61430, "SRR12749700", "SRX9221655", "SRS7455356", "SRP285950", "PRJNA666695", "Single cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae", "GSE158851", "Transcriptome Analysis", "Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single cell RNA sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation.  Methods: 150 of regenerating caudal fin cut and intact caudal fine uncut samples were dissociated and loaded into the 10x Genomics Chromium Platform  and sequenced using Illumina NovaSeq 6000.  Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single molecule based sequencing technology for high throughput profiling of both intact uncut and regenerating caudal fin samples cut at 24hpA. We confirmed the presence of macrophage subsets  previously described by our group to govern zebrafish fin regeneration  and identified a novel blastemal cell population. Overall design: Cells from intact and regenerating caudal fin were used for single cell RNA sequencing 10xGenomics Chromium Platform  and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection UMAP.", null, "pubmed:34732706;pubmed:35664055", null, "Uncut caudal fin scRNA", "GSM4812244", null, "source name:caudal fin|tissue:caudal fin|developmental stage:larvae|treatment:uncut|time:24 hours post amputation", "Uncut caudal fin scRNA", "Image analyses and base calling were performed using the NovaSeq Control Software and Real Time Analysis component Illumina. Demultiplexing was performed using cellranger mkfastq v3.1.0. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV Sequencing Analysis Viewer. cellranger count v3.1.0 was used to align reads to the reference genome and generate the raw and filtered gene barcodes matrices. cellranger aggr v3.1.0 was used to combine the results of the two samples. Genome build: danRer11 Supplementary files format and content: MEX file format\u00a0: the matrix.mtx file contains the filtered gene barcode matrix total UMI count per cell and gene combination\u00a0; the .tsv files contain all annotated genes and cell barcodes represented in the mtx file. In the file Aggregation barcodes.tsv  barcodes appended with ' 1' represent the sample 'Cut' and barcodes appended with ' 2' represent the sample 'UnCut'.", "caudal fin", null, "Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/\u03bcl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer\u2019s instructions using Chromium\u2122 Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.", null, "tissue:caudal fin|developmental stage:larvae|treatment:uncut|time:24 hours post amputation", "GSM4812244", "GSM4812244: Uncut caudal fin scRNA; Danio rerio; RNA Seq", "GSM4812244", null, "1", "Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/\u03bcl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer's instructions using Chromium\u2122 Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.", "GEO Accession:GSM4812244", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP285950", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=Uncut S8 L002 R1 001.fastq.gz   read2PairFiles=Uncut S8 L002 R2 001.fastq.gz   read3PairFiles=Uncut S8 L002 I1 001.fastq.gz", "Uncut_S8_L002_I1_001.fastq.gz Uncut_S8_L002_R1_001.fastq.gz Uncut_S8_L002_R2_001.fastq.gz", "fastq fastq fastq", 18967585107.0, 154208009.0, "GSM4812244 r2", "0:28 1:87 2:8", "A:5236542259;C:4292274179;G:4804216460;T:4633355352;N:1196857", 28, 87, 8, null, 5236542259, 4292274179, 4804216460, 4633355352, 1196857, "SRX9221655", "SRS7455356", "SRA1136463", "GEO", "Institute for Regenerative Medecine and Biotherapy, University Hospital of Montpellier, Inserm", 1, 0.63437, null, 0.11726, null, 0.83857, null, 0.5661, null, 87, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "France", "2020-09-30", "Larval", "Larval", "Fin", "Surface Structure"], [61431, "SRR12749697", "SRX9221654", "SRS7455355", "SRP285950", "PRJNA666695", "Single cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae", "GSE158851", "Transcriptome Analysis", "Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single cell RNA sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation.  Methods: 150 of regenerating caudal fin cut and intact caudal fine uncut samples were dissociated and loaded into the 10x Genomics Chromium Platform  and sequenced using Illumina NovaSeq 6000.  Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single molecule based sequencing technology for high throughput profiling of both intact uncut and regenerating caudal fin samples cut at 24hpA. We confirmed the presence of macrophage subsets  previously described by our group to govern zebrafish fin regeneration  and identified a novel blastemal cell population. Overall design: Cells from intact and regenerating caudal fin were used for single cell RNA sequencing 10xGenomics Chromium Platform  and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection UMAP.", null, "pubmed:34732706;pubmed:35664055", null, "Cut caudal fin scRNA", "GSM4812243", null, "source name:caudal fin|tissue:caudal fin|developmental stage:larvae|treatment:cut|time:24 hours", "Cut caudal fin scRNA", "Image analyses and base calling were performed using the NovaSeq Control Software and Real Time Analysis component Illumina. Demultiplexing was performed using cellranger mkfastq v3.1.0. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV Sequencing Analysis Viewer. cellranger count v3.1.0 was used to align reads to the reference genome and generate the raw and filtered gene barcodes matrices. cellranger aggr v3.1.0 was used to combine the results of the two samples. Genome build: danRer11 Supplementary files format and content: MEX file format\u00a0: the matrix.mtx file contains the filtered gene barcode matrix total UMI count per cell and gene combination\u00a0; the .tsv files contain all annotated genes and cell barcodes represented in the mtx file. In the file Aggregation barcodes.tsv  barcodes appended with ' 1' represent the sample 'Cut' and barcodes appended with ' 2' represent the sample 'UnCut'.", "caudal fin", null, "Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/\u03bcl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer\u2019s instructions using Chromium\u2122 Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.", null, "tissue:caudal fin|developmental stage:larvae|treatment:cut|time:24 hours", "GSM4812243", "GSM4812243: Cut caudal fin scRNA; Danio rerio; RNA Seq", "GSM4812243", null, "1", "Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/\u03bcl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer's instructions using Chromium\u2122 Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.", "GEO Accession:GSM4812243", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP285950", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=Cut S7 L001 R1 001.fastq.gz   read2PairFiles=Cut S7 L001 R2 001.fastq.gz   read3PairFiles=Cut S7 L001 I1 001.fastq.gz", "Cut_S7_L001_I1_001.fastq.gz Cut_S7_L001_R1_001.fastq.gz Cut_S7_L001_R2_001.fastq.gz", "fastq fastq fastq", 17453571711.0, 141898957.0, "GSM4812243 r1", "0:28 1:87 2:8", "A:4820960991;C:3908308491;G:4347557585;T:4375565175;N:1179469", 28, 87, 8, null, 4820960991, 3908308491, 4347557585, 4375565175, 1179469, "SRX9221654", "SRS7455355", "SRA1136463", "GEO", "Institute for Regenerative Medecine and Biotherapy, University Hospital of Montpellier, Inserm", 1, 0.63902, null, 0.11232, null, 0.82235, null, 0.50797, null, 87, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "France", "2020-09-30", "Larval", "Larval", "Fin", "Surface Structure"], [61432, "SRR12749698", "SRX9221654", "SRS7455355", "SRP285950", "PRJNA666695", "Single cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae", "GSE158851", "Transcriptome Analysis", "Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single cell RNA sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation.  