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Sample GSM3380229

Query DataSets for GSM3380229

Status

Public on Sep 08, 2018

Title

replicate 1 of A3

Sample type

SRA

Source name

total RNA

Organism

Lactococcus lactis

Characteristics

strain: robust derivative A3

Treatment protocol

In exponential phase of growth (OD 0.8-1.1) samples were taken for RNA isolation.

Growth protocol

SK11 and its robust derivatives A3, A5, B1, B2 and B7 were cultured in duplicate in 50 ml GM17 at 30°C.

Extracted molecule

total RNA

Extraction protocol

RNA isolation was performed using routine procedures, as described previously (Bron et al., 2012) with minor adjustments. Aliquots of 5 ml of culture were centrifuged at 4000 × g for 3 minutes at 2°C and cells were resuspended in 0.5 ml cold TE buffer. To this suspension, 500 µl 1:1 phenol/chloroform, 30 µl 10% SDS, 30 µl 3M sodium acetate pH 5.2 and 500 mg 0.1 mm zirconia beads (Biospec Products, Inc., Bartlesville, USA) was added in a 2 ml screw-cap tube and samples were frozen in liquid nitrogen and stored at -80°C.
cDNA synthesis and sequencing with an Ion Proton system using an Ion PI-chip (Life Technologies) was performed by PrimBio Research Institute (Exton, USA).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Ion Torrent Proton

Description

a3.1

Data processing

Demultiplexed fastq-files were analyzed using Transcriptor with default settings (Todt TJ, Derks M, Siezen RJ, van Hijum SAFT, submitted for publication). Read data were mapped against the reference genome sequence of SK11 using Bowtie2 (Langmead and Salzberg, 2012). Transcripts were determined by applying a segmentation algorithm to the alignment results (Todt et al., 2012). Segments with read coverage above a minimum read count threshold of five reads were identified and adjacent segments were joined. For each sample, transcripts were annotated by matching them with gene annotations provided by the selected reference genome.
Genome_build: NC_008527
Supplementary_files_format_and_content: Read counts were used to to identify differentially expressed genes across the different derivatives and the original SK11 strain using edgeR (Robinson et al., 2010). P-values were corrected for multiple testing using the Benjamini and Hochberg procedure provided by the edgeR package.

Submission date

Sep 07, 2018

Last update date

Sep 10, 2018

Contact name

Annereinou Dijkstra

E-mail(s)

annereinou.dijkstra@nizo.com

Organization name

NIZO food research

Street address

Kernhemseweg 2