|
| Status |
Public on Feb 07, 2024 |
| Title |
RIAILs_Batch3_QX559 |
| Sample type |
SRA |
| |
|
| Source name |
QX559
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: QX559
treatment: Cntrl
|
| Treatment protocol |
Synchronized worms from each strain were few with E. coli HT115
|
| Growth protocol |
Worms of each strain were cultured on plates seeded with E. coli OP50, then eggs were obtained by alkaline hypochlorite treatment of gravid adults. A synchronized L1 population was obtained by incubating the egg suspension in M9 butter overnight at room temperature. Approximately 2000 L1 worms were transferred onto plates seeded with E. coli HT115. L4 worms were harvested after 50 h by three times of washing with M9 buffer. Tubes containing worm pellets were immediately submerged in liquid nitrogen for snap freezing and stored at -80ºC until use.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
On the day of the extraction, 1 mL of TriPure Isolation Reagent was added to each tube. The samples were then frozen and thawed quickly eight times with liquid nitrogen and 37ºC water bath to rupture cell membranes. RNA was then extracted by using a column-based kit from Macherey-Nagel.
BGISeq-500 library construction Protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
FastQC (default parameters) was used to verify the quality of the reads. No low-quality reads were present and no trimming was needed.
Alignment was performed against worm genome (WBcel235 sm-toplevel) following the STAR (version 2.73a) manual guidelines
Counts for each sample features (outputed by STAR) where read into R
The STAR gene-counts for each alignment were analyzed for differentially expressed genes using the R package DESeq2
Assembly: WBcel235 sm-toplevel
Supplementary files format and content: tab-delimited text files include raw mapped read counts per feature (generated by STAR - per strand and combined strands)
|
| |
|
| Submission date |
Jan 05, 2024 |
| Last update date |
Feb 07, 2024 |
| Contact name |
Gaby El Alam |
| E-mail(s) |
gaby.elalam@epfl.ch
|
| Organization name |
École polytechnique fédérale de Lausanne
|
| Department |
SV LISP
|
| Lab |
Laboratory of Integrative Systems Physiology
|
| Street address |
Station 15
|
| City |
Lausanne |
| State/province |
Vaud |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL25145 |
| Series (1) |
| GSE252593 |
High-content phenotypic analysis defines generalizable genetic and molecular regulators of lifespan in a C. elegans recombinant inbred population |
|
| Relations |
| BioSample |
SAMN39271105 |
| SRA |
SRX23109650 |