Methods: 150 of regenerating caudal fin cut and intact caudal fine uncut samples were dissociated and loaded into the 10x Genomics Chromium Platform  and sequenced using Illumina NovaSeq 6000.  Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single molecule based sequencing technology for high throughput profiling of both intact uncut and regenerating caudal fin samples cut at 24hpA. We confirmed the presence of macrophage subsets  previously described by our group to govern zebrafish fin regeneration  and identified a novel blastemal cell population. Overall design: Cells from intact and regenerating caudal fin were used for single cell RNA sequencing 10xGenomics Chromium Platform  and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection UMAP.", null, "pubmed:34732706;pubmed:35664055", null, "Cut caudal fin scRNA", "GSM4812243", null, "source name:caudal fin|tissue:caudal fin|developmental stage:larvae|treatment:cut|time:24 hours", "Cut caudal fin scRNA", "Image analyses and base calling were performed using the NovaSeq Control Software and Real Time Analysis component Illumina. Demultiplexing was performed using cellranger mkfastq v3.1.0. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV Sequencing Analysis Viewer. cellranger count v3.1.0 was used to align reads to the reference genome and generate the raw and filtered gene barcodes matrices. cellranger aggr v3.1.0 was used to combine the results of the two samples. Genome build: danRer11 Supplementary files format and content: MEX file format\u00a0: the matrix.mtx file contains the filtered gene barcode matrix total UMI count per cell and gene combination\u00a0; the .tsv files contain all annotated genes and cell barcodes represented in the mtx file. In the file Aggregation barcodes.tsv  barcodes appended with ' 1' represent the sample 'Cut' and barcodes appended with ' 2' represent the sample 'UnCut'.", "caudal fin", null, "Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/\u03bcl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer\u2019s instructions using Chromium\u2122 Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.", null, "tissue:caudal fin|developmental stage:larvae|treatment:cut|time:24 hours", "GSM4812243", "GSM4812243: Cut caudal fin scRNA; Danio rerio; RNA Seq", "GSM4812243", null, "1", "Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/\u03bcl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer's instructions using Chromium\u2122 Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.", "GEO Accession:GSM4812243", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP285950", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=Cut S7 L002 R1 001.fastq.gz   read2PairFiles=Cut S7 L002 R2 001.fastq.gz   read3PairFiles=Cut S7 L002 I1 001.fastq.gz", "Cut_S7_L002_I1_001.fastq.gz Cut_S7_L002_R1_001.fastq.gz Cut_S7_L002_R2_001.fastq.gz", "fastq fastq fastq", 17511283926.0, 142368162.0, "GSM4812243 r2", "0:28 1:87 2:8", "A:4836849959;C:3920920286;G:4362769830;T:4389644044;N:1099807", 28, 87, 8, null, 4836849959, 3920920286, 4362769830, 4389644044, 1099807, "SRX9221654", "SRS7455355", "SRA1136463", "GEO", "Institute for Regenerative Medecine and Biotherapy, University Hospital of Montpellier, Inserm", 1, 0.63847, null, 0.11249, null, 0.82231, null, 0.51524, null, 87, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "France", "2020-09-30", "Larval", "Larval", "Fin", "Surface Structure"], [65645, "SRR15458886", "SRX11758247", "SRS9777785", "SRP332539", "PRJNA754591", "Next Generation Sequencing Facilitates Quantitative Analysis of Uncut and Injured Larval Zebrafish Fin Fold Transcriptomes", "GSE182113", "Transcriptome Analysis", "We report increased expression of mitochondrial biogenesis genes in regnerating larval fin fold Overall design: Larval fin fold mRNA profiles of 3 dpf control and fin amputated zebrafish", null, "pubmed:34622167", null, "Uncut fin fold rep3", "GSM5518678", null, "source name:larval fin fold|tissue:larval fin fold|treatment:uncut", "Uncut fin fold rep3", "Tophat and Cufflinks DESeq2 Differential Analysis in R Supplementary files format and content: raw count and normalized counts", "larval fin fold", null, "Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina", null, "tissue:larval fin fold|treatment:uncut", "GSM5518678", "GSM5518678: Uncut fin fold rep3; Danio rerio; RNA Seq", "GSM5518678", null, "1", "Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina", "GEO Accession:GSM5518678", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332539", null, null, "unDMSO-3_S9_L008_R1_001.fastq.gz", "fastq", 1463248650.0, 28691150.0, "GSM5518678 r1", "0:51 1:0", "A:397962408;C:373148163;G:352701142;T:339050095;N:386842", 51, 0, null, null, 397962408, 373148163, 352701142, 339050095, 386842, "SRX11758247", "SRS9777785", "SRA1278109", "GEO", "National Tsing-Hua University", 1, 0.91418, null, 0.06051, null, 0.77958, null, 0.45543, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Taiwan", "2021-08-14", "Larval", "Larval", "Fin", "Surface Structure"], [65646, "SRR15458885", "SRX11758246", "SRS9777786", "SRP332539", "PRJNA754591", "Next Generation Sequencing Facilitates Quantitative Analysis of Uncut and Injured Larval Zebrafish Fin Fold Transcriptomes", "GSE182113", "Transcriptome Analysis", "We report increased expression of mitochondrial biogenesis genes in regnerating larval fin fold Overall design: Larval fin fold mRNA profiles of 3 dpf control and fin amputated zebrafish", null, "pubmed:34622167", null, "Uncut fin fold rep2", "GSM5518677", null, "source name:larval fin fold|tissue:larval fin fold|treatment:uncut", "Uncut fin fold rep2", "Tophat and Cufflinks DESeq2 Differential Analysis in R Supplementary files format and content: raw count and normalized counts", "larval fin fold", null, "Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina", null, "tissue:larval fin fold|treatment:uncut", "GSM5518677", "GSM5518677: Uncut fin fold rep2; Danio rerio; RNA Seq", "GSM5518677", null, "1", "Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina", "GEO Accession:GSM5518677", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332539", null, null, "unDMSO-2_S5_L008_R1_001.fastq.gz", "fastq", 1534053174.0, 30079474.0, "GSM5518677 r1", "0:51 1:0", "A:375567653;C:393670046;G:387649149;T:376851052;N:315274", 51, 0, null, null, 375567653, 393670046, 387649149, 376851052, 315274, "SRX11758246", "SRS9777786", "SRA1278109", "GEO", "National Tsing-Hua University", 1, 0.95025, null, 0.06073, null, 0.7245, null, 0.46029, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Taiwan", "2021-08-14", "Larval", "Larval", "Fin", "Surface Structure"], [65647, "SRR15458884", "SRX11758245", "SRS9777784", "SRP332539", "PRJNA754591", "Next Generation Sequencing Facilitates