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The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.", null, "pubmed:40392591", null, "KO12. 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The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.", null, "pubmed:40392591", null, "KO11 Ctla 4 knockout", "GSM8068838", null, "source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO|geo loc name:missing|collection date:missing", "KO11 Ctla 4 knockout", "The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. 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The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.", null, "pubmed:40392591", null, "KO9 Ctla 4 knockout", "GSM8068837", null, "source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO|geo loc name:missing|collection date:missing", "KO9 Ctla 4 knockout", "The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "intestine", null, "Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.", null, "tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO", "GSM8068837", "GSM8068837: KO9 Ctla 4 knockout; Danio rerio; RNA Seq", "GSM8068837 r1", "GSM8068837", "1", "Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP488782", null, "loader:fastq load.py", "KO9_Clean_Data2.fq.gz KO9_Clean_Data1.fq.gz", "fastq fastq", 5971590749.0, 20072217.0, "GSM8068837 r1", "0:148.76 1:148.75", "A:1640322573;C:1334570646;G:1352953128;T:1643708463;N:35939", 148, 148, null, null, 1640322573, 1334570646, 1352953128, 1643708463, 35939, "SRX23567384", "SRS20412876", "SRA1799527", "zhejiang university", "zhejiang university", 2, 0.86793, 0.86937, 0.07855, 0.07588, 0.74393, 0.74523, 0.50694, 0.51104, 149, 149, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "China", "2024-02-07", "Undetermined", "Undetermined", "Gut", "Digestive System"], [30623, "SRR27907611", "SRX23567383", "SRS20412875", "SRP488782", "PRJNA1074407", "Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq]", "GSE255304", "Transcriptome Analysis", "Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.", null, "pubmed:40392591", null, "WT8 control", "GSM8068836", null, "source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Wildtype|geo loc name:missing|collection date:missing", "WT8 control", "The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "intestine", null, "Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.", null, "tissue:intestine|cell type:leukocyte|genotype:Wildtype", "GSM8068836", "GSM8068836: WT8 control; Danio rerio; RNA Seq", "GSM8068836 r1", "GSM8068836", "1", "Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP488782", null, "loader:fastq load.py", "WT8_Clean_Data1.fq.gz WT8_Clean_Data2.fq.gz", "fastq fastq", 5740688401.0, 19287992.0, "GSM8068836 r1", "0:148.82 1:148.81", "A:1586419463;C:1274440057;G:1291660517;T:1588132746;N:35618", 148, 148, null, null, 1586419463, 1274440057, 1291660517, 1588132746, 35618, "SRX23567383", "SRS20412875", "SRA1799527", "zhejiang university", "zhejiang university", 2, 0.85516, 0.85653, 0.07987, 0.07551, 0.74515, 0.74497, 0.52575, 0.52057, 149, 149, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "China", "2024-02-07", "Undetermined", "Undetermined", "Gut", "Digestive System"], [30624, "SRR27907612", "SRX23567382", "SRS20412874", "SRP488782", "PRJNA1074407", "Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq]", "GSE255304", "Transcriptome Analysis", "Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.", null, "pubmed:40392591", null, "WT7 control", "GSM8068835", null, "source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Wildtype|geo loc name:missing|collection date:missing", "WT7 control", "The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "intestine", null, "Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.", null, "tissue:intestine|cell type:leukocyte|genotype:Wildtype", "GSM8068835", "GSM8068835: WT7 control; Danio rerio; RNA Seq", "GSM8068835 r1", "GSM8068835", "1", "Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP488782", null, "loader:fastq load.py", "WT7_Clean_Data2.fq.gz WT7_Clean_Data1.fq.gz", "fastq fastq", 5810188177.0, 19521216.0, "GSM8068835 r1", "0:148.82 1:148.81", "A:1609284873;C:1285068093;G:1302652710;T:1613147856;N:34645", 148, 148, null, null, 1609284873, 1285068093, 1302652710, 1613147856, 34645, "SRX23567382", "SRS20412874", "SRA1799527", "zhejiang university", "zhejiang university", 2, 0.83558, 0.83684, 0.08427, 0.08011, 0.75741, 0.75836, 0.52403, 0.52405, 149, 149, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "China", "2024-02-07", "Undetermined", "Undetermined", "Gut", "Digestive System"], [30625, "SRR27907613", "SRX23567381", "SRS20412873", "SRP488782", "PRJNA1074407", "Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq]", "GSE255304", "Transcriptome Analysis", "Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.", null, "pubmed:40392591", null, "WT1 control", "GSM8068834", null, "source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Wildtype|geo loc name:missing|collection date:missing", "WT1 control", "The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "intestine", null, "Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.", null, "tissue:intestine|cell type:leukocyte|genotype:Wildtype", "GSM8068834", "GSM8068834: WT1 control; Danio rerio; RNA Seq", "GSM8068834 r1", "GSM8068834", "1", "Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP488782", null, "loader:fastq load.py", "WT1_Clean_Data2.fq.gz WT1_Clean_Data1.fq.gz", "fastq fastq", 5771161671.0, 19396834.0, "GSM8068834 r1", "0:148.77 1:148.76", "A:1593780869;C:1284499295;G:1300298518;T:1592548515;N:34474", 148, 148, null, null, 1593780869, 1284499295, 1300298518, 1592548515, 34474, "SRX23567381", "SRS20412873", "SRA1799527", "zhejiang university", "zhejiang university", 2, 0.85731, 0.85944, 0.0704, 0.06703, 0.76601, 0.76607, 0.53065, 0.53445, 149, 149, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "China", "2024-02-07", "Undetermined", "Undetermined", "Gut", "Digestive System"], [30626, "SRR27907720", "SRX23567476", "SRS20412967", "SRP488787", "PRJNA1074408", "Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [scRNA seq]", "GSE255303", "Transcriptome Analysis", "Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: intestine leukocyte WT and KO Ctla 4 deficiency of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.", null, "pubmed:40392591", null, "KO scRNAseq", "GSM8068833", null, "source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO|geo loc name:missing|collection date:missing", "KO scRNAseq", "The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "intestine", null, "Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 \u03bcg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO", "GSM8068833", "GSM8068833: KO scRNAseq; Danio rerio; RNA Seq", "GSM8068833 r1", "GSM8068833", "1", "Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 \u03bcg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP488787", null, "loader:fastq load.py", "KO_S1_L001_R2_001.fastq.gz KO_S1_L001_R1_001.fastq.gz", "fastq fastq", 40958285011.0, 344187269.0, "GSM8068833 r1", "0:28 1:91", "A:11614416767;C:9247684357;G:9480911439;T:10614469263;N:803185", 28, 91, null, null, 11614416767, 9247684357, 9480911439, 10614469263, 803185, "SRX23567476", "SRS20412967", "SRA1799569", "zhejiang university", "zhejiang university", 2, 0.00982, 0.9431, 0.00356, 0.10625, 0.99277, 0.8187, 0.41297, 0.63838, 28, 91, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2024-02-07", "Undetermined", "Undetermined", "Gut", "Digestive System"], [30627, "SRR27907721", "SRX23567475", "SRS20412966", "SRP488787", "PRJNA1074408", "Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [scRNA seq]", "GSE255303", "Transcriptome Analysis", "Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: intestine leukocyte WT and KO Ctla 4 deficiency of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.", null, "pubmed:40392591", null, "WT scRNAseq", "GSM8068832", null, "source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Wildtype|geo loc name:missing|collection date:missing", "WT scRNAseq", "The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "intestine", null, "Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 \u03bcg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "tissue:intestine|cell type:leukocyte|genotype:Wildtype", "GSM8068832", "GSM8068832: WT scRNAseq; Danio rerio; RNA Seq", "GSM8068832 r1", "GSM8068832", "1", "Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 \u03bcg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP488787", null, "loader:fastq load.py", "WT_S1_L001_R1_001.fastq.gz WT_S1_L001_R2_001.fastq.gz", "fastq fastq", 36724066995.0, 308605605.0, "GSM8068832 r1", "0:28 1:91", "A:10425178276;C:8399183780;G:8411777361;T:9487202777;N:724801", 28, 91, null, null, 10425178276, 8399183780, 8411777361, 9487202777, 724801, "SRX23567475", "SRS20412966", "SRA1799569", "zhejiang university", "zhejiang university", 2, 0.01141, 0.94944, 0.0039, 0.1092, 0.99324, 0.841, 0.43558, 0.73314, 28, 91, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2024-02-07", "Undetermined", "Undetermined", "Gut", "Digestive System"], [33351, "SRR30125634", "SRX25595192", "SRS22245033", "SRP524094", "PRJNA1144090", "Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis", "GSE273916", "Transcriptome Analysis", "The aim of this study is to explore through transcriptomics \u00df \u00df Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.", null, null, null, "SBM1 3", "GSM8439539", null, "source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing", "SBM1 3", "CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample", "intestine", null, "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "tissue:intestine", "GSM8439539", "GSM8439539: SBM1 3; Danio rerio; RNA Seq", "GSM8439539 r1", "GSM8439539", "1", "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP524094", null, null, "SBM1-3.R1.fq.gz SBM1-3.R2.fq.gz", "fastq fastq", 6920938402.0, 24030624.0, "GSM8439539 r1", "0:144.00 1:144.00", "A:1848518187;C:1602695225;G:1609135376;T:1860572175;N:17439", 144, 144, null, null, 1848518187, 1602695225, 1609135376, 1860572175, 17439, "SRX25595192", "SRS22245033", "SRA1939628", "Beibu Gulf University", "Beibu Gulf University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-08-04", "Undetermined", "Undetermined", "Gut", "Digestive System"], [33352, "SRR30125635", "SRX25595191", "SRS22245032", "SRP524094", "PRJNA1144090", "Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis", "GSE273916", "Transcriptome Analysis", "The aim of this study is to explore through transcriptomics \u00df \u00df Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.", null, null, null, "SBM1 2", "GSM8439538", null, "source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing", "SBM1 2", "CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample", "intestine", null, "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "tissue:intestine", "GSM8439538", "GSM8439538: SBM1 2; Danio rerio; RNA Seq", "GSM8439538 r1", "GSM8439538", "1", "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP524094", null, null, "SBM1-2.R1.fq.gz SBM1-2.R2.fq.gz", "fastq fastq", 6873386097.0, 23812133.0, "GSM8439538 r1", "0:144.32 1:144.33", "A:1794801562;C:1631426136;G:1638460090;T:1808681001;N:17308", 144, 144, null, null, 1794801562, 1631426136, 1638460090, 1808681001, 17308, "SRX25595191", "SRS22245032", "SRA1939628", "Beibu Gulf University", "Beibu Gulf University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-08-04", "Undetermined", "Undetermined", "Gut", "Digestive System"], [33353, "SRR30125636", "SRX25595190", "SRS22245031", "SRP524094", "PRJNA1144090", "Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis", "GSE273916", "Transcriptome Analysis", "The aim of this study is to explore through transcriptomics \u00df \u00df Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.", null, null, null, "SBM1 1", "GSM8439537", null, "source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing", "SBM1 1", "CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample", "intestine", null, "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "tissue:intestine", "GSM8439537", "GSM8439537: SBM1 1; Danio rerio; RNA Seq", "GSM8439537 r1", "GSM8439537", "1", "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP524094", null, null, "SBM1-1.R1.fq.gz SBM1-1.R2.fq.gz", "fastq fastq", 6893638362.0, 23881631.0, "GSM8439537 r1", "0:144.33 1:144.33", "A:1801507713;C:1634518350;G:1642455999;T:1815139080;N:17220", 144, 144, null, null, 1801507713, 1634518350, 1642455999, 1815139080, 17220, "SRX25595190", "SRS22245031", "SRA1939628", "Beibu Gulf University", "Beibu Gulf University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-08-04", "Undetermined", "Undetermined", "Gut", "Digestive System"], [33354, "SRR30125637", "SRX25595189", "SRS22245030", "SRP524094", "PRJNA1144090", "Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis", "GSE273916", "Transcriptome Analysis", "The aim of this study is to explore through transcriptomics \u00df \u00df Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.", null, null, null, "FM1 3", "GSM8439536", null, "source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing", "FM1 3", "CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample", "intestine", null, "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "tissue:intestine", "GSM8439536", "GSM8439536: FM1 3; Danio rerio; RNA Seq", "GSM8439536 r1", "GSM8439536", "1", "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP524094", null, null, "FM1-3.R1.fq.gz FM1-3.R2.fq.gz", "fastq fastq", 6926890624.0, 24044310.0, "GSM8439536 r1", "0:144.04 1:144.05", "A:1814868011;C:1638590076;G:1645410775;T:1828004537;N:17225", 144, 144, null, null, 1814868011, 1638590076, 1645410775, 1828004537, 17225, "SRX25595189", "SRS22245030", "SRA1939628", "Beibu Gulf University", "Beibu Gulf University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-08-04", "Undetermined", "Undetermined", "Gut", "Digestive System"], [33355, "SRR30125638", "SRX25595188", "SRS22245029", "SRP524094", "PRJNA1144090", "Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis", "GSE273916", "Transcriptome