run_metadata: 44928
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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| 44928 | SRR6298094 | SRX3399037 | SRS2693217 | SRP125111 | PRJNA418766 | Age dependent increase of oxidative stress regulates microRNA 29 family preserving cardiac health | GSE107003 | Transcriptome Analysis | The short lived turquoise killifish Nothobranchius furzeri Nfu is a valid model for aging studies. Here we investigated its age associated cardiac function. We observed oxidative stress accumulation and an engagement of microRNAs miRNAs in the aging heart. MiRNA sequencing of 5 week young 12 21 week adult and 28 wpf 40 wpf Nfu hearts revealed 23 up regulated and 18 down regulated miRNAs with age. MiR 29 family turned out as one of the most up regulated miRNAs during aging. MiR 29 family increase induces a decrease of known targets like collagens and DNA methyl transferases DNMTs paralleled by 5´methyl cytosine 5mC level decrease. To further investigate miR 29 family role in the fish heart we generated a transgenic zebrafish model where miR 29 was knocked down. In this model we found significant morphological and functional cardiac alterations and an impairment of oxygen dependent pathways by transcriptome analysis leading to hypoxic marker up regulation. To get insights the possible hypoxic regulation of miR 29 family we exposed human cardiac fibroblasts ttwo xxx% O2 levels. In hypoxic condition we found miR 29 down modulation responsible for the accumulation of collagens and 5mC. Overall our data suggest that miR 29 family up regulation might represent an endogenous mechanism aimed at ameliorating the age dependent cardiac damage leading to hypertrophy and fibrosis. Overall design: RNA was isolated from zebrafish heart samples 3 wt and 3 miR 29 sponge and sequenced. | pubmed:29203887 | ZF mir29 1 | GSM2859323 | source name:Heart tissue|construct:mir29 sponge|tissue:heart | ZF mir29 1 | Raw reads were assessed for quality adapter content and duplication rates with FastQC version 0.11.2. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 5 nucleotides. Only reads above 30 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl zebrafish genome version GRCz10 using STAR 2.5.2b with the parameters “ outFilterMismatchNoverLmax 0.1 alignMatesGapMax 1000 alignIntronMax 200000”. The number of reads aligning to genes was counted with featureCounts 1.5.0 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Raw counts were normalized using DESeq2 and rounded to the next integer. Genome build: GRCz10 Supplementary files format and content: matrix.txt contains DESeq2 normalized count values for all genes overlapped by at least one read. | Heart tissue | For next generation sequencing NGS RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA and libraries integrity were verified with a BioAnalyzer 2100 Agilent or LabChip Gx Touch 24 Perkin Elmer. 500 ng total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit HI Mammalian Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry with 2x75bp paired end setup. | construct:mir29 sponge|tissue:heart | GSM2859323 | GSM2859323: ZF mir29 1; Danio rerio; RNA Seq | GSM2859323 | 1 | For next generation sequencing NGS RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA and libraries integrity were verified with a BioAnalyzer 2100 Agilent or LabChip Gx Touch 24 Perkin Elmer. 500 ng total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit HI Mammalian Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry with 2x75bp paired end setup. | GEO Accession:GSM2859323 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP125111 | ZF_mir29_1_R1.fastq.gz ZF_mir29_1_R2.fastq.gz | fastq fastq | 5308216436.0 | 35690404.0 | GSM2859323 r1 | 0:74.36 1:74.37 | A:1509798660;C:1127748899;G:1159263867;T:1505497024;N:5907986 | 74 | 74 | 1509798660 | 1127748899 | 1159263867 | 1505497024 | 5907986 | SRX3399037 | SRS2693217 | SRA631359 | GEO | Bioinformatics, Max Planck Institute for Heart and Lung Research | 2 | 0.90409 | 0.91666 | 0.26447 | 0.2644 | 0.82615 | 0.83991 | 0.77524 | 0.76594 | 74 | 75 | B | B | biological fallback assumption | illumina | nextseq | full_length | small_rna | smarter | bulk | unknown | unknown | Germany | 2017-11-16 | Undetermined | Undetermined | Heart | Cardiovascular System |