|
| Status |
Public on Nov 11, 2023 |
| Title |
OPd8_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Whole
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: Whole
strain: Bristol N2
cell type: hermaphrodite
genotype: wild-type
treatment: feeding OP50
age: three-day-old
|
| Treatment protocol |
Three-day-old worms were cultured for five days on mNGM plates covered with OP50 (control group) or ETEC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Approximately 200 worms in each group were collected and soaked in RNAlater solution (Qiagen). Total RNA was isolated using the RNeasy Lipid Tissue kit (Qiagen).
mRNAs were purified using the NEBNext Poly(A) mRNA Magnetic Isolation Module. Libraries were prepared using the SMARTer® Stranded Total RNA-Seq Kit (Clontech)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina Real-Time Analysis (RTA) software used for basecalling.
The raw reads were trimmed and quality-filtered using the Trim Galore! (ver. 0.6.5), Trimmomatic (ver. 0.39) and cutadapt (ver. 2.7) software. Clean reads were aligned versus the N2 Caenorhabditis elegans reference genome ce11 (WBcel235.98) using STAR (ver. 2.7.2b).
The read count of gene features was performed with the featureCounts tool (ver. 1.6.4)
Supplementary files format and content: ce11
Supplementary files format and content: tab-delimited text files include featureCount values for each sample
|
| |
|
| Submission date |
Nov 06, 2023 |
| Last update date |
Nov 11, 2023 |
| Contact name |
Eriko Kage-Nakadai |
| E-mail(s) |
nakadai@omu.ac.jp
|
| Organization name |
Osaka Metropolitan Univ.
|
| Street address |
3-3-138, Sugimoto, Sumiyoshi-ku
|
| City |
Osaka |
| State/province |
Osaka |
| ZIP/Postal code |
558-8585 |
| Country |
Japan |
| |
|
| Platform ID |
GPL22765 |
| Series (1) |
| GSE247108 |
Characterization of the genes that were regulated by infection with enterotoxigenic E. coli (ETEC) |
|
| Relations |
| BioSample |
SAMN38120827 |
| SRA |
SRX22383131 |
