{"database": "metadata", "table": "run_metadata", "rows": [[76730, "SRR25320260", "SRX21062490", "SRS18332758", "SRP450092", "PRJNA996066", "Multi omics analysis of zebrafish response to tick saliva reveals biological processes associated with alpha Gal syndrome", "GSE237627", "Transcriptome Analysis", "This study provides a multi omics approach to determine the effect on the transcriptome and proteome gut profiles of zebrafish inoculated with tick saliva followed by mammalian meat consumption. With bioinformatics analysis using the R software  we sought for significant biological and metabolic pathway changes  in order to fill up some of the current knowledge gaps associated with the alpha Gal syndrome AGS. In addition  ortholog mapping allowed to obtain highly concordant biological 1:1 human ortholog genes for the detection of gene disease associations GDAs and disease enriched pathways. Further data validation was performed using reverse transcriptase quantitative PCR RT qPCR and Western Blot WB analysis on target differentially expressed genes DEGs and differentially represented proteins DRPs  respectively. We found that treatment with tick saliva increased mortality and caused significant higher incidence of hemorrhagic type allergic reactions  changes in behavior and feeding patterns. Transcriptomics analysis showed downregulation of biological and metabolic pathways correlated with anti Gal IgE and allergic reactions to tick saliva such as blood circulation  cardiac and vascular smooth muscle contraction  behavior and sensory perception. Disease enrichment analysis revealed that downregulated orthologous genes were mostly associated with human disorders affecting the nervous  musculoskeletal  and cardiovascular systems. Proteomics analysis predominantly revealed suppression of biological and metabolic pathways associated with the immune system production of reactive oxygen species ROS and cardiac muscle contraction. The underrepresented proteins were mainly linked to nervous and nutritional/metabolic human disorders. Furthermore  12 DEGs were found to have concomitant protein level representation. Lastly  the integration of transcriptomics and proteomics layers through multi omics pathway enrichment revealed inhibition of pathways associated with adrenergic signaling in cardiomyocytes  as well as heart and muscle contraction. This research contributed to the discovery of AGS related biological pathways  reinforcing disease multisystemic organ involvement and linking a Gal sensitization with other illnesses. Furthermore  our results shed light on novel bioinformatic strategies for the identification of key genes and proteins that may serve as potential disease biomarkers. Overall design: RNA seq was performed on a total of 6 pooled zebrafish Danio rerio intestinal tissue samples. For the treatment group tick saliva  6 independent biological samples were pooled in pairs 2 per pool  while the other 9 control PBS samples were pooled in groups of three 3 per pool.", null, "pubmed:37922649", null, "Intestine  PBS 3 Control", "GSM7634950", null, "source name:Intestine|tissue:Intestine|treatment:Control|geo loc name:missing|collection date:missing", "Intestine  PBS 3 Control", "Around 18.4 to 49.3 million M of total reads were generated from each library for the RNA sequencing RNA Seq data. The Read 1 and Read 2 FASTQ files were analyzed by FastQC 0.11.5 and primary quality control QC was performed. The UMI reads were identified  and adapter and poly A/T sequences were trimmed by using UMI tools 1.1.2 and Cutadapt 3.7. The STAR 2.7.3 aligner was used to align reads to the Danio Rerio reference genome GRCz11.107. post alignment  the final BAM files were deduplicated with UMI tools and quantified with featureCounts function available in Bioconductor R package Rsubread by GRCz11.107 annotations. Assembly: Danio Rerio reference genome GRCz11.107 Supplementary files format and content: MS Excel spreadsheet contains raw counts for each sample.", "Intestine", null, "Total mRNA was isolated from samples using the AllPrep DNA/RNA/Protein Mini Kit Qiagen  Hilden  Germany  following manufacturer\u2019s instructions. RNA libraries for RNA seq were prepared using the CORALL mRNA Seq V1 Library Prep Kit Lexogen  Wien  Austria  following manufacturer's protocol.", null, "tissue:Intestine|treatment:Control", "GSM7634950", "GSM7634950: Intestine  PBS 3 Control; Danio rerio; RNA Seq", "GSM7634950 r1", "GSM7634950", "1", "Total mRNA was isolated from samples using the AllPrep DNA/RNA/Protein Mini Kit Qiagen  Hilden  Germany  following manufacturer's instructions. RNA libraries for RNA seq were prepared using the CORALL mRNA Seq V1 Library Prep Kit Lexogen  Wien  Austria  following manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP450092", null, null, "PBS_3_int_1.fastq.gz PBS_3_int_2.fastq.gz", "fastq fastq", 9696842802.0, 32108751.0, "GSM7634950 r1", "0:151 1:151", "A:2392641265;C:2385685766;G:2716165649;T:2201854741;N:495381", 151, 151, null, null, 2392641265, 2385685766, 2716165649, 2201854741, 495381, "SRX21062490", "SRS18332758", "SRA1675308", "SaBio, Instituto de Investigaci\u00f3n en Recursos Cineg\u00e9ticos (IREC) - University of Castilla-La Mancha (UCLM)", "SaBio, Instituto de Investigaci\u00f3n en Recursos Cineg\u00e9ticos (IREC) - University of Castilla-La Mancha (UCLM)", 2, 0.36834, 0.36601, 0.05164, 0.09738, 0.95572, 0.95526, 0.90835, 0.32256, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "Spain", "2023-07-18", "Undetermined", "Undetermined", "Gut", "Digestive System"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["76730"], "units": {}, "query_ms": 9.675844998128014}