|
| Status |
Public on Aug 22, 2024 |
| Title |
WT_Her_1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole body
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: Whole body
strain: N2
genotype: wild type
developmental stage: Prefertile adult to day 1 adult
Sex: Hermaphrodite
|
| Growth protocol |
All strains were maintained on E. coli OP50-seeded nematode growth media (NGM) plates at 20°C. Males were generated by heat shock at 37°C for 1 h of L4 stage larval WT or mutant worms. Male worms were maintained by crossing between hermaphrodites and males.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from prefertile adult to day 1 adult WT and hlh-30(tm1978) hermaphrodites and males, three times independently. Synchronized hermaphrodites were harvested using S-basal buffer. Males were picked and harvested using S-basal buffer every day. One set of total RNA of males was extracted from the samples collected for about 20 days. Total RNA was isolated using RNAiso plus following the manufacturer’s instructions.
cDNA library was prepared for paired-end RNA seq using Illumina NovaSeq 6000 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing pairs were aligned to the C. elegans genome WBcel235 (ce11) and Ensembl transcriptome (release 104) by using STAR (v.2.7.0e). Aligned pairs on genes or transcripts were quantified by using RSEM (v.1.3.1). Detailed parameters of alignment and quantification were calculated by following guidelines of ENCODE long RNA-Seq processing pipeline.
Assembly: WBcel235 (ce11)
Supplementary files format and content: txt files with read counts were generated by using RSEM (v.1.3.1)
|
| |
|
| Submission date |
Oct 16, 2023 |
| Last update date |
Aug 22, 2024 |
| Contact name |
Seung-Jae V Lee |
| E-mail(s) |
seungjaevlee@kaist.ac.kr
|
| Organization name |
KAIST
|
| Department |
Life Sciences
|
| Lab |
Room 4203
|
| Street address |
291 Daehak-ro
|
| City |
Daejeon |
| ZIP/Postal code |
34141 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL26672 |
| Series (1) |
| GSE245430 |
HLH-30/TFEB-regulated autophagy mediates sexual dimorphism in immunity in Caenorhabditis elegans |
|
| Relations |
| BioSample |
SAMN37831063 |
| SRA |
SRX22099598 |
