|
| Status |
Public on Oct 22, 2024 |
| Title |
N2 worms, DMSO, rep 4 |
| Sample type |
SRA |
| |
|
| Source name |
whole worm
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole worm
strain: N2-PD1073
age: adult day 4
genotype: WT
treatment: DMSO control
|
| Treatment protocol |
Tretinoin (all-trans retinoic acid) (Sigma-Aldrich PHR1187) was obtained as a solid and dissolved in DMSO (dimethyl sulfoxide) to obtain a stock solution. DMSO stock solutions were mixed with water to form a working solution before being added to plates. In-plate concentrations were calculated by presuming the final volume to be equal to that of the volume of agar. For 150 µM atRA plates, stock solutions formed precipitates at working solution concentrations, requiring working solutions to be prepared individually for each plate.
|
| Growth protocol |
C. elegans strains N2-PD1073, PS3551 [hsf-1(sy441)], and RB754 [aak-2(ok524)] were maintained on nematode growth medium (NGM) plates seeded with Escherichia coli OP50-1 at 20˚C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
To generate populations for RNA sequencing, we pooled animals from 4 plates to generate populations of ~200 animals, on day four of adulthood. RNA was collected using standard techniques.
RNA libraries for RNA-seq were prepared with the KAPA mRNA HyperPrep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
alignments/tretinoin/D11_N2_DMSO_4.bam
N2_featureCounts.txt
|
| Data processing |
Subread v2.0.2 was used to build a custom C. elegans reference genome package with default parameters.
Sequenced reads contained in paired-end FASTQ files were mapped to the WBcel235 reference genome using Subread with parameter -t 0.
Uniquely mapped reads were assigned to genes using the Subread featureCounts package with parameters -t exon -g gene_id.
Assembly: WBcel235 (build 104)
Supplementary files format and content: Tab-delimited tables of raw gene counts for every gene and sample.
|
| |
|
| Submission date |
Jul 18, 2024 |
| Last update date |
Oct 22, 2024 |
| Contact name |
Patrick Phillips |
| Organization name |
University of Oregon
|
| Department |
Institute of Ecology and Evolution
|
| Street address |
5289 University of Oregon
|
| City |
Eugene |
| State/province |
OR |
| ZIP/Postal code |
97403-5289 |
| Country |
USA |
| |
|
| Platform ID |
GPL22765 |
| Series (1) |
| GSE272535 |
Computer prediction and genetic analysis identifies retinoic acid modulation as a driver of conserved longevity pathways in genetically-diverse Caenorhabditis nematodes. |
|
| Relations |
| BioSample |
SAMN42581472 |
| SRA |
SRX25374042 |
