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Series GSE162063 Query DataSets for GSE162063
Status Public on Jul 01, 2021
Title Using Auxin-inducible-degradation System to Interrogate Tissue-specific Transcriptional Programs of HSF-1 in Reproduction and Heat Shock Response. [ChIP-Seq]
Organism Caenorhabditis elegans
Experiment type Expression profiling by high throughput sequencing
Summary To understand the roles of HSF-1 and its regulation in reproduction and heat shock response in a tissue-specific manner, we coupled tissue-specific HSF-1 depletion in C. elegans by auxin-inducible degron (AID) with genome-wide transcriptional analyses in whole animals. We used ChIP-seq to analyze the occupancy of HSF-1 (tagged with AID::GFP) and RNA Pol II in young adult (YA) animals grown at 20°C or upon heat shock (HS) at 34°C for 30 min following an acute depletion of HSF-1 by AID for 2 hours either in the somatic or in the germline cells. Depletion by AID was performed by transferring worms expressing the E3 ligase TIR1 and carrying AID insertion to endogenous HSF-1 (JTL611 or JTL621) to NGM plates containing 1mM auxin (indole- 3-acetic acid, Sigma). The mock treatment was done by transferring worms to plates only containing the vehicle ethanol (EtOH). In parallel, we used RNA-seq to analyze the heat shock respnse upon depletion of HSF-1 in the soma or the germline for 2 hours. In addition, we also analyzed the transcriptomic changes by RNA-seq upon tissue-specific depletion of HSF-1 initiated at young adult stage for different length of time. In all RNA-seq analyses, we included the strains that only express TIR1 but do not have degron insertion at HSF-1 (CA1200 and CA1199) to control for the effects of auxin treatment and AID insertion into HSF-1.
 
Overall design Experiment type: ChIP-seq, RNA-seq. Biological Source: strain: JTL611, JTL621, CA1200 and CA1199. Developmental dtage: young adult. Experimental Factors: temperature: 20 degree celsius (non-heat-shock, NHS), 34 degree celsius (heat-shock, HS); antibodies: anti-GFP (clontech, polyclonal), anti-Pol II (8WG16, BioLegend).
 
Contributor(s) Li J
Citation(s) 34469721, 35899092
Submission date Nov 24, 2020
Last update date Aug 03, 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
 
Platforms (1)
GPL26672 Illumina NovaSeq 6000 (Caenorhabditis elegans)
Samples (40)
GSM4932454 soma-control-NHS-HSF1_ChIP_replicate1
GSM4932455 germline-control-NHS-HSF1_ChIP_replicate1
GSM4932456 soma-control-NHS-HSF1_ChIP_replicate2
This SubSeries is part of SuperSeries:
GSE162067 Using Auxin-inducible-degradation System to Interrogate Tissue-specific Transcriptional Programs of HSF-1 in Reproduction, Lifespan Assurance and Heat Shock Response.
Relations
BioProject PRJNA680485
SRA SRP293849

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE162063_HSF-1_ChIP_peaks.xlsx 96.8 Kb (ftp)(http) XLSX
GSE162063_common-HS-HSF1-peaksummits_EtOH_.bed.gz 6.7 Kb (ftp)(http) BED
GSE162063_common-NHS-HSF1-peaksummits_EtOH_.bed.gz 7.7 Kb (ftp)(http) BED
GSE162063_germline-ctrl-HS-HSF1_combined_treat_pileup.bedgraph.gz 48.5 Mb (ftp)(http) BEDGRAPH
GSE162063_germline-ctrl-HS-Pol_combined_treat_pileup.bedgraph.gz 32.4 Mb (ftp)(http) BEDGRAPH
GSE162063_germline-ctrl-NHS-HSF1_combined_treat_pileup.bedgraph.gz 46.4 Mb (ftp)(http) BEDGRAPH
GSE162063_germline-ctrl-NHS-Pol_combined_treat_pileup.bedgraph.gz 46.6 Mb (ftp)(http) BEDGRAPH
GSE162063_germline-depl-HS-HSF1_combined_treat_pileup.bedgraph.gz 50.9 Mb (ftp)(http) BEDGRAPH
GSE162063_germline-depl-HS-Pol_combined_treat_pileup.bedgraph.gz 43.5 Mb (ftp)(http) BEDGRAPH
GSE162063_germline-depl-NHS-HSF1_combined_treat_pileup.bedgraph.gz 45.3 Mb (ftp)(http) BEDGRAPH
GSE162063_germline-depl-NHS-Pol_combined_treat_pileup.bedgraph.gz 54.2 Mb (ftp)(http) BEDGRAPH
GSE162063_soma-ctrl-HS-HSF1_combined_treat_pileup.bedgraph.gz 42.4 Mb (ftp)(http) BEDGRAPH
GSE162063_soma-ctrl-HS-Pol_combined_treat_pileup.bedgraph.gz 38.0 Mb (ftp)(http) BEDGRAPH
GSE162063_soma-ctrl-NHS-HSF1_combined_treat_pileup.bedgraph.gz 34.6 Mb (ftp)(http) BEDGRAPH
GSE162063_soma-ctrl-NHS-Pol_combined_treat_pileup.bedgraph.gz 74.6 Mb (ftp)(http) BEDGRAPH
GSE162063_soma-depl-HS-HSF1_combined_treat_pileup.bedgraph.gz 48.9 Mb (ftp)(http) BEDGRAPH
GSE162063_soma-depl-HS-Pol_combined_treat_pileup.bedgraph.gz 42.5 Mb (ftp)(http) BEDGRAPH
GSE162063_soma-depl-NHS-HSF1_combined_treat_pileup.bedgraph.gz 30.0 Mb (ftp)(http) BEDGRAPH
GSE162063_soma-depl-NHS-Pol_combined_treat_pileup.bedgraph.gz 73.4 Mb (ftp)(http) BEDGRAPH
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