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96 rows where devstage_curation = "Undetermined" and tissue_curation = "Gut"

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technology 4

devstage_curation_coarse 4

experiment.library_selection 3

experiment.library_strategy 2

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Gut · 96 ✖

experiment.platform 1

devstage_curation 1

  • Undetermined · 96 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
24918 24918 SRR25594442 SRX21322829 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome Z 2 1.fq Z 2 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     Z-2_2.fq.gz Z-2_1.fq.gz fastq fastq 5621492400.0 18738308.0 Z 2 1.fq.gz 0:150 1:150 A:1483421677;C:1306378425;G:1338052121;T:1493618330;N:21847 150 150     1483421677 1306378425 1338052121 1493618330 21847 SRX21322829 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94389 0.93819 0.03702 0.03621 0.71758 0.72423 0.43774 0.4558 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24919 24919 SRR25594443 SRX21322828 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome Z 1 1.fq Z 1 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     Z-1_2.fq.gz Z-1_1.fq.gz fastq fastq 6301274700.0 21004249.0 Z 1 1.fq.gz 0:150 1:150 A:1671253253;C:1458678359;G:1491311308;T:1680006330;N:25450 150 150     1671253253 1458678359 1491311308 1680006330 25450 SRX21322828 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94339 0.93817 0.03831 0.03813 0.71752 0.72293 0.42611 0.43548 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24920 24920 SRR25594444 SRX21322827 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome K 3 1.fq K 3 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     K-3_2.fq.gz K-3_1.fq.gz fastq fastq 5519682000.0 18398940.0 K 3 1.fq.gz 0:150 1:150 A:1469946965;C:1270791684;G:1304075220;T:1474846842;N:21289 150 150     1469946965 1270791684 1304075220 1474846842 21289 SRX21322827 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94356 0.93561 0.03986 0.03923 0.71877 0.72697 0.44771 0.44936 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24921 24921 SRR25594445 SRX21322826 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome K 2 1.fq K 2 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     K-2_1.fq.gz K-2_2.fq.gz fastq fastq 5808261300.0 19360871.0 K 2 1.fq.gz 0:150 1:150 A:1538012312;C:1343217111;G:1375887577;T:1551118640;N:25660 150 150     1538012312 1343217111 1375887577 1551118640 25660 SRX21322826 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94469 0.94137 0.03929 0.03857 0.7175 0.71946 0.44395 0.44354 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24922 24922 SRR25594446 SRX21322825 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome ZP 3 1.fq ZP 3 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     ZP-3_1.fq.gz ZP-3_2.fq.gz fastq fastq 5397938100.0 17993127.0 ZP 3 1.fq.gz 0:150 1:150 A:1438191584;C:1244532731;G:1271700792;T:1443491138;N:21855 150 150     1438191584 1244532731 1271700792 1443491138 21855 SRX21322825 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94839 0.94406 0.04345 0.04279 0.71719 0.72362 0.42772 0.4311 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24923 24923 SRR25594447 SRX21322824 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome ZP 2 1.fq ZP 2 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     ZP-2_1.fq.gz ZP-2_2.fq.gz fastq fastq 6062424900.0 20208083.0 ZP 2 1.fq.gz 0:150 1:150 A:1612595576;C:1398589726;G:1427536119;T:1623678727;N:24752 150 150     1612595576 1398589726 1427536119 1623678727 24752 SRX21322824 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.95013 0.94657 0.04364 0.04342 0.71565 0.71908 0.44652 0.44832 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24924 24924 SRR25594448 SRX21322823 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome ZP 1 1.fq ZP 1 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     ZP-1_2.fq.gz ZP-1_1.fq.gz fastq fastq 6487607100.0 21625357.0 ZP 1 1.fq.gz 0:150 1:150 A:1728514584;C:1494175744;G:1521726756;T:1743164500;N:25516 150 150     1728514584 1494175744 1521726756 1743164500 25516 SRX21322823 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94867 0.94432 0.04535 0.0449 0.71926 0.72348 0.43747 0.44661 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24925 24925 SRR25594449 SRX21322822 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome Z 3 1.fq Z 3 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     Z-3_1.fq.gz Z-3_2.fq.gz fastq fastq 8111204700.0 27037349.0 Z 3 1.fq.gz 0:150 1:150 A:2143712842;C:1879826122;G:1918517283;T:2169119328;N:29125 150 150     2143712842 1879826122 1918517283 2169119328 29125 SRX21322822 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94485 0.94083 0.03886 0.03798 0.71362 0.71768 0.44066 0.44713 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24926 24926 SRR25594450 SRX21322821 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome K 1 1.fq K 1 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     K-1_1.fq.gz K-1_2.fq.gz fastq fastq 7164142200.0 23880474.0 K 1 1.fq.gz 0:150 1:150 A:1896647470;C:1661542391;G:1700422400;T:1905500150;N:29789 150 150     1896647470 1661542391 1700422400 1905500150 29789 SRX21322821 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94635 0.94209 0.03738 0.03664 0.71961 0.72571 0.45014 0.44857 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
30620 30620 SRR27907608 SRX23567386 SRS20412878 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.   pubmed:40392591   KO12. Ctla 4 knockout GSM8068839   source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO|geo loc name:missing|collection date:missing KO12. 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   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.   tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO GSM8068839 GSM8068839: KO12. Ctla 4 knockout; Danio rerio; RNA Seq GSM8068839 r1 GSM8068839 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP488782   loader:fastq load.py KO12_Clean_Data2.fq.gz KO12_Clean_Data1.fq.gz fastq fastq 5415971621.0 18199812.0 GSM8068839 r1 0:148.79 1:148.79 A:1482389043;C:1213758088;G:1232295642;T:1487496355;N:32493 148 148     1482389043 1213758088 1232295642 1487496355 32493 SRX23567386 SRS20412878 SRA1799527 zhejiang university zhejiang university 2 0.86496 0.86584 0.08493 0.08156 0.73553 0.73588 0.50941 0.5104 149 149 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext sc_generic single_cell_generic generic-scrnaseq-only   China 2024-02-07 Undetermined Undetermined Gut Digestive System
30621 30621 SRR27907609 SRX23567385 SRS20412877 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.   pubmed:40392591   KO11 Ctla 4 knockout GSM8068838   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. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files intestine   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.   tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO GSM8068838 GSM8068838: KO11 Ctla 4 knockout; Danio rerio; RNA Seq GSM8068838 r1 GSM8068838 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP488782   loader:fastq load.py KO11_Clean_Data2.fq.gz KO11_Clean_Data1.fq.gz fastq fastq 5443694370.0 18290488.0 GSM8068838 r1 0:148.81 1:148.81 A:1480267395;C:1230300897;G:1247791644;T:1485302181;N:32253 148 148     1480267395 1230300897 1247791644 1485302181 32253 SRX23567385 SRS20412877 SRA1799527 zhejiang university zhejiang university 2 0.86445 0.86409 0.07094 0.06652 0.74738 0.74897 0.51339 0.51762 149 149 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext sc_generic single_cell_generic generic-scrnaseq-only   China 2024-02-07 Undetermined Undetermined Gut Digestive System
30622 30622 SRR27907610 SRX23567384 SRS20412876 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.   pubmed:40392591   KO9 Ctla 4 knockout GSM8068837   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP488782   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     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   China 2024-02-07 Undetermined Undetermined Gut Digestive System
30623 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.   pubmed:40392591   WT8 control GSM8068836   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP488782   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     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   China 2024-02-07 Undetermined Undetermined Gut Digestive System
30624 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.   pubmed:40392591   WT7 control GSM8068835   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP488782   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     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   China 2024-02-07 Undetermined Undetermined Gut Digestive System
30625 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.   pubmed:40392591   WT1 control GSM8068834   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP488782   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     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   China 2024-02-07 Undetermined Undetermined Gut Digestive System
30626 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.   pubmed:40392591   KO scRNAseq GSM8068833   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   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 μm 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 μg/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 3’ 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.   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 μm 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 μg/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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP488787   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     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   China 2024-02-07 Undetermined Undetermined Gut Digestive System