Quantitative Analysis of Uncut and Injured Larval Zebrafish Fin Fold Transcriptomes", "GSE182113", "Transcriptome Analysis", "We report increased expression of mitochondrial biogenesis genes in regnerating larval fin fold Overall design: Larval fin fold mRNA profiles of 3 dpf control and fin amputated zebrafish", null, "pubmed:34622167", null, "Uncut fin fold rep1", "GSM5518676", null, "source name:larval fin fold|tissue:larval fin fold|treatment:uncut", "Uncut fin fold rep1", "Tophat and Cufflinks DESeq2 Differential Analysis in R Supplementary files format and content: raw count and normalized counts", "larval fin fold", null, "Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina", null, "tissue:larval fin fold|treatment:uncut", "GSM5518676", "GSM5518676: Uncut fin fold rep1; Danio rerio; RNA Seq", "GSM5518676", null, "1", "Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina", "GEO Accession:GSM5518676", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332539", null, null, "unDMSO-1_S1_L008_R1_001.fastq.gz", "fastq", 1174809939.0, 23035489.0, "GSM5518676 r1", "0:51 1:0", "A:288665248;C:299039651;G:296219712;T:290639919;N:245409", 51, 0, null, null, 288665248, 299039651, 296219712, 290639919, 245409, "SRX11758245", "SRS9777784", "SRA1278109", "GEO", "National Tsing-Hua University", 1, 0.94689, null, 0.06026, null, 0.73204, null, 0.44369, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Taiwan", "2021-08-14", "Larval", "Larval", "Fin", "Surface Structure"], [65648, "SRR15458889", "SRX11758244", "SRS9777782", "SRP332539", "PRJNA754591", "Next Generation Sequencing Facilitates Quantitative Analysis of Uncut and Injured Larval Zebrafish Fin Fold Transcriptomes", "GSE182113", "Transcriptome Analysis", "We report increased expression of mitochondrial biogenesis genes in regnerating larval fin fold Overall design: Larval fin fold mRNA profiles of 3 dpf control and fin amputated zebrafish", null, "pubmed:34622167", null, "4hpa rep3", "GSM5518681", null, "source name:larval fin fold|tissue:larval fin fold|treatment:4h post amputation", "4hpa rep3", "Tophat and Cufflinks DESeq2 Differential Analysis in R Supplementary files format and content: raw count and normalized counts", "larval fin fold", null, "Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina", null, "tissue:larval fin fold|treatment:4h post amputation", "GSM5518681", "GSM5518681: 4hpa rep3; Danio rerio; RNA Seq", "GSM5518681", null, "1", "Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina", "GEO Accession:GSM5518681", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332539", null, null, "4hDMSO-3_S11_L008_R1_001.fastq.gz", "fastq", 1550745576.0, 30406776.0, "GSM5518681 r1", "0:51 1:0", "A:387174249;C:402754112;G:383357587;T:377128496;N:331132", 51, 0, null, null, 387174249, 402754112, 383357587, 377128496, 331132, "SRX11758244", "SRS9777782", "SRA1278109", "GEO", "National Tsing-Hua University", 1, 0.9503, null, 0.06384, null, 0.71723, null, 0.4534, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Taiwan", "2021-08-14", "Larval", "Larval", "Fin", "Surface Structure"], [65649, "SRR15458888", "SRX11758243", "SRS9777783", "SRP332539", "PRJNA754591", "Next Generation Sequencing Facilitates Quantitative Analysis of Uncut and Injured Larval Zebrafish Fin Fold Transcriptomes", "GSE182113", "Transcriptome Analysis", "We report increased expression of mitochondrial biogenesis genes in regnerating larval fin fold Overall design: Larval fin fold mRNA profiles of 3 dpf control and fin amputated zebrafish", null, "pubmed:34622167", null, "4hpa rep2", "GSM5518680", null, "source name:larval fin fold|tissue:larval fin fold|treatment:4h post amputation", "4hpa rep2", "Tophat and Cufflinks DESeq2 Differential Analysis in R Supplementary files format and content: raw count and normalized counts", "larval fin fold", null, "Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina", null, "tissue:larval fin fold|treatment:4h post amputation", "GSM5518680", "GSM5518680: 4hpa rep2; Danio rerio; RNA Seq", "GSM5518680", null, "1", "Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina", "GEO Accession:GSM5518680", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332539", null, null, "4hDMSO-2_S7_L008_R1_001.fastq.gz", "fastq", 1410871038.0, 27664138.0, "GSM5518680 r1", "0:51 1:0", "A:366166995;C:357462752;G:343178962;T:343741181;N:321148", 51, 0, null, null, 366166995, 357462752, 343178962, 343741181, 321148, "SRX11758243", "SRS9777783", "SRA1278109", "GEO", "National Tsing-Hua University", 1, 0.93684, null, 0.06834, null, 0.71705, null, 0.46343, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Taiwan", "2021-08-14", "Larval", "Larval", "Fin", "Surface Structure"], [65650, "SRR15458887", "SRX11758242", "SRS9777781", "SRP332539", "PRJNA754591", "Next Generation Sequencing Facilitates Quantitative Analysis of Uncut and Injured Larval Zebrafish Fin Fold Transcriptomes", "GSE182113", "Transcriptome Analysis", "We report increased expression of mitochondrial biogenesis genes in regnerating larval fin fold Overall design: Larval fin fold mRNA profiles of 3 dpf control and fin amputated zebrafish", null, "pubmed:34622167", null, "4hpa rep1", "GSM5518679", null, "source name:larval fin fold|tissue:larval fin fold|treatment:4h post amputation", "4hpa rep1", "Tophat and Cufflinks DESeq2 Differential Analysis in R Supplementary files format and content: raw count and normalized counts", "larval fin fold", null, "Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina", null, "tissue:larval fin fold|treatment:4h post amputation", "GSM5518679", "GSM5518679: 4hpa rep1; Danio rerio; RNA Seq", "GSM5518679", null, "1", "Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina", "GEO Accession:GSM5518679", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332539", null, null, "4hDMSO-1_S3_L008_R1_001.fastq.gz", "fastq", 1262762193.0, 24760043.0, "GSM5518679 r1", "0:51 1:0", "A:314766829;C:319337908;G:315265233;T:313124694;N:267529", 51, 0, null, null, 314766829, 319337908, 315265233, 313124694, 267529, "SRX11758242", "SRS9777781", "SRA1278109", "GEO", "National Tsing-Hua University", 1, 0.9491, null, 0.0613, null, 0.7135, null, 0.45795, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Taiwan", "2021-08-14", "Larval", "Larval", "Fin", "Surface Structure"], [76699, "SRR25258795", "SRX21004794", "SRS18278659", "SRP449335", "PRJNA994500", "Infection induced inflammation impairs wound healing through IL 1b signaling", "GSE237265", "Transcriptome Analysis", "Wound healing is impaired by infection; however  how microbe induced inflammation modulates tissue repair remains unclear. We took advantage of the optical transparency of zebrafish and a genetically tractable microbe  Listeria monocytogenes  to probe the role of infection and inflammation in wound healing. We found a critical window of microbial clearance necessary to limit persistent inflammation and enable efficient wound repair. Infection with bacteria engineered to activate the inflammasome  Lm Pyro  induced persistent inflammation and impaired healing despite low bacterial burden. In contrast  infection with an anti inflammatory  apoptosis inducing strain  Lm Apo  had similar infectious burden but was associated with rapid wound repair. Inflammatory infections induced il 1b expression and