run_metadata: 53375
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 |
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| 53375 | SRR9849277 | SRX6603810 | SRS5168859 | SRP216556 | PRJNA556842 | aKlotho regulates age associated vascular calcification and lifespan in zebrafish | PRJNA556842 | Transcriptome Analysis | The hormone aKlotho regulates lifespan in mice as knockouts die early of what appears to be accelerated aging due to hyperphosphatemia and soft tissue calcification. In contrast its overexpression increases lifespan. Given the severe mouse phenotype we generated zebrafish mutants for aklotho as well as its binding partner fibroblast growth factor 23 fgf23. Both mutations cause shortened lifespan in zebrafish with abrupt onset of behavioral and degenerative physical changes at around five months of age. There is calcification of vessels throughout the body most dramatically in the outflow tract of the heart the bulbus arteriosus BA. This calcification is associated with ectopic activation of osteoclast differentiation pathways. These findings suggest that the gradual loss of aKlotho found in normal aging might give rise to ectopic calcification. | wildtype gill 3 mpf replicate 2 | wt 14746 e gill | strain:AB|age:3months|sex:male|tissue:gills|genotype:wildtype|Replicate:Bilogical replicate 2|BioSampleModel:Model organism or animal | wildtype gill 3 mpf replicate 2 | wt 14746 e gill | wt 14746 e gill | Tissue collection and dissection: Adult zebrafish were euthanized by exposure to chilled water 0 4C. Gills heart and kidney were collected from 32 individual fish at two time points namely at 3 mpf and 5 mpf for klotho mutants and wildtype sibling controls AB background; 8 fish per genotype per time point 4 males 4 females for a total of 96 samples. Tissues were dissected in cold PBS and immediately stored in RNALater Stabilization Solution ThermoFisher Cat# AM7021. RNALater was removed post an overnight incubation at 4C and samples were stored at 80C until processing. RNA extraction: All tissues were homogenized using the TissueLyser II Qiagen plus Lysis buffer containing mercaptoethanol and stored at 80C. RNA extraction was performed using the automated protocol in the QIAcube workstation utilizing the RNeasy Fibrous Tissue Mini kit Qiagen Cat No./ID: 74704. RNA integrity and quality were assessed by Agilent TapeStation using High Sensitivity RNA ScreenTapes. Samples were normalized and 300ng of RNA was used for library prep for each sample. ERCC RNA Spike in mix was added for quality control. mRNA was captured using poly T oligos attached beads for library selection. | RNA-Seq | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP216556 | wt-14746-e-gill_merged_S87-1.fastq.gz wt-14746-e-gill_merged_S87-2.fastq.gz | fastq fastq | 3327810713.0 | 22620977.0 | wt 14746 e gill merged S87 1.fastq.gz | 0:73.57 1:73.54 | A:790747041;C:826908991;G:822421934;T:811444797;N:76287950 | 73 | 73 | 790747041 | 826908991 | 822421934 | 811444797 | 76287950 | SRX6603810 | SRS5168859 | SRA927891 | Novartis Institutes for Biomedical Research|Chemical Biology and Therapeutics | Novartis Institutes for Biomedical Research | 2 | 0.95403 | 0.95572 | 0.0703 | 0.07016 | 0.70291 | 0.70443 | 0.49483 | 0.50182 | 76 | 76 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Germany | 2019-07-27 | Adult | Adult | Gill | Respiratory System |