Analysis", "The aim of this study is to explore through transcriptomics \u00df \u00df Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.", null, null, null, "FM1 2", "GSM8439535", null, "source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing", "FM1 2", "CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample", "intestine", null, "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "tissue:intestine", "GSM8439535", "GSM8439535: FM1 2; Danio rerio; RNA Seq", "GSM8439535 r1", "GSM8439535", "1", "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP524094", null, null, "FM1-2.R1.fq.gz FM1-2.R2.fq.gz", "fastq fastq", 6932329149.0, 24050700.0, "GSM8439535 r1", "0:144.12 1:144.12", "A:1821635965;C:1634568957;G:1641356498;T:1834750114;N:17615", 144, 144, null, null, 1821635965, 1634568957, 1641356498, 1834750114, 17615, "SRX25595188", "SRS22245029", "SRA1939628", "Beibu Gulf University", "Beibu Gulf University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-08-04", "Undetermined", "Undetermined", "Gut", "Digestive System"], [33356, "SRR30125639", "SRX25595187", "SRS22245028", "SRP524094", "PRJNA1144090", "Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis", "GSE273916", "Transcriptome Analysis", "The aim of this study is to explore through transcriptomics \u00df \u00df Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.", null, null, null, "FM1 1", "GSM8439534", null, "source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing", "FM1 1", "CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample", "intestine", null, "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "tissue:intestine", "GSM8439534", "GSM8439534: FM1 1; Danio rerio; RNA Seq", "GSM8439534 r1", "GSM8439534", "1", "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP524094", null, null, "FM1-1.R1.fq.gz FM1-1.R2.fq.gz", "fastq fastq", 6915521492.0, 24044109.0, "GSM8439534 r1", "0:143.81 1:143.81", "A:1851629842;C:1595942468;G:1602547587;T:1865384194;N:17401", 143, 143, null, null, 1851629842, 1595942468, 1602547587, 1865384194, 17401, "SRX25595187", "SRS22245028", "SRA1939628", "Beibu Gulf University", "Beibu Gulf University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-08-04", "Undetermined", "Undetermined", "Gut", "Digestive System"], [33357, "SRR30125640", "SRX25595186", "SRS22245027", "SRP524094", "PRJNA1144090", "Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis", "GSE273916", "Transcriptome Analysis", "The aim of this study is to explore through transcriptomics \u00df \u00df Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.", null, null, null, "D3 4 3", "GSM8439533", null, "source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing", "D3 4 3", "CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample", "intestine", null, "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "tissue:intestine", "GSM8439533", "GSM8439533: D3 4 3; Danio rerio; RNA Seq", "GSM8439533 r1", "GSM8439533", "1", "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP524094", null, null, "D3-4-3.R1.fq.gz D3-4-3.R2.fq.gz", "fastq fastq", 6934859246.0, 24095045.0, "GSM8439533 r1", "0:143.91 1:143.91", "A:1815846879;C:1641161510;G:1648091770;T:1829741658;N:17429", 143, 143, null, null, 1815846879, 1641161510, 1648091770, 1829741658, 17429, "SRX25595186", "SRS22245027", "SRA1939628", "Beibu Gulf University", "Beibu Gulf University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-08-04", "Undetermined", "Undetermined", "Gut", "Digestive System"], [33358, "SRR30125641", "SRX25595185", "SRS22245026", "SRP524094", "PRJNA1144090", "Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis", "GSE273916", "Transcriptome Analysis", "The aim of this study is to explore through transcriptomics \u00df \u00df Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.", null, null, null, "D3 4 2", "GSM8439532", null, "source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing", "D3 4 2", "CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample", "intestine", null, "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "tissue:intestine", "GSM8439532", "GSM8439532: D3 4 2; Danio rerio; RNA Seq", "GSM8439532 r1", "GSM8439532", "1", "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP524094", null, null, "D3-4-2.R1.fq.gz D3-4-2.R2.fq.gz", "fastq fastq", 7053487385.0, 24519028.0, "GSM8439532 r1", "0:143.83 1:143.84", "A:1888591272;C:1630003556;G:1636509489;T:1898365125;N:17943", 143, 143, null, null, 1888591272, 1630003556, 1636509489, 1898365125, 17943, "SRX25595185", "SRS22245026", "SRA1939628", "Beibu Gulf University", "Beibu Gulf University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-08-04", "Undetermined", "Undetermined", "Gut", "Digestive System"], [33359, "SRR30125642", "SRX25595184", "SRS22245025", "SRP524094", "PRJNA1144090", "Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis", "GSE273916", "Transcriptome Analysis", "The aim of this study is to explore through transcriptomics \u00df \u00df Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.", null, null, null, "D3 4 1", "GSM8439531", null, "source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing", "D3 4 1", "CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample", "intestine", null, "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "tissue:intestine", "GSM8439531", "GSM8439531: D3 4 1; Danio rerio; RNA Seq", "GSM8439531 r1", "GSM8439531", "1", "RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP524094", null, null, "D3-4-1.R1.fq.gz D3-4-1.R2.fq.gz", "fastq fastq", 6996797279.0, 24229469.0, "GSM8439531 r1", "0:144.38 1:144.39", "A:1841905352;C:1647600285;G:1654313322;T:1852960597;N:17723", 144, 144, null, null, 1841905352, 1647600285, 1654313322, 1852960597, 17723, "SRX25595184", "SRS22245025", "SRA1939628", "Beibu Gulf University", "Beibu Gulf University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-08-04", "Undetermined", "Undetermined", "Gut", "Digestive System"], [41078, "SRR3655795", "SRX1836009", "SRS1495472", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption: RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects and tested this in a zebrafish SBS model. Methods: With IACUC approval adult male wild type zebrafish underwent SBS laparotomy proximal stoma distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks the proximal intestine was harvested RNA isolated and external RNA controls consortium ERCC controls spiked into each sample sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed. CyclinD1 CyclinB1 SAA1 IFN gamma and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling complement system coagulation cell proliferation cellular barrier production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis gluconeogenesis glycogenolysis fatty acid oxidation & activation and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher CyclinB1 2.8 fold higher SAA1 4.5 fold higher IFN gamma 2.1 fold higher and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 wks post sham surgery #3", "GSM2195932", null, "tissue:full thickness intestine|status:SHAM", "Proximal S1 intestine in zebrafish 2 wks post sham surgery #3", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values counts DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SHAM", "GSM2195932", "GSM2195932: Proximal S1 intestine in zebrafish 2 wks post sham surgery #3; Danio rerio; RNA Seq", "GSM2195932", null, "1", "Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195932", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "02May15_KS383.fastq.gz", "fastq", 1510741670.0, 20138480.0, "GSM2195932 r1", "0:75.02 1:0", "A:374411447;C:361418430;G:359803924;T:415021333;N:86536", 75, 0, null, null, 374411447, 361418430, 359803924, 415021333, 86536, "SRX1836009", "SRS1495472", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.94789, null, 0.05269, null, 0.77753, null, 0.53939, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Undetermined", "Undetermined", "Gut", "Digestive System"], [41079, "SRR3655796", "SRX1836009", "SRS1495472", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption: RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects and tested this in a zebrafish SBS model. Methods: With IACUC approval adult male wild type zebrafish underwent SBS laparotomy proximal stoma distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks the proximal intestine was harvested RNA isolated and external RNA controls consortium ERCC controls spiked into each sample sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed. CyclinD1 CyclinB1 SAA1 IFN gamma and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling complement system coagulation cell proliferation cellular barrier production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis gluconeogenesis glycogenolysis fatty acid oxidation & activation and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher CyclinB1 2.8 fold higher SAA1 4.5 fold higher IFN gamma 2.1 fold higher and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 wks post sham surgery #3", "GSM2195932", null, "tissue:full thickness intestine|status:SHAM", "Proximal S1 intestine in zebrafish 2 wks post sham surgery #3", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values counts DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SHAM", "GSM2195932", "GSM2195932: Proximal S1 intestine in zebrafish 2 wks post sham surgery #3; Danio rerio; RNA Seq", "GSM2195932", null, "1", "Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195932", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "27May15_KS383.fastq.gz", "fastq", 3623681121.0, 48303841.0, "GSM2195932 r2", "0:75.02 1:0", "A:881893112;C:869893713;G:867139931;T:1004485159;N:269206", 75, 0, null, null, 881893112, 869893713, 867139931, 1004485159, 269206, "SRX1836009", "SRS1495472", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.95546, null, 0.05225, null, 0.77218, null, 0.53519, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Undetermined", "Undetermined", "Gut", "Digestive System"], [41080, "SRR3655793", "SRX1836008", "SRS1495473", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption: RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects and tested this in a zebrafish SBS model. Methods: With IACUC approval adult male wild type zebrafish underwent SBS laparotomy proximal stoma distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks the proximal intestine was harvested RNA isolated and external RNA controls consortium ERCC controls spiked into each sample sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed. CyclinD1 CyclinB1 SAA1 IFN gamma and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling complement system coagulation cell proliferation cellular barrier production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis gluconeogenesis glycogenolysis fatty acid oxidation & activation and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher CyclinB1 2.8 fold higher SAA1 4.5 fold higher IFN gamma 2.1 fold higher and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 wks post sham surgery #2", "GSM2195931", null, "tissue:full thickness intestine|status:SHAM", "Proximal S1 intestine in zebrafish 2 wks post sham surgery #2", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values counts DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SHAM", "GSM2195931", "GSM2195931: Proximal S1 intestine in zebrafish 2 wks post sham surgery #2; Danio rerio; RNA Seq", "GSM2195931", null, "1", "Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195931", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "02May15_KS381.fastq.gz", "fastq", 1348860046.0, 17985061.0, "GSM2195931 r1", "0:75.00 1:0", "A:350940564;C:313266568;G:309387786;T:375159308;N:105820", 75, 0, null, null, 350940564, 313266568, 309387786, 375159308, 105820, "SRX1836008", "SRS1495473", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.92348, null, 0.06356, null, 0.77252, null, 0.52707, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Undetermined", "Undetermined", "Gut", "Digestive System"], [41081, "SRR3655794", "SRX1836008", "SRS1495473", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption: RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects and tested this in a zebrafish SBS model. Methods: With IACUC approval adult male wild type zebrafish underwent SBS laparotomy proximal stoma distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks the proximal intestine was harvested RNA isolated and external RNA controls consortium ERCC controls spiked into each sample sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed. CyclinD1 CyclinB1 SAA1 IFN gamma and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling complement system coagulation cell proliferation cellular barrier production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis gluconeogenesis glycogenolysis fatty acid oxidation & activation and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher CyclinB1 2.8 fold higher SAA1 4.5 fold higher IFN gamma 2.1 fold higher and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 wks post sham surgery #2", "GSM2195931", null, "tissue:full thickness intestine|status:SHAM", "Proximal S1 intestine in zebrafish 2 wks post sham surgery #2", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values counts DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SHAM", "GSM2195931", "GSM2195931: Proximal S1 intestine in zebrafish 2 wks post sham surgery #2; Danio rerio; RNA Seq", "GSM2195931", null, "1", "Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195931", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "27May15_KS381.fastq.gz", "fastq", 3298786881.0, 43979655.0, "GSM2195931 r2", "0:75.01 1:0", "A:829523096;C:775146066;G:763427556;T:930352935;N:337228", 75, 0, null, null, 829523096, 775146066, 763427556, 930352935, 337228, "SRX1836008", "SRS1495473", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.9361, null, 0.06336, null, 0.76353, null, 0.54746, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Undetermined", "Undetermined", "Gut", "Digestive System"], [41082, "SRR3655791", "SRX1836007", "SRS1495471", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption: RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects and tested this in a zebrafish SBS model. Methods: With IACUC approval adult male wild type zebrafish underwent SBS laparotomy proximal stoma distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks the proximal intestine was harvested RNA isolated and external RNA controls consortium ERCC controls spiked into each sample sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed. CyclinD1 CyclinB1 SAA1 IFN gamma and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling complement system coagulation cell proliferation cellular barrier production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis gluconeogenesis glycogenolysis fatty acid oxidation & activation and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher CyclinB1 2.8 fold higher SAA1 4.5 fold higher IFN gamma 2.1 fold higher and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 wks post sham surgery #1", "GSM2195930", null, "tissue:full thickness intestine|status:SHAM", "Proximal S1 intestine in zebrafish 2 wks post sham surgery #1", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values counts DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SHAM", "GSM2195930", "GSM2195930: Proximal S1 intestine in zebrafish 2 wks post sham surgery #1; Danio rerio; RNA Seq", "GSM2195930", null, "1", "Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195930", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "02May15_KS380.fastq.gz", "fastq", 1448364484.0, 19307379.0, "GSM2195930 r1", "0:75.02 1:0", "A:359052072;C:343824905;G:344804667;T:400589883;N:92957", 75, 0, null, null, 359052072, 343824905, 344804667, 400589883, 92957, "SRX1836007", "SRS1495471", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.94277, null, 0.05284, null, 0.77881, null, 0.57769, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Undetermined", "Undetermined", "Gut", "Digestive System"], [41083, "SRR3655792", "SRX1836007", "SRS1495471", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption: RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects and tested this in a zebrafish SBS model. Methods: With IACUC approval adult male wild type zebrafish underwent SBS laparotomy proximal stoma distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks the proximal intestine was harvested RNA isolated and external RNA controls consortium ERCC controls spiked into each sample sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed. CyclinD1 CyclinB1 SAA1 IFN gamma and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling complement system coagulation cell proliferation cellular barrier production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis gluconeogenesis glycogenolysis fatty acid oxidation & activation and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher CyclinB1 2.8 fold higher SAA1 4.5 fold higher IFN gamma 2.1 fold higher and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 wks post sham surgery #1", "GSM2195930", null, "tissue:full thickness intestine|status:SHAM", "Proximal S1 intestine in zebrafish 2 wks post sham surgery #1", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values counts DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SHAM", "GSM2195930", "GSM2195930: Proximal S1 intestine in zebrafish 2 wks post sham surgery #1; Danio rerio; RNA Seq", "GSM2195930", null, "1", "Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195930", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "27May15_KS380.fastq.gz", "fastq", 3599154025.0, 47976708.0, "GSM2195930 r2", "0:75.02 1:0", "A:875615940;C:857379635;G:859609503;T:1006260031;N:288916", 75, 0, null, null, 875615940, 857379635, 859609503, 1006260031, 288916, "SRX1836007", "SRS1495471", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.95037, null, 0.0525, null, 0.77147, null, 0.5711, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "Undetermined", "Undetermined", "Gut", "Digestive System"], [45003, "SRR6411472", "SRX3504487", "SRS2782041", "SRP127390", "PRJNA427283", "RNA profiling of the liver and gut tissues in zebrafish Danio rerio [mRNA]", "GSE108435", "Transcriptome Analysis", "Compared to other fish models miRNAs are currently most extensively studied and identified in zebrafish. Approximately 415 dre miRNAs have been identified and several articles have studied some aspect of miRNA function in zebrafish such as their role in basic development and in disease pathways. However this field of research is in its infancy and the function of several dre miRNAs as well as their tissue specific expression profile are yet to be defined. In this study the liver and gut were dissected wildtype/untreated fish total and small RNA were extracted mRNA and miRNA libraries constructed and subjected to high throughput sequencing HTS using standard approaches. We carried out differential expression DE analysis and compared liver miRNA expression to gut using established bioinformatics pipelines. Through bioinformatics analysis known and putative novel miRNAs were identified. Finally we constructed a \u201cmiRNA matrix\u201d that connects both total RNA Seq and miRNA Seq. Overall design: Examination of transcriptome in an in vivo model organism in two defined tissues liver and gut.", "parent bioproject:PRJNA427275", "pubmed:30386173", null, "Gut 4 mRNA", "GSM2898184", null, "source name:Gut|Sex:male|tissue:Gut", "Gut 4 mRNA", "Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics San Diego CA. OnRamp\u2019s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: Tab delimited .txt files include the DESEQ2 output for the gut vs liver Comparison. Columns to the right of the Base Mean column represent standard DEseq2 output. Gut 1 Gut 2 Liver 1 and Liver 2 contain raw count data for the two gut and two liver RNAseq libraries respectively. The ensembl gene id external gene name description represent zebrafish gene identifiers. The human homologs as determined by Ensembl homology are described using the following human gene identifiers hsapiens homolog ensembl gene hgnc symbol Human description and Human entrez geneid", "Gut", "Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26\u201329 \u00b0C and the light\u2013dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 . Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra Germany. Fish were acclimated for one week prior to extracting the tissues i.e. liver and intestine. Tissue samples were immediately frozen in liquid nitrogen and stored at \u201370 \u00b0C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.", "Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the RNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina San Diego CA 100 200 ng of total RNA was used following the protocol described by the manufacturer.", null, "Sex:male|tissue:Gut", "GSM2898184", "GSM2898184: Gut 4 mRNA; Danio rerio; RNA Seq", "GSM2898184", null, "1", "Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the RNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina San Diego CA 100 200 ng of total RNA was used following the protocol described by the manufacturer.", "GEO Accession:GSM2898184", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP127390", null, null, "Gut_2.fastq.gz", "fastq", 2511580170.0, 49246670.0, "GSM2898184 r1", "0:51", "A:634532680;C:591744395;G:630819200;T:654046479;N:437416", 51, null, null, null, 634532680, 591744395, 630819200, 654046479, 437416, "SRX3504487", "SRS2782041", "SRA641251", "GEO", "Walton RS311, Pathology, Medical University of South Carolina", 1, 0.91491, null, 0.06302, null, 0.79632, null, 0.54435, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2017-12-22", "Undetermined", "Undetermined", "Gut", "Digestive System"], [45004, "SRR6411471", "SRX3504486", "SRS2782040", "SRP127390", "PRJNA427283", "RNA profiling of the liver and gut tissues in zebrafish Danio rerio [mRNA]", "GSE108435", "Transcriptome Analysis", "Compared to other fish models miRNAs are currently most extensively studied and identified in zebrafish. Approximately 415 dre miRNAs have been identified and several articles have studied some aspect of miRNA function in zebrafish such as their role in basic development and in disease pathways. However this field of research is in its infancy and the function of several dre miRNAs as well as their tissue specific expression profile are yet to be defined. In this study the liver and gut were dissected wildtype/untreated fish total and small RNA were extracted mRNA and miRNA libraries constructed and subjected to high throughput sequencing HTS using standard approaches. We carried out differential expression DE analysis and compared liver miRNA expression to gut using established bioinformatics pipelines. Through bioinformatics analysis known and putative novel miRNAs were identified. Finally we constructed a \u201cmiRNA matrix\u201d that connects both total RNA Seq and miRNA Seq. Overall design: Examination of transcriptome in an in vivo model organism in two defined tissues liver and gut.", "parent bioproject:PRJNA427275", "pubmed:30386173", null, "Gut 3 mRNA", "GSM2898183", null, "source name:Gut|Sex:male|tissue:Gut", "Gut 3 mRNA", "Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics San Diego CA. OnRamp\u2019s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: Tab delimited .txt files include the DESEQ2 output for the gut vs liver Comparison. Columns to the right of the Base Mean column represent standard DEseq2 output. Gut 1 Gut 2 Liver 1 and Liver 2 contain raw count data for the two gut and two liver RNAseq libraries respectively. The ensembl gene id external gene name description represent zebrafish gene identifiers. The human homologs as determined by Ensembl homology are described using the following human gene identifiers hsapiens homolog ensembl gene hgnc symbol Human description and Human entrez geneid", "Gut", "Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26\u201329 \u00b0C and the light\u2013dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 . Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra Germany. Fish were acclimated for one week prior to extracting the tissues i.e. liver and intestine. Tissue samples were immediately frozen in liquid nitrogen and stored at \u201370 \u00b0C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.", "Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the RNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina San Diego CA 100 200 ng of total RNA was used following the protocol described by the manufacturer.", null, "Sex:male|tissue:Gut", "GSM2898183", "GSM2898183: Gut 3 mRNA; Danio rerio; RNA Seq", "GSM2898183", null, "1", "Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the RNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina San Diego CA 100 200 ng of total RNA was used following the protocol described by the manufacturer.", "GEO Accession:GSM2898183", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP127390", null, null, "Gut_1.fastq.gz", "fastq", 2336820153.0, 45820003.0, "GSM2898183 r1", "0:51", "A:592745033;C:551283776;G:583859269;T:608544280;N:387795", 51, null, null, null, 592745033, 551283776, 583859269, 608544280, 387795, "SRX3504486", "SRS2782040", "SRA641251", "GEO", "Walton RS311, Pathology, Medical University of South Carolina", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2017-12-22", "Undetermined", "Undetermined", "Gut", "Digestive System"], [63810, "SRR14060980", "SRX10435564", "SRS8569035", "SRP311962", "PRJNA716978", "Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model", "GSE169522", "Transcriptome Analysis", "We hypothesised that induction of a torpor like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis a torpor like state was induced in zebrafish using melatonin treatment and cold temperature and radiation exposure was administered twice over the course of 10 days. The protective effects of induced torpor were assessed via RNA sequencing of mRNA extracted from the GIT. A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation torpor and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response including steroidal signalling and changes to metabolism damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis proliferation cell survival signals and expression of genes involved in protection against the adverse effects of radiation particularly in neurons suggesting a radioprotective effect conferred by a torpor state. This proof of concept model provides compelling initial evidence for utilizing an induced torpor like state as a potential countermeasure for radiation exposure. Overall design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, "pubmed:33920039", null, "Torpor+radiation [18 24 M2 RAD]", "GSM5208645", null, "tissue:Gastrointestinal tract", "Torpor+radiation [18 24 M2 RAD]", "Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Genome build: zebrafish genome GRCz11 Supplementary files format and content: HTSeq counts DESeq output", "Gastrointestinal tract", "A melatonin group 28.5 melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen Hilden Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina San Diego CA USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer\u2019s protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility Chapel Hill NC and the Queens University Belfast Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", null, "radiation cgy:32.64|temperature \u00b0c:18.5|melatonin \u00b5m:24", "GSM5208645", "GSM5208645: Torpor+radiation [18 24 M2 RAD]; Danio rerio; RNA Seq", "GSM5208645", null, "1", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen Hilden Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina San Diego CA USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer's protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility Chapel Hill NC and the Queens University Belfast Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", "GEO Accession:GSM5208645", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP311962", null, "loader:fastq load.py", "18-24-M2-RAD_GTGAAA_S103_L008_R1_001.fastq.gz", "fastq", 1589596300.0, 31791926.0, "GSM5208645 r1", "0:50", "A:343218732;C:412078303;G:480421414;T:353581599;N:296252", 50, null, null, null, 