{"database": "metadata", "table": "run_metadata", "rows": [[70205, "SRR19571685", "SRX15623684", "SRS13323913", "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.", null, null, null, "Brain  WT  2months  rep1", "GSM6215399", null, "source name:brain|tissue:brain|strain:AB background|genotype:WT|age:2 month", "Brain  WT  2months  rep1", "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", null, "Whole tissues were dissected in cold PBS Sigma Aldrich  transferred to a microcentrifuge tube containing 100 \u03bcl of Trizol Thermo Fisher Scientific  snap frozen in dry ice and stored at  80\u00b0. To isolate the RNA  extra 50 \u03bcl 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 \u03bcl 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\u00b0C. 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\u00b0C. Finally  the pellet was twice washed in 250 \u03bcl of ice cold 75% ethanol and left to air dry  before resuspended in 14 \u03bcl 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 \u22659. 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\u00ae Ultra\u2122 RNA Library Prep Kit for Illumina  following the manufacturer\u2019s instructions New England Biolabs Inc.", "Zebrafish were maintained at the standard conditions of 27 28\u00baC  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:WT|age:2 month", "GSM6215399", "GSM6215399: Brain  WT  2months  rep1; Danio rerio; RNA Seq", "GSM6215399 r1", "GSM6215399", "1", "Whole tissues were dissected in cold PBS Sigma Aldrich  transferred to a microcentrifuge tube containing 100 \u03bcl of Trizol Thermo Fisher Scientific  snap frozen in dry ice and stored at  80\u00b0. To isolate the RNA  extra 50 \u03bcl 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 \u03bcl 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\u00b0C. 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\u00b0C. Finally  the pellet was twice washed in 250 \u03bcl of ice cold 75% ethanol and left to air dry  before resuspended in 14 \u03bcl 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 \u22659. 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\u00ae Ultra\u2122 RNA Library Prep Kit for Illumina  following the manufacturer's instructions New England Biolabs Inc.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiScanSQ", null, "SRP378890", null, null, "B2.fastq.gz", "fastq", 1656790668.0, 16403868.0, "GSM6215399 r1", "0:101 1:0", "A:449703718;C:368586926;G:363343184;T:467072556;N:8084284", 101, 0, null, null, 449703718, 368586926, 363343184, 467072556, 8084284, "SRX15623684", "SRS13323913", "SRA1433223", "Tissue Repair & Immunity in ageing, Oncology & Metabolism, The University of Sheffield", "Tissue Repair & Immunity in ageing, Oncology & Metabolism, The University of Sheffield", 1, 0.92658, null, 0.16686, null, 0.69731, null, 0.49794, null, 101, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2022-06-07", "Juvenile", "Juvenile", "Brain", "Nervous 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": ["70205"], "units": {}, "query_ms": 9.724224000819959}