|
| Status |
Public on Aug 27, 2024 |
| Title |
Retina_18w_F09 |
| Sample type |
SRA |
| |
|
| Source name |
Neural Retina
|
| Organism |
Nothobranchius furzeri |
| Characteristics |
tissue: Neural Retina
genotype: Wildtype
treatment: None
condition: 18 weeks
|
| Growth protocol |
Killifish of the GRZ-AD inbred strain were housed in a standarised system maintaining constant pH (7.0), conducitivty (600µs) and temperature (28,0°C).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Fish were euthanized using 0.1% tris buffered tricaine. Retinas were collected after retinal pigment epithelium removal. Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer's protocol.
Libraries were generated using the QuantSeq 3' (Lexogen) mRNA protocol according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Reads were trimmed using Trim-Galore! (v0.6.7), a wrapper for Cutadapt (v3.4) and FastQC (v0.11.9)
Trimmed reads were mapped to the custom-built transcriptome using STAR (v2.7.0)
Mapped reads were cleaned using Samtools (v1.9.4)
Gene counts were generated by HTseq (v0.11.2) and comparative analysis between individual ages was performed using EdgeR (v3.42.4)
Assembly: PRJEB5837
Supplementary files format and content: Tab-delimited text file including raw counts for each sample
|
| |
|
| Submission date |
Feb 08, 2024 |
| Last update date |
Aug 27, 2024 |
| Contact name |
Lieve Moons |
| E-mail(s) |
lieve.moons@kuleuven.be
|
| Organization name |
KU Leuven
|
| Department |
Biology
|
| Lab |
Neural Circuit Development and Regeneration research group
|
| Street address |
Naamsestraat 61
|
| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL30851 |
| Series (1) |
| GSE255363 |
Effect of ageing on gene expression in the African turquiose killifish retina |
|
| Relations |
| BioSample |
SAMN39894310 |
| SRA |
SRX23580772 |