343218732, 412078303, 480421414, 353581599, 296252, "SRX10435564", "SRS8569035", "SRA1209926", "GEO", "Hardiman Lab, Institute for Global Food Security, Queen's University Belfast", 1, 0.61709, null, 0.13219, null, 0.8379, null, 0.67633, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2021-03-24", "Undetermined", "Undetermined", "Gut", "Digestive System"], [63811, "SRR14060979", "SRX10435563", "SRS8569036", "SRP311962", "PRJNA716978", "Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model", "GSE169522", "Transcriptome Analysis", "We hypothesised that induction of a torpor like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis a torpor like state was induced in zebrafish using melatonin treatment and cold temperature and radiation exposure was administered twice over the course of 10 days. The protective effects of induced torpor were assessed via RNA sequencing of mRNA extracted from the GIT. A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation torpor and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response including steroidal signalling and changes to metabolism damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis proliferation cell survival signals and expression of genes involved in protection against the adverse effects of radiation particularly in neurons suggesting a radioprotective effect conferred by a torpor state. This proof of concept model provides compelling initial evidence for utilizing an induced torpor like state as a potential countermeasure for radiation exposure. Overall design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, "pubmed:33920039", null, "Torpor+radiation [18 24 M1 RAD]", "GSM5208644", null, "tissue:Gastrointestinal tract", "Torpor+radiation [18 24 M1 RAD]", "Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Genome build: zebrafish genome GRCz11 Supplementary files format and content: HTSeq counts DESeq output", "Gastrointestinal tract", "A melatonin group 28.5 melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen Hilden Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina San Diego CA USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer\u2019s protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility Chapel Hill NC and the Queens University Belfast Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", null, "radiation cgy:32.64|temperature \u00b0c:18.5|melatonin \u00b5m:24", "GSM5208644", "GSM5208644: Torpor+radiation [18 24 M1 RAD]; Danio rerio; RNA Seq", "GSM5208644", null, "1", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen Hilden Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina San Diego CA USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer's protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility Chapel Hill NC and the Queens University Belfast Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", "GEO Accession:GSM5208644", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP311962", null, "loader:fastq load.py", "18-24-M1-RAD_GTCCGC_S102_L008_R1_001.fastq.gz", "fastq", 1826597250.0, 36531945.0, "GSM5208644 r1", "0:50", "A:400114581;C:473398494;G:532511254;T:420225243;N:347678", 50, null, null, null, 400114581, 473398494, 532511254, 420225243, 347678, "SRX10435563", "SRS8569036", "SRA1209926", "GEO", "Hardiman Lab, Institute for Global Food Security, Queen's University Belfast", 1, 0.58111, null, 0.13543, null, 0.86419, null, 0.68781, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2021-03-24", "Undetermined", "Undetermined", "Gut", "Digestive System"], [63812, "SRR14060978", "SRX10435562", "SRS8569034", "SRP311962", "PRJNA716978", "Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model", "GSE169522", "Transcriptome Analysis", "We hypothesised that induction of a torpor like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis a torpor like state was induced in zebrafish using melatonin treatment and cold temperature and radiation exposure was administered twice over the course of 10 days. The protective effects of induced torpor were assessed via RNA sequencing of mRNA extracted from the GIT. A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation torpor and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response including steroidal signalling and changes to metabolism damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis proliferation cell survival signals and expression of genes involved in protection against the adverse effects of radiation particularly in neurons suggesting a radioprotective effect conferred by a torpor state. This proof of concept model provides compelling initial evidence for utilizing an induced torpor like state as a potential countermeasure for radiation exposure. Overall design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, "pubmed:33920039", null, "Torpor+radiation [18 24 F2 RAD]", "GSM5208643", null, "tissue:Gastrointestinal tract", "Torpor+radiation [18 24 F2 RAD]", "Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Genome build: zebrafish genome GRCz11 Supplementary files format and content: HTSeq counts DESeq output", "Gastrointestinal tract", "A melatonin group 28.5 melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen Hilden Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina San Diego CA USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer\u2019s protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility Chapel Hill NC and the Queens University Belfast Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", null, "radiation cgy:32.64|temperature \u00b0c:18.5|melatonin \u00b5m:24", "GSM5208643", "GSM5208643: Torpor+radiation [18 24 F2 RAD]; Danio rerio; RNA Seq", "GSM5208643", null, "1", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen Hilden Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina San Diego CA USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer's protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility Chapel Hill NC and the Queens University Belfast Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", "GEO Accession:GSM5208643", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP311962", null, "loader:fastq load.py", "18-24-F2-RAD_GTTTCG_S101_L008_R1_001.fastq.gz", "fastq", 2006121600.0, 40122432.0, "GSM5208643 r1", "0:50", "A:418454946;C:561035530;G:571770538;T:454478879;N:381707", 50, null, null, null, 418454946, 561035530, 571770538, 454478879, 381707, "SRX10435562", "SRS8569034", "SRA1209926", "GEO", "Hardiman Lab, Institute for Global Food Security, Queen's University Belfast", 1, 0.76053, null, 0.17325, null, 0.83954, null, 0.64698, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2021-03-24", "Undetermined", "Undetermined", "Gut", "Digestive System"], [63813, "SRR14060977", "SRX10435561", "SRS8569033", "SRP311962", "PRJNA716978", "Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model", "GSE169522", "Transcriptome Analysis", "We hypothesised that induction of a torpor like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis a torpor like state was induced in zebrafish using melatonin treatment and cold temperature and radiation exposure was administered twice over the course of 10 days. The protective effects of induced torpor were assessed via RNA sequencing of mRNA extracted from the GIT. A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation torpor and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response including steroidal signalling and changes to metabolism damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis proliferation cell survival signals and expression of genes involved in protection against the adverse effects of radiation particularly in neurons suggesting a radioprotective effect conferred by a torpor state. This proof of concept model provides compelling initial evidence for utilizing an induced torpor like state as a potential countermeasure for radiation exposure. Overall design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, "pubmed:33920039", null, "Torpor+radiation [18 24 F1 RAD]", "GSM5208642", null, "tissue:Gastrointestinal tract", "Torpor+radiation [18 24 F1 RAD]", "Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Genome build: zebrafish genome GRCz11 Supplementary files format and content: HTSeq counts DESeq output", "Gastrointestinal tract", "A melatonin group 28.5 melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen Hilden Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina San Diego CA USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer\u2019s protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility Chapel Hill NC and the Queens University Belfast Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", null, "radiation cgy:32.64|temperature \u00b0c:18.5|melatonin \u00b5m:24", "GSM5208642", "GSM5208642: Torpor+radiation [18 24 F1 RAD]; Danio rerio; RNA Seq", "GSM5208642", null, "1", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen Hilden Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina San Diego CA USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer's protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility Chapel Hill NC and the Queens University Belfast Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", "GEO Accession:GSM5208642", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP311962", null, "loader:fastq load.py", "18-24-F1-RAD_GTGGCC_S100_L008_R1_001.fastq.gz", "fastq", 2369508350.0, 47390167.0, "GSM5208642 r1", "0:50", "A:509515197;C:623307582;G:694019366;T:542224292;N:441913", 50, null, null, null, 509515197, 623307582, 694019366, 542224292, 441913, "SRX10435561", "SRS8569033", "SRA1209926", "GEO", "Hardiman Lab, Institute for Global Food Security, Queen's University Belfast", 1, 0.62827, null, 0.14038, null, 0.828, null, 0.66975, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2021-03-24", "Undetermined", "Undetermined", "Gut", "Digestive System"], [63814, "SRR14060976", "SRX10435560", "SRS8569032", "SRP311962", "PRJNA716978", "Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model", "GSE169522", "Transcriptome Analysis", "We hypothesised that induction of a torpor like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis a torpor like state was induced in zebrafish using melatonin treatment and cold temperature and radiation exposure was administered twice over the course of 10 days. The protective effects of induced torpor were assessed via RNA sequencing of mRNA extracted from the GIT. A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation torpor and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response including steroidal signalling and changes to metabolism damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis proliferation cell survival signals and expression of genes involved in protection against the adverse effects of radiation particularly in neurons suggesting a radioprotective effect conferred by a torpor state. This proof of concept model provides compelling initial evidence for utilizing an induced torpor like state as a potential countermeasure for radiation exposure. Overall design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, "pubmed:33920039", null, "Radiation [C M1 RAD]", "GSM5208641", null, "tissue:Gastrointestinal tract", "Radiation [C M1 RAD]", "Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Genome build: zebrafish genome GRCz11 Supplementary files format and content: HTSeq counts DESeq output", "Gastrointestinal tract", "A melatonin group 28.5 melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen Hilden Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina San Diego CA USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer\u2019s protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility Chapel Hill NC and the Queens University Belfast Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", null, "radiation cgy:32.64|temperature \u00b0c:28.5|melatonin \u00b5m:0", "GSM5208641", "GSM5208641: Radiation [C M1 RAD]; Danio rerio; RNA Seq", "GSM5208641", null, "1", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen Hilden Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina San Diego CA USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer's protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility Chapel Hill NC and the Queens University Belfast Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", "GEO Accession:GSM5208641", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP311962", null, "loader:fastq load.py", "C-M1-RAD_GATCAG_S111_L008_R1_001.fastq.gz", "fastq", 599190900.0, 11983818.0, "GSM5208641 r1", "0:50", "A:136269333;C:152654300;G:156807839;T:153346367;N:113061", 50, null, null, null, 136269333, 152654300, 156807839, 153346367, 113061, "SRX10435560", "SRS8569032", "SRA1209926", "GEO", "Hardiman Lab, Institute for Global Food Security, Queen's University Belfast", 1, 0.77484, null, 0.14395, null, 0.78405, null, 0.5761, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2021-03-24", "Undetermined", "Undetermined", "Gut", "Digestive System"], [63815, "SRR14060975", "SRX10435559", "SRS8569031", "SRP311962", "PRJNA716978", "Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model", "GSE169522", "Transcriptome Analysis", "We hypothesised that induction of a torpor like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis a torpor like state was induced in zebrafish using melatonin treatment and cold temperature and radiation exposure was administered twice over the course of 10 days. The protective effects of induced torpor were assessed via RNA sequencing of mRNA extracted from the GIT. A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation torpor and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response including steroidal signalling and changes to metabolism damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis proliferation cell survival signals and expression of genes involved in protection against the adverse effects of radiation particularly in neurons suggesting a radioprotective effect conferred by a torpor state. This proof of concept model provides compelling initial evidence for utilizing an induced torpor like state as a potential countermeasure for radiation