run_metadata: 11173
This data as json
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| 11173 | ERR10047706 | ERX9587594 | ERS12570305 | ERP140136 | PRJEB55250 | Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease | 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 | Other | Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. | ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 | RNA seq Wild type Male 1 | WM1 | SAMEA110472282 | Computational Biology Unit | ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472282|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29722|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29722|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 10 08 2022 10:54:39:368 85523 | WM1 | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP140136 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 | WM5_1.fq.gz WM5_2.fq.gz | fastq fastq | 9558564300.0 | 31861881.0 | ena RUN TAB 10 08 2022 10:54:39:369 85524 | 0:150 1:150 | A:2556941509;C:2249230277;G:2236855770;T:2515442411;N:94333 | 150 | 150 | 2556941509 | 2249230277 | 2236855770 | 2515442411 | 94333 | ERX9587594 | ERS12570305 | ERA16825549 | Computational Biology Unit|European Nucleotide Archive | Computational Biology Unit | 2 | 0.95505 | 0.95484 | 0.05372 | 0.05318 | 0.71798 | 0.71898 | 0.52584 | 0.52042 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Unknown | 2022-09-15 | Undetermined | Undetermined | Kidney | Renal System |