blocking IL 1R signaling partially rescued wound healing in the presence of persistent infection. Taken together  our findings suggest that the dynamics of microbe induced tissue inflammation impacts repair in complex tissue damage independent of bacterial load  with a critical early window for efficient tissue repair. Overall design: RNA seq gene expression analysis of caudal fins of 4 dpf zebrafish post wounding and infection n = 9: 3 replicates from each of 3 treatments", null, "pubmed:38577110", null, "D9 uninfected", "GSM7598093", null, "source name:caudal fin|tissue:caudal fin|tissue id:ZFA:0001058|line:AB|age:Larval:Day 4|age id:ZFS:0000036|treatment:control|treatment id:EFO:0001461|geo loc name:missing|collection date:missing", "D9 uninfected", "Reads were aligned to the genome using STAR v2.7.8a with default parameters except for except for outFilterMismatchNoverLmax 0.1  outFilterScoreMinOverLread 0.33  and outFilterMatchNminOverLread 0.33  Gene abundances were estimated using RSEM v1.3.3 with additonal parameters   paired end    estimate rspd  and   strandedness none Assembly: GRCz11 Ensembl 95 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file", "caudal fin", "3 dpf zebrafish were placed in 5 mL E3 medium containing Tricaine with 5x108 CFU L. monocytogenes and caudal fins of larvae were transected using surgical blade Feather no. 10 at the tip of the notochord without xxx to the notochord. For uninfected wounds  sterile PBS was added in the medium instead of bacterial resuspension.", "Tail fins of 50 larvae were pooled and collected in ice cold PBS for each condition in each biological replicate. RNA was extracted from pooled tail fins using TRIzol reagent and RNAqueous Micro Kit Invitrogen. PolyA  NEBNext\u00ae Ultra\u2122 II RNA Library Prep Kit for Illumina\u00ae was used for library construction.", "Upon fertilization  zebrafish embryos were transferred into E3 medium and maintained at 28.5\u00b0C.", "tissue:caudal fin|tissue id:ZFA:0001058|line:AB|age:Larval:Day 4|age id:ZFS:0000036|treatment:control|treatment id:EFO:0001461", "GSM7598093", "GSM7598093: D9 uninfected; Danio rerio; RNA Seq", "GSM7598093 r1", "GSM7598093", "1", "Tail fins of 50 larvae were pooled and collected in ice cold PBS for each condition in each biological replicate. RNA was extracted from pooled tail fins using TRIzol reagent and RNAqueous Micro Kit Invitrogen. PolyA  NEBNext\u00ae Ultra\u2122 II RNA Library Prep Kit for Illumina\u00ae was used for library construction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP449335", null, "loader:fastq load.py", "D9_R1_001.fastq.gz D9_R2_001.fastq.gz", "fastq fastq", 8686889570.0, 28764535.0, "GSM7598093 r1", "0:151 1:151", "A:2296370538;C:2049767640;G:2085089469;T:2255082220;N:579703", 151, 151, null, null, 2296370538, 2049767640, 2085089469, 2255082220, 579703, "SRX21004794", "SRS18278659", "SRA1672430", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 2, 0.936, 0.93538, 0.07614, 0.07655, 0.70153, 0.70826, 0.48553, 0.48537, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-07-13", "Larval", "Larval", "Fin", "Surface Structure"], [76700, "SRR25258796", "SRX21004793", "SRS18278656", "SRP449335", "PRJNA994500", "Infection induced inflammation impairs wound healing through IL 1b signaling", "GSE237265", "Transcriptome Analysis", "Wound healing is impaired by infection; however  how microbe induced inflammation modulates tissue repair remains unclear. We took advantage of the optical transparency of zebrafish and a genetically tractable microbe  Listeria monocytogenes  to probe the role of infection and inflammation in wound healing. We found a critical window of microbial clearance necessary to limit persistent inflammation and enable efficient wound repair. Infection with bacteria engineered to activate the inflammasome  Lm Pyro  induced persistent inflammation and impaired healing despite low bacterial burden. In contrast  infection with an anti inflammatory  apoptosis inducing strain  Lm Apo  had similar infectious burden but was associated with rapid wound repair. Inflammatory infections induced il 1b expression and blocking IL 1R signaling partially rescued wound healing in the presence of persistent infection. Taken together  our findings suggest that the dynamics of microbe induced tissue inflammation impacts repair in complex tissue damage independent of bacterial load  with a critical early window for efficient tissue repair. Overall design: RNA seq gene expression analysis of caudal fins of 4 dpf zebrafish post wounding and infection n = 9: 3 replicates from each of 3 treatments", null, "pubmed:38577110", null, "D8 uninfected", "GSM7598092", null, "source name:caudal fin|tissue:caudal fin|tissue id:ZFA:0001058|line:AB|age:Larval:Day 4|age id:ZFS:0000036|treatment:control|treatment id:EFO:0001461|geo loc name:missing|collection date:missing", "D8 uninfected", "Reads were aligned to the genome using STAR v2.7.8a with default parameters except for except for outFilterMismatchNoverLmax 0.1  outFilterScoreMinOverLread 0.33  and outFilterMatchNminOverLread 0.33  Gene abundances were estimated using RSEM v1.3.3 with additonal parameters   paired end    estimate rspd  and   strandedness none Assembly: GRCz11 Ensembl 95 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file", "caudal fin", "3 dpf zebrafish were placed in 5 mL E3 medium containing Tricaine with 5x108 CFU L. monocytogenes and caudal fins of larvae were transected using surgical blade Feather no. 10 at the tip of the notochord without xxx to the notochord. For uninfected wounds  sterile PBS was added in the medium instead of bacterial resuspension.", "Tail fins of 50 larvae were pooled and collected in ice cold PBS for each condition in each biological replicate. RNA was extracted from pooled tail fins using TRIzol reagent and RNAqueous Micro Kit Invitrogen. PolyA  NEBNext\u00ae Ultra\u2122 II RNA Library Prep Kit for Illumina\u00ae was used for library construction.", "Upon fertilization  zebrafish embryos were transferred into E3 medium and maintained at 28.5\u00b0C.", "tissue:caudal fin|tissue id:ZFA:0001058|line:AB|age:Larval:Day 4|age id:ZFS:0000036|treatment:control|treatment id:EFO:0001461", "GSM7598092", "GSM7598092: D8 uninfected; Danio rerio; RNA Seq", "GSM7598092 r1", "GSM7598092", "1", "Tail fins of 50 larvae were pooled and collected in ice cold PBS for each condition in each biological replicate. RNA was extracted from pooled tail fins using TRIzol reagent and RNAqueous Micro Kit Invitrogen. PolyA  NEBNext\u00ae Ultra\u2122 II RNA Library Prep Kit for Illumina\u00ae was used for library construction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP449335", null, null, "D8_R1_001.fastq.gz D8_R2_001.fastq.gz", "fastq fastq", 10575785100.0, 35252617.0, "GSM7598092 r1", "0:150 1:150", "A:2714405274;C:2542916577;G:2686344419;T:2631858115;N:260715", 150, 150, null, null, 2714405274, 2542916577, 2686344419, 2631858115, 260715, "SRX21004793", "SRS18278656", "SRA1672430", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 2, 0.94863, 0.84087, 0.05806, 0.0499, 0.70266, 0.7151, 0.45917, 0.46455, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-07-13", "Larval", "Larval", "Fin", "Surface Structure"], [76701, "SRR25258797", "SRX21004792", "SRS18278657", "SRP449335", "PRJNA994500", "Infection