exposure. Overall design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, "pubmed:33920039", null, "Radiation [C F7 RAD]", "GSM5208640", null, "tissue:Gastrointestinal tract", "Radiation [C F7 RAD]", "Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Genome build: zebrafish genome GRCz11 Supplementary files format and content: HTSeq counts DESeq output", "Gastrointestinal tract", "A melatonin group 28.5 melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen Hilden Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina San Diego CA USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer\u2019s protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility Chapel Hill NC and the Queens University Belfast Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", null, "radiation cgy:32.64|temperature \u00b0c:28.5|melatonin \u00b5m:0", "GSM5208640", "GSM5208640: Radiation [C F7 RAD]; Danio rerio; RNA Seq", "GSM5208640", null, "1", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen Hilden Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina San Diego CA USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer's protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility Chapel Hill NC and the Queens University Belfast Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", "GEO Accession:GSM5208640", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP311962", null, "loader:fastq load.py", "C-F7-RAD_TAGCTT_S110_L008_R1_001.fastq.gz", "fastq", 1820356400.0, 36407128.0, "GSM5208640 r1", "0:50", "A:396601070;C:476853550;G:517846835;T:428710396;N:344549", 50, null, null, null, 396601070, 476853550, 517846835, 428710396, 344549, "SRX10435559", "SRS8569031", "SRA1209926", "GEO", "Hardiman Lab, Institute for Global Food Security, Queen's University Belfast", 1, 0.71064, null, 0.16141, null, 0.81544, null, 0.63869, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2021-03-24", "Undetermined", "Undetermined", "Gut", "Digestive System"], [63816, "SRR14060974", "SRX10435558", "SRS8569030", "SRP311962", "PRJNA716978", "Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model", "GSE169522", "Transcriptome Analysis", "We hypothesised that induction of a torpor like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis a torpor like state was induced in zebrafish using melatonin treatment and cold temperature and radiation exposure was administered twice over the course of 10 days. The protective effects of induced torpor were assessed via RNA sequencing of mRNA extracted from the GIT. A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation torpor and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response including steroidal signalling and changes to metabolism damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis proliferation cell survival signals and expression of genes involved in protection against the adverse effects of radiation particularly in neurons suggesting a radioprotective effect conferred by a torpor state. This proof of concept model provides compelling initial evidence for utilizing an induced torpor like state as a potential countermeasure for radiation exposure. Overall design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, "pubmed:33920039", null, "Radiation [C F2 RAD]", "GSM5208639", null, "tissue:Gastrointestinal tract", "Radiation [C F2 RAD]", "Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Genome build: zebrafish genome GRCz11 Supplementary files format and content: HTSeq counts DESeq output", "Gastrointestinal tract", "A melatonin group 28.5 melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen Hilden Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina San Diego CA USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer\u2019s protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility Chapel Hill NC and the Queens University Belfast Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", null, "radiation cgy:32.64|temperature \u00b0c:28.5|melatonin \u00b5m:0", "GSM5208639", "GSM5208639: Radiation [C F2 RAD]; Danio rerio; RNA Seq", "GSM5208639", null, "1", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen Hilden Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina San Diego CA USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer's protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility Chapel Hill NC and the Queens University Belfast Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", "GEO Accession:GSM5208639", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP311962", null, "loader:fastq load.py", "C-F2-RAD_GGCTAC_S107_L008_R1_001.fastq.gz", "fastq", 1227644200.0, 24552884.0, "GSM5208639 r1", "0:50", "A:270072562;C:315451890;G:350204178;T:291687838;N:227732", 50, null, null, null, 270072562, 315451890, 350204178, 291687838, 227732, "SRX10435558", "SRS8569030", "SRA1209926", "GEO", "Hardiman Lab, Institute for Global Food Security, Queen's University Belfast", 1, 0.70512, null, 0.15321, null, 0.81491, null, 0.65123, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2021-03-24", "Undetermined", "Undetermined", "Gut", "Digestive System"], [63817, "SRR14060973", "SRX10435557", "SRS8569029", "SRP311962", "PRJNA716978", "Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model", "GSE169522", "Transcriptome Analysis", "We hypothesised that induction of a torpor like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis a torpor like state was induced in zebrafish using melatonin treatment and cold temperature and radiation exposure was administered twice over the course of 10 days. The protective effects of induced torpor were assessed via RNA sequencing of mRNA extracted from the GIT. A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation torpor and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response including steroidal signalling and changes to metabolism damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis proliferation cell survival signals and expression of genes involved in protection against the adverse effects of radiation particularly in neurons suggesting a radioprotective effect conferred by a torpor state. This proof of concept model provides compelling initial evidence for utilizing an induced torpor like state as a potential countermeasure for radiation exposure. Overall design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, "pubmed:33920039", null, "Torpor [PN0186 0016]", "GSM5208638", null, "tissue:Gastrointestinal tract", "Torpor [PN0186 0016]", "Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Genome build: zebrafish genome GRCz11 Supplementary files format and content: HTSeq counts DESeq output", "Gastrointestinal tract", "A melatonin group 28.5 melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen Hilden Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina San Diego CA USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer\u2019s protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility Chapel Hill NC and the Queens University Belfast Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", null, "radiation cgy:0|temperature \u00b0c:18.5|melatonin \u00b5m:24", "GSM5208638", "GSM5208638: Torpor [PN0186 0016]; Danio rerio; RNA Seq", "GSM5208638", null, "1", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen Hilden Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina San Diego CA USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer's protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility Chapel Hill NC and the Queens University Belfast Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", "GEO Accession:GSM5208638", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP311962", null, "loader:fastq load.py", "PN0186_0016_S14_L001_R1_001.fastq.gz PN0186_0016_S14_L001_R2_001.fastq.gz", "fastq fastq", 2449064243.0, 24243950.0, "GSM5208638 r1", "0:50.52 1:50.50", "A:628344435;C:569804022;G:583968351;T:666534485;N:412950", 50, 50, null, null, 628344435, 569804022, 583968351, 666534485, 412950, "SRX10435557", "SRS8569029", "SRA1209926", "GEO", "Hardiman Lab, Institute for Global Food Security, Queen's University Belfast", 2, 0.91773, 0.92221, 0.09858, 0.09273, 0.73576, 0.7376, 0.56051, 0.56142, 50, 48, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2021-03-24", "Undetermined", "Undetermined", "Gut", "Digestive System"], [63818, "SRR14060972", "SRX10435556", "SRS8569027", "SRP311962", "PRJNA716978", "Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model", "GSE169522", "Transcriptome Analysis", "We hypothesised that induction of a torpor like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis a torpor like state was induced in zebrafish using melatonin treatment and cold temperature and radiation exposure was administered twice over the course of 10 days. The protective effects of induced torpor were assessed via RNA sequencing of mRNA extracted from the GIT. A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation torpor and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response including steroidal signalling and changes to metabolism damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis proliferation cell survival signals and expression of genes involved in protection against the adverse effects of radiation particularly in neurons suggesting a radioprotective effect conferred by a torpor state. This proof of concept model provides compelling initial evidence for utilizing an induced torpor like state as a potential countermeasure for radiation exposure. Overall design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, "pubmed:33920039", null, "Torpor [PN0186 0015]", "GSM5208637", null, "tissue:Gastrointestinal tract", "Torpor [PN0186 0015]", "Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Genome build: zebrafish genome GRCz11 Supplementary files format and content: HTSeq counts DESeq output", "Gastrointestinal tract", "A melatonin group 28.5 melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen Hilden Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina San Diego CA USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer\u2019s protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility Chapel Hill NC and the Queens University Belfast Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", null, "radiation cgy:0|temperature \u00b0c:18.5|melatonin \u00b5m:24", "GSM5208637", "GSM5208637: Torpor [PN0186 0015]; Danio rerio; RNA Seq", "GSM5208637", null, "1", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen Hilden Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina San Diego CA USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer's protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility Chapel Hill NC and the Queens University Belfast Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", "GEO Accession:GSM5208637", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP311962", null, "loader:fastq load.py", "PN0186_0015_S16_L001_R1_001.fastq.gz PN0186_0015_S16_L001_R2_001.fastq.gz", "fastq fastq", 5094423752.0, 50418906.0, "GSM5208637 r1", "0:50.54 1:50.50", "A:1307749024;C:1199138488;G:1222319042;T:1365034295;N:182903", 50, 50, null, null, 1307749024, 1199138488, 1222319042, 1365034295, 182903, "SRX10435556", "SRS8569027", "SRA1209926", "GEO", "Hardiman Lab, Institute for Global Food Security, Queen's University Belfast", 2, 0.92343, 0.92896, 0.08466, 0.08149, 0.74194, 0.74229, 0.56671, 0.55917, 49, 51, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2021-03-24", "Undetermined", "Undetermined", "Gut", "Digestive System"], [63819, "SRR14060971", "SRX10435555", "SRS8569026", "SRP311962", "PRJNA716978", "Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model", "GSE169522", "Transcriptome Analysis", "We hypothesised that induction of a torpor like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis a torpor like state was induced in zebrafish using melatonin treatment and cold temperature and radiation exposure was administered twice over the course of 10 days. The protective effects of induced torpor were assessed via RNA sequencing of mRNA extracted from the GIT. A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation torpor and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response including steroidal signalling and changes to metabolism damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis proliferation cell survival signals and expression of genes involved in protection against the adverse effects of radiation particularly in neurons suggesting a radioprotective effect conferred by a torpor state. This proof of concept model provides compelling initial evidence for utilizing an induced torpor like state as a potential countermeasure for radiation exposure. Overall design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, "pubmed:33920039", null, "Control [C F7 NORAD]", "GSM5208636", null, "tissue:Gastrointestinal tract", "Control [C F7 NORAD]", "Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Genome build: zebrafish genome GRCz11 Supplementary files format and content: HTSeq counts DESeq output", "Gastrointestinal tract", "A melatonin group 28.5 melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen Hilden Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina San Diego CA USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer\u2019s protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility Chapel Hill NC and the Queens University Belfast Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", null, "radiation cgy:0|temperature \u00b0c:28.5|melatonin \u00b5m:0", "GSM5208636", "GSM5208636: Control [C F7 NORAD]; Danio rerio; RNA Seq", "GSM5208636", null, "1", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen Hilden Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina San Diego CA USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer's protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility Chapel Hill NC and the Queens University Belfast Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", "GEO Accession:GSM5208636", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP311962", null, "loader:fastq load.py", "C-F7-NORAD_CTTGTA_S109_L008_R1_001.fastq.gz", "fastq", 1433736900.0, 28674738.0, "GSM5208636 