run_metadata: 76729
This data as json
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| 76729 | SRR25320259 | SRX21062491 | SRS18332760 | SRP450092 | PRJNA996066 | Multi omics analysis of zebrafish response to tick saliva reveals biological processes associated with alpha Gal syndrome | GSE237627 | Transcriptome Analysis | This study provides a multi omics approach to determine the effect on the transcriptome and proteome gut profiles of zebrafish inoculated with tick saliva followed by mammalian meat consumption. With bioinformatics analysis using the R software we sought for significant biological and metabolic pathway changes in order to fill up some of the current knowledge gaps associated with the alpha Gal syndrome AGS. In addition ortholog mapping allowed to obtain highly concordant biological 1:1 human ortholog genes for the detection of gene disease associations GDAs and disease enriched pathways. Further data validation was performed using reverse transcriptase quantitative PCR RT qPCR and Western Blot WB analysis on target differentially expressed genes DEGs and differentially represented proteins DRPs respectively. We found that treatment with tick saliva increased mortality and caused significant higher incidence of hemorrhagic type allergic reactions changes in behavior and feeding patterns. Transcriptomics analysis showed downregulation of biological and metabolic pathways correlated with anti Gal IgE and allergic reactions to tick saliva such as blood circulation cardiac and vascular smooth muscle contraction behavior and sensory perception. Disease enrichment analysis revealed that downregulated orthologous genes were mostly associated with human disorders affecting the nervous musculoskeletal and cardiovascular systems. Proteomics analysis predominantly revealed suppression of biological and metabolic pathways associated with the immune system production of reactive oxygen species ROS and cardiac muscle contraction. The underrepresented proteins were mainly linked to nervous and nutritional/metabolic human disorders. Furthermore 12 DEGs were found to have concomitant protein level representation. Lastly the integration of transcriptomics and proteomics layers through multi omics pathway enrichment revealed inhibition of pathways associated with adrenergic signaling in cardiomyocytes as well as heart and muscle contraction. This research contributed to the discovery of AGS related biological pathways reinforcing disease multisystemic organ involvement and linking a Gal sensitization with other illnesses. Furthermore our results shed light on novel bioinformatic strategies for the identification of key genes and proteins that may serve as potential disease biomarkers. Overall design: RNA seq was performed on a total of 6 pooled zebrafish Danio rerio intestinal tissue samples. For the treatment group tick saliva 6 independent biological samples were pooled in pairs 2 per pool while the other 9 control PBS samples were pooled in groups of three 3 per pool. | 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 |