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| Status |
Public on Jul 01, 2020 |
| Title |
N2-vrk1-3 |
| Sample type |
SRA |
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| Source name |
Whole body
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| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
genotype: wild type
developmental stage: Day 0 adult
treatment: vrk-1 RNAi
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| Treatment protocol |
Wild-type N2 and isp-1(qm150) mutant animals were synchronized by using an embryo bleaching method, and synchronized larvae were fed with either control or vrk-1 RNAi bacteria until the worms reached young adult stage. To induce RNAi, 10 mM IPTG was treated on the bacteria seeded NGM plates. Worms were harvested with M9 buffer, washed to remove remaining bacteria.
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| Growth protocol |
Worms were grown on NGM plates as previously described in 'Maintenance of C. elegans (Stiernagle T, WormBook, 2006)'.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed as previously described (Son et al., Nature Comm, 2017). Total RNA in the animals was extracted using RNAiso plus (Takara, Seta, Kyoto, Japan).
Libraries were constructed with TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, CA, USA) by Macrogen Inc. (Seoul, South Korea) following the manufacture’s instruction.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Sequencing reads were aligned to the C. elegans trascriptome and genome WBcel235.87 (ce11) by using HISAT2 (v.2.0.5). Aligned transcripts were assembled and quantified by using SeqMonk
Genome_build: WBcel235.87 (ce11)
Supplementary_files_format_and_content: txt files with read counts were generated by using SeqMonk
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| Submission date |
Sep 29, 2019 |
| Last update date |
Jul 02, 2020 |
| Contact name |
Seung-Jae V Lee |
| E-mail(s) |
seungjaevlee@kaist.ac.kr
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| Organization name |
KAIST
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| Department |
Life Sciences
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| Lab |
Room 5216
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| Street address |
291 Daehak-ro
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| City |
Daejeon |
| ZIP/Postal code |
34141 |
| Country |
South Korea |
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| Platform ID |
GPL18245 |
| Series (1) |
| GSE138129 |
VRK-1 Extends Lifespan by Activation of AMPK via Phosphorylation |
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| Relations |
| BioSample |
SAMN12870232 |
| SRA |
SRX6920360 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4100772_N2-vrk1-3.txt.gz |
158.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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