30627 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.   pubmed:40392591   WT scRNAseq GSM8068832   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   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 μm 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 μg/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 3’ 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.   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 μm 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 μg/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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP488787   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     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   China 2024-02-07 Undetermined Undetermined Gut Digestive System
33351 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 ß ß 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.       SBM1 3 GSM8439539   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524094     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     1848518187 1602695225 1609135376 1860572175 17439 SRX25595192 SRS22245033 SRA1939628 Beibu Gulf University Beibu Gulf University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-08-04 Undetermined Undetermined Gut Digestive System
33352 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 ß ß 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.       SBM1 2 GSM8439538   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524094     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     1794801562 1631426136 1638460090 1808681001 17308 SRX25595191 SRS22245032 SRA1939628 Beibu Gulf University Beibu Gulf University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-08-04 Undetermined Undetermined Gut Digestive System
33353 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 ß ß 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.       SBM1 1 GSM8439537   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524094     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     1801507713 1634518350 1642455999 1815139080 17220 SRX25595190 SRS22245031 SRA1939628 Beibu Gulf University Beibu Gulf University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-08-04 Undetermined Undetermined Gut Digestive System
33354 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 ß ß 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.       FM1 3 GSM8439536   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524094     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     1814868011 1638590076 1645410775 1828004537 17225 SRX25595189 SRS22245030 SRA1939628 Beibu Gulf University Beibu Gulf University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-08-04 Undetermined Undetermined Gut Digestive System
33355 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 ß ß 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.       FM1 2 GSM8439535   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524094     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     1821635965 1634568957 1641356498 1834750114 17615 SRX25595188 SRS22245029 SRA1939628 Beibu Gulf University Beibu Gulf University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-08-04 Undetermined Undetermined Gut Digestive System
33356 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 ß ß 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.       FM1 1 GSM8439534   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524094     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     1851629842 1595942468 1602547587 1865384194 17401 SRX25595187 SRS22245028 SRA1939628 Beibu Gulf University Beibu Gulf University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-08-04 Undetermined Undetermined Gut Digestive System
33357 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 ß ß 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.       D3 4 3 GSM8439533   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524094     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     1815846879 1641161510 1648091770 1829741658 17429 SRX25595186 SRS22245027 SRA1939628 Beibu Gulf University Beibu Gulf University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-08-04 Undetermined Undetermined Gut Digestive System
33358 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 ß ß 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.       D3 4 2 GSM8439532   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524094     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     1888591272 1630003556 1636509489 1898365125 17943 SRX25595185 SRS22245026 SRA1939628 Beibu Gulf University Beibu Gulf University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-08-04 Undetermined Undetermined Gut Digestive System
33359 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 ß ß 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.       D3 4 1 GSM8439531   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524094     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     1841905352 1647600285 1654313322 1852960597 17723 SRX25595184 SRS22245025 SRA1939628 Beibu Gulf University Beibu Gulf University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-08-04 Undetermined Undetermined Gut Digestive System
38009 38009 SRR1265748 SRX529142 SRS598839 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Female Gut Replicate 3 sRNAseq GSM1376631   source name:Female Gut|gender:female|tissue:Gut|genetic background:Wild type Singapore strain Female Gut Replicate 3 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Female Gut N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Female|tissue:Gut|genetic background:Wild type Singapore strain GSM1376631 GSM1376631: Female Gut Replicate 3 sRNAseq; Danio rerio; miRNA Seq GSM1376631   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376631 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZG012_TTAGGC_L008_R1.fastq.gz fastq 425902173.0 8351023.0 GSM1376631 r1 0:51 A:85733692;C:98728458;G:130104130;T:111282282;N:53611 51       85733692 98728458 130104130 111282282 53611 SRX529142 SRS598839 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.00598   0.00074   0.99565   0.68818   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Gut Digestive System
38010 38010 SRR1265747 SRX529141 SRS598838 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Female Gut Replicate 2 sRNAseq GSM1376630   source name:Female Gut|gender:female|tissue:Gut|genetic background:Wild type Singapore strain Female Gut Replicate 2 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Female Gut N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Female|tissue:Gut|genetic background:Wild type Singapore strain GSM1376630 GSM1376630: Female Gut Replicate 2 sRNAseq; Danio rerio; miRNA Seq GSM1376630   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376630 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZG011_CGATGT_L008_R1.fastq.gz fastq 464997192.0 9117592.0 GSM1376630 r1 0:51 A:94817360;C:107530735;G:141688278;T:120903676;N:57143 51       94817360 107530735 141688278 120903676 57143 SRX529141 SRS598838 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.00297   0.00033   0.9975   0.62721   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Gut Digestive System
38011 38011 SRR1265746 SRX529140 SRS598837 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Female Gut Replicate 1 sRNAseq GSM1376629   source name:Female Gut|gender:female|tissue:Gut|genetic background:Wild type Singapore strain Female Gut Replicate 1 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Female Gut N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Female|tissue:Gut|genetic background:Wild type Singapore strain GSM1376629 GSM1376629: Female Gut Replicate 1 sRNAseq; Danio rerio; miRNA Seq GSM1376629   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376629 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZG010_ATCACG_L008_R1.fastq.gz fastq 798808308.0 15662908.0 GSM1376629 r1 0:51 A:163944400;C:183125028;G:240040726;T:211597768;N:100386 51       163944400 183125028 240040726 211597768 100386 SRX529140 SRS598837 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.01106   0.00122   0.99466   0.66862   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Gut Digestive System
38012 38012 SRR1265745 SRX529139 SRS598836 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Male Gut Replicate 3 sRNAseq GSM1376628   source name:Male Gut|gender:male|tissue:Gut|genetic background:Wild type Singapore strain Male Gut Replicate 3 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Male Gut N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Male|tissue:Gut|genetic background:Wild type Singapore strain GSM1376628 GSM1376628: Male Gut Replicate 3 sRNAseq; Danio rerio; miRNA Seq GSM1376628   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376628 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZG009_GCCAAT_L007_R1.fastq.gz fastq 224291778.0 4397878.0 GSM1376628 r1 0:51 A:45043664;C:58692343;G:66840019;T:53695301;N:20451 51       45043664 58692343 66840019 53695301 20451 SRX529139 SRS598836 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.0015   0.00021   0.99829   0.69477   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Gut Digestive System
38013 38013 SRR1265743 SRX529138 SRS598835 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Male Gut Replicate 1 sRNAseq GSM1376626   source name:Male Gut|gender:male|tissue:Gut|genetic background:Wild type Singapore strain Male Gut Replicate 1 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Male Gut N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Male|tissue:Gut|genetic background:Wild type Singapore strain GSM1376626 GSM1376626: Male Gut Replicate 1 sRNAseq; Danio rerio; miRNA Seq GSM1376626   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376626 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZG007_TGACCA_L007_R1.fastq.gz fastq 1058961552.0 20763952.0 GSM1376626 r1 0:51 A:205056709;C:273349362;G:322710601;T:257753257;N:91623 51       205056709 273349362 322710601 257753257 91623 SRX529138 SRS598835 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.00382   0.00043   0.99746   0.683   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Gut Digestive System