induced inflammation impairs wound healing through IL 1b signaling", "GSE237265", "Transcriptome Analysis", "Wound healing is impaired by infection; however  how microbe induced inflammation modulates tissue repair remains unclear. We took advantage of the optical transparency of zebrafish and a genetically tractable microbe  Listeria monocytogenes  to probe the role of infection and inflammation in wound healing. We found a critical window of microbial clearance necessary to limit persistent inflammation and enable efficient wound repair. Infection with bacteria engineered to activate the inflammasome  Lm Pyro  induced persistent inflammation and impaired healing despite low bacterial burden. In contrast  infection with an anti inflammatory  apoptosis inducing strain  Lm Apo  had similar infectious burden but was associated with rapid wound repair. Inflammatory infections induced il 1b expression and blocking IL 1R signaling partially rescued wound healing in the presence of persistent infection. Taken together  our findings suggest that the dynamics of microbe induced tissue inflammation impacts repair in complex tissue damage independent of bacterial load  with a critical early window for efficient tissue repair. Overall design: RNA seq gene expression analysis of caudal fins of 4 dpf zebrafish post wounding and infection n = 9: 3 replicates from each of 3 treatments", null, "pubmed:38577110", null, "D7 uninfected", "GSM7598091", null, "source name:caudal fin|tissue:caudal fin|tissue id:ZFA:0001058|line:AB|age:Larval:Day 4|age id:ZFS:0000036|treatment:control|treatment id:EFO:0001461|geo loc name:missing|collection date:missing", "D7 uninfected", "Reads were aligned to the genome using STAR v2.7.8a with default parameters except for except for outFilterMismatchNoverLmax 0.1  outFilterScoreMinOverLread 0.33  and outFilterMatchNminOverLread 0.33  Gene abundances were estimated using RSEM v1.3.3 with additonal parameters   paired end    estimate rspd  and   strandedness none Assembly: GRCz11 Ensembl 95 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file", "caudal fin", "3 dpf zebrafish were placed in 5 mL E3 medium containing Tricaine with 5x108 CFU L. monocytogenes and caudal fins of larvae were transected using surgical blade Feather no. 10 at the tip of the notochord without xxx to the notochord. For uninfected wounds  sterile PBS was added in the medium instead of bacterial resuspension.", "Tail fins of 50 larvae were pooled and collected in ice cold PBS for each condition in each biological replicate. RNA was extracted from pooled tail fins using TRIzol reagent and RNAqueous Micro Kit Invitrogen. PolyA  NEBNext\u00ae Ultra\u2122 II RNA Library Prep Kit for Illumina\u00ae was used for library construction.", "Upon fertilization  zebrafish embryos were transferred into E3 medium and maintained at 28.5\u00b0C.", "tissue:caudal fin|tissue id:ZFA:0001058|line:AB|age:Larval:Day 4|age id:ZFS:0000036|treatment:control|treatment id:EFO:0001461", "GSM7598091", "GSM7598091: D7 uninfected; Danio rerio; RNA Seq", "GSM7598091 r1", "GSM7598091", "1", "Tail fins of 50 larvae were pooled and collected in ice cold PBS for each condition in each biological replicate. RNA was extracted from pooled tail fins using TRIzol reagent and RNAqueous Micro Kit Invitrogen. PolyA  NEBNext\u00ae Ultra\u2122 II RNA Library Prep Kit for Illumina\u00ae was used for library construction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP449335", null, "loader:fastq load.py", "D7_R1_001.fastq.gz D7_R2_001.fastq.gz", "fastq fastq", 10054909404.0, 33294402.0, "GSM7598091 r1", "0:151 1:151", "A:2660409229;C:2376884409;G:2416003829;T:2600945907;N:666030", 151, 151, null, null, 2660409229, 2376884409, 2416003829, 2600945907, 666030, "SRX21004792", "SRS18278657", "SRA1672430", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 2, 0.93592, 0.93417, 0.07725, 0.07699, 0.70029, 0.70796, 0.47595, 0.47628, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-07-13", "Larval", "Larval", "Fin", "Surface Structure"], [76702, "SRR25258798", "SRX21004791", "SRS18278658", "SRP449335", "PRJNA994500", "Infection induced inflammation impairs wound healing through IL 1b signaling", "GSE237265", "Transcriptome Analysis", "Wound healing is impaired by infection; however  how microbe induced inflammation modulates tissue repair remains unclear. We took advantage of the optical transparency of zebrafish and a genetically tractable microbe  Listeria monocytogenes  to probe the role of infection and inflammation in wound healing. We found a critical window of microbial clearance necessary to limit persistent inflammation and enable efficient wound repair. Infection with bacteria engineered to activate the inflammasome  Lm Pyro  induced persistent inflammation and impaired healing despite low bacterial burden. In contrast  infection with an anti inflammatory  apoptosis inducing strain  Lm Apo  had similar infectious burden but was associated with rapid wound repair. Inflammatory infections induced il 1b expression and blocking IL 1R signaling partially rescued wound healing in the presence of persistent infection. Taken together  our findings suggest that the dynamics of microbe induced tissue inflammation impacts repair in complex tissue damage independent of bacterial load  with a critical early window for efficient tissue repair. Overall design: RNA seq gene expression analysis of caudal fins of 4 dpf zebrafish post wounding and infection n = 9: 3 replicates from each of 3 treatments", null, "pubmed:38577110", null, "D6 Pyro", "GSM7598090", null, "source name:caudal fin|tissue:caudal fin|tissue id:ZFA:0001058|line:AB|age:Larval:Day 4|age id:ZFS:0000036|treatment:infection|treatment id:EFO:0001196|pathogen:Listeria monocytogenes 10403S|pathogen id:NCBITaxon:393133|pathogen genotype:Pyro|geo loc name:missing|collection date:missing", "D6 Pyro", "Reads were aligned to the genome using STAR v2.7.8a with default parameters except for except for outFilterMismatchNoverLmax 0.1  outFilterScoreMinOverLread 0.33  and outFilterMatchNminOverLread 0.33  Gene abundances were estimated using RSEM v1.3.3 with additonal parameters   paired end    estimate rspd  and   strandedness none Assembly: GRCz11 Ensembl 95 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file", "caudal fin", "3 dpf zebrafish were placed in 5 mL E3 medium containing Tricaine with 5x108 CFU L. monocytogenes and caudal fins of larvae were transected using surgical blade Feather no. 10 at the tip of the notochord without xxx to the notochord. For uninfected wounds  sterile PBS was added in the medium instead of bacterial resuspension.", "Tail fins of 50 larvae were pooled and collected in ice cold PBS for each condition in each biological replicate. RNA was extracted from pooled tail fins using TRIzol reagent and RNAqueous Micro Kit Invitrogen. PolyA  NEBNext\u00ae Ultra\u2122 II RNA Library Prep Kit for Illumina\u00ae was used for library construction.", "Upon fertilization  zebrafish embryos were transferred into E3 medium and maintained at 28.5\u00b0C.", "tissue:caudal fin|tissue id:ZFA:0001058|line:AB|age:Larval:Day 4|age id:ZFS:0000036|treatment:infection|treatment id:EFO:0001196|pathogen:Listeria monocytogenes 10403S|pathogen id:NCBITaxon:393133|pathogen