r1", "0:50", "A:320793907;C:370334561;G:393244317;T:349086384;N:277731", 50, null, null, null, 320793907, 370334561, 393244317, 349086384, 277731, "SRX10435555", "SRS8569026", "SRA1209926", "GEO", "Hardiman Lab, Institute for Global Food Security, Queen's University Belfast", 1, 0.74343, null, 0.14223, null, 0.8322, null, 0.411, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2021-03-24", "Undetermined", "Undetermined", "Gut", "Digestive System"], [63820, "SRR14060970", "SRX10435554", "SRS8569028", "SRP311962", "PRJNA716978", "Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model", "GSE169522", "Transcriptome Analysis", "We hypothesised that induction of a torpor like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis a torpor like state was induced in zebrafish using melatonin treatment and cold temperature and radiation exposure was administered twice over the course of 10 days. The protective effects of induced torpor were assessed via RNA sequencing of mRNA extracted from the GIT. A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation torpor and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response including steroidal signalling and changes to metabolism damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis proliferation cell survival signals and expression of genes involved in protection against the adverse effects of radiation particularly in neurons suggesting a radioprotective effect conferred by a torpor state. This proof of concept model provides compelling initial evidence for utilizing an induced torpor like state as a potential countermeasure for radiation exposure. Overall design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, "pubmed:33920039", null, "Control [C F3 NORAD]", "GSM5208635", null, "tissue:Gastrointestinal tract", "Control [C F3 NORAD]", "Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Genome build: zebrafish genome GRCz11 Supplementary files format and content: HTSeq counts DESeq output", "Gastrointestinal tract", "A melatonin group 28.5 melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen Hilden Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina San Diego CA USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer\u2019s protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility Chapel Hill NC and the Queens University Belfast Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", null, "radiation cgy:0|temperature \u00b0c:28.5|melatonin \u00b5m:0", "GSM5208635", "GSM5208635: Control [C F3 NORAD]; Danio rerio; RNA Seq", "GSM5208635", null, "1", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen Hilden Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina San Diego CA USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer's protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility Chapel Hill NC and the Queens University Belfast Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", "GEO Accession:GSM5208635", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP311962", null, "loader:fastq load.py", "C-F3-NORAD_AGTCAA_S108_L008_R1_001.fastq.gz", "fastq", 1341408250.0, 26828165.0, "GSM5208635 r1", "0:50", "A:293343570;C:349728046;G:383602727;T:314473091;N:260816", 50, null, null, null, 293343570, 349728046, 383602727, 314473091, 260816, "SRX10435554", "SRS8569028", "SRA1209926", "GEO", "Hardiman Lab, Institute for Global Food Security, Queen's University Belfast", 1, 0.70261, null, 0.14107, null, 0.81791, null, 0.57017, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2021-03-24", "Undetermined", "Undetermined", "Gut", "Digestive System"], [63907, "SRR14213386", "SRX10579904", "SRS8684372", "SRP314470", "PRJNA721381", "RNA Seq from zebrafish adult tissues", "GSE171906", "Transcriptome Analysis", "The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.", null, "pubmed:34556579", null, "Intestine3", "GSM5237128", null, "source name:zebrafish intestine|genotype:wild type|tissue:intestine|strain:TLAB", "Intestine3", "Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 102. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM", "zebrafish intestine", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|tissue:intestine|strain:TLAB", "GSM5237128", "GSM5237128: Intestine3; Danio rerio; RNA Seq", "GSM5237128", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM5237128", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP314470", null, null, "Intestine3.fastq", "fastq", 1569173300.0, 15691733.0, "GSM5237128 r1", "0:100", "A:386685730;C:390640575;G:379186629;T:412599551;N:60815", 100, null, null, null, 386685730, 390640575, 379186629, 412599551, 60815, "SRX10579904", "SRS8684372", "SRA1217576", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.95006, null, 0.08193, null, 0.78015, null, 0.56907, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2021-04-12", "Undetermined", "Undetermined", "Gut", "Digestive System"], [63908, "SRR14213385", "SRX10579903", "SRS8684371", "SRP314470", "PRJNA721381", "RNA Seq from zebrafish adult tissues", "GSE171906", "Transcriptome Analysis", "The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.", null, "pubmed:34556579", null, "Intestine2", "GSM5237127", null, "source name:zebrafish intestine|genotype:wild type|tissue:intestine|strain:TLAB", "Intestine2", "Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 102. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM", "zebrafish intestine", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|tissue:intestine|strain:TLAB", "GSM5237127", "GSM5237127: Intestine2; Danio rerio; RNA Seq", "GSM5237127", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM5237127", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP314470", null, null, "Intestine2.fastq", "fastq", 2130566800.0, 21305668.0, "GSM5237127 r1", "0:100", "A:526261017;C:530944116;G:514882717;T:558396882;N:82068", 100, null, null, null, 526261017, 530944116, 514882717, 558396882, 82068, "SRX10579903", "SRS8684371", "SRA1217576", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.95, null, 0.0797, null, 0.77382, null, 0.56644, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2021-04-12", "Undetermined", "Undetermined", "Gut", "Digestive System"], [63909, "SRR14213384", "SRX10579902", "SRS8684370", "SRP314470", "PRJNA721381", "RNA Seq from zebrafish adult tissues", "GSE171906", "Transcriptome Analysis", "The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.", null, "pubmed:34556579", null, "Intestine1", "GSM5237126", null, "source name:zebrafish intestine|genotype:wild type|tissue:intestine|strain:TLAB", "Intestine1", "Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 102. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM", "zebrafish intestine", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|tissue:intestine|strain:TLAB", "GSM5237126", "GSM5237126: Intestine1; Danio rerio; RNA Seq", "GSM5237126", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM5237126", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP314470", null, null, "Intestine1.fastq", "fastq", 1573976900.0, 15739769.0, "GSM5237126 r1", "0:100", "A:387753454;C:390843684;G:380063787;T:415255739;N:60236", 100, null, null, null, 387753454, 390843684, 380063787, 415255739, 60236, "SRX10579902", "SRS8684370", "SRA1217576", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.95269, null, 0.07992, null, 0.77311, null, 0.57635, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2021-04-12", "Undetermined", "Undetermined", "Gut", "Digestive System"], [75099, "SRR24295703", "SRX20091106", "SRS17422802", "SRP434294", "PRJNA961336", "Single cell transcriptome sequence of intestinal regeneration in zebrafish", "PRJNA961336", "Other", "The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.", null, null, null, null, "20201026 S3 S0hpt S26 L003 R1 001.fastq", null, "strain:not applicable|dev stage:MTZ 0 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 9|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of zebrafish intestine: MTZ 0 hpt", "20201026 S3 S0hpt S26 L003 R1 001", "20201026 S3 S0hpt S26 L003 R1 001", "Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 30 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP434294", null, null, "20201026_S3_S0hpt_S26_L003_R1_001.fastq.gz 20201026_S3_S0hpt_S26_L003_R2_001.fastq.gz", "fastq fastq", 9523579187.0, 53204353.0, "20201026 S3 S0hpt S26 L003 R1 001.fastq.gz", "0:28 1:151", "A:2683643441;C:2130409626;G:2213828474;T:2495632325;N:65321", 28, 151, null, null, 2683643441, 2130409626, 2213828474, 2495632325, 65321, "SRX20091106", "SRS17422802", "SRA1626787", "Southwest University|Institute of Developmental Biology and Regenerativ", "Southwest University", 2, 0.00736, 0.92902, 0.00193, 0.10378, 0.98815, 0.81525, 0.45394, 0.60873, 28, 151, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "sc", "single_cell_droplet", "10x", null, "China", "2023-04-25", "Undetermined", "Undetermined", "Gut", "Digestive System"], [75100, "SRR24295704", "SRX20091105", "SRS17422801", "SRP434294", "PRJNA961336", "Single cell transcriptome sequence of intestinal regeneration in zebrafish", "PRJNA961336", "Other", "The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.", null, null, null, null, "20201026 S3 S0hpt S8 L004 R1 001.fastq", null, "strain:not applicable|dev stage:MTZ 0 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of zebrafish intestine: MTZ 0 hpt", "20201026 S3 S0hpt S8 L004 R1 001", "20201026 S3 S0hpt S8 L004 R1 001", "Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 28 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP434294", null, null, "20201026_S3_S0hpt_S8_L004_R1_001.fastq.gz 20201026_S3_S0hpt_S8_L004_R2_001.fastq.gz", "fastq fastq", 11268103342.0, 62950298.0, "20201026 S3 S0hpt S8 L004 R1 001.fastq.gz", "0:28 1:151", "A:3165223318;C:2522144425;G:2624994106;T:2955567304;N:174189", 28, 151, null, null, 3165223318, 2522144425, 2624994106, 2955567304, 174189, "SRX20091105", "SRS17422801", "SRA1626787", "Southwest University|Institute of Developmental Biology and Regenerativ", "Southwest University", 2, 0.00779, 0.92717, 0.00206, 0.1034, 0.98776, 0.81544, 0.48375, 0.57614, 28, 151, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "sc", "single_cell_droplet", "10x", null, "China", "2023-04-25", "Undetermined", "Undetermined", "Gut", "Digestive System"], [75101, "SRR24295705", "SRX20091104", "SRS17422800", "SRP434294", "PRJNA961336", "Single cell transcriptome sequence of intestinal regeneration in zebrafish", "PRJNA961336", "Other", "The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.", null, null, null, null, "20201026 S3 S0hpt S8 L003 R1 001.fastq", null, "strain:not applicable|dev stage:MTZ 0 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of zebrafish intestine: MTZ 0 hpt", "20201026 S3 S0hpt S8 L003 R1 001", "20201026 S3 S0hpt S8 L003 R1 001", "Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 26 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP434294", null, null, "20201026_S3_S0hpt_S8_L003_R1_001.fastq.gz 20201026_S3_S0hpt_S8_L003_R2_001.fastq.gz", "fastq fastq", 11318791667.0, 63233473.0, "20201026 S3 S0hpt S8 L003 R1 001.fastq.gz", "0:28 1:151", "A:3185910303;C:2527965947;G:2631985020;T:2972741298;N:189099", 28, 151, null, null, 3185910303, 2527965947, 2631985020, 2972741298, 189099, "SRX20091104", "SRS17422800", "SRA1626787", "Southwest University|Institute of Developmental Biology and Regenerativ", "Southwest University", 2, 0.00736, 0.92879, 0.00199, 0.10456, 0.98827, 0.81643, 0.49224, 0.57699, 28, 151, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "sc", "single_cell_droplet", "10x", null, "China", "2023-04-25", "Undetermined", "Undetermined", "Gut", "Digestive System"], [75102, "SRR24295706", "SRX20091103", "SRS17422798", "SRP434294", "PRJNA961336", "Single cell transcriptome sequence of intestinal regeneration in zebrafish", "PRJNA961336", "Other", "The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.", null, null, null, null, "20201026 S3 S0hpt S8 L002 R1 001.fastq", null, "strain:not applicable|dev stage:MTZ 0 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of zebrafish intestine: MTZ 0 hpt", "20201026 S3 S0hpt S8 L002 R1 001", "20201026 S3 S0hpt S8 L002 R1 001", "Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 24 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP434294", null, null, "20201026_S3_S0hpt_S8_L002_R1_001.fastq.gz 20201026_S3_S0hpt_S8_L002_R2_001.fastq.gz", "fastq fastq", 11212565191.0, 62640029.0, "20201026 S3 S0hpt S8 L002 R1 001.fastq.gz", "0:28 1:151", "A:3151088961;C:2508604162;G:2610615892;T:2942050613;N:205563", 28, 151, null, null, 3151088961, 2508604162, 2610615892, 2942050613, 205563, "SRX20091103", "SRS17422798", "SRA1626787", "Southwest University|Institute of Developmental Biology and Regenerativ", "Southwest University", 2, 0.00781, 0.92808, 0.00205, 0.10455, 0.98744, 0.81489, 0.50675, 0.61614, 28, 151, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "sc", "single_cell_droplet", "10x", null, "China", "2023-04-25", "Undetermined", "Undetermined", "Gut", "Digestive System"], [75103, "SRR24295707", "SRX20091102", "SRS17422799", "SRP434294", "PRJNA961336", "Single cell transcriptome sequence of intestinal regeneration in zebrafish", "PRJNA961336", "Other", "The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.", null, null, null, null, "20201026 S3 S0hpt S8 L001 R1 001.fastq", null, "strain:not applicable|dev stage:MTZ 0 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of zebrafish intestine: MTZ 0 hpt", "20201026 S3 S0hpt S8 L001 R1 001", "20201026 S3 S0hpt S8 L001 R1 001", "Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 22 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP434294", null, null, "20201026_S3_S0hpt_S8_L001_R1_001.fastq.gz 20201026_S3_S0hpt_S8_L001_R2_001.fastq.gz", "fastq fastq", 11551003355.0, 64530745.0, "20201026 S3 S0hpt S8 L001 R1 001.fastq.gz", "0:28 1:151", "A:3248866155;C:2582279236;G:2687784274;T:3031856357;N:217333", 28, 151, null, null, 3248866155, 2582279236, 2687784274, 3031856357, 217333, "SRX20091102", "SRS17422799", "SRA1626787", "Southwest University|Institute of Developmental Biology and Regenerativ", "Southwest University", 2, 0.00773, 0.92693, 0.00213, 0.10378, 0.98796, 0.81458, 0.48003, 0.61476, 28, 151, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "sc", "single_cell_droplet", "10x", null, "China", "2023-04-25", "Undetermined", "Undetermined", "Gut", "Digestive System"], [75107, "SRR24295711", "SRX20091098", "SRS17422794", "SRP434294", "PRJNA961336", "Single cell transcriptome sequence of intestinal regeneration in zebrafish", "PRJNA961336", "Other", "The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.", null, null, null, null, "20201026 S2 S48hpt S25 L003 R1 001.fastq", null, "strain:not applicable|dev stage:MTZ 48 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 9|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of zebrafish intestine: MTZ 48 hpt", "20201026 S2 S48hpt S25 L003 R1 001", "20201026 S2 S48hpt S25 L003 R1 001", "Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 40 bp UMI. 