38023 38023 SRR1265744 SRX529128 SRS598826 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Male Gut Replicate 2 sRNAseq GSM1376627   source name:Male Gut|gender:male|tissue:Gut|genetic background:Wild type Singapore strain Male Gut Replicate 2 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Male Gut N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Male|tissue:Gut|genetic background:Wild type Singapore strain GSM1376627 GSM1376627: Male Gut Replicate 2 sRNAseq; Danio rerio; miRNA Seq GSM1376627   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376627 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZG008_ACAGTG_L007_R1.fastq.gz fastq 541064457.0 10609107.0 GSM1376627 r1 0:51 A:104798947;C:136927266;G:166713427;T:132575036;N:49781 51       104798947 136927266 166713427 132575036 49781 SRX529128 SRS598826 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.00679   0.00072   0.99655   0.72132   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Gut Digestive System
41078 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.   pubmed:28118819   Proximal S1 intestine in zebrafish 2 wks post sham surgery #3 GSM2195932   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   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   status:SHAM GSM2195932 GSM2195932: Proximal S1 intestine in zebrafish 2 wks post sham surgery #3; Danio rerio; RNA Seq GSM2195932   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   SRP076398     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     374411447 361418430 359803924 415021333 86536 SRX1836009 SRS1495472 SRA432774 GEO Children's Hospital Los Angeles 1 0.94789   0.05269   0.77753   0.53939   75   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2016-06-09 Undetermined Undetermined Gut Digestive System
41079 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.   pubmed:28118819   Proximal S1 intestine in zebrafish 2 wks post sham surgery #3 GSM2195932   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   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   status:SHAM GSM2195932 GSM2195932: Proximal S1 intestine in zebrafish 2 wks post sham surgery #3; Danio rerio; RNA Seq GSM2195932   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   SRP076398     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     881893112 869893713 867139931 1004485159 269206 SRX1836009 SRS1495472 SRA432774 GEO Children's Hospital Los Angeles 1 0.95546   0.05225   0.77218   0.53519   75   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2016-06-09 Undetermined Undetermined Gut Digestive System
41080 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.   pubmed:28118819   Proximal S1 intestine in zebrafish 2 wks post sham surgery #2 GSM2195931   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   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   status:SHAM GSM2195931 GSM2195931: Proximal S1 intestine in zebrafish 2 wks post sham surgery #2; Danio rerio; RNA Seq GSM2195931   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   SRP076398     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     350940564 313266568 309387786 375159308 105820 SRX1836008 SRS1495473 SRA432774 GEO Children's Hospital Los Angeles 1 0.92348   0.06356   0.77252   0.52707   75   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2016-06-09 Undetermined Undetermined Gut Digestive System
41081 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.   pubmed:28118819   Proximal S1 intestine in zebrafish 2 wks post sham surgery #2 GSM2195931   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   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   status:SHAM GSM2195931 GSM2195931: Proximal S1 intestine in zebrafish 2 wks post sham surgery #2; Danio rerio; RNA Seq GSM2195931   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   SRP076398     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     829523096 775146066 763427556 930352935 337228 SRX1836008 SRS1495473 SRA432774 GEO Children's Hospital Los Angeles 1 0.9361   0.06336   0.76353   0.54746   75   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2016-06-09 Undetermined Undetermined Gut Digestive System
41082 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.   pubmed:28118819   Proximal S1 intestine in zebrafish 2 wks post sham surgery #1 GSM2195930   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   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   status:SHAM GSM2195930 GSM2195930: Proximal S1 intestine in zebrafish 2 wks post sham surgery #1; Danio rerio; RNA Seq GSM2195930   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   SRP076398     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     359052072 343824905 344804667 400589883 92957 SRX1836007 SRS1495471 SRA432774 GEO Children's Hospital Los Angeles 1 0.94277   0.05284   0.77881   0.57769   74   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2016-06-09 Undetermined Undetermined Gut Digestive System
41083 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.   pubmed:28118819   Proximal S1 intestine in zebrafish 2 wks post sham surgery #1 GSM2195930   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   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   status:SHAM GSM2195930 GSM2195930: Proximal S1 intestine in zebrafish 2 wks post sham surgery #1; Danio rerio; RNA Seq GSM2195930   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   SRP076398     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     875615940 857379635 859609503 1006260031 288916 SRX1836007 SRS1495471 SRA432774 GEO Children's Hospital Los Angeles 1 0.95037   0.0525   0.77147   0.5711   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2016-06-09 Undetermined Undetermined Gut Digestive System
44999 44999 SRR6411468 SRX3504483 SRS2782037 SRP127389 PRJNA427282 RNA profiling of the liver and gut tissues in zebrafish Danio rerio [miRNA] GSE108436 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 “miRNA matrix” that connects both total RNA Seq and miRNA Seq. Overall design: Examination of miRNome in adult zebrafish tissues gut and liver under homesostasis. parent bioproject:PRJNA427275 pubmed:30386173   Gut 4 miRNA GSM2898188   source name:Gut|tissue:Gut|Sex:male Gut 4 miRNA 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’s 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 Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing alignment mature/precursor/ novel miRNA detection and quantification and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep a tool for miRNA identification from RNA sequencing data and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR 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 EdgeR output for the BPA vs Control Comparison. Columns to the right of the logFC column represent EdgeR output. Gut 1 Gut 2 Liver 1 and Liver 2 contain raw count data for the two gut and liver miRNAseq libraries respectively. Symbol GeneID Description and MirBaseID represent miRNA annotation and description information. Gut Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C and the light–dark 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 –70 °C. 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 miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA   tissue:Gut|Sex:male GSM2898188 GSM2898188: Gut 4 miRNA; Danio rerio; miRNA Seq GSM2898188   1 Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA GEO Accession:GSM2898188 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP127389     4.fastq.gz fastq 643103727.0 12609877.0 GSM2898188 r1 0:51 A:158299708;C:154230134;G:180978224;T:147874496;N:1721165 51       158299708 154230134 180978224 147874496 1721165 SRX3504483 SRS2782037 SRA641250 GEO Walton RS311, Pathology, Medical University of South Carolina 1 0.0075   0.00106   0.99671   0.56044   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   United States 2017-12-22 Undetermined Adult Gut Digestive System
45000 45000 SRR6411467 SRX3504482 SRS2782036 SRP127389 PRJNA427282 RNA profiling of the liver and gut tissues in zebrafish Danio rerio [miRNA] GSE108436 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 “miRNA matrix” that connects both total RNA Seq and miRNA Seq. Overall design: Examination of miRNome in adult zebrafish tissues gut and liver under homesostasis. parent bioproject:PRJNA427275 pubmed:30386173   Gut 3 miRNA GSM2898187   source name:Gut|tissue:Gut|Sex:male Gut 3 miRNA 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’s 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 Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing alignment mature/precursor/ novel miRNA detection and quantification and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep a tool for miRNA identification from RNA sequencing data and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR 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 EdgeR output for the BPA vs Control Comparison. Columns to the right of the logFC column represent EdgeR output. Gut 1 Gut 2 Liver 1 and Liver 2 contain raw count data for the two gut and liver miRNAseq libraries respectively. Symbol GeneID Description and MirBaseID represent miRNA annotation and description information. Gut Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C and the light–dark 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 –70 °C. 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 miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA   tissue:Gut|Sex:male GSM2898187 GSM2898187: Gut 3 miRNA; Danio rerio; miRNA Seq GSM2898187   1 Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA GEO Accession:GSM2898187 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP127389     3.fastq.gz fastq 657326148.0 12888748.0 GSM2898187 r1 0:51 A:155617794;C:161709285;G:186002579;T:152250836;N:1745654 51       155617794 161709285 186002579 152250836 1745654 SRX3504482 SRS2782036 SRA641250 GEO Walton RS311, Pathology, Medical University of South Carolina 1 0.11293   0.00924   0.99399   0.58458   51   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   United States 2017-12-22 Undetermined Adult Gut Digestive System
