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Sample GSM2339172

Query DataSets for GSM2339172

Status

Public on Jan 20, 2017

Title

SM-3

Sample type

SRA

Source name

Biofilm cells

Organism

Staphylococcus aureus

Characteristics

strain: IPLA 1
tissue: Biofilm cells
treatment: untreated control

Growth protocol

Biofilms were formed for 24 hours at 37ºC, then adhered cells were harvested

Extracted molecule

total RNA

Extraction protocol

Bacterial cells were harvested, treated with RNA protect (Qiagen) and kept at -80ºC until RNA purification. RNA was obtained by mechanical disruption in the presence of acid phenol and subsequent purification was carried out with illustra RNA spin minikit (GE Healthcare)
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

Quality of the sequences was verified with FastQC 0.11.2
EDGE-pro 1.3.1 workflow was employed for read processing. The pipeline as described by T.Magoc, et al., Evolutionary Bioinformatics, 2013, employs Bowtie2 (v2.2.3) to map reads to the reference genome (NCTC 8325), filters multimapped reads based on scoring alignments and determines read coverage for each genomic position and gene.
EDGE-pro output files were formated using the edgeToDeseq script provided in the EDGE-pro package and used as input for DESeq2 (v1.12.4) to calculate RPKMs per gene and quantify differential expression between conditions.
Unaligned reads for RODI replicates to the NCTC 8325 reference genome were collected and reprocessed using the EDGE-pro 1.3.1 and DESeq2, using phiIPLA-RODI's reference genome.
Genome_build: S. aureus subsp. aureus NCTC 8325 (Assembly GCA_000013425.1, Mar 2010) and phage phiIPLA-RODI (Assembly GCF_001504675.1, May 2015)
Supplementary_files_format_and_content: SM_vs_RODI.txt: Tab-delimited text File. The file includes RPKM values for NCTC 8325 genes in SM and RODI replicates as well as differential expression estimations, expressed as a log2 fold change between conditions.
Supplementary_files_format_and_content: phiIPLA-RODI_RPKMs.txt: Tab-delimited text file. The file includes read counts and RPKM values for phage phiIPLA-RODI genes in each RODI replicate.

Submission date

Oct 06, 2016

Last update date

May 15, 2019

Contact name

Lucia Fernandez

E-mail(s)

lucia.fernandez@ipla.csic.es

Organization name

Instituto de Productos Lacteos de Asturias (IPLA-CSIC)

Street address

Paseo Rio Linares s/n