{"database": "metadata", "table": "run_metadata", "rows": [[48077, "SRR7008284", "SRX3940772", "SRS3171573", "SRP140471", "PRJNA450343", "A Zebrafish Acromegaly Model Elevates DNA Damage and Impairs DNA Repair Pathways", "GSE113169", "Transcriptome Analysis", "Acromegaly is a pathological condition due to excess growth hormone GH secretion. Acromegaly patients exhibit a deterioration of health and many associated complications  such as cardiovascular issues  arthritis  kidney diseases  muscular weakness  and colon cancer. Since these complications are generalized throughout the body  we investigated the effect of GH excess on cellular integrity. Here  we established stable acromegaly model zebrafish lines that overexpress tilapia GH and the red fluorescence protein RFP reporter gene for tracking GH gene expression throughout generations  and performed RNA Seq data analysis from different organs. Intriguingly  heatmap and Expression2Kinases X2K analysis revealed the enrichment of DNA damage markers in various organs. Moreover  H2A.X immunostaining analysis in acromegaly zebrafish larvae and the adult acromegaly model brain and muscle showed a robust increase in the number of DNA damaged cells. Using Gene Set Enrichment Analysis GSEA  we found that the acromegaly zebrafish model had impaired DNA repair pathways in the liver  such as double strand break DSB  homologous recombination repair HRR  non homologous end joining NHEJ  nucleotide excision repair NER  and translesion synthesis TLS. Interestingly  the impairment of DNA repair was even more prominent in acromegaly model than in aged zebrafish three years old. Thus  our study demonstrates that affection of cellular integrity is characteristic of acromegaly Overall design: Total mRNA obtained from 1 years old acromegaly zebrafish model muscle  brain  kidney  liver and 3 dpf larvae compared to wild type WT zebrafish were generated by deep sequencing using Illumina.", null, "pubmed:30336646;pubmed:32517323;pubmed:33849304", null, "Kidney ACRO rep2", "GSM3098420", null, "source name:Kidney|genotype:Acromegaly zebrafish model|tissue:Kidney|age:1 year old", "Kidney ACRO rep2", "Illumina Casava1.7 software used for basecalling. HISAT2 software was used according to the instructions from the program designers to map the raw reads of acromegaly and WT samples to zebrafish genome reference GRCz10 retrieved from Ensembl database together with the annotation file. The Cufflinks pipeline was used to assign reads to known transcripts and test for differential expression between acromegaly model and the WT samples. The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads FPKM. Genome build: GRCz10 Supplementary files format and content: One tab delimited text file containing all FPKM values for all Samples.", "Kidney", null, "tissues were removed  and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.", null, "genotype:Acromegaly zebrafish model|tissue:Kidney|age:1 year old", "GSM3098420", "GSM3098420: Kidney ACRO rep2; Danio rerio; RNA Seq", "GSM3098420", null, "1", "tissues were removed  and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.", "GEO Accession:GSM3098420", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP140471", null, null, "GH_K2_Kidney_18_1.fq.gz GH_K2_Kidney_18_2.fq.gz", "fastq fastq", 554022000.0, 2770110.0, "GSM3098420 r1", "0:100 1:100", "A:145695233;C:130810207;G:130333919;T:147099701;N:82940", 100, 100, null, null, 145695233, 130810207, 130333919, 147099701, 82940, "SRX3940772", "SRS3171573", "SRA690975", "GEO", "Aquatic Molecular Biology and Biotechnology, Aquatic Bioscience, The University of Tokyo", 2, 0.94063, 0.94251, 0.08052, 0.07972, 0.72316, 0.72372, 0.51706, 0.53029, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-04-16", "Adult", "Adult", "Kidney", "Renal 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": ["48077"], "units": {}, "query_ms": 11.644564998277929}