run_metadata: 70193

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
70193	SRR19571673	SRX15623696	SRS13323925	SRP378890	PRJNA846700	Telomerase Dependent Ageing In The Zebrafish Brain	GSE205601	Transcriptome Analysis	Decreased telomerase expression telomere shortening senescence associated markers and inflammation have all been independently observed in the ageing brain and associated with disease. However causality between limited telomerase expression and brain senescence and neuro inflammation in the natural ageing setting is yet to be established. Here we address these questions using the zebrafish as an ageing model which akin to humans displays premature ageing and death in the absence of telomerase and where telomere shortening is a driver of cellular senescence. Our work shows for the first time that telomerase deficiency tert / accelerates key hallmarks of ageing identified in the Wild Type WT zebrafish brain at transcriptional cellular tissue and functional levels. We show that Tert dependent transcriptomic changes associated with dysregulation of gene expression stress response and dysregulation of immune genes are accompanied by accelerated accumulation of senescence associated markers and inflammation in the aged brain. Importantly In vivo these changes correlate with increased blood brain barrier permeability and altered cognitive behaviour. Of note telomerase dependent accumulation of senescence associated markers in the brain occurs not only in the expected proliferative areas but also in non proliferative ones where it is unlikely due to telomere dependent replicative exhaustion suggesting that non canonical roles of telomerase may be involved. Together our work suggests that telomerase has a protective role in the zebrafish brain against the accumulation of senescence and neuro inflammation and is required for blood brain barrier integrity. Overall design: RNA Sequencing of whole brain tissues throughout the lifespan of WT and telomerase deficient tert / fish. The data 4 age groups of WT 2 9 22 and >30 month corresponding to young adult median lifespan and old; and 3 age groups of telomerase deficient fish 2 9 and 22 month which correspond to young medium lifespan and old. Each group has a sample size of 3 animals. To identify signatures of ageing WT brain samples were subjected separately to DESEq2 analysis comparing the time points 9 22 and >30 month with the time point of 2 month. Then tert / samples at 2 9 month and 22 month were compared with WT at 2 month to identify telomerase dependent ageing processes.				Brain tert 2months rep2	GSM6215411		source name:brain\|tissue:brain\|strain:AB background\|genotype:tert \|age:2 month	Brain tert 2months rep2	Quality control was performed using MultiQC version 1.9. Cutadapt version 3.0 was used for trimming the first 13 bases from the reads to remove poor quality base pairs in the reads. Read alignment: Single end reads were aligned against the reference genome Danio rerio.GRCz11.dna. primary assembly.fa using STAR. A bespoke alignment index was built using annotation file Danio rerio.GRCz11.103.gtf and an expected read length of 88 bp. Ht seq count was run in non stranded mode to obtain per gene read counts. Assembly: Danio rerio.GRCz11.dna. Supplementary files format and content: tab delimited text files include RPKM values for each Sample	brain		Whole tissues were dissected in cold PBS Sigma Aldrich transferred to a microcentrifuge tube containing 100 μl of Trizol Thermo Fisher Scientific snap frozen in dry ice and stored at 80°. To isolate the RNA extra 50 μl of Trizol was added to each sample and the tissue was homogenized with a mechanical homogenizer VWR International and a 1.5 pestle Kimble Chase Vineland NJ USA. post 5 min incubation at room temperature RT 30 μl of chloroform 1:5 VWR International was added and the samples were incubated for further 3 min at RT before centrifuged at 13 000g for 30 min at 4°C. Isopropanol Thermo Fisher Scientific was then added to the aqueous phase of the solution and the resultant mix was incubated for 10 min at RT before centrifuged 13 000g for 15 min at 4°C. Finally the pellet was twice washed in 250 μl of ice cold 75% ethanol and left to air dry before resuspended in 14 μl of nuclease free water. RNA integrity was assessed with the bioanalyzer Agilent 2100 Bioanalyzer Agilent Santa Clara CA USA. All the samples had a RNA integrity number RIN ≥9. Library preparation was performed following the Illumina methodology. mRNA was extracted from 500 ng of RNA with oligo dT beads capturing polyA tails using the NEBNext PolyA mRNA Magnetic Isolation Module New England Biolabs Inc. cDNA libraries were made with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer’s instructions New England Biolabs Inc.	Zebrafish were maintained at the standard conditions of 27 28ºC in a 14:10 hour light dark cycle and fed twice a day with Artemia live rotifers and Sparus dry food.	tissue:brain\|strain:AB background\|genotype:tert \|age:2 month	GSM6215411	GSM6215411: Brain tert 2months rep2; Danio rerio; RNA Seq	GSM6215411 r1	GSM6215411	1	Whole tissues were dissected in cold PBS Sigma Aldrich transferred to a microcentrifuge tube containing 100 μl of Trizol Thermo Fisher Scientific snap frozen in dry ice and stored at 80°. To isolate the RNA extra 50 μl of Trizol was added to each sample and the tissue was homogenized with a mechanical homogenizer VWR International and a 1.5 pestle Kimble Chase Vineland NJ USA. post 5 min incubation at room temperature RT 30 μl of chloroform 1:5 VWR International was added and the samples were incubated for further 3 min at RT before centrifuged at 13 000g for 30 min at 4°C. Isopropanol Thermo Fisher Scientific was then added to the aqueous phase of the solution and the resultant mix was incubated for 10 min at RT before centrifuged 13 000g for 15 min at 4°C. Finally the pellet was twice washed in 250 μl of ice cold 75% ethanol and left to air dry before resuspended in 14 μl of nuclease free water. RNA integrity was assessed with the bioanalyzer Agilent 2100 Bioanalyzer Agilent Santa Clara CA USA. All the samples had a RNA integrity number RIN ≥9. Library preparation was performed following the Illumina methodology. mRNA was extracted from 500 ng of RNA with oligo dT beads capturing polyA tails using the NEBNext PolyA mRNA Magnetic Isolation Module New England Biolabs Inc. cDNA libraries were made with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer's instructions New England Biolabs Inc.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiScanSQ		SRP378890			B20.fastq.gz	fastq	1589807064.0	15740664.0	GSM6215411 r1	0:101 1:0	A:425523566;C:356671503;G:351309194;T:448559151;N:7743650	101	0			425523566	356671503	351309194	448559151	7743650	SRX15623696	SRS13323925	SRA1433223	Tissue Repair & Immunity in ageing, Oncology & Metabolism, The University of Sheffield	Tissue Repair & Immunity in ageing, Oncology & Metabolism, The University of Sheffield	1	0.93342		0.15617		0.68801		0.49533		101		B		usable mapping rate	illumina	early_illumina	unknown	poly_a	nebnext	bulk	unknown	unknown		United Kingdom	2022-06-07	Juvenile	Juvenile	Brain	Nervous System