|
| Status |
Public on Jul 01, 2021 |
| Title |
JTL621_Auxin_2h_NHS_R3 |
| Sample type |
SRA |
| |
|
| Source name |
JTL621 (hsf-1::aid::gfpI;unc-119(ed3)III;ieSi38[sun-1p::TIR1::mRuby::sun-1_3'UTR+Cbr-unc-119(+)]IV)
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
age: young adults
tissue of tir1: germline
strain: JTL621 (hsf-1::aid::gfpI;unc-119(ed3)III;ieSi38[sun-1p::TIR1::mRuby::sun-1_3'UTR+Cbr-unc-119(+)]IV)
treatment: Auxin;NHS
|
| Treatment protocol |
Worms were transferred to either auxin or ethanol (EtOH) plates, and kept for 2 hours. Following this, worms were either directly collected or subjected to heat shock performed in a water bath pre-heated to 34°C. For heat shock, NGM plates were wrapped with parafilm and submerged for 30 min.
|
| Growth protocol |
The HSF-1 AID animals (JTL611 and JTL621) and the corresponding control animals that only express TIR1 (CA1200 and CA1199) were synchronized by treatment of alkaline hypochlorite solution (bleach). Synchronized L1 larvae were grown on 10 cm normal NGM plates (~500 worms per plate) for 51 hr to develop into young 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 |
Li_RNA_084
edgeR_JTL621(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL621(germ)_2h.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.
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.
Genome_build: WS235/ce11
|
| |
|
| Submission date |
Nov 24, 2020 |
| Last update date |
Jul 01, 2021 |
| 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) |
| GSE162064 |
Using Auxin-inducible-degradation System to Interrogate Tissue-specific Transcriptional Programs of HSF-1 in Reproduction and Heat Shock Response. [HS response] |
| GSE162067 |
Using Auxin-inducible-degradation System to Interrogate Tissue-specific Transcriptional Programs of HSF-1 in Reproduction, Lifespan Assurance and Heat Shock Response. |
|
| Relations |
| BioSample |
SAMN16881502 |
| SRA |
SRX9567251 |
