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Sample GSM3574695 Query DataSets for GSM3574695
Status Public on Apr 15, 2019
Title wild type 48 °C [B_48C_I]
Sample type SRA
Source name wild type 48 °C
Organism Bacillus subtilis
Characteristics genotype/variation: amyE::rrnJp1 lacZ cm
treatment: 48 °C 15 min
replicate: I
polyphosphatase treatment: yes
Treatment protocol The culture was divided and treated either with 48 °C or left untreated for 15 min. Then, both cultures were transferred to a 53 °C water bath for another 15 min. Samples of 25 mL were harvested by centrifugation for 3 min and flash-frozen in luqid nitrogen.
Growth protocol Cells were grown in LB medium to the mid-exponential phase (OD 0.4) in a water bath with orbital shaking at 200 rpm.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from flash-frozen cells using phenol/TRIzol extraction as described in Lamy et al. (2004) Molecular Microbiology, 54: 1250-1268 and treated with DAase using the TURBO DNA-free kit (Ambion). RNA integrity was checked on a Bioanalyzer 2100
rRNA was depleted using the MICROBExpress Kit (Invitrogen). mRNA was supplemented with ERCC ExFold RNA Spike-In Mixes, treated with 5'RNA-polyphosphatase, sonicated and treated with PNK. The library was generated using the NEB Next Small RNA Kit as described by Manufacturer. In addition, one replicate without ERCC was not treated with polypphosphatase
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description 2anu11_S4_L001
Data processing library quality assessment using FastQC
alignment vs. reference genome using Bowtie2 with default parametrization
read count quantification using htseq-count ( and subsequent RPKM normalization
Detection of differentially expressed genes using DeSEQ2 with raw count data and default parametrization
Genome_build: Bacillus subtils 168 genome with insertion of rrnJp1-lacZ in the amyE site (amyE::rrnJp1-lacZ Cm). For reference sequence/annotation see files: B.subtilis_168_BHS220_modified_chr_spike.fna and B.subtilis_168_BHS220_modified_chr_spike.gff
Supplementary_files_format_and_content: htseqcounts*.tab files: raw read counts per gene; htseqcounts*.rpkm files: RPKM normalized read counts per gene; DESeq2_genes_diffexp*.csv: CSV files with differentially expressed genes; Fasta and GFF files with genomic reference and annotation
Submission date Jan 22, 2019
Last update date Apr 16, 2019
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
Platform ID GPL18561
Series (1)
GSE125467 The role of (p)ppGpp in the heat shock response in B. subtilis
BioSample SAMN10788817
SRA SRX5278701

Supplementary file Size Download File type/resource
GSM3574695_htseqcounts_2anu11_S4_L001_R1_001.fastq.rpkm.gz 46.1 Kb (ftp)(http) RPKM 17.5 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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