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To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.", null, null, null, null, "20201026 S2 S48hpt S7 L003 R1 001.fastq", null, "strain:not applicable|dev stage:MTZ 48 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of zebrafish intestine: MTZ 48 hpt", "20201026 S2 S48hpt S7 L003 R1 001", "20201026 S2 S48hpt S7 L003 R1 001", "Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. 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To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.", null, null, null, null, "20201026 S2 S48hpt S7 L002 R1 001.fastq", null, "strain:not applicable|dev stage:MTZ 48 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of zebrafish intestine: MTZ 48 hpt", "20201026 S2 S48hpt S7 L002 R1 001", "20201026 S2 S48hpt S7 L002 R1 001", "Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. 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To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.", null, null, null, null, "20201026 S2 S48hpt S7 L001 R1 001.fastq", null, "strain:not applicable|dev stage:MTZ 48 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of zebrafish intestine: MTZ 48 hpt", "20201026 S2 S48hpt S7 L001 R1 001", "20201026 S2 S48hpt S7 L001 R1 001", "Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. 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With bioinformatics analysis using the R software we sought for significant biological and metabolic pathway changes in order to fill up some of the current knowledge gaps associated with the alpha Gal syndrome AGS. In addition ortholog mapping allowed to obtain highly concordant biological 1:1 human ortholog genes for the detection of gene disease associations GDAs and disease enriched pathways. Further data validation was performed using reverse transcriptase quantitative PCR RT qPCR and Western Blot WB analysis on target differentially expressed genes DEGs and differentially represented proteins DRPs respectively. We found that treatment with tick saliva increased mortality and caused significant higher incidence of hemorrhagic type allergic reactions changes in behavior and feeding patterns. Transcriptomics analysis showed downregulation of biological and metabolic pathways correlated with anti Gal IgE and allergic reactions to tick saliva such as blood circulation cardiac and vascular smooth muscle contraction behavior and sensory perception. Disease enrichment analysis revealed that downregulated orthologous genes were mostly associated with human disorders affecting the nervous musculoskeletal and cardiovascular systems. Proteomics analysis predominantly revealed suppression of biological and metabolic pathways associated with the immune system production of reactive oxygen species ROS and cardiac muscle contraction. The underrepresented proteins were mainly linked to nervous and nutritional/metabolic human disorders. Furthermore 12 DEGs were found to have concomitant protein level representation. Lastly the integration of transcriptomics and proteomics layers through multi omics pathway enrichment revealed inhibition of pathways associated with adrenergic signaling in cardiomyocytes as well as heart and muscle contraction. This research contributed to the discovery of AGS related biological pathways reinforcing disease multisystemic organ involvement and linking a Gal sensitization with other illnesses. Furthermore our results shed light on novel bioinformatic strategies for the identification of key genes and proteins that may serve as potential disease biomarkers. Overall design: RNA seq was performed on a total of 6 pooled zebrafish Danio rerio intestinal tissue samples. For the treatment group tick saliva 6 independent biological samples were pooled in pairs 2 per pool while the other 9 control PBS samples were pooled in groups of three 3 per pool.", null, "pubmed:37922649", null, "Intestine Saliva 3 Treatment", "GSM7634953", null, "source name:Intestine|tissue:Intestine|treatment:tick saliva|geo loc name:missing|collection date:missing", "Intestine Saliva 3 Treatment", "Around 18.4 to 49.3 million M of total reads were generated from each library for the RNA sequencing RNA Seq data. The Read 1 and Read 2 FASTQ files were analyzed by FastQC 0.11.5 and primary quality control QC was performed. The UMI reads were identified and adapter and poly A/T sequences were trimmed by using UMI tools 1.1.2 and Cutadapt 3.7. The STAR 2.7.3 aligner was used to align reads to the Danio Rerio reference genome GRCz11.107. post alignment the final BAM files were deduplicated with UMI tools and quantified with featureCounts function available in Bioconductor R package Rsubread by GRCz11.107 annotations. Assembly: Danio Rerio reference genome GRCz11.107 Supplementary files format and content: MS Excel spreadsheet contains raw counts for each sample.", "Intestine", null, "Total mRNA was isolated from samples using the AllPrep DNA/RNA/Protein Mini Kit Qiagen Hilden Germany following manufacturer\u2019s instructions. 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With bioinformatics analysis using the R software we sought for significant biological and metabolic pathway changes in order to fill up some of the current knowledge gaps associated with the alpha Gal syndrome AGS. In addition ortholog mapping allowed to obtain highly concordant biological 1:1 human ortholog genes for the detection of gene disease associations GDAs and disease enriched pathways. Further data validation was performed using reverse transcriptase quantitative PCR RT qPCR and Western Blot WB analysis on target differentially expressed genes DEGs and differentially represented proteins DRPs respectively. We found that treatment with tick saliva increased mortality and caused significant higher incidence of hemorrhagic type allergic reactions changes in behavior and feeding patterns. Transcriptomics analysis showed downregulation of biological and metabolic pathways correlated with anti Gal IgE and allergic reactions to tick saliva such as blood circulation cardiac and vascular smooth muscle contraction behavior and sensory perception. Disease enrichment analysis revealed that downregulated orthologous genes were mostly associated with human disorders affecting the nervous musculoskeletal and cardiovascular systems. Proteomics analysis predominantly revealed suppression of biological and metabolic pathways associated with the immune system production of reactive oxygen species ROS and cardiac muscle contraction. The underrepresented proteins were mainly linked to nervous and nutritional/metabolic human disorders. Furthermore 12 DEGs were found to have concomitant protein level representation. Lastly the integration of transcriptomics and proteomics layers through multi omics pathway enrichment revealed inhibition of pathways associated with adrenergic signaling in cardiomyocytes as well as heart and muscle contraction. This research contributed to the discovery of AGS related biological pathways reinforcing disease multisystemic organ involvement and linking a Gal sensitization with other illnesses. Furthermore our results shed light on novel bioinformatic strategies for the identification of key genes and proteins that may serve as potential disease biomarkers. Overall design: RNA seq was performed on a total of 6 pooled zebrafish Danio rerio intestinal tissue samples. For the treatment group tick saliva 6 independent biological samples were pooled in pairs 2 per pool while the other 9 control PBS samples were pooled in groups of three 3 per pool.", null, "pubmed:37922649", null, "Intestine Saliva 2 Treatment", "GSM7634952", null, "source name:Intestine|tissue:Intestine|treatment:tick saliva|geo loc name:missing|collection date:missing", "Intestine Saliva 2 Treatment", "Around 18.4 to 49.3 million M of total reads were generated from each library for the RNA sequencing RNA Seq data. The Read 1 and Read 2 FASTQ files were analyzed by FastQC 0.11.5 and primary quality control QC was performed. The UMI reads were identified and adapter and poly A/T sequences were trimmed by using UMI tools 1.1.2 and Cutadapt 3.7. The STAR 2.7.3 aligner was used to align reads to the Danio Rerio reference genome GRCz11.107. post alignment the final BAM files were deduplicated with UMI tools and quantified with featureCounts function available in Bioconductor R package Rsubread by GRCz11.107 annotations. Assembly: Danio Rerio reference genome GRCz11.107 Supplementary files format and content: MS Excel spreadsheet contains raw counts for each sample.", "Intestine", null, "Total mRNA was isolated from samples using the AllPrep DNA/RNA/Protein Mini Kit Qiagen Hilden Germany following manufacturer\u2019s instructions. RNA libraries for RNA seq were prepared using the CORALL mRNA Seq V1 Library Prep Kit Lexogen Wien Austria following manufacturer's protocol.", null, "tissue:Intestine|treatment:tick saliva", "GSM7634952", "GSM7634952: Intestine Saliva 2 Treatment; Danio rerio; RNA Seq", "GSM7634952 r1", "GSM7634952", "1", "Total mRNA was isolated from samples using the AllPrep DNA/RNA/Protein Mini Kit Qiagen Hilden Germany following manufacturer's instructions. RNA libraries for RNA seq were prepared using the CORALL mRNA Seq V1 Library Prep Kit Lexogen Wien Austria following manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP450092", null, null, "Saliva_2_int_1.fastq.gz Saliva_2_int_2.fastq.gz", "fastq fastq", 15236132540.0, 50450770.0, "GSM7634952 r1", "0:151 1:151", "A:3951807456;C:3613697125;G:4175903766;T:3493941159;N:783034", 151, 151, null, null, 3951807456, 3613697125, 4175903766, 3493941159, 783034, "SRX21062492", "SRS18332759", "SRA1675308", "SaBio, Instituto de Investigaci\u00f3n en Recursos Cineg\u00e9ticos (IREC) - University of Castilla-La Mancha (UCLM)", "SaBio, Instituto de Investigaci\u00f3n en Recursos Cineg\u00e9ticos (IREC) - University of Castilla-La Mancha (UCLM)", 2, 0.23841, 0.2333, 0.03181, 0.06942, 0.99415, 0.99456, 0.9369, 0.25964, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "Spain", "2023-07-18", "Undetermined", "Undetermined", "Gut", "Digestive System"], [76729, "SRR25320259", "SRX21062491", "SRS18332760", "SRP450092", "PRJNA996066", "Multi omics analysis of zebrafish response to tick saliva reveals biological processes associated with alpha Gal syndrome", "GSE237627", "Transcriptome Analysis", "This study provides a multi omics approach to determine the effect on the transcriptome and proteome gut profiles of zebrafish inoculated with tick saliva followed by mammalian meat consumption. With bioinformatics analysis using the R software we sought for significant biological and metabolic pathway changes in order to fill up some of the current knowledge gaps associated with the alpha Gal syndrome AGS. In addition ortholog mapping allowed to obtain highly concordant biological 1:1 human ortholog genes for the detection of gene disease associations GDAs and disease enriched pathways. Further data validation was performed using reverse transcriptase quantitative PCR RT qPCR and Western Blot WB analysis on target differentially expressed genes DEGs and differentially represented proteins DRPs respectively. We found that treatment with tick saliva increased mortality and caused significant higher incidence of hemorrhagic type allergic reactions changes in behavior and feeding patterns. Transcriptomics analysis showed downregulation of biological and metabolic pathways correlated with anti Gal IgE and allergic reactions to tick saliva such as blood circulation cardiac and vascular smooth muscle contraction behavior and sensory perception. Disease enrichment analysis revealed that downregulated orthologous genes were mostly associated with human disorders affecting the nervous musculoskeletal and cardiovascular systems. Proteomics analysis predominantly revealed suppression of biological and metabolic pathways associated with the immune system production of reactive oxygen species ROS and cardiac muscle contraction. The underrepresented proteins were mainly linked to nervous and nutritional/metabolic human disorders. Furthermore 12 DEGs were found to have concomitant protein level representation. Lastly the integration of transcriptomics and proteomics layers through multi omics pathway enrichment revealed inhibition of pathways associated with adrenergic signaling in cardiomyocytes as well as heart and muscle contraction. This research contributed to the discovery of AGS related biological pathways reinforcing disease multisystemic organ involvement and linking a Gal sensitization with other illnesses. Furthermore our results shed light on novel bioinformatic strategies for the identification of key genes and proteins that may serve as potential disease biomarkers. Overall design: RNA seq was performed on a total of 6 pooled zebrafish Danio rerio intestinal tissue samples. For the treatment group tick saliva 6 independent biological samples were pooled in pairs 2 per pool while the other 9 control PBS samples were pooled in groups of three 3 per pool.", null, "pubmed:37922649", null, "Intestine Saliva 1 Treatment", "GSM7634951", null, "source name:Intestine|tissue:Intestine|treatment:tick saliva|geo loc name:missing|collection date:missing", "Intestine Saliva 1 Treatment", "Around 18.4 to 49.3 million M of