|
| Status |
Public on Jul 18, 2023 |
| Title |
C. elegans, raga-1::AID; Neuronal::TIR1, no auxin, Day 3 adult, biol rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
lysate from ~400 whole nematodes
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: lysate from ~400 whole nematodes
strain: WBM1250
genotype: raga-1(wbm40) [raga-1::degron::EmGFP] II; wbmIs83 [rab-3p::3xflag::TIR1::rab-3 3'UTR *wbmIs66] IV
treatment: no auxin
time: Day 3 of adulthood
|
| Treatment protocol |
At day 1 of adulthood (3 days after hatch), animals were either transferred to plates with 0.15 mM auxin or "control" plates containing an equivalent amount of ethanol (the auxin solvent)
|
| Growth protocol |
C. elegans were maintained on 6 cm NGM plates with Carbenicillin at 20 degrees celsius.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
On Day 3, animals were snap frozen in Qiazol Lysis Reagent and RNA was extracted using the Qiagen RNeasy Mini Kit.
Libraries were prepared using a SciClone G3 NGSx workstation (Perkin Elmer) using the Kapa mRNA HyperPrep kit (Roche Applied Science)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Neuronal RAGA-1 strain untreated
|
| Data processing |
Raw reads were examined for quality using FastQC(v0.11.5)
To perform additonal quality checks, all reads were aligned to Ensembl assembly of the C. elegans (PRJNA13758) genome WBcel235_release104 using STAR (v.2.7.0)
Alignments were checked for biases, evenness of coverage, rRNA content, genomic content of alignments, complexity and other quality checks using a combination of FastQC, Qualimap, and MultiQC
To quantify the abundance of reads corresponding to each transcript, alignment and quantification was performed using Salmon (1.4.0)
In R (version 4.1.2) counts were normalized and pairwise comparisons of the differential gene expression between the various conditions was performed using DESeq2_1.34.0 from tximport with a p-vaule cutoff of 0.01
Assembly: Ensembl assembly of the C. elegans (PRJNA13758) genome WBcel235_release104
Supplementary files format and content: Excel file contains normalized counts for all genes for all samples.
Supplementary files format and content: Gene names are listed as WormBase IDs.
|
| |
|
| Submission date |
Jul 11, 2023 |
| Last update date |
Jul 18, 2023 |
| Contact name |
Hannah Josephine Smith |
| E-mail(s) |
[email protected]
|
| Organization name |
Harvard University T.H. Chan School of Public Health
|
| Department |
Molecular Metabolism
|
| Lab |
William Mair Lab
|
| Street address |
665 Huntington Avenue, Building 1, Room 512
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL26672 |
| Series (1) |
| GSE237060 |
Neuronal mTORC1 inhibition promotes longevity without suppressing anabolic growth and reproduction in C. elegans |
|
| Relations |
| BioSample |
SAMN36405995 |
| SRA |
SRX20980376 |
