run_metadata: 26383
This data as json
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| 26383 | SRR25897911 | SRX21618256 | SRS18790601 | SRP458313 | PRJNA1012699 | Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish | GSE242251 | Transcriptome Analysis | LMNA mutations cause laminopathies a group of rare genetic diseases with no known cure only symptomatic treatment and supportive care. In this study we characterized five LMNA mutations LMNAL35P LMNAA539V LMNAW520G LMNAE358K and LMNAR453W identified from patients diagnosed with muscular laminopathy in the zebrafish model. Overall design: We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior muscle endurance and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq. | pubmed:38834813 | RNA seq LMNA WT 3 | GSM7757078 | source name:muscle|tissue:muscle|genotype:LMNA WT|treatment:N1|geo loc name:missing|collection date:missing | RNA seq LMNA WT 3 | Raw data qulity contol by fastQC Trimmomatic those that meet the following conditions will be deleted: 1 Base quality <3 from either 3’ or 5’ end. 2 Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3 Read length <36. Post Trimming quality control read alignmnet by HISAT2 Supplementary files format and content: Differential expression analysis by DESeq2 with biological replicates Supplementary files format and content: tab delimited text files include RPKM values for each Sample | muscle | RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep | We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility TZFC which operates under an automatic 14/10 hour light/dark cycle and maintains the water temperature at 28 °C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned. | tissue:muscle|genotype:LMNA WT|treatment:N1 | GSM7757078 | GSM7757078: RNA seq LMNA WT 3; Danio rerio; RNA Seq | GSM7757078 r1 | GSM7757078 | 1 | RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP458313 | loader:fastq load.py | C9M_WT_3_1_paired.fq C9M_WT_3_2_paired.fq | fastq fastq | 2628000986.0 | 8856042.0 | GSM7757078 r1 | 0:148.09 1:148.66 | A:662710830;C:644088161;G:643223497;T:677949643;N:28855 | 148 | 148 | 662710830 | 644088161 | 643223497 | 677949643 | 28855 | SRX21618256 | SRS18790601 | SRA1704662 | Institute of Molecular and Genomic Medicine, National Health Research Institutes | Institute of Molecular and Genomic Medicine, National Health Research Institutes | 2 | 0.9176 | 0.93277 | 0.04117 | 0.04045 | 0.78017 | 0.7792 | 0.55638 | 0.56128 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Taiwan | 2023-09-04 | Adult | Adult | Muscle | Muscular System |