total reads were generated from each library for the RNA sequencing RNA Seq data. The Read 1 and Read 2 FASTQ files were analyzed by FastQC 0.11.5 and primary quality control QC was performed. The UMI reads were identified and adapter and poly A/T sequences were trimmed by using UMI tools 1.1.2 and Cutadapt 3.7. The STAR 2.7.3 aligner was used to align reads to the Danio Rerio reference genome GRCz11.107. post alignment the final BAM files were deduplicated with UMI tools and quantified with featureCounts function available in Bioconductor R package Rsubread by GRCz11.107 annotations. Assembly: Danio Rerio reference genome GRCz11.107 Supplementary files format and content: MS Excel spreadsheet contains raw counts for each sample.", "Intestine", null, "Total mRNA was isolated from samples using the AllPrep DNA/RNA/Protein Mini Kit Qiagen Hilden Germany following manufacturer\u2019s instructions. RNA libraries for RNA seq were prepared using the CORALL mRNA Seq V1 Library Prep Kit Lexogen Wien Austria following manufacturer's protocol.", null, "tissue:Intestine|treatment:tick saliva", "GSM7634951", "GSM7634951: Intestine Saliva 1 Treatment; Danio rerio; RNA Seq", "GSM7634951 r1", "GSM7634951", "1", "Total mRNA was isolated from samples using the AllPrep DNA/RNA/Protein Mini Kit Qiagen Hilden Germany following manufacturer's instructions. RNA libraries for RNA seq were prepared using the CORALL mRNA Seq V1 Library Prep Kit Lexogen Wien Austria following manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP450092", null, null, "Saliva_1_int_1.fastq.gz Saliva_1_int_2.fastq.gz", "fastq fastq", 10107874768.0, 33469784.0, "GSM7634951 r1", "0:151 1:151", "A:2611676156;C:2385768928;G:2685002752;T:2424917421;N:509511", 151, 151, null, null, 2611676156, 2385768928, 2685002752, 2424917421, 509511, "SRX21062491", "SRS18332760", "SRA1675308", "SaBio, Instituto de Investigaci\u00f3n en Recursos Cineg\u00e9ticos (IREC) - University of Castilla-La Mancha (UCLM)", "SaBio, Instituto de Investigaci\u00f3n en Recursos Cineg\u00e9ticos (IREC) - University of Castilla-La Mancha (UCLM)", 2, 0.28863, 0.29294, 0.03741, 0.0548, 0.86269, 0.86097, 0.73709, 0.4059, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "Spain", "2023-07-18", "Undetermined", "Undetermined", "Gut", "Digestive System"], [76730, "SRR25320260", "SRX21062490", "SRS18332758", "SRP450092", "PRJNA996066", "Multi omics analysis of zebrafish response to tick saliva reveals biological processes associated with alpha Gal syndrome", "GSE237627", "Transcriptome Analysis", "This study provides a multi omics approach to determine the effect on the transcriptome and proteome gut profiles of zebrafish inoculated with tick saliva followed by mammalian meat consumption. With bioinformatics analysis using the R software we sought for significant biological and metabolic pathway changes in order to fill up some of the current knowledge gaps associated with the alpha Gal syndrome AGS. In addition ortholog mapping allowed to obtain highly concordant biological 1:1 human ortholog genes for the detection of gene disease associations GDAs and disease enriched pathways. Further data validation was performed using reverse transcriptase quantitative PCR RT qPCR and Western Blot WB analysis on target differentially expressed genes DEGs and differentially represented proteins DRPs respectively. We found that treatment with tick saliva increased mortality and caused significant higher incidence of hemorrhagic type allergic reactions changes in behavior and feeding patterns. Transcriptomics analysis showed downregulation of biological and metabolic pathways correlated with anti Gal IgE and allergic reactions to tick saliva such as blood circulation cardiac and vascular smooth muscle contraction behavior and sensory perception. Disease enrichment analysis revealed that downregulated orthologous genes were mostly associated with human disorders affecting the nervous musculoskeletal and cardiovascular systems. Proteomics analysis predominantly revealed suppression of biological and metabolic pathways associated with the immune system production of reactive oxygen species ROS and cardiac muscle contraction. The underrepresented proteins were mainly linked to nervous and nutritional/metabolic human disorders. Furthermore 12 DEGs were found to have concomitant protein level representation. Lastly the integration of transcriptomics and proteomics layers through multi omics pathway enrichment revealed inhibition of pathways associated with adrenergic signaling in cardiomyocytes as well as heart and muscle contraction. This research contributed to the discovery of AGS related biological pathways reinforcing disease multisystemic organ involvement and linking a Gal sensitization with other illnesses. Furthermore our results shed light on novel bioinformatic strategies for the identification of key genes and proteins that may serve as potential disease biomarkers. Overall design: RNA seq was performed on a total of 6 pooled zebrafish Danio rerio intestinal tissue samples. For the treatment group tick saliva 6 independent biological samples were pooled in pairs 2 per pool while the other 9 control PBS samples were pooled in groups of three 3 per pool.", null, "pubmed:37922649", null, "Intestine PBS 3 Control", "GSM7634950", null, "source name:Intestine|tissue:Intestine|treatment:Control|geo loc name:missing|collection date:missing", "Intestine PBS 3 Control", "Around 18.4 to 49.3 million M of total reads were generated from each library for the RNA sequencing RNA Seq data. The Read 1 and Read 2 FASTQ files were analyzed by FastQC 0.11.5 and primary quality control QC was performed. The UMI reads were identified and adapter and poly A/T sequences were trimmed by using UMI tools 1.1.2 and Cutadapt 3.7. The STAR 2.7.3 aligner was used to align reads to the Danio Rerio reference genome GRCz11.107. post alignment the final BAM files were deduplicated with UMI tools and quantified with featureCounts function available in Bioconductor R package Rsubread by GRCz11.107 annotations. Assembly: Danio Rerio reference genome GRCz11.107 Supplementary files format and content: MS Excel spreadsheet contains raw counts for each sample.", "Intestine", null, "Total mRNA was isolated from samples using the AllPrep DNA/RNA/Protein Mini Kit Qiagen Hilden Germany following manufacturer\u2019s instructions. RNA libraries for RNA seq were prepared using the CORALL mRNA Seq V1 Library Prep Kit Lexogen Wien Austria following manufacturer's protocol.", null, "tissue:Intestine|treatment:Control", "GSM7634950", "GSM7634950: Intestine PBS 3 Control; Danio rerio; RNA Seq", "GSM7634950 r1", "GSM7634950", "1", "Total mRNA was isolated from samples using the AllPrep DNA/RNA/Protein Mini Kit Qiagen Hilden Germany following manufacturer's instructions. RNA libraries for RNA seq were prepared using the CORALL mRNA Seq V1 Library Prep Kit Lexogen Wien Austria following manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP450092", null, null, "PBS_3_int_1.fastq.gz PBS_3_int_2.fastq.gz", "fastq fastq", 9696842802.0, 32108751.0, "GSM7634950 r1", "0:151 1:151", "A:2392641265;C:2385685766;G:2716165649;T:2201854741;N:495381", 151, 151, null, null, 2392641265, 2385685766, 2716165649, 2201854741, 495381, "SRX21062490", "SRS18332758", "SRA1675308", "SaBio, Instituto de Investigaci\u00f3n en Recursos Cineg\u00e9ticos (IREC) - University of Castilla-La Mancha (UCLM)", "SaBio, Instituto de Investigaci\u00f3n en Recursos Cineg\u00e9ticos (IREC) - University of Castilla-La Mancha (UCLM)", 2, 0.36834, 0.36601, 0.05164, 0.09738, 0.95572, 0.95526, 0.90835, 0.32256, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "Spain", "2023-07-18", "Undetermined", "Undetermined", "Gut", "Digestive System"], [76731, "SRR25320261", "SRX21062489", "SRS18332757", "SRP450092", "PRJNA996066", "Multi omics analysis of zebrafish response to tick saliva reveals biological processes associated with alpha Gal syndrome", "GSE237627", "Transcriptome Analysis", "This study provides a multi omics approach to determine the effect on the transcriptome and proteome gut profiles of zebrafish inoculated with tick saliva followed by mammalian meat consumption. With bioinformatics analysis using the R software we sought for significant biological and metabolic pathway changes in order to fill up some of the current knowledge gaps associated with the alpha Gal syndrome AGS. In addition ortholog mapping allowed to obtain highly concordant biological 1:1 human ortholog genes for the detection of gene disease associations GDAs and disease enriched pathways. Further data validation was performed using reverse transcriptase quantitative PCR RT qPCR and Western Blot WB analysis on target differentially expressed genes DEGs and differentially represented proteins DRPs respectively. We found that treatment with tick saliva increased mortality and caused significant higher incidence of hemorrhagic type allergic reactions changes in behavior and feeding patterns. Transcriptomics analysis showed downregulation of biological and metabolic pathways correlated with anti Gal IgE and allergic reactions to tick saliva such as blood circulation cardiac and vascular smooth muscle contraction behavior and sensory perception. Disease enrichment analysis revealed that downregulated orthologous genes were mostly associated with human disorders affecting the nervous musculoskeletal and cardiovascular systems. Proteomics analysis predominantly revealed suppression of biological and metabolic pathways associated with the immune system production of reactive oxygen species ROS and cardiac muscle contraction. The underrepresented proteins were mainly linked to nervous and nutritional/metabolic human disorders. Furthermore 12 DEGs were found to have concomitant protein level representation. Lastly the integration of transcriptomics and proteomics layers through multi omics pathway enrichment revealed inhibition of pathways associated with adrenergic signaling in cardiomyocytes as well as heart and muscle contraction. This research contributed to the discovery of AGS related biological pathways reinforcing disease multisystemic organ involvement and linking a Gal sensitization with other illnesses. Furthermore our results shed light on novel bioinformatic strategies for the identification of key genes and proteins that may serve as potential disease biomarkers. Overall design: RNA seq was performed on a total of 6 pooled zebrafish Danio rerio intestinal tissue samples. For the treatment group tick saliva 6 independent biological samples were pooled in pairs 2 per pool while the other 9 control PBS samples were pooled in groups of three 3 per pool.", null, "pubmed:37922649", null, "Intestine PBS 2 Control", "GSM7634949", null, "source name:Intestine|tissue:Intestine|treatment:Control|geo loc name:missing|collection date:missing", "Intestine PBS 2 Control", "Around 18.4 to 49.3 million M of total reads were generated from each library for the RNA sequencing RNA Seq data. The Read 1 and Read 2 FASTQ files were analyzed by FastQC 0.11.5 and primary quality control QC was performed. The UMI reads were identified and adapter and poly A/T sequences were trimmed by using UMI tools 1.1.2 and Cutadapt 3.7. The STAR 2.7.3 aligner was used to align reads to the Danio Rerio reference genome GRCz11.107. post alignment the final BAM files were deduplicated with UMI tools and quantified with featureCounts function available in Bioconductor R package Rsubread by GRCz11.107 annotations. Assembly: Danio Rerio reference genome GRCz11.107 Supplementary files format and content: MS Excel spreadsheet contains raw counts for each sample.", "Intestine", null, "Total mRNA was isolated from samples using the AllPrep DNA/RNA/Protein Mini Kit Qiagen Hilden Germany following manufacturer\u2019s instructions. 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Transcriptomics analysis showed downregulation of biological and metabolic pathways correlated with anti Gal IgE and allergic reactions to tick saliva such as blood circulation cardiac and vascular smooth muscle contraction behavior and sensory perception. Disease enrichment analysis revealed that downregulated orthologous genes were mostly associated with human disorders affecting the nervous musculoskeletal and cardiovascular systems. Proteomics analysis predominantly revealed suppression of biological and metabolic pathways associated with the immune system production of reactive oxygen species ROS and cardiac muscle contraction. The underrepresented proteins were mainly linked to nervous and nutritional/metabolic human disorders. Furthermore 12 DEGs were found to have concomitant protein level representation. Lastly the integration of transcriptomics and proteomics layers through multi omics pathway enrichment revealed inhibition of pathways associated with adrenergic signaling in cardiomyocytes as well as heart and muscle contraction. This research contributed to the discovery of AGS related biological pathways reinforcing disease multisystemic organ involvement and linking a Gal sensitization with other illnesses. Furthermore our results shed light on novel bioinformatic strategies for the identification of key genes and proteins that may serve as potential disease biomarkers. Overall design: RNA seq was performed on a total of 6 pooled zebrafish Danio rerio intestinal tissue samples. For the treatment group tick saliva 6 independent biological samples were pooled in pairs 2 per pool while the other 9 control PBS samples were pooled in groups of three 3 per pool.", null, "pubmed:37922649", null, "Intestine PBS 1 Control", "GSM7634948", null, "source name:Intestine|tissue:Intestine|treatment:Control|geo loc name:missing|collection date:missing", "Intestine PBS 1 Control", "Around 18.4 to 49.3 million M of total reads were generated from each library for the RNA sequencing RNA Seq data. The Read 1 and Read 2 FASTQ files were analyzed by FastQC 0.11.5 and primary quality control QC was performed. The UMI reads were identified and adapter and poly A/T sequences were trimmed by using UMI tools 1.1.2 and Cutadapt 3.7. 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