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| Status |
Public on Feb 26, 2021 |
| Title |
WT_D1_2 |
| Sample type |
SRA |
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| Source name |
Whole body
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| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
genotype: wild type
development stage: adult at day1
tissue: Whole body
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| Treatment protocol |
Synchronized wild-type(N2) and daf-2(e1370) animals were treated with 50 μM FUdR when worms reached L4 or young adult stage on OP50. At indicated ages (day 1 or day 9 adulthood), worms were harvested with M9 buffer, and washed 2-3 times, and frozen in liquid nitrogen. Three biological repeats of the samples were used for all conditions.
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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 (unstranded) RNA Library Prep Kit v2 (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 pairs were aligned to the C. elegans genome WBcel235 (ce11) and Ensembl transcriptome (release 97) 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.
Differentially expressed genes (fold change > 1.5 and adjusted p value < 0.1) were identified by using DESeq2 (v.1.22.2). Wald test p values are adjusted for multiple testing using the procedure of BH.
Genome_build: WBcel235 (ce11)
Supplementary_files_format_and_content: txt files with read counts were generated by using RSEM (v.1.3.1)
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| Submission date |
Sep 23, 2019 |
| Last update date |
Feb 28, 2021 |
| Contact name |
Seung-Jae V Lee |
| E-mail(s) |
[email protected]
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| Organization name |
KAIST
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| Department |
Life Sciences
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| Lab |
Room 4203
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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) |
| GSE137861 |
FOXO and HSF1 rejuvenate immunity via positive feedback regulation of insulin/IGF-1 signaling |
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| Relations |
| BioSample |
SAMN12821251 |
| SRA |
SRX6889450 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4090268_WT_D1_2.txt.gz |
141.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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