45003 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 “miRNA matrix” 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   Gut 4 mRNA GSM2898184   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’s 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 26–29 °C and the light–dark 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 –70 °C. 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.   Sex:male|tissue:Gut GSM2898184 GSM2898184: Gut 4 mRNA; Danio rerio; RNA Seq GSM2898184   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   SRP127390     Gut_2.fastq.gz fastq 2511580170.0 49246670.0 GSM2898184 r1 0:51 A:634532680;C:591744395;G:630819200;T:654046479;N:437416 51       634532680 591744395 630819200 654046479 437416 SRX3504487 SRS2782041 SRA641251 GEO Walton RS311, Pathology, Medical University of South Carolina 1 0.91491   0.06302   0.79632   0.54435   51   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   United States 2017-12-22 Undetermined Undetermined Gut Digestive System
45004 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 “miRNA matrix” 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   Gut 3 mRNA GSM2898183   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’s 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 26–29 °C and the light–dark 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 –70 °C. 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.   Sex:male|tissue:Gut GSM2898183 GSM2898183: Gut 3 mRNA; Danio rerio; RNA Seq GSM2898183   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   SRP127390     Gut_1.fastq.gz fastq 2336820153.0 45820003.0 GSM2898183 r1 0:51 A:592745033;C:551283776;G:583859269;T:608544280;N:387795 51       592745033 551283776 583859269 608544280 387795 SRX3504486 SRS2782040 SRA641251 GEO Walton RS311, Pathology, Medical University of South Carolina                       B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk unknown unknown   United States 2017-12-22 Undetermined Undetermined Gut Digestive System
59456 59456 SRR11917488 SRX8463993 SRS6765214 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   CV3 IEC GSM4588952   tissue:intestine|group:Conventionalized|cell type:Other intestinal epithelium cells CV3 IEC Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Conventionalized|cell type:Other intestinal epithelium cells GSM4588952 GSM4588952: CV3 IEC; Danio rerio; RNA Seq GSM4588952   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588952 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S12_S12_L006_R1_001.fastq.gz fastq 989770770.0 19407270.0 GSM4588952 r1 0:51 1:0 A:281534917;C:214882196;G:215847745;T:277443986;N:61926 51 0     281534917 214882196 215847745 277443986 61926 SRX8463993 SRS6765214 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.85529   0.16671   0.87886   0.67632   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
59457 59457 SRR11917489 SRX8463993 SRS6765214 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   CV3 IEC GSM4588952   tissue:intestine|group:Conventionalized|cell type:Other intestinal epithelium cells CV3 IEC Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Conventionalized|cell type:Other intestinal epithelium cells GSM4588952 GSM4588952: CV3 IEC; Danio rerio; RNA Seq GSM4588952   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588952 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S12_S12_L007_R1_001.fastq.gz fastq 970629807.0 19031957.0 GSM4588952 r2 0:51 1:0 A:276238559;C:210614378;G:211564800;T:272166193;N:45877 51 0     276238559 210614378 211564800 272166193 45877 SRX8463993 SRS6765214 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.85557   0.16793   0.87819   0.68247   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
59458 59458 SRR11917486 SRX8463992 SRS6765213 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   CV3 EEC GSM4588951   tissue:intestine|group:Conventionalized|cell type:Enteroendocrine cells CV3 EEC Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Conventionalized|cell type:Enteroendocrine cells GSM4588951 GSM4588951: CV3 EEC; Danio rerio; RNA Seq GSM4588951   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588951 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S11_S11_L006_R1_001.fastq.gz fastq 1116941667.0 21900817.0 GSM4588951 r1 0:51 1:0 A:320236417;C:240301779;G:240594328;T:315739633;N:69510 51 0     320236417 240301779 240594328 315739633 69510 SRX8463992 SRS6765213 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.60354   0.13851   0.86699   0.49869   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
59459 59459 SRR11917487 SRX8463992 SRS6765213 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   CV3 EEC GSM4588951   tissue:intestine|group:Conventionalized|cell type:Enteroendocrine cells CV3 EEC Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Conventionalized|cell type:Enteroendocrine cells GSM4588951 GSM4588951: CV3 EEC; Danio rerio; RNA Seq GSM4588951   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588951 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S11_S11_L007_R1_001.fastq.gz fastq 1100752584.0 21583384.0 GSM4588951 r2 0:51 1:0 A:315761089;C:236724849;G:236992907;T:311222165;N:51574 51 0     315761089 236724849 236992907 311222165 51574 SRX8463992 SRS6765213 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.60449   0.13991   0.86519   0.49824   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
59460 59460 SRR11917484 SRX8463991 SRS6765212 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   GF3 IEC GSM4588950   tissue:intestine|group:Germ free|cell type:Other intestinal epithelium cells GF3 IEC Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Germ free|cell type:Other intestinal epithelium cells GSM4588950 GSM4588950: GF3 IEC; Danio rerio; RNA Seq GSM4588950   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588950 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S10_S10_L006_R1_001.fastq.gz fastq 1158251565.0 22710815.0 GSM4588950 r1 0:51 1:0 A:329413690;C:252108273;G:252469757;T:324185740;N:74105 51 0     329413690 252108273 252469757 324185740 74105 SRX8463991 SRS6765212 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.8667   0.17916   0.81631   0.60631   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
59461 59461 SRR11917485 SRX8463991 SRS6765212 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   GF3 IEC GSM4588950   tissue:intestine|group:Germ free|cell type:Other intestinal epithelium cells GF3 IEC Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Germ free|cell type:Other intestinal epithelium cells GSM4588950 GSM4588950: GF3 IEC; Danio rerio; RNA Seq GSM4588950   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588950 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S10_S10_L007_R1_001.fastq.gz fastq 1140502902.0 22362802.0 GSM4588950 r2 0:51 1:0 A:324550812;C:248145888;G:248413979;T:319338762;N:53461 51 0     324550812 248145888 248413979 319338762 53461 SRX8463991 SRS6765212 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.86472   0.17957   0.81604   0.60323   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
59462 59462 SRR11917482 SRX8463990 SRS6765211 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   GF3 EEC GSM4588949   tissue:intestine|group:Germ free|cell type:Enteroendocrine cells GF3 EEC Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Germ free|cell type:Enteroendocrine cells GSM4588949 GSM4588949: GF3 EEC; Danio rerio; RNA Seq GSM4588949   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588949 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S9_S9_L006_R1_001.fastq.gz fastq 1124335902.0 22045802.0 GSM4588949 r1 0:51 1:0 A:323779238;C:243076994;G:243426022;T:313982480;N:71168 51 0     323779238 243076994 243426022 313982480 71168 SRX8463990 SRS6765211 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.82417   0.22133   0.82262   0.53921   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
59463 59463 SRR11917483 SRX8463990 SRS6765211 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   GF3 EEC GSM4588949   tissue:intestine|group:Germ free|cell type:Enteroendocrine cells GF3 EEC Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Germ free|cell type:Enteroendocrine cells GSM4588949 GSM4588949: GF3 EEC; Danio rerio; RNA Seq GSM4588949   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588949 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S9_S9_L007_R1_001.fastq.gz fastq 1102409217.0 21615867.0 GSM4588949 r2 0:51 1:0 A:317592665;C:238208950;G:238561212;T:307994643;N:51747 51 0     317592665 238208950 238561212 307994643 51747 SRX8463990 SRS6765211 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.82287   0.22204   0.82037   0.54199   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
