run_metadata: 52919
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 52919 | SRR9596463 | SRX6362166 | SRS5024083 | SRP211964 | PRJNA551130 | Induction of adult cardiomyocyte renewal by Klf1 | PRJNA551130 | Other | In highly regenerative animals cardiac regeneration occurs innately through cardiomyocyte dedifferentiation and proliferation although the regenerative mechanisms remain unclear. This project contains raw sequencing data sets that were used to identify that klf1 a Kruppel like transcription factor essential for red blood cell development is also necessary and sufficient in the myocardium for the induction of cardiomyocyte dedifferentiation and proliferation in adult zebrafish hearts | klf1 over expressing | klf1 | strain:EKW|breed:n1|cultivar:n1|ecotype:n1|dev stage:Adult|sex:pooled male and female|tissue:hearts|genotype:klf1 overexpressing|sample type:tissue sample|treatment:untreated|BioSampleModel:Model organism or animal | RNA Seq of zebrafish cardiac tissue | OE4 RNASEQ | OE4 RNASEQ | Tissue was resuspended in 700ul Trizol and total RNA was extracted using miRNeasy kit following manufacturers description. Total RNA integrity was assessed and quantified on a RNA nano Agilent chip following manufacturers description. RNA libraries were prepared 500ng input using the Kapa stranded RNA Seq kit using the oligo dT module to enrich for mRNA transcripts. Libraries were pooled to equimolar concentrations and sequenced on an Illumina HiSeq2500 paired end reads using v4 high output chemistry. | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP211964 | CCB6CANXX_5_180204_CFL--007_Other_GATCAG_R_180116_DAVHUM_LIB2500_M003_R1.fastq.gz CCB6CANXX_5_180204_CFL--007_Other_GATCAG_R_180116_DAVHUM_LIB2500_M003_R2.fastq.gz | fastq fastq | 7295330500.0 | 29181322.0 | CCB6CANXX 5 180204 CFL 007 Other GATCAG R 180116 DAVHUM LIB2500 M003 R1.fastq.gz | 0:125 1:125 | A:2032530437;C:1615271949;G:1627524722;T:2018148293;N:1855099 | 125 | 125 | 2032530437 | 1615271949 | 1627524722 | 2018148293 | 1855099 | SRX6362166 | SRS5024083 | SRA913571 | Victor Chang Cardiac Research Institute|Genome core | Victor Chang Cardiac Research Institute | 2 | 0.9317 | 0.93743 | 0.11776 | 0.11755 | 0.73497 | 0.73888 | 0.51221 | 0.53503 | 125 | 125 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Australia | 2019-06-26 | Adult | Adult | Heart | Cardiovascular System |