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Sample GSM4932540 Query DataSets for GSM4932540
Status Public on Jul 01, 2021
Title JTL621_EtOH_2h_HS_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: EtOH;HS
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_087
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 SAMN16881501
SRA SRX9567252

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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