|
| Status |
Public on Sep 08, 2023 |
| Title |
RNA-seq, LMNA A539V-1 |
| Sample type |
SRA |
| |
|
| Source name |
muscle
|
| Organism |
Danio rerio |
| Characteristics |
tissue: muscle
genotype: LMNA A539V
treatment: None
|
| Growth protocol |
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.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
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
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
T9M_A_1
|
| Data processing |
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
|
| |
|
| Submission date |
Sep 04, 2023 |
| Last update date |
Sep 08, 2023 |
| Contact name |
Chiou Hwa Yuh |
| E-mail(s) |
chyun@nhri.edu.tw
|
| Organization name |
National Health Research Institutes
|
| Department |
Institute of Molecular and Genomic Medicine
|
| Street address |
35, Keyan Road
|
| City |
Zhunan |
| ZIP/Postal code |
350 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL24995 |
| Series (1) |
| GSE242251 |
Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish |
|
| Relations |
| BioSample |
SAMN37270891 |
| SRA |
SRX21618257 |
