|
| Status |
Public on Mar 16, 2017 |
| Title |
Lys-1 |
| Sample type |
SRA |
| |
|
| Source name |
Biofilm cells, LysH5
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain/background: IPLA 1
cell type: Biofilm
treatment: NaPi buffer + LysH5
|
| Growth protocol |
Biofilms were formed for 24 hours at 25ºC, then adhered cells were treated with NaPi buffer alone or containing subinhibitory endolysin LysH5 for 30 minutes and subsequently harvested for RNA purification.
|
| 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 |
Processed data file: NaPi_vs_Lys.txt
|
| 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 formatted 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.
Genome_build: S. aureus subsp. aureus NCTC 8325 (Assembly ASM1342v1, GCA_000013425.1, Mar 2010).
Supplementary_files_format_and_content: NaPi_vs_Lys.txt: Tab-delimited text file includes RPKM values for NCTC 8325 genes in NaPi and Lys replicates as well as differential expression estimations, expressed as a log2 fold change between conditions.
|
| |
|
| Submission date |
Feb 03, 2017 |
| 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
|
| City |
Villaviciosa |
| ZIP/Postal code |
33300 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17452 |
| Series (1) |
| GSE94512 |
Downregulation of autolysin-encoding genes by phage-derived lytic proteins inhibits biofilm formation in Staphylococcus aureus |
|
| Relations |
| BioSample |
SAMN06295872 |
| SRA |
SRX2537892 |
