run_metadata: 39807
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 39807 | SRR2146367 | SRX1134126 | SRS1024034 | SRP062067 | PRJNA292013 | Telomerase is essential for zebrafish heart regeneration | GSE71755 | Transcriptome Analysis | Unlike human hearts zebrafish hearts efficiently xxx post injury. Regeneration is driven by the strong proliferation response of its cardiomyocytes to injury. In this study we show that active telomerase is required for cardiomyocyte proliferation and full organ recovery supporting the potential of telomerase therapy as a means of stimulating cell proliferation upon myocardial infarction. Overall design: Heart transcriptomes of WT and telomerase defective adult zebrafish animals were profiled by RNASeq in control conditions and 3 days post heart cryoinjury. | pubmed:26321646 | WT Ctrl 2 | GSM1844642 | source name:Heart|genotype/variation:WT|stress:Control|tissue:heart | WT Ctrl 2 | Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Zv9 Ensembl gene build 66 Supplementary files format and content: matrix table.txt contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample. | Heart | Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 μg with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA. | All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l. | genotype/variation:WT|stress:Control|tissue:heart | GSM1844642 | GSM1844642: WT Ctrl 2; Danio rerio; RNA Seq | GSM1844642 | 1 | Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 μg with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA. | GEO Accession:GSM1844642 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP062067 | R34_WC2_CGATGT_L001_R1_001.fastq.gz | fastq | 658475520.0 | 10974592.0 | GSM1844642 r1 | 0:60 | A:181534641;C:149368098;G:146492820;T:180957879;N:122082 | 60 | 181534641 | 149368098 | 146492820 | 180957879 | 122082 | SRX1134126 | SRS1024034 | SRA282285 | GEO | Bioinformatics Unit, CNIC | 1 | 0.92851 | 0.09073 | 0.76067 | 0.49777 | 60 | B | usable mapping rate | illumina | early_illumina | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Spain | 2015-08-05 | Adult | Adult | Heart | Cardiovascular System |