genotype:Pyro", "GSM7598090", "GSM7598090: D6 Pyro; Danio rerio; RNA Seq", "GSM7598090 r1", "GSM7598090", "1", "Tail fins of 50 larvae were pooled and collected in ice cold PBS for each condition in each biological replicate. RNA was extracted from pooled tail fins using TRIzol reagent and RNAqueous Micro Kit Invitrogen. PolyA  NEBNext\u00ae Ultra\u2122 II RNA Library Prep Kit for Illumina\u00ae was used for library construction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP449335", null, "loader:fastq load.py", "D6_R1_001.fastq.gz D6_R2_001.fastq.gz", "fastq fastq", 9679996034.0, 32052967.0, "GSM7598090 r1", "0:151 1:151", "A:2545578236;C:2305578076;G:2337426105;T:2490773237;N:640380", 151, 151, null, null, 2545578236, 2305578076, 2337426105, 2490773237, 640380, "SRX21004791", "SRS18278658", "SRA1672430", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 2, 0.93484, 0.93442, 0.07774, 0.07775, 0.69775, 0.7041, 0.49166, 0.47935, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-07-13", "Larval", "Larval", "Fin", "Surface Structure"], [76703, "SRR25258799", "SRX21004790", "SRS18278655", "SRP449335", "PRJNA994500", "Infection induced inflammation impairs wound healing through IL 1b signaling", "GSE237265", "Transcriptome Analysis", "Wound healing is impaired by infection; however  how microbe induced inflammation modulates tissue repair remains unclear. We took advantage of the optical transparency of zebrafish and a genetically tractable microbe  Listeria monocytogenes  to probe the role of infection and inflammation in wound healing. We found a critical window of microbial clearance necessary to limit persistent inflammation and enable efficient wound repair. Infection with bacteria engineered to activate the inflammasome  Lm Pyro  induced persistent inflammation and impaired healing despite low bacterial burden. In contrast  infection with an anti inflammatory  apoptosis inducing strain  Lm Apo  had similar infectious burden but was associated with rapid wound repair. Inflammatory infections induced il 1b expression and blocking IL 1R signaling partially rescued wound healing in the presence of persistent infection. Taken together  our findings suggest that the dynamics of microbe induced tissue inflammation impacts repair in complex tissue damage independent of bacterial load  with a critical early window for efficient tissue repair. Overall design: RNA seq gene expression analysis of caudal fins of 4 dpf zebrafish post wounding and infection n = 9: 3 replicates from each of 3 treatments", null, "pubmed:38577110", null, "D5 Pyro", "GSM7598089", null, "source name:caudal fin|tissue:caudal fin|tissue id:ZFA:0001058|line:AB|age:Larval:Day 4|age id:ZFS:0000036|treatment:infection|treatment id:EFO:0001196|pathogen:Listeria monocytogenes 10403S|pathogen id:NCBITaxon:393133|pathogen genotype:Pyro|geo loc name:missing|collection date:missing", "D5 Pyro", "Reads were aligned to the genome using STAR v2.7.8a with default parameters except for except for outFilterMismatchNoverLmax 0.1  outFilterScoreMinOverLread 0.33  and outFilterMatchNminOverLread 0.33  Gene abundances were estimated using RSEM v1.3.3 with additonal parameters   paired end    estimate rspd  and   strandedness none Assembly: GRCz11 Ensembl 95 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file", "caudal fin", "3 dpf zebrafish were placed in 5 mL E3 medium containing Tricaine with 5x108 CFU L. monocytogenes and caudal fins of larvae were transected using surgical blade Feather no. 10 at the tip of the notochord without xxx to the notochord. For uninfected wounds  sterile PBS was added in the medium instead of bacterial resuspension.", "Tail fins of 50 larvae were pooled and collected in ice cold PBS for each condition in each biological replicate. RNA was extracted from pooled tail fins using TRIzol reagent and RNAqueous Micro Kit Invitrogen. PolyA  NEBNext\u00ae Ultra\u2122 II RNA Library Prep Kit for Illumina\u00ae was used for library construction.", "Upon fertilization  zebrafish embryos were transferred into E3 medium and maintained at 28.5\u00b0C.", "tissue:caudal fin|tissue id:ZFA:0001058|line:AB|age:Larval:Day 4|age id:ZFS:0000036|treatment:infection|treatment id:EFO:0001196|pathogen:Listeria monocytogenes 10403S|pathogen id:NCBITaxon:393133|pathogen genotype:Pyro", "GSM7598089", "GSM7598089: D5 Pyro; Danio rerio; RNA Seq", "GSM7598089 r1", "GSM7598089", "1", "Tail fins of 50 larvae were pooled and collected in ice cold PBS for each condition in each biological replicate. RNA was extracted from pooled tail fins using TRIzol reagent and RNAqueous Micro Kit Invitrogen. PolyA  NEBNext\u00ae Ultra\u2122 II RNA Library Prep Kit for Illumina\u00ae was used for library construction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP449335", null, "loader:fastq load.py", "D5_R1_001.fastq.gz D5_R2_001.fastq.gz", "fastq fastq", 10307322212.0, 34130206.0, "GSM7598089 r1", "0:151 1:151", "A:2723306687;C:2440848684;G:2483343280;T:2659134971;N:688590", 151, 151, null, null, 2723306687, 2440848684, 2483343280, 2659134971, 688590, "SRX21004790", "SRS18278655", "SRA1672430", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 2, 0.9343, 0.93282, 0.0843, 0.08409, 0.69881, 0.70516, 0.47461, 0.48764, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-07-13", "Larval", "Larval", "Fin", "Surface Structure"], [76704, "SRR25258800", "SRX21004789", "SRS18278654", "SRP449335", "PRJNA994500", "Infection induced inflammation impairs wound healing through IL 1b signaling", "GSE237265", "Transcriptome Analysis", "Wound healing is impaired by infection; however  how microbe induced inflammation modulates tissue repair remains unclear. We took advantage of the optical transparency of zebrafish and a genetically tractable microbe  Listeria monocytogenes  to probe the role of infection and inflammation in wound healing. We found a critical window of microbial clearance necessary to limit persistent inflammation and enable efficient wound repair. Infection with bacteria engineered to activate the inflammasome  Lm Pyro  induced persistent inflammation and impaired healing despite low bacterial burden. In contrast  infection with an anti inflammatory  apoptosis inducing strain  Lm Apo  had similar infectious burden but was associated with rapid wound repair. Inflammatory infections induced il 1b expression and blocking IL 1R signaling partially rescued wound healing in the presence of persistent infection. Taken together  our findings suggest that the dynamics of microbe induced tissue inflammation impacts repair in complex tissue damage independent of bacterial load  with a critical early window for efficient tissue repair. Overall design: RNA seq gene expression analysis of caudal fins of 4 dpf zebrafish post wounding and infection n = 9: 3 replicates from each of 3 treatments", null, "pubmed:38577110", null, "D4 Pyro", "GSM7598088", null, "source name:caudal fin|tissue:caudal fin|tissue id:ZFA:0001058|line:AB|age:Larval:Day 4|age id:ZFS:0000036|treatment:infection|treatment id:EFO:0001196|pathogen:Listeria monocytogenes 10403S|pathogen id:NCBITaxon:393133|pathogen genotype:Pyro|geo loc name:missing|collection date:missing", "D4 Pyro", "Reads were aligned to the genome using STAR v2.7.8a with default parameters except for except for outFilterMismatchNoverLmax 0.1  