59464 59464 SRR11917480 SRX8463989 SRS6765210 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   CV2 IED GSM4588948   tissue:intestine|group:Conventionalized|cell type:Other intestinal epithelium cells CV2 IED Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Conventionalized|cell type:Other intestinal epithelium cells GSM4588948 GSM4588948: CV2 IED; Danio rerio; RNA Seq GSM4588948   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588948 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S8_S8_L006_R1_001.fastq.gz fastq 1153200474.0 22611774.0 GSM4588948 r1 0:51 1:0 A:325960158;C:253028514;G:253402635;T:320734834;N:74333 51 0     325960158 253028514 253402635 320734834 74333 SRX8463989 SRS6765210 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.87013   0.18232   0.74217   0.52659   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
59465 59465 SRR11917481 SRX8463989 SRS6765210 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   CV2 IED GSM4588948   tissue:intestine|group:Conventionalized|cell type:Other intestinal epithelium cells CV2 IED Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Conventionalized|cell type:Other intestinal epithelium cells GSM4588948 GSM4588948: CV2 IED; Danio rerio; RNA Seq GSM4588948   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588948 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S8_S8_L007_R1_001.fastq.gz fastq 1129915098.0 22155198.0 GSM4588948 r2 0:51 1:0 A:319498713;C:247882461;G:248181774;T:314298474;N:53676 51 0     319498713 247882461 248181774 314298474 53676 SRX8463989 SRS6765210 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.8695   0.18113   0.74156   0.52983   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
59466 59466 SRR11917478 SRX8463988 SRS6765209 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   CV2 EEC GSM4588947   tissue:intestine|group:Conventionalized|cell type:Enteroendocrine cells CV2 EEC Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Conventionalized|cell type:Enteroendocrine cells GSM4588947 GSM4588947: CV2 EEC; Danio rerio; RNA Seq GSM4588947   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588947 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S7_S7_L006_R1_001.fastq.gz fastq 1378636692.0 27032092.0 GSM4588947 r1 0:51 1:0 A:391264014;C:300388051;G:302055880;T:384841320;N:87427 51 0     391264014 300388051 302055880 384841320 87427 SRX8463988 SRS6765209 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.86069   0.20189   0.74643   0.48529   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
59467 59467 SRR11917479 SRX8463988 SRS6765209 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   CV2 EEC GSM4588947   tissue:intestine|group:Conventionalized|cell type:Enteroendocrine cells CV2 EEC Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Conventionalized|cell type:Enteroendocrine cells GSM4588947 GSM4588947: CV2 EEC; Danio rerio; RNA Seq GSM4588947   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588947 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S7_S7_L007_R1_001.fastq.gz fastq 1355490597.0 26578247.0 GSM4588947 r2 0:51 1:0 A:384933467;C:295204222;G:296869394;T:378419448;N:64066 51 0     384933467 295204222 296869394 378419448 64066 SRX8463988 SRS6765209 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.86045   0.20313   0.74667   0.48228   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
59468 59468 SRR11917476 SRX8463987 SRS6765208 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   GF2 IEC GSM4588946   tissue:intestine|group:Germ free|cell type:Other intestinal epithelium cells GF2 IEC Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Germ free|cell type:Other intestinal epithelium cells GSM4588946 GSM4588946: GF2 IEC; Danio rerio; RNA Seq GSM4588946   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588946 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S6_S6_L006_R1_001.fastq.gz fastq 1096567014.0 21501314.0 GSM4588946 r1 0:51 1:0 A:310133103;C:241356167;G:241726971;T:303281850;N:68923 51 0     310133103 241356167 241726971 303281850 68923 SRX8463987 SRS6765208 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.87328   0.17387   0.86657   0.64049   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
59469 59469 SRR11917477 SRX8463987 SRS6765208 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   GF2 IEC GSM4588946   tissue:intestine|group:Germ free|cell type:Other intestinal epithelium cells GF2 IEC Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Germ free|cell type:Other intestinal epithelium cells GSM4588946 GSM4588946: GF2 IEC; Danio rerio; RNA Seq GSM4588946   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588946 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S6_S6_L007_R1_001.fastq.gz fastq 1077795036.0 21133236.0 GSM4588946 r2 0:51 1:0 A:305006168;C:237104899;G:237493375;T:298139724;N:50870 51 0     305006168 237104899 237493375 298139724 50870 SRX8463987 SRS6765208 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.87121   0.17225   0.86776   0.65328   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
59470 59470 SRR11917474 SRX8463986 SRS6765207 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   GF2 EEC GSM4588945   tissue:intestine|group:Germ free|cell type:Enteroendocrine cells GF2 EEC Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Germ free|cell type:Enteroendocrine cells GSM4588945 GSM4588945: GF2 EEC; Danio rerio; RNA Seq GSM4588945   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588945 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S5_S5_L006_R1_001.fastq.gz fastq 993591180.0 19482180.0 GSM4588945 r1 0:51 1:0 A:282890765;C:216703865;G:217669683;T:276263863;N:63004 51 0     282890765 216703865 217669683 276263863 63004 SRX8463986 SRS6765207 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.84026   0.15974   0.84542   0.62819   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
59471 59471 SRR11917475 SRX8463986 SRS6765207 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   GF2 EEC GSM4588945   tissue:intestine|group:Germ free|cell type:Enteroendocrine cells GF2 EEC Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Germ free|cell type:Enteroendocrine cells GSM4588945 GSM4588945: GF2 EEC; Danio rerio; RNA Seq GSM4588945   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588945 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S5_S5_L007_R1_001.fastq.gz fastq 974360049.0 19105099.0 GSM4588945 r2 0:51 1:0 A:277539322;C:212402095;G:213358281;T:271014144;N:46207 51 0     277539322 212402095 213358281 271014144 46207 SRX8463986 SRS6765207 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.84253   0.16032   0.84723   0.62874   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
59472 59472 SRR11917472 SRX8463985 SRS6765206 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   CV1 IEC GSM4588944   tissue:intestine|group:Conventionalized|cell type:Other intestinal epithelium cells CV1 IEC Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Conventionalized|cell type:Other intestinal epithelium cells GSM4588944 GSM4588944: CV1 IEC; Danio rerio; RNA Seq GSM4588944   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588944 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S4_S4_L006_R1_001.fastq.gz fastq 1125747633.0 22073483.0 GSM4588944 r1 0:51 1:0 A:318281873;C:249238273;G:249957107;T:308199627;N:70753 51 0     318281873 249238273 249957107 308199627 70753 SRX8463985 SRS6765206 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.89074   0.12353   0.82816   0.68204   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
59473 59473 SRR11917473 SRX8463985 SRS6765206 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   CV1 IEC GSM4588944   tissue:intestine|group:Conventionalized|cell type:Other intestinal epithelium cells CV1 IEC Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Conventionalized|cell type:Other intestinal epithelium cells GSM4588944 GSM4588944: CV1 IEC; Danio rerio; RNA Seq GSM4588944   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588944 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S4_S4_L007_R1_001.fastq.gz fastq 1105934796.0 21684996.0 GSM4588944 r2 0:51 1:0 A:312851469;C:244757781;G:245446410;T:302827147;N:51989 51 0     312851469 244757781 245446410 302827147 51989 SRX8463985 SRS6765206 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.88843   0.12342   0.82873   0.67656   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
59474 59474 SRR11917470 SRX8463984 SRS6765204 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   CV1 EEC GSM4588943   tissue:intestine|group:Conventionalized|cell type:Enteroendocrine cells CV1 EEC Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Conventionalized|cell type:Enteroendocrine cells GSM4588943 GSM4588943: CV1 EEC; Danio rerio; RNA Seq GSM4588943   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588943 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S3_S3_L006_R1_001.fastq.gz fastq 942559764.0 18481564.0 GSM4588943 r1 0:51 1:0 A:263978139;C:208960440;G:211142234;T:258419586;N:59365 51 0     263978139 208960440 211142234 258419586 59365 SRX8463984 SRS6765204 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.84651   0.13502   0.87334   0.60719   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
59475 59475 SRR11917471 SRX8463984 SRS6765204 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   CV1 EEC GSM4588943   tissue:intestine|group:Conventionalized|cell type:Enteroendocrine cells CV1 EEC Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Conventionalized|cell type:Enteroendocrine cells GSM4588943 GSM4588943: CV1 EEC; Danio rerio; RNA Seq GSM4588943   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588943 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S3_S3_L007_R1_001.fastq.gz fastq 923680839.0 18111389.0 GSM4588943 r2 0:51 1:0 A:258844956;C:204695214;G:206849563;T:253247421;N:43685 51 0     258844956 204695214 206849563 253247421 43685 SRX8463984 SRS6765204 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.84566   0.13508   0.8746   0.60113   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
