run_metadata: 48076

This data as json

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
48076	SRR7008285	SRX3940773	SRS3171574	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.		pubmed:30336646;pubmed:32517323;pubmed:33849304		Kidney ACRO rep3	GSM3098421		source name:Kidney\|genotype:Acromegaly zebrafish model\|tissue:Kidney\|age:1 year old	Kidney ACRO rep3	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		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.		genotype:Acromegaly zebrafish model\|tissue:Kidney\|age:1 year old	GSM3098421	GSM3098421: Kidney ACRO rep3; Danio rerio; RNA Seq	GSM3098421		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:GSM3098421	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP140471			GH_K3_Kidney_19_1.fq.gz GH_K3_Kidney_19_2.fq.gz	fastq fastq	516366800.0	2581834.0	GSM3098421 r1	0:100 1:100	A:139000034;C:118629581;G:117673967;T:140984276;N:78942	100	100			139000034	118629581	117673967	140984276	78942	SRX3940773	SRS3171574	SRA690975	GEO	Aquatic Molecular Biology and Biotechnology, Aquatic Bioscience, The University of Tokyo	2	0.93368	0.93424	0.08046	0.07881	0.73032	0.73125	0.52305	0.51853	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown		Japan	2018-04-16	Adult	Adult	Kidney	Renal System