GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM4467324

Query DataSets for GSM4467324

Status

Public on Dec 04, 2020

Title

WT replicate 2

Sample type

SRA

Source name

Sgg UCN34

Organism

Streptococcus gallolyticus UCN34

Characteristics

deleted gene: None

Growth protocol

The WT strain and the three regulatory mutants Δgsp, Δghk and Δgrr were inoculated at DO=0,1 in liquid THY (10mL) from fresh agar plates and incubated without agitation at 37°C.

Extracted molecule

total RNA

Extraction protocol

At DO(600)=0,5, RNA were extracted with the MP Biomedicals™ FastRNA™ Pro Blue Kit and treated with DNase (Invitrogen™ Ambion™ TURBO DNA-free Kit) to remove residual DNA. DNase was inactivated with the DNase inactivation reagent present in the kit.
rRNA were depleted from 0,5 μg of total RNA using the Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina. Sequencing libraries were constructed using the TruSeq Stranded mRNA Sample preparation kit (20020595) following the manufacturer’s instructions (Illumina). The directional libraries were controlled on Bioanalyzer DNA1000 Chips (Agilent Technologies) and concentrations measured with the Qubit® dsDNA HS Assay Kit (ThermoFisher). Sequences of 65 bases were generated on the Illumina Hiseq 2500 sequencer.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

WT-2

Data processing

Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11 . Only sequences at least 25 nt in length were considered for further analysis.
Bowtie version 1.2.2, with default parameters, was used for alignment on the reference genome (NC_013798.1, from NCBI).
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t gene -g locus_tag -s 1).
Count data were analyzed using R version 3.5.1 and the Bioconductor package DESeq2 version 1.20.0. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between the WT, 13, 14 and 15 biological conditions. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Genome_build: Streptococcus gallolyticus UCN34 (NC_013798.1, from NCBI)
Supplementary_files_format_and_content: Output file from DESzq2

Submission date

Apr 09, 2020

Last update date

Dec 04, 2020

Contact name

Rachel Legendre

E-mail(s)

[email protected]

Organization name

Institut Pasteur

Department

Research and Resource Center for Scientific Informatics