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Sample GSM3020211

Query DataSets for GSM3020211

Status

Public on Aug 20, 2018

Title

450-2

Sample type

SRA

Source name

Biofilm cells

Organism

Staphylococcus aureus

Characteristics

strain: RN450
cell state: cells adhered to biofilm

Growth protocol

Biofilms were formed for 5 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

Description

450-2

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.
Reads for phi11 and phi80 replicates were reprocessed using the EDGE-pro 1.3.1 and DESeq2, using phi11 and phi80alpha reference genomes.
Genome_build: S. aureus subsp. aureus NCTC 8325 (Assembly GCA_000013425.1, Mar 2010), phage phi11 (Assembly GCA_000841245.1, February 2002) and phage phi80alpha (Assembly GCA_000871605.1, May 2006)
Supplementary_files_format_and_content: 450_vs_Phi11.txt: Tab-delimited text File. The file includes RPKM values for NCTC 8325 genes in 450 and phi11 replicates as well as differential expression estimations, expressed as a log2 fold change between conditions.
phi11.phage_11.RPKM.txt: Tab-delimited text file. The file includes read counts and RPKM values for phage phi11 genes in each phi11 replicate.
450_vs_Phi80.txt: Tab-delimited text File. The file includes RPKM values for NCTC 8325 genes in 450 and phi80 replicates as well as differential expression estimations, expressed as a log2 fold change between conditions.
phi80.phage_80_alpha.RPKM.txt: Tab-delimited text file. The file includes read counts and RPKM values for phage phi80alpha genes in each phi80 replicate.

Submission date

Feb 22, 2018

Last update date

Aug 20, 2018

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