|
| Status |
Public on Nov 06, 2023 |
| Title |
N2_Untreated [Control] |
| Sample type |
SRA |
| |
|
| Source name |
Whole nematodes
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: Whole nematodes
genotype: Wild-type
treatment: Untreated
|
| Treatment protocol |
Wild-type N2 nematodes with or without 2 mM of AbaPep#07 treatment from L4 stage were collected at day 10 of adulthood, washed with M9 buffer at least 3 times, and immediately flash-frozen in liquid nitrogen.
|
| Growth protocol |
Wild-type N2 nematodes were cultured in S medium with E. coli NA22 as food in a shaking incubator at 20°C and 120 rpm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from whole nematodes using TRIzol kit (Invitrogen).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then first-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
The raw sequencing data was subjected to quality control with SOAPnuke (v1.5.2) software. The clean reads were aligned to the C. elegans reference genome WBcel235 using HISAT2 (v2.0.4). Ericscript (v0.5.5) was subsequently used to detect fusion genes, and rMATS (v3.2.5) was used to identify differential splicing genes. Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, and the expression level of genes was calculated by RSEM (v1.2.12).
Differential expression analysis was performed using PossionDis with a significance threshold of false discovery rate ≤ 0.05 and fold change ≥ 2 (i.e. |log2(fold change)| ≥ 1).
Assembly: WBcel235
Supplementary files format and content: Tab-delimited text file include raw Read Count, TPM and FPKM for each Sample.
|
| |
|
| Submission date |
Nov 01, 2023 |
| Last update date |
Nov 06, 2023 |
| Contact name |
Qiangqiang Wang |
| E-mail(s) |
wqq@whu.edu.cn, fewqq@mail.scut.edu.cn
|
| Organization name |
South China University of Technology
|
| Department |
School of Food Science and Engineering
|
| Lab |
Prof. Huang Zebo
|
| Street address |
Waihuan East Road, No. 381
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
450006 |
| Country |
China |
| |
|
| Platform ID |
GPL25145 |
| Series (1) |
| GSE246759 |
Abalone peptide increases stress resilience and cost-free longevity via SKN-1-governed transcriptional metabolic reprogramming in C. elegans |
|
| Relations |
| BioSample |
SAMN38061067 |
| SRA |
SRX22328660 |
