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Sample GSM8078370

Query DataSets for GSM8078370

Status

Public on Jun 13, 2024

Title

WT_CDMDEB

Sample type

SRA

Source name

bacterial cell

Organism

Lactococcus lactis

Characteristics

strain: DGCC12653
genetic modification: none
genotype: WT
treatment: diauxic shift
cell type: bacterial cell

Treatment protocol

For codY- and covRS-deletion mutants and their controls, cells were harvested at their respective glucose-maltose diauxix shift. For comX overepression and its control, cells were harvested at mid log phase.

Growth protocol

codY- and covRS-deletion mutants and wild-type controls were grown at 30°C without agitation in their respective efficient competence-activating medium (CDM*-DEB and CDM* for DcodY mutant and DcovRS mutant, respectively). The WT strain carrying an empty vector and the strain overexpressing the master comptence regulator ComX ((PxylT-comX fusion carried by a plasmid) were grown as reported above but in M17X medium containing Xylose as inducer.

Extracted molecule

total RNA

Extraction protocol

RNA was harvested using Rneasy plus according to manufacturer indications. Samples were adjusted to 100 ng/µl and checked for integrity with an RNA Nano Chip (Agilent Technologies).
RNA sequencing library preparation was prepared using NEBNext rRNA Depletion Kit (Bacteria) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA)
The sequencing libraries were multiplexed and clustered on the flowcell. After clustering, the flowcell was loaded on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

Raw data were processed on the Galaxy server (use.galaxy.org) using Bowtie2 algorithm to yield BAM files
BAM files were analyzed using Seqmonk to count the number of reads per coding sequence
The dataset was exported into Excel for further analyses
Assembly: SL12653_transcripts_fasta.txt (DGCC12653)
Supplementary files format and content: the xls file (sheet 1) reporting RNAseq data is organized in columns as follows: column A: locus tag, column B: raw counts of WT grown in CDM*-DEB, column C: raw counts of WT grown in CDM*, column D: raw counts of WT (empty vector) grown in M17X, column E: raw counts of DcodY grown in CDM*-DEB, column F: raw counts of DcovRS grown in CDM*, column G: raw counts of WT overexpressing comX grown in M17X, column H: normalized counts of WT grown in CDM*-DEB, column I: normalized counts of WT grown in CDM*, column J: normalized counts of WT (empty vector) grown in M17X, column K: normalized counts of DcodY grown in CDM*-DEB, column L: normalized counts of DcovRS grown in CDM*, column M: normalized counts of WT overepressing comX grown in M17X, column N: ratio between normalized counts of DcodY and WT, column O: ratio between normalized counts of DcovRS and WT, column P: ratio between normalized counts of comX overpression and WT.

Submission date

Feb 13, 2024

Last update date

Jun 13, 2024

Contact name

Frédéric Toussaint

E-mail(s)

frederic.toussaint@uclouvain.be

Organization name

UCLouvain

Street address

Place de l'Université 1