|
| Status |
Public on Apr 23, 2023 |
| Title |
daf-2; daf-42, 52 Hours after eggs laid, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
whole animal
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole animal
cell line: LJ2703
cell type: whole animal
genotype: daf-2 (e1370); daf-42(ys54)
treatment: worms were raised at 25 degree C
|
| Growth protocol |
Synchronized daf-2 and daf-2; daf-42 embryos were obtained by placing 20 adult worms each on six NGM plates with OP50 for 2 hours at 15°C and then incubated at 25°C for dauer induction.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
At 52 HAE and 60 HAE, the worms were harvested with M9 and washed with distilled water five times. The, 250 μL of TRIzol was added to 50 μL of washed worm harvest, and the worm samples were freeze-thawed 10–15 times for disruption. Harvest daf-2; daf-42 at 60 HAE included both live and dead L2d worms. RNA was extracted through chloroform—isopropanol precipitation.
Theragen Bio Inc. (South Korea) prepared a library with TruSeq Stranded mRNA Sample Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Kallisto v.0.46.1 was used to create cDNA index file and pseudoalignment (100 bootstraps)
Assembly: WBcel235, ensembl 103
Supplementary files format and content: tsv (tab-separated values) files generated by Kallisto, containing abundance information in estimated counts and tpm, for each sample
|
| |
|
| Submission date |
Apr 22, 2023 |
| Last update date |
Apr 23, 2023 |
| Contact name |
Daisy Sunghee Lim |
| E-mail(s) |
[email protected]
|
| Organization name |
Seoul National University
|
| Street address |
1 Gwanak-ro, Gwanak-gu
|
| City |
Seoul |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL26672 |
| Series (1) |
| GSE230353 |
RNAseq of dauer-forming C. elegans L2d in daf-2 and daf-2;daf-42 |
|
| Relations |
| BioSample |
SAMN30427474 |
| SRA |
SRX17159066 |