59476 59476 SRR11917468 SRX8463983 SRS6765205 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   GF1 IEC GSM4588942   tissue:intestine|group:Germ free|cell type:Other intestinal epithelium cells GF1 IEC Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Germ free|cell type:Other intestinal epithelium cells GSM4588942 GSM4588942: GF1 IEC; Danio rerio; RNA Seq GSM4588942   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588942 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S2_S2_L006_R1_001.fastq.gz fastq 1238473698.0 24283798.0 GSM4588942 r1 0:51 1:0 A:341609725;C:281085121;G:281016378;T:334683690;N:78784 51 0     341609725 281085121 281016378 334683690 78784 SRX8463983 SRS6765205 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.88819   0.1308   0.81357   0.57234   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
59477 59477 SRR11917469 SRX8463983 SRS6765205 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   GF1 IEC GSM4588942   tissue:intestine|group:Germ free|cell type:Other intestinal epithelium cells GF1 IEC Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Germ free|cell type:Other intestinal epithelium cells GSM4588942 GSM4588942: GF1 IEC; Danio rerio; RNA Seq GSM4588942   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588942 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S2_S2_L007_R1_001.fastq.gz fastq 1215535785.0 23834035.0 GSM4588942 r2 0:51 1:0 A:335462084;C:275714789;G:275686585;T:328614149;N:58178 51 0     335462084 275714789 275686585 328614149 58178 SRX8463983 SRS6765205 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.88988   0.13024   0.81262   0.57631   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
59478 59478 SRR11917466 SRX8463982 SRS6765203 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   GF1 EEC GSM4588941   tissue:intestine|group:Germ free|cell type:Enteroendocrine cells GF1 EEC Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Germ free|cell type:Enteroendocrine cells GSM4588941 GSM4588941: GF1 EEC; Danio rerio; RNA Seq GSM4588941   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588941 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S1_S1_L006_R1_001.fastq.gz fastq 1106448264.0 21695064.0 GSM4588941 r1 0:51 1:0 A:312177906;C:243246164;G:244584142;T:306370900;N:69152 51 0     312177906 243246164 244584142 306370900 69152 SRX8463982 SRS6765203 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.7883   0.14389   0.88158   0.55008   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
59479 59479 SRR11917467 SRX8463982 SRS6765203 SRP265808 PRJNA637035 Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways GSE151711 Transcriptome Analysis RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.   pubmed:38577841   GF1 EEC GSM4588941   tissue:intestine|group:Germ free|cell type:Enteroendocrine cells GF1 EEC Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample intestine no treatment Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols Gnotobiotic zebrafish group:Germ free|cell type:Enteroendocrine cells GSM4588941 GSM4588941: GF1 EEC; Danio rerio; RNA Seq GSM4588941   1 Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4588941 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP265808     LY-S1_S1_L007_R1_001.fastq.gz fastq 1082299917.0 21221567.0 GSM4588941 r2 0:51 1:0 A:305489640;C:237873171;G:239135258;T:299751004;N:50844 51 0     305489640 237873171 239135258 299751004 50844 SRX8463982 SRS6765203 SRA1082774 GEO Rawls lab, MGM Department, Duke University 1 0.78533   0.14463   0.88229   0.56056   51   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   United States 2020-06-03 Undetermined Larval Gut Digestive System
63810 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   pubmed:33920039   Torpor+radiation [18 24 M2 RAD] GSM5208645   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 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM 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; 100–200 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.   radiation cgy:32.64|temperature °c:18.5|melatonin µm:24 GSM5208645 GSM5208645: Torpor+radiation [18 24 M2 RAD]; Danio rerio; RNA Seq GSM5208645   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; 100–200 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   SRP311962   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       343218732 412078303 480421414 353581599 296252 SRX10435564 SRS8569035 SRA1209926 GEO Hardiman Lab, Institute for Global Food Security, Queen's University Belfast 1 0.61709   0.13219   0.8379   0.67633   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United Kingdom 2021-03-24 Undetermined Undetermined Gut Digestive System
63811 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   pubmed:33920039   Torpor+radiation [18 24 M1 RAD] GSM5208644   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 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM 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; 100–200 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.   radiation cgy:32.64|temperature °c:18.5|melatonin µm:24 GSM5208644 GSM5208644: Torpor+radiation [18 24 M1 RAD]; Danio rerio; RNA Seq GSM5208644   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; 100–200 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   SRP311962   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       400114581 473398494 532511254 420225243 347678 SRX10435563 SRS8569036 SRA1209926 GEO Hardiman Lab, Institute for Global Food Security, Queen's University Belfast 1 0.58111   0.13543   0.86419   0.68781   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United Kingdom 2021-03-24 Undetermined Undetermined Gut Digestive System
63812 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   pubmed:33920039   Torpor+radiation [18 24 F2 RAD] GSM5208643   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 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM 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; 100–200 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.   radiation cgy:32.64|temperature °c:18.5|melatonin µm:24 GSM5208643 GSM5208643: Torpor+radiation [18 24 F2 RAD]; Danio rerio; RNA Seq GSM5208643   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; 100–200 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   SRP311962   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       418454946 561035530 571770538 454478879 381707 SRX10435562 SRS8569034 SRA1209926 GEO Hardiman Lab, Institute for Global Food Security, Queen's University Belfast 1 0.76053   0.17325   0.83954   0.64698   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United Kingdom 2021-03-24 Undetermined Undetermined Gut Digestive System
63813 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   pubmed:33920039   Torpor+radiation [18 24 F1 RAD] GSM5208642   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 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM 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; 100–200 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.   radiation cgy:32.64|temperature °c:18.5|melatonin µm:24 GSM5208642 GSM5208642: Torpor+radiation [18 24 F1 RAD]; Danio rerio; RNA Seq GSM5208642   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; 100–200 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   SRP311962   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       509515197 623307582 694019366 542224292 441913 SRX10435561 SRS8569033 SRA1209926 GEO Hardiman Lab, Institute for Global Food Security, Queen's University Belfast 1 0.62827   0.14038   0.828   0.66975   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United Kingdom 2021-03-24 Undetermined Undetermined Gut Digestive System
63814 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   pubmed:33920039   Radiation [C M1 RAD] GSM5208641   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 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM 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; 100–200 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.   radiation cgy:32.64|temperature °c:28.5|melatonin µm:0 GSM5208641 GSM5208641: Radiation [C M1 RAD]; Danio rerio; RNA Seq GSM5208641   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; 100–200 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   SRP311962   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       136269333 152654300 156807839 153346367 113061 SRX10435560 SRS8569032 SRA1209926 GEO Hardiman Lab, Institute for Global Food Security, Queen's University Belfast 1 0.77484   0.14395   0.78405   0.5761   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United Kingdom 2021-03-24 Undetermined Undetermined Gut Digestive System
63815 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   pubmed:33920039   Radiation [C F7 RAD] GSM5208640   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 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM 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; 100–200 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.   radiation cgy:32.64|temperature °c:28.5|melatonin µm:0 GSM5208640 GSM5208640: Radiation [C F7 RAD]; Danio rerio; RNA Seq GSM5208640   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; 100–200 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   SRP311962   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       396601070 476853550 517846835 428710396 344549 SRX10435559 SRS8569031 SRA1209926 GEO Hardiman Lab, Institute for Global Food Security, Queen's University Belfast 1 0.71064   0.16141   0.81544   0.63869   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United Kingdom 2021-03-24 Undetermined Undetermined Gut Digestive System
