run_metadata: 35562
This data as json
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| 35562 | SRR32880278 | SRX28160879 | SRS24513817 | SRP573530 | PRJNA1242724 | Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration | GSE293062 | Transcriptome Analysis | Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading initiated before or during blastema formation resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program including for hyaluronic acid HA synthesis. Like exercise loading HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction. HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair where early exercise—applied during blastema establishment—impairs regeneration while delayed loading during outgrowth does not suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control | 3dpa blastema unexercised control bio rep 5 | GSM8875048 | source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing | 3dpa blastema unexercised control bio rep 5 | Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files | whole caudal fin 3 dpa blastema | Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later. | RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library. | Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily | tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control | GSM8875048 | GSM8875048: 3dpa blastema unexercised control bio rep 5; Danio rerio; RNA Seq | GSM8875048 r1 | GSM8875048 | 1 | RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | SRP573530 | Control_5_raw.fastq.gz | fastq | 3076092628.0 | 25213874.0 | GSM8875048 r1 | 0:122 | A:850913805;C:643783202;G:725071885;T:856245838;N:77898 | 122 | 850913805 | 643783202 | 725071885 | 856245838 | 77898 | SRX28160879 | SRS24513817 | SRA2100952 | Stankunas, Institute of Molecular Biology, University of Oregon | Stankunas, Institute of Molecular Biology, University of Oregon | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | United States | 2025-03-27 | Adult | Adult | Fin | Surface Structure |