{"database": "metadata", "table": "run_metadata", "rows": [[24652, "SRR25487068", "SRX21218619", "SRS18475798", "SRP452670", "PRJNA1000968", "CRISPR/Cas9 mediated Nexilin deficiency interferes with cardiac contractile function in zebrafish in vivo", "GSE239788", "Transcriptome Analysis", "Nexilin NEXN plays a crucial role in stabilizing the sarcomeric Z disk of striated muscle fibers and  when mutated   leads to dilated cardiomyopathy in humans. Due to its early neonatal lethality in mice  the detailed impact of the  constitutive homozygous NEXN knockout on heart and skeletal muscle morphology and function is insufficiently investigated.  We characterized a constitutive homozygous CRISPR/Cas9 mediated nexn knockout zebrafish model. We found that Nexn deficient embryos developed significantly reduced cardiac contractility and under stressed conditions also impaired  skeletal muscle organization whereas skeletal muscle function seemed not to be affected. Remarkably  in contrast to nexn  morphants  CRISPR/Cas9 nexn /  knockout embryos showed a milder phenotype without xxx development of a pronounced  pericardial edema or blood congestion. nexn specific expression analysis as well as whole transcriptome profiling suggest  some degree of compensatory mechanisms. Transcripts of numerous essential sarcomeric proteins were massively induced  and may mediate a sarcomere stabilizing function in nexn /  knockout embryos. Overall design: To investigate the influence of nexn knockout on cardiac and skeletal muslce  we generated a CRISPR/Cas9 mediated nexn  knockout zebrafish model. We then performed gene expression profiling analysis using data obtained from RNA seq.", null, "pubmed:38114601", null, "nexn /   biological replicate 2", "GSM7673294", null, "source name:whole organism|tissue:whole organism|genotype:nexn knockout|geo loc name:missing|collection date:missing", "nexn /   biological replicate 2", "Raw sequencing data is screened for reads originating from rRNA using RiboDetector eurofins genomics  INVIEW transcriptome High quality sequence reads are aligned to the reference genome using STAR Spliced Transcripts Alignment to a Reference  run through Sentieon framework  along with the known gene models. eurofins genomics  INVIEW transcriptome Gene wise quantification is achieved by inspecting transcriptome alignments using RSEM tool. eurofins genomics  INVIEW transcriptome Assembly: GRCz11 Supplementary files format and content: Sample wise  gene wise read counts  TPM value and FPKM value", "whole organism", null, "RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 \u00b5g total RNA was used for library preparation. 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