run_metadata: 69536
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 69536 | SRR18837603 | SRX14935575 | SRS12686397 | SRP371323 | PRJNA828542 | RNA seq experiments on heart regeneration in WT foxm1 and dusp6 mutants. | GSE201139 | Transcriptome Analysis | The study compares gene expression profile at several stages post amputation of the adult zebrafish ventricular heart between zebrafish mutants and WT siblings. The first experiment was to identify genes that are activated in response to cardiac injury at 3 and 7 dy post amputation dpa. Dusp6 mutant hearts were reported to show an enhanced regenerative response. For this experiment bulk RNA seq was obtained from WT and Dusp6 mutant hearts and genes increased at 3 and 7 dpa were identified. The forkhead transcription factor foxm1 showed increased expression in cardiomyocytes and follow up studies show that it is required to regulate cardiomyocyte proliferation. This was further explored with RNA seq experiments comparing WT and foxm1 mutant hearts at 3dpa. We identified genes normally expressed in proliferating cells to be decreased in the foxm1 mutants. Overall design: Ventricular resection was performed on WT dusp6 and foxm1 mutant hearts. Uninjured adult hearts were used as control to compare to hearts at 3 and 7 dy post amputation dpa. | pubmed:36846912 | Dusp6 mutant heart 3dpa expt. 1 | GSM6051599 | source name:Heart|tissue:Heart|genotype:dusp6 pt30a/pt30a | Dusp6 mutant heart 3dpa expt. 1 | fastq files were analyzed using CLC genomics workbench 20.0 sequence reads were mapped onto Danio rerio GRC.z11 EDGE test was performed using CLC genomics workbench Assembly: Danio rerio GRC.z11 Supplementary files format and content: Zuppo 3dpa vs. uninj.xlsx Supplementary files format and content: Zuppo WT vs foxm1mut 3dpa.xlsx | Heart | Adutls hearts were injured through ventricular resection and allowed to recover until 3 dy post amputation. Ventricles were removed flash frozen on dry ice and RNA was harvested using Trizol reagent and Quiagen RNeasy micro kit Cat# 74004. | Zebrafish adult at 6 1year of age | tissue:Heart|genotype:dusp6 pt30a/pt30a | GSM6051599 | GSM6051599: Dusp6 mutant heart 3dpa expt. 1; Danio rerio; RNA Seq | GSM6051599 r1 | GSM6051599 | 1 | Adutls hearts were injured through ventricular resection and allowed to recover until 3 dy post amputation. Ventricles were removed flash frozen on dry ice and RNA was harvested using Trizol reagent and Quiagen RNeasy micro kit Cat# 74004. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP371323 | Sample_4_5_Dusp6-KO_3dpa.R1.fastq | fastq | 10458082424.0 | 69258824.0 | GSM6051599 r1 | 0:151 1:0 | A:2921567231;C:2380184370;G:2341511961;T:2813882994;N:935868 | 151 | 0 | 2921567231 | 2380184370 | 2341511961 | 2813882994 | 935868 | SRX14935575 | SRS12686397 | SRA1407669 | Developmental Biology, University of Pittsburgh | Developmental Biology, University of Pittsburgh | 1 | 0.91981 | 0.09262 | 0.74828 | 0.50789 | 151 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2022-04-20 | Adult | Adult | Heart | Cardiovascular System |