|
| Status |
Public on Jul 14, 2020 |
| Title |
muscle_20wk_2 |
| Sample type |
SRA |
| |
|
| Source name |
skeletal muscle
|
| Organism |
Nothobranchius furzeri |
| Characteristics |
tissue: skeletal muscle
age (weeks): 20
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from skeletal muscle tissue from 3 fishes for each condition (young, adult and old) using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA and libraries integrity were verified with LabChip Gx Touch 24 (Perkin Elmer).
1µg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech). Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry, resulting in average of 30M reads per library with 2x75bp paired end setup.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Read quality trimming was performed with Trimmomatic version 0.33 (java -jar trimmomatic-0.33.jar PE ... SLIDINGWINDOW:5:20 MINLEN:30).
Reads were mapped versus Nothobranchius furzeri genome version NotFur1 using STAR 2.4.2a (--outFilterMismatchNoverLmax 0.1).
Reads were counted per gene with featureCounts 1.4.5-p1 from the Subread package using default parameters.
The raw gene counts were joined to a common matrix.
The matrix of gene counts was normalized with DESeq.
Genome_build: Nothobranchius furzeri NotFur1
Supplementary_files_format_and_content: The tab-delimited text file (matrix.txt) contains DESeq normalized counts for all homologous genes.
|
| |
|
| Submission date |
Jul 29, 2019 |
| Last update date |
Jul 14, 2020 |
| Contact name |
Carsten Kuenne |
| E-mail(s) |
Carsten.Kuenne@mpi-bn.mpg.de
|
| Organization name |
Max Planck Institute for Heart and Lung Research
|
| Department |
Bioinformatics
|
| Street address |
Ludwigstrasse 43
|
| City |
Bad Nauheim |
| ZIP/Postal code |
61231 |
| Country |
Germany |
| |
|
| Platform ID |
GPL26990 |
| Series (1) |
| GSE135032 |
Aging triggers H3K27 trimethylation hoarding in the chromatin of Nothobranchius furzeri skeletal muscle. |
|
| Relations |
| BioSample |
SAMN12390518 |
| SRA |
SRX6608754 |