63816 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   pubmed:33920039   Radiation [C F2 RAD] GSM5208639   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 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM 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; 100–200 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.   radiation cgy:32.64|temperature °c:28.5|melatonin µm:0 GSM5208639 GSM5208639: Radiation [C F2 RAD]; Danio rerio; RNA Seq GSM5208639   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; 100–200 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   SRP311962   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       270072562 315451890 350204178 291687838 227732 SRX10435558 SRS8569030 SRA1209926 GEO Hardiman Lab, Institute for Global Food Security, Queen's University Belfast 1 0.70512   0.15321   0.81491   0.65123   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United Kingdom 2021-03-24 Undetermined Undetermined Gut Digestive System
63817 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   pubmed:33920039   Torpor [PN0186 0016] GSM5208638   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 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM 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; 100–200 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.   radiation cgy:0|temperature °c:18.5|melatonin µm:24 GSM5208638 GSM5208638: Torpor [PN0186 0016]; Danio rerio; RNA Seq GSM5208638   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; 100–200 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   SRP311962   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     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   United Kingdom 2021-03-24 Undetermined Undetermined Gut Digestive System
63818 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   pubmed:33920039   Torpor [PN0186 0015] GSM5208637   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 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM 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; 100–200 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.   radiation cgy:0|temperature °c:18.5|melatonin µm:24 GSM5208637 GSM5208637: Torpor [PN0186 0015]; Danio rerio; RNA Seq GSM5208637   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; 100–200 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   SRP311962   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     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   United Kingdom 2021-03-24 Undetermined Undetermined Gut Digestive System
63819 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   pubmed:33920039   Control [C F7 NORAD] GSM5208636   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 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM 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; 100–200 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.   radiation cgy:0|temperature °c:28.5|melatonin µm:0 GSM5208636 GSM5208636: Control [C F7 NORAD]; Danio rerio; RNA Seq GSM5208636   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; 100–200 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   SRP311962   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       320793907 370334561 393244317 349086384 277731 SRX10435555 SRS8569026 SRA1209926 GEO Hardiman Lab, Institute for Global Food Security, Queen's University Belfast 1 0.74343   0.14223   0.8322   0.411   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United Kingdom 2021-03-24 Undetermined Undetermined Gut Digestive System
63820 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   pubmed:33920039   Control [C F3 NORAD] GSM5208635   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 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM 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; 100–200 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.   radiation cgy:0|temperature °c:28.5|melatonin µm:0 GSM5208635 GSM5208635: Control [C F3 NORAD]; Danio rerio; RNA Seq GSM5208635   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; 100–200 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   SRP311962   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       293343570 349728046 383602727 314473091 260816 SRX10435554 SRS8569028 SRA1209926 GEO Hardiman Lab, Institute for Global Food Security, Queen's University Belfast 1 0.70261   0.14107   0.81791   0.57017   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United Kingdom 2021-03-24 Undetermined Undetermined Gut Digestive System
63907 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.   pubmed:34556579   Intestine3 GSM5237128   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   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°C water temperature; 14/10 hour light/dark cycle genotype:wild type|tissue:intestine|strain:TLAB GSM5237128 GSM5237128: Intestine3; Danio rerio; RNA Seq GSM5237128   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   SRP314470     Intestine3.fastq fastq 1569173300.0 15691733.0 GSM5237128 r1 0:100 A:386685730;C:390640575;G:379186629;T:412599551;N:60815 100       386685730 390640575 379186629 412599551 60815 SRX10579904 SRS8684372 SRA1217576 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.95006   0.08193   0.78015   0.56907   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2021-04-12 Undetermined Undetermined Gut Digestive System
63908 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.   pubmed:34556579   Intestine2 GSM5237127   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   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°C water temperature; 14/10 hour light/dark cycle genotype:wild type|tissue:intestine|strain:TLAB GSM5237127 GSM5237127: Intestine2; Danio rerio; RNA Seq GSM5237127   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   SRP314470     Intestine2.fastq fastq 2130566800.0 21305668.0 GSM5237127 r1 0:100 A:526261017;C:530944116;G:514882717;T:558396882;N:82068 100       526261017 530944116 514882717 558396882 82068 SRX10579903 SRS8684371 SRA1217576 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.95   0.0797   0.77382   0.56644   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2021-04-12 Undetermined Undetermined Gut Digestive System
63909 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.   pubmed:34556579   Intestine1 GSM5237126   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   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°C water temperature; 14/10 hour light/dark cycle genotype:wild type|tissue:intestine|strain:TLAB GSM5237126 GSM5237126: Intestine1; Danio rerio; RNA Seq GSM5237126   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   SRP314470     Intestine1.fastq fastq 1573976900.0 15739769.0 GSM5237126 r1 0:100 A:387753454;C:390843684;G:380063787;T:415255739;N:60236 100       387753454 390843684 380063787 415255739 60236 SRX10579902 SRS8684370 SRA1217576 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.95269   0.07992   0.77311   0.57635   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2021-04-12 Undetermined Undetermined Gut Digestive System
75099 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.         20201026 S3 S0hpt S26 L003 R1 001.fastq   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                 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.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     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     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   China 2023-04-25 Undetermined Undetermined Gut Digestive System
75100 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.         20201026 S3 S0hpt S8 L004 R1 001.fastq   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                 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.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     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     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   China 2023-04-25 Undetermined Undetermined Gut Digestive System
75101 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.         20201026 S3 S0hpt S8 L003 R1 001.fastq   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                 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.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     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     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   China 2023-04-25 Undetermined Undetermined Gut Digestive System
75102 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.         20201026 S3 S0hpt S8 L002 R1 001.fastq   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                 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.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     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     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   China 2023-04-25 Undetermined Undetermined Gut Digestive System
75103 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.         20201026 S3 S0hpt S8 L001 R1 001.fastq   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                 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.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     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     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   China 2023-04-25 Undetermined Undetermined Gut Digestive System
75107 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.         20201026 S2 S48hpt S25 L003 R1 001.fastq   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                 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. Sequencing these libraries produce a standard Illumina BCL data output folder.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     20201026_S2_S48hpt_S25_L003_R1_001.fastq.gz 20201026_S2_S48hpt_S25_L003_R2_001.fastq.gz fastq fastq 14964717009.0 83601771.0 20201026 S2 S48hpt S25 L003 R1 001.fastq.gz 0:28 1:151 A:4042811725;C:3465477701;G:3602852950;T:3853470560;N:104073 28 151     4042811725 3465477701 3602852950 3853470560 104073 SRX20091098 SRS17422794 SRA1626787 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 2 0.00811 0.9409 0.00196 0.08687 0.98922 0.85001 0.51973 0.65526 28 151 T B sc-like readlen illumina novaseq_era unknown poly_a trueseq sc single_cell_droplet 10x   China 2023-04-25 Undetermined Undetermined Gut Digestive System