outFilterScoreMinOverLread 0.33  and outFilterMatchNminOverLread 0.33  Gene abundances were estimated using RSEM v1.3.3 with additonal parameters   paired end    estimate rspd  and   strandedness none Assembly: GRCz11 Ensembl 95 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file", "caudal fin", "3 dpf zebrafish were placed in 5 mL E3 medium containing Tricaine with 5x108 CFU L. monocytogenes and caudal fins of larvae were transected using surgical blade Feather no. 10 at the tip of the notochord without xxx to the notochord. For uninfected wounds  sterile PBS was added in the medium instead of bacterial resuspension.", "Tail fins of 50 larvae were pooled and collected in ice cold PBS for each condition in each biological replicate. RNA was extracted from pooled tail fins using TRIzol reagent and RNAqueous Micro Kit Invitrogen. PolyA  NEBNext\u00ae Ultra\u2122 II RNA Library Prep Kit for Illumina\u00ae was used for library construction.", "Upon fertilization  zebrafish embryos were transferred into E3 medium and maintained at 28.5\u00b0C.", "tissue:caudal fin|tissue id:ZFA:0001058|line:AB|age:Larval:Day 4|age id:ZFS:0000036|treatment:infection|treatment id:EFO:0001196|pathogen:Listeria monocytogenes 10403S|pathogen id:NCBITaxon:393133|pathogen genotype:Pyro", "GSM7598088", "GSM7598088: D4 Pyro; Danio rerio; RNA Seq", "GSM7598088 r1", "GSM7598088", "1", "Tail fins of 50 larvae were pooled and collected in ice cold PBS for each condition in each biological replicate. RNA was extracted from pooled tail fins using TRIzol reagent and RNAqueous Micro Kit Invitrogen. PolyA  NEBNext\u00ae Ultra\u2122 II RNA Library Prep Kit for Illumina\u00ae was used for library construction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP449335", null, "loader:fastq load.py", "D4_R1_001.fastq.gz D4_R2_001.fastq.gz", "fastq fastq", 7916342610.0, 26213055.0, "GSM7598088 r1", "0:151 1:151", "A:2084049033;C:1874567183;G:1915421205;T:2041783072;N:522117", 151, 151, null, null, 2084049033, 1874567183, 1915421205, 2041783072, 522117, "SRX21004789", "SRS18278654", "SRA1672430", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 2, 0.93413, 0.93359, 0.08557, 0.08654, 0.69483, 0.70141, 0.49226, 0.48972, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-07-13", "Larval", "Larval", "Fin", "Surface Structure"], [76705, "SRR25258801", "SRX21004788", "SRS18278652", "SRP449335", "PRJNA994500", "Infection induced inflammation impairs wound healing through IL 1b signaling", "GSE237265", "Transcriptome Analysis", "Wound healing is impaired by infection; however  how microbe induced inflammation modulates tissue repair remains unclear. We took advantage of the optical transparency of zebrafish and a genetically tractable microbe  Listeria monocytogenes  to probe the role of infection and inflammation in wound healing. We found a critical window of microbial clearance necessary to limit persistent inflammation and enable efficient wound repair. Infection with bacteria engineered to activate the inflammasome  Lm Pyro  induced persistent inflammation and impaired healing despite low bacterial burden. In contrast  infection with an anti inflammatory  apoptosis inducing strain  Lm Apo  had similar infectious burden but was associated with rapid wound repair. Inflammatory infections induced il 1b expression and blocking IL 1R signaling partially rescued wound healing in the presence of persistent infection. Taken together  our findings suggest that the dynamics of microbe induced tissue inflammation impacts repair in complex tissue damage independent of bacterial load  with a critical early window for efficient tissue repair. Overall design: RNA seq gene expression analysis of caudal fins of 4 dpf zebrafish post wounding and infection n = 9: 3 replicates from each of 3 treatments", null, "pubmed:38577110", null, "D3 wt listeria", "GSM7598087", null, "source name:caudal fin|tissue:caudal fin|tissue id:ZFA:0001058|line:AB|age:Larval:Day 4|age id:ZFS:0000036|treatment:infection|treatment id:EFO:0001196|pathogen:Listeria monocytogenes 10403S|pathogen id:NCBITaxon:393133|pathogen genotype:wild type|geo loc name:missing|collection date:missing", "D3 wt listeria", "Reads were aligned to the genome using STAR v2.7.8a with default parameters except for except for outFilterMismatchNoverLmax 0.1  outFilterScoreMinOverLread 0.33  and outFilterMatchNminOverLread 0.33  Gene abundances were estimated using RSEM v1.3.3 with additonal parameters   paired end    estimate rspd  and   strandedness none Assembly: GRCz11 Ensembl 95 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file", "caudal fin", "3 dpf zebrafish were placed in 5 mL E3 medium containing Tricaine with 5x108 CFU L. monocytogenes and caudal fins of larvae were transected using surgical blade Feather no. 10 at the tip of the notochord without xxx to the notochord. For uninfected wounds  sterile PBS was added in the medium instead of bacterial resuspension.", "Tail fins of 50 larvae were pooled and collected in ice cold PBS for each condition in each biological replicate. RNA was extracted from pooled tail fins using TRIzol reagent and RNAqueous Micro Kit Invitrogen. PolyA  NEBNext\u00ae Ultra\u2122 II RNA Library Prep Kit for Illumina\u00ae was used for library construction.", "Upon fertilization  zebrafish embryos were transferred into E3 medium and maintained at 28.5\u00b0C.", "tissue:caudal fin|tissue id:ZFA:0001058|line:AB|age:Larval:Day 4|age id:ZFS:0000036|treatment:infection|treatment id:EFO:0001196|pathogen:Listeria monocytogenes 10403S|pathogen id:NCBITaxon:393133|pathogen genotype:wild type", "GSM7598087", "GSM7598087: D3 wt listeria; Danio rerio; RNA Seq", "GSM7598087 r1", "GSM7598087", "1", "Tail fins of 50 larvae were pooled and collected in ice cold PBS for each condition in each biological replicate. RNA was extracted from pooled tail fins using TRIzol reagent and RNAqueous Micro Kit Invitrogen. PolyA  NEBNext\u00ae Ultra\u2122 II RNA Library Prep Kit for Illumina\u00ae was used for library construction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP449335", null, "loader:fastq load.py", "D3_R1_001.fastq.gz D3_R2_001.fastq.gz", "fastq fastq", 7222815918.0, 23916609.0, "GSM7598087 r1", "0:151 1:151", "A:1922870702;C:1695561482;G:1725898053;T:1877998208;N:487473", 151, 151, null, null, 1922870702, 1695561482, 1725898053, 1877998208, 487473, "SRX21004788", "SRS18278652", "SRA1672430", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 2, 0.93956, 0.93811, 0.08851, 0.08827, 0.69773, 0.70522, 0.48303, 0.45858, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-07-13", "Larval", "Larval", "Fin", "Surface Structure"], [76706, "SRR25258802", "SRX21004787", "SRS18278653", "SRP449335", "PRJNA994500", "Infection induced inflammation impairs wound healing through IL 1b signaling", "GSE237265", "Transcriptome Analysis", "Wound healing is impaired by infection; however  how microbe induced inflammation modulates tissue repair remains unclear. We took advantage of the optical transparency of zebrafish and a genetically tractable microbe  Listeria monocytogenes  to probe the role of infection and inflammation in wound healing. We found a critical window of microbial clearance necessary to limit persistent inflammation and enable efficient wound repair. Infection with bacteria