run_metadata: 31898
This data as json
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| 31898 | SRR28745434 | SRX24311223 | SRS21073228 | SRP502845 | PRJNA1102356 | flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response | GSE264406 | Transcriptome Analysis | VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however many challenges remain. Here we investigate a different approach to augmenting VEGFA bioavailability one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1 a VEGFA decoy receptor. We find that following cryoinjury zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion increased cardiomyocyte dedifferentiation and proliferation and decreased scarring. Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion. Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3. Using genetic tools we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation. These data suggest that with enhanced VEGFA bioavailability the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury. | pubmed:39612288 | wild type heart 96 hours post cryoinjury 1 | GSM8217702 | source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing | wild type heart 96 hours post cryoinjury 1 | Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al. Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5 multiple testing adjusted p value < 0.05 and 0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix | heart ventricle border zone and injured area | A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set Qiagen 4µg of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture’s protocol Vazyme. | tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury | GSM8217702 | GSM8217702: wild type heart 96 hours post cryoinjury 1; Danio rerio; RNA Seq | GSM8217702 r1 | GSM8217702 | 1 | A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set Qiagen 4µg of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 2000 | SRP502845 | loader:fastq load.py | E23_4173_Armaad_Lib_WT1_R1.fastq.gz | fastq | 3571478400.0 | 52133215.0 | GSM8217702 r1 | 0:68.51 | A:928171678;C:814216251;G:835024543;T:992630615;N:1435313 | 68 | 928171678 | 814216251 | 835024543 | 992630615 | 1435313 | SRX24311223 | SRS21073228 | SRA1849558 | MPI for heart and lung research | MPI for heart and lung research | 1 | 0.94111 | 0.08647 | 0.72922 | 0.50812 | 42 | B | usable mapping rate | illumina | nextseq_v2 | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-04-19 | Undetermined | Undetermined | Heart | Cardiovascular System |