75108 75108 SRR24295712 SRX20091097 SRS17422793 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.         20201026 S2 S48hpt S7 L004 R1 001.fastq   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 7|BioSampleModel:Model organism or animal                 scRNA seq of zebrafish intestine: MTZ 48 hpt 20201026 S2 S48hpt S7 L004 R1 001 20201026 S2 S48hpt S7 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 38 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     20201026_S2_S48hpt_S7_L004_R1_001.fastq.gz 20201026_S2_S48hpt_S7_L004_R2_001.fastq.gz fastq fastq 10669333843.0 59605217.0 20201026 S2 S48hpt S7 L004 R1 001.fastq.gz 0:28 1:151 A:2876329901;C:2471017739;G:2573143323;T:2748679474;N:163406 28 151     2876329901 2471017739 2573143323 2748679474 163406 SRX20091097 SRS17422793 SRA1626787 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 2 0.00841 0.93868 0.00188 0.08847 0.98879 0.85149 0.54358 0.6538 28 151 T B sc-like readlen illumina novaseq_era unknown poly_a trueseq sc single_cell_droplet 10x   China 2023-04-25 Undetermined Undetermined Gut Digestive System
75109 75109 SRR24295713 SRX20091096 SRS17422791 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.         20201026 S2 S48hpt S7 L003 R1 001.fastq   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                 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. 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 36 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     20201026_S2_S48hpt_S7_L003_R1_001.fastq.gz 20201026_S2_S48hpt_S7_L003_R2_001.fastq.gz fastq fastq 10613956434.0 59295846.0 20201026 S2 S48hpt S7 L003 R1 001.fastq.gz 0:28 1:151 A:2867387827;C:2453215650;G:2555390367;T:2737785596;N:176994 28 151     2867387827 2453215650 2555390367 2737785596 176994 SRX20091096 SRS17422791 SRA1626787 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 2 0.00804 0.93909 0.00204 0.09014 0.98912 0.85289 0.53052 0.65123 28 151 T B sc-like readlen illumina novaseq_era unknown poly_a trueseq sc single_cell_droplet 10x   China 2023-04-25 Undetermined Undetermined Gut Digestive System
75110 75110 SRR24295714 SRX20091095 SRS17422792 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.         20201026 S2 S48hpt S7 L002 R1 001.fastq   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                 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. 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 34 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     20201026_S2_S48hpt_S7_L002_R1_001.fastq.gz 20201026_S2_S48hpt_S7_L002_R2_001.fastq.gz fastq fastq 10590029325.0 59162175.0 20201026 S2 S48hpt S7 L002 R1 001.fastq.gz 0:28 1:151 A:2855935581;C:2451968029;G:2552761582;T:2729169108;N:195025 28 151     2855935581 2451968029 2552761582 2729169108 195025 SRX20091095 SRS17422792 SRA1626787 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 2 0.00831 0.93901 0.00202 0.0879 0.98942 0.85072 0.5438 0.66125 28 151 T B sc-like readlen illumina novaseq_era unknown poly_a trueseq sc single_cell_droplet 10x   China 2023-04-25 Undetermined Undetermined Gut Digestive System
75111 75111 SRR24295715 SRX20091094 SRS17422790 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.         20201026 S2 S48hpt S7 L001 R1 001.fastq   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                 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. 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 32 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     20201026_S2_S48hpt_S7_L001_R2_001.fastq.gz 20201026_S2_S48hpt_S7_L001_R1_001.fastq.gz fastq fastq 10843243262.0 60576778.0 20201026 S2 S48hpt S7 L001 R1 001.fastq.gz 0:28 1:151 A:2926797989;C:2508866130;G:2611743790;T:2795632661;N:202692 28 151     2926797989 2508866130 2611743790 2795632661 202692 SRX20091094 SRS17422790 SRA1626787 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 2 0.00842 0.93796 0.00207 0.08873 0.98906 0.85204 0.53927 0.66266 28 151 T B sc-like readlen illumina novaseq_era unknown poly_a trueseq sc single_cell_droplet 10x   China 2023-04-25 Undetermined Undetermined Gut Digestive System
76727 76727 SRR25320257 SRX21062493 SRS18332761 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 an…   pubmed:37922649   Intestine Saliva 3 Treatment GSM7634953   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   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.   tissue:Intestine|treatment:tick saliva GSM7634953 GSM7634953: Intestine Saliva 3 Treatment; Danio rerio; RNA Seq GSM7634953 r1 GSM7634953 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP450092     Saliva_3_int_1.fastq.gz Saliva_3_int_2.fastq.gz fastq fastq 9904689772.0 32796986.0 GSM7634953 r1 0:151 1:151 A:2719308632;C:2108316310;G:2611487888;T:2465060625;N:516317 151 151     2719308632 2108316310 2611487888 2465060625 516317 SRX21062493 SRS18332761 SRA1675308 SaBio, Instituto de Investigación en Recursos Cinegéticos (IREC) - University of Castilla-La Mancha (UCLM) SaBio, Instituto de Investigación en Recursos Cinegéticos (IREC) - University of Castilla-La Mancha (UCLM) 2 0.07924 0.08219 0.01173 0.01712 0.93533 0.93432 0.73867 0.37657 151 151 T T mates < 9% mapping rate illumina hiseq_era unknown poly_a lexogen bulk unknown unknown   Spain 2023-07-18 Undetermined Undetermined Gut Digestive System
76728 76728 SRR25320258 SRX21062492 SRS18332759 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 an…   pubmed:37922649   Intestine Saliva 2 Treatment GSM7634952   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP450092     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     3951807456 3613697125 4175903766 3493941159 783034 SRX21062492 SRS18332759 SRA1675308 SaBio, Instituto de Investigación en Recursos Cinegéticos (IREC) - University of Castilla-La Mancha (UCLM) SaBio, Instituto de Investigación en Recursos Cinegéticos (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   Spain 2023-07-18 Undetermined Undetermined Gut Digestive System
76729 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 an…   pubmed:37922649   Intestine Saliva 1 Treatment GSM7634951   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP450092     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     2611676156 2385768928 2685002752 2424917421 509511 SRX21062491 SRS18332760 SRA1675308 SaBio, Instituto de Investigación en Recursos Cinegéticos (IREC) - University of Castilla-La Mancha (UCLM) SaBio, Instituto de Investigación en Recursos Cinegéticos (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   Spain 2023-07-18 Undetermined Undetermined Gut Digestive System
76730 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 an…   pubmed:37922649   Intestine PBS 3 Control GSM7634950   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP450092     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     2392641265 2385685766 2716165649 2201854741 495381 SRX21062490 SRS18332758 SRA1675308 SaBio, Instituto de Investigación en Recursos Cinegéticos (IREC) - University of Castilla-La Mancha (UCLM) SaBio, Instituto de Investigación en Recursos Cinegéticos (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   Spain 2023-07-18 Undetermined Undetermined Gut Digestive System
76731 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 an…   pubmed:37922649   Intestine PBS 2 Control GSM7634949   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   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.   tissue:Intestine|treatment:Control GSM7634949 GSM7634949: Intestine PBS 2 Control; Danio rerio; RNA Seq GSM7634949 r1 GSM7634949 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP450092     PBS_2_int_1.fastq.gz PBS_2_int_2.fastq.gz fastq fastq 10238848846.0 33903473.0 GSM7634949 r1 0:151 1:151 A:2590753223;C:2496955346;G:2795939748;T:2354682584;N:517945 151 151     2590753223 2496955346 2795939748 2354682584 517945 SRX21062489 SRS18332757 SRA1675308 SaBio, Instituto de Investigación en Recursos Cinegéticos (IREC) - University of Castilla-La Mancha (UCLM) SaBio, Instituto de Investigación en Recursos Cinegéticos (IREC) - University of Castilla-La Mancha (UCLM) 2 0.26382 0.26067 0.03501 0.06806 0.98987 0.99121 0.93394 0.3187 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a lexogen bulk unknown unknown   Spain 2023-07-18 Undetermined Undetermined Gut Digestive System
76732 76732 SRR25320262 SRX21062488 SRS18332756 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 an…   pubmed:37922649   Intestine PBS 1 Control GSM7634948   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. 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   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.   tissue:Intestine|treatment:Control GSM7634948 GSM7634948: Intestine PBS 1 Control; Danio rerio; RNA Seq GSM7634948 r1 GSM7634948 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP450092     PBS_1_int_1.fastq.gz PBS_1_int_2.fastq.gz fastq fastq 10862418144.0 35968272.0 GSM7634948 r1 0:151 1:151 A:2930477767;C:2461578237;G:2848406965;T:2621397581;N:557594 151 151     2930477767 2461578237 2848406965 2621397581 557594 SRX21062488 SRS18332756 SRA1675308 SaBio, Instituto de Investigación en Recursos Cinegéticos (IREC) - University of Castilla-La Mancha (UCLM) SaBio, Instituto de Investigación en Recursos Cinegéticos (IREC) - University of Castilla-La Mancha (UCLM) 2 0.03805 0.03966 0.01084 0.01304 0.96008 0.9598 0.68502 0.38227 151 151 T T mates < 9% mapping rate illumina hiseq_era unknown poly_a lexogen bulk unknown unknown   Spain 2023-07-18 Undetermined Undetermined Gut Digestive System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;