engineered to activate the inflammasome  Lm Pyro  induced persistent inflammation and impaired healing despite low bacterial burden. In contrast  infection with an anti inflammatory  apoptosis inducing strain  Lm Apo  had similar infectious burden but was associated with rapid wound repair. Inflammatory infections induced il 1b expression and blocking IL 1R signaling partially rescued wound healing in the presence of persistent infection. Taken together  our findings suggest that the dynamics of microbe induced tissue inflammation impacts repair in complex tissue damage independent of bacterial load  with a critical early window for efficient tissue repair. Overall design: RNA seq gene expression analysis of caudal fins of 4 dpf zebrafish post wounding and infection n = 9: 3 replicates from each of 3 treatments", null, "pubmed:38577110", null, "D2 wt listeria", "GSM7598086", null, "source name:caudal fin|tissue:caudal fin|tissue id:ZFA:0001058|line:AB|age:Larval:Day 4|age id:ZFS:0000036|treatment:infection|treatment id:EFO:0001196|pathogen:Listeria monocytogenes 10403S|pathogen id:NCBITaxon:393133|pathogen genotype:wild type|geo loc name:missing|collection date:missing", "D2 wt listeria", "Reads were aligned to the genome using STAR v2.7.8a with default parameters except for except for outFilterMismatchNoverLmax 0.1  outFilterScoreMinOverLread 0.33  and outFilterMatchNminOverLread 0.33  Gene abundances were estimated using RSEM v1.3.3 with additonal parameters   paired end    estimate rspd  and   strandedness none Assembly: GRCz11 Ensembl 95 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file", "caudal fin", "3 dpf zebrafish were placed in 5 mL E3 medium containing Tricaine with 5x108 CFU L. monocytogenes and caudal fins of larvae were transected using surgical blade Feather no. 10 at the tip of the notochord without xxx to the notochord. For uninfected wounds  sterile PBS was added in the medium instead of bacterial resuspension.", "Tail fins of 50 larvae were pooled and collected in ice cold PBS for each condition in each biological replicate. RNA was extracted from pooled tail fins using TRIzol reagent and RNAqueous Micro Kit Invitrogen. PolyA  NEBNext\u00ae Ultra\u2122 II RNA Library Prep Kit for Illumina\u00ae was used for library construction.", "Upon fertilization  zebrafish embryos were transferred into E3 medium and maintained at 28.5\u00b0C.", "tissue:caudal fin|tissue id:ZFA:0001058|line:AB|age:Larval:Day 4|age id:ZFS:0000036|treatment:infection|treatment id:EFO:0001196|pathogen:Listeria monocytogenes 10403S|pathogen id:NCBITaxon:393133|pathogen genotype:wild type", "GSM7598086", "GSM7598086: D2 wt listeria; Danio rerio; RNA Seq", "GSM7598086 r1", "GSM7598086", "1", "Tail fins of 50 larvae were pooled and collected in ice cold PBS for each condition in each biological replicate. RNA was extracted from pooled tail fins using TRIzol reagent and RNAqueous Micro Kit Invitrogen. PolyA  NEBNext\u00ae Ultra\u2122 II RNA Library Prep Kit for Illumina\u00ae was used for library construction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP449335", null, "loader:fastq load.py", "D2_R1_001.fastq.gz D2_R2_001.fastq.gz", "fastq fastq", 8041241656.0, 26626628.0, "GSM7598086 r1", "0:151 1:151", "A:2119939468;C:1905930310;G:1940854712;T:2073977628;N:539538", 151, 151, null, null, 2119939468, 1905930310, 1940854712, 2073977628, 539538, "SRX21004787", "SRS18278653", "SRA1672430", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 2, 0.93686, 0.93593, 0.07981, 0.08034, 0.69812, 0.70293, 0.48298, 0.4863, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-07-13", "Larval", "Larval", "Fin", "Surface Structure"], [76707, "SRR25258803", "SRX21004786", "SRS18278650", "SRP449335", "PRJNA994500", "Infection induced inflammation impairs wound healing through IL 1b signaling", "GSE237265", "Transcriptome Analysis", "Wound healing is impaired by infection; however  how microbe induced inflammation modulates tissue repair remains unclear. We took advantage of the optical transparency of zebrafish and a genetically tractable microbe  Listeria monocytogenes  to probe the role of infection and inflammation in wound healing. We found a critical window of microbial clearance necessary to limit persistent inflammation and enable efficient wound repair. Infection with bacteria engineered to activate the inflammasome  Lm Pyro  induced persistent inflammation and impaired healing despite low bacterial burden. In contrast  infection with an anti inflammatory  apoptosis inducing strain  Lm Apo  had similar infectious burden but was associated with rapid wound repair. Inflammatory infections induced il 1b expression and blocking IL 1R signaling partially rescued wound healing in the presence of persistent infection. Taken together  our findings suggest that the dynamics of microbe induced tissue inflammation impacts repair in complex tissue damage independent of bacterial load  with a critical early window for efficient tissue repair. Overall design: RNA seq gene expression analysis of caudal fins of 4 dpf zebrafish post wounding and infection n = 9: 3 replicates from each of 3 treatments", null, "pubmed:38577110", null, "D1 wt listeria", "GSM7598085", null, "source name:caudal fin|tissue:caudal fin|tissue id:ZFA:0001058|line:AB|age:Larval:Day 4|age id:ZFS:0000036|treatment:infection|treatment id:EFO:0001196|pathogen:Listeria monocytogenes 10403S|pathogen id:NCBITaxon:393133|pathogen genotype:wild type|geo loc name:missing|collection date:missing", "D1 wt listeria", "Reads were aligned to the genome using STAR v2.7.8a with default parameters except for except for outFilterMismatchNoverLmax 0.1  outFilterScoreMinOverLread 0.33  and outFilterMatchNminOverLread 0.33  Gene abundances were estimated using RSEM v1.3.3 with additonal parameters   paired end    estimate rspd  and   strandedness none Assembly: GRCz11 Ensembl 95 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file", "caudal fin", "3 dpf zebrafish were placed in 5 mL E3 medium containing Tricaine with 5x108 CFU L. monocytogenes and caudal fins of larvae were transected using surgical blade Feather no. 10 at the tip of the notochord without xxx to the notochord. For uninfected wounds  sterile PBS was added in the medium instead of bacterial resuspension.", "Tail fins of 50 larvae were pooled and collected in ice cold PBS for each condition in each biological replicate. RNA was extracted from pooled tail fins using TRIzol reagent and RNAqueous Micro Kit Invitrogen. PolyA  NEBNext\u00ae Ultra\u2122 II RNA Library Prep Kit for Illumina\u00ae was used for library construction.", "Upon fertilization  zebrafish embryos were transferred into E3 medium and maintained at 28.5\u00b0C.", "tissue:caudal fin|tissue id:ZFA:0001058|line:AB|age:Larval:Day 4|age id:ZFS:0000036|treatment:infection|treatment id:EFO:0001196|pathogen:Listeria monocytogenes 10403S|pathogen id:NCBITaxon:393133|pathogen genotype:wild type", "GSM7598085", "GSM7598085: D1 wt listeria; Danio rerio; RNA Seq", "GSM7598085 r1", "GSM7598085", "1", "Tail fins of 50 larvae were pooled and collected in ice cold PBS for each condition in each biological replicate. RNA was extracted from pooled tail fins using TRIzol reagent and RNAqueous Micro Kit Invitrogen. 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