|
| Status |
Public on May 19, 2022 |
| Title |
JTL667(glp-1)_EtOH_D1_48h_R3 |
| Sample type |
SRA |
| |
|
| Source name |
young adults
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue of tir1: soma
strain: JTL667 (glp-1(e2141)III; hsf-1::aid::gfpI;ieSi57[eft-3p::TIR1::mRuby::unc-54_3'UTR+Cbr-unc-119(+)]II)
agent: Auxin
time point: 48h
|
| Treatment protocol |
For each condition, ~120 worms were transferred to either auxin or ethanol (EtOH) plates by picking, and kept for indicated time.
|
| Growth protocol |
The HSF-1 AID animals in the wild-type background (JTL611) and the corresponding control animals that only express TIR1 in the soma (CA1200) were synchronized by treatment of alkaline hypochlorite solution (bleach). Synchronized L1 larvae were grown on 10 cm normal NGM plates (~500 worms per plate) at 20 °C for 51 hr to develop into young adults. The HSF-1 AID models in the longlived glp-1(e2141) temperature-sensitive mutant background (JTL667) and the control fem-3(q20) background (JTL670) were synchronized by treatment of alkaline hypochlorite solution (bleach). Synchronized L1 larvae were grown on 10 cm normal NGM plates at 25°C for 48 hr to develop into Day1 adults.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using 300 uL Trizol reagent. Worms were vortexed continuously for 20 minutes at 4°C and then went through one cycle of freeze-thaw to help release RNA. Following this, RNA was purified using Direct-zol RNA MiniPrep kit (Zymo Research) as per manufacturer’s instructions using on column DNase I digestion to remove genomic DNA.
Total RNAs were polyA enriched, and directional RNA-seq libraries were prepared using NEBNext Ultra II RNA library prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
TableS2_DE genes caused by HSF-1 depletion in soma.xlsx
edgeR_normcounts_glp1&fem3.tsv
|
| Data processing |
RNA-seq reads were mapped to Ensembl WBcel235 genome using RNA STAR (Dobin et al., 2013) with --alignIntronMax 120000 to set the intron size, and --outFilterMultimapNmax 200 to allow multi-mapped reads. All paired-end reads were trimmed to 50 bp to make downstream mapping and analyses consistent.
The mapped reads were then subject to FeatureCounts in Rsubread (Liao et al., 2019) for quantification with the setting -p -B -P -C -M -O --fraction –largestOverlap. The settings in STAR and FeatureCounts enabled proper quantification of those heat shock genes (e.g. hsp-70 and hsp-16s) that are duplicated in C. elegans genome.
Differential expression (DE) analyses were then done using edgeR (Robinson et al., 2010) with default settings except of using Likelyhood Ratio Test and filtering out those lowly expressed genes with CPM (counts per million) value less than 1 in more than 75% samples. For each time point, to control for effects by auxin and by insertion of AID:GFP to HSF-1, we pooled EtOH treated CA1199 and EtOH treated JTL621 with auxin treated CA1199 to calculate the expression levels in control condition, and then compare them to auxin treated JTL621. This analysis reports only DE genes caused by HSF-1 depletion (as HSF-1 depletion vs. control).
Assembly: WS235/ce11
Supplementary files format and content: norm counts
|
| |
|
| Submission date |
May 16, 2022 |
| Last update date |
May 25, 2022 |
| Contact name |
Jian Li |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
New York Medical College
|
| Street address |
15 Dana Road
|
| City |
Valhalla |
| State/province |
NY |
| ZIP/Postal code |
10595 |
| Country |
USA |
| |
|
| Platform ID |
GPL26672 |
| Series (2) |
| GSE162067 |
Using Auxin-inducible-degradation System to Interrogate Tissue-specific Transcriptional Programs of HSF-1 in Reproduction, Lifespan Assurance and Heat Shock Response. |
| GSE203087 |
Using Auxin-inducible-degradation System to Interrogate Tissue-specific Transcriptional Programs of HSF-1 in Lifespan Assurance [HSF-1 transcriptome in the soma] |
|
| Relations |
| BioSample |
SAMN28448621 |
| SRA |
SRX15447946 |
