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Series GSE125467 Query DataSets for GSE125467
Status Public on Apr 15, 2019
Title The role of (p)ppGpp in the heat shock response in B. subtilis
Organism Bacillus subtilis
Experiment type Expression profiling by high throughput sequencing
Summary Bacterial and eukaryotic cells survive an otherwise lethal heat shock once they are primed by a mild pre-heat shock. Using B. subtilis as a model organism, we investigated transcriptional changes during thermotolerance development at 37 °C, 48 °C, 53 °C and 48/53 °C and observed a comprehensive upregulation of genes of the general and heat shock response and the downregulation of many translation-related genes. In addition, strains lacking (p)ppGpp (ppGpp0) or with elevated (p)ppGpp levels (ΔrelA) were analyzed at 37 °C and 48 °C, revealing broad and pleiotropic transcripional changes mediated by (p)ppGpp in the ΔrelA mutant. In addition, our data suggests a contribution of the (p)ppGpp-mediated stringent response in the heat-mediated transcripional down-regulation of ribosomal genes and additional processes.
 
Overall design RNA of heat shocked B subtilis wild type, (p)ppGpp0 and ΔrelA strains
Please note that the *NoPP samples are special 5' enriched/depleted libraries which were used for TSS and promotor analysis and therefore, no processed (count or RPKM) data was generated.
 
Contributor(s) Schäfer H, Nuss A, Beckstette M, Dersch P, Turgay K
Citation(s) 32176689
Submission date Jan 22, 2019
Last update date Apr 06, 2020
Contact name Michael Beckstette
Organization name Helmholtz Centre for Infection Research
Department Molecular Infection Biology
Lab Experimental Immunology
Street address Inhoffenstrase 7
City Braunschweig
State/province Lower Saxony
ZIP/Postal code 38124
Country Germany
 
Platforms (1)
GPL18561 Illumina HiSeq 2000 (Bacillus subtilis)
Samples (32)
GSM3574692 wild type 37 °C control [A_37C_I]
GSM3574693 wild type 37 °C control [A_37C_II]
GSM3574694 wild type 37 °C control [A_37C_III]
Relations
BioProject PRJNA516445
SRA SRP181188

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
GSE125467_B.subtilis_168_BHS220_modified_chr_spike.fna.gz 1.3 Mb (ftp)(http) FNA
GSE125467_B.subtilis_168_BHS220_modified_chr_spike.gff.gz 111.6 Kb (ftp)(http) GFF
GSE125467_DESeq2_genes_diffexp_by_fc_A_37C_vs_B_48C.csv.gz 1.1 Mb (ftp)(http) CSV
GSE125467_DESeq2_genes_diffexp_by_fc_A_37C_vs_C_37-53C.csv.gz 1.1 Mb (ftp)(http) CSV
GSE125467_DESeq2_genes_diffexp_by_fc_A_37C_vs_D_48-53C.csv.gz 1.2 Mb (ftp)(http) CSV
GSE125467_DESeq2_genes_diffexp_by_fc_A_37C_vs_E_37C_delta_relA.csv.gz 1.1 Mb (ftp)(http) CSV
GSE125467_DESeq2_genes_diffexp_by_fc_A_37C_vs_F_48C_delta_relA.csv.gz 1.2 Mb (ftp)(http) CSV
GSE125467_DESeq2_genes_diffexp_by_fc_A_37C_vs_ppGpp_Null_37C.csv.gz 1.0 Mb (ftp)(http) CSV
GSE125467_DESeq2_genes_diffexp_by_fc_A_37C_vs_ppGpp_Null_48C.csv.gz 1.1 Mb (ftp)(http) CSV
GSE125467_DESeq2_genes_diffexp_by_fc_B_48C_vs_F_48C_delta_relA.csv.gz 1.2 Mb (ftp)(http) CSV
GSE125467_DESeq2_genes_diffexp_by_fc_B_48C_vs_ppGpp_Null_48C.csv.gz 1.1 Mb (ftp)(http) CSV
GSE125467_DESeq2_genes_diffexp_by_fc_E_37C_delta_relA_vs_F_48C_delta_relA.csv.gz 1.1 Mb (ftp)(http) CSV
GSE125467_DESeq2_genes_diffexp_by_fc_ppGpp_Null_37C_vs_E_37C_delta_relA.csv.gz 1.1 Mb (ftp)(http) CSV
GSE125467_DESeq2_genes_diffexp_by_fc_ppGpp_Null_37C_vs_ppGpp_Null_48C.csv.gz 1.1 Mb (ftp)(http) CSV
GSE125467_RAW.tar 1.5 Mb (http)(custom) TAR (of RPKM, TAB)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record
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