|
| Status |
Public on Feb 12, 2021 |
| Title |
CI1149_pH7-4_09-04-2019_S29_R1_001 |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria from patient pus
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: Clinical isolate CI-1149
ph condition: pH 7.4
replicate: Replicate 2
|
| Treatment protocol |
DMEM was buffered with either 50mM HEPES for pH 7.4 or with 0.077 mM Na2HPO4 and 0.0614 mM citric acid for pH 5.5.
|
| Growth protocol |
S. aureus was inoculated into defined pH media (pH 5.5 and 7.4) at a starting OD600 of 0.2 and incubated at 37°C and 5% CO2 for three days. DMEM was supplemented with 10% FBS and 4 mM of L-glutamine.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Bacteria were collected by centrifugation, washed twice with PBS, and total RNA was isolated using the RNeasy Mini kit (Qiagen) following the manufactures protocol
Vertis Biotechnologie AG, Germany, carried out the rRNA depletion, RNA fragmentation, strand-specific cDNA library preparation, and Illumina NextSeq500 single-read sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina NextSeq 500 system was used for RNA sequencing with read length of 75bp.
Quality control of the sequencing reads was done with FastQC v0.11.8 using the default parameters.
Reference genome S. aureus USA300 FPR3757 was indexed using STAR 2.6.0c, with parameters --runMode genomeGenerate, --genomeSAindexNbases 8, --sjdbGTFfeatureExon CDS, --sjdbOverhang 80, --genomeFastaFiles USA300_FPR3757.fasta, --sjdbGTFfile USA300_FPR3757.gtf.
Reads were aligned to the indexed reference genome and counted into annotated genes using the software STAR 2.6.0c . The following parameters were used: --runMode alignReads, --twopassMode Basic, --outSAMtype BAM SortedByCoordinate, --quantMode GeneCounts, --sjdbGTFfile USA300_FPR3757.gtf, --sjdbGTFfeatureExon CDS.
Raw read counts were imported to DESeq2 1.24.0, which facilitated an internal normalization and tested the transcripts for differential expression between conditions.
Genome_build: GenBank CP000255.1
Supplementary_files_format_and_content: Tab-delimited text file showing read counts per gene in each condition
|
| |
|
| Submission date |
Apr 02, 2020 |
| Last update date |
Feb 12, 2021 |
| Contact name |
Markus Huemer |
| E-mail(s) |
Markus.Huemer@usz.ch
|
| Organization name |
University Hospital Zurich
|
| Department |
Division of Infectious Diseases and Hospital Epidemiology
|
| Lab |
Annelies Zinkernagel Laboratory
|
| Street address |
Sternwartstrasse 14, Lab F39
|
| City |
Zurich |
| State/province |
Zurich |
| ZIP/Postal code |
CH-8091 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL24034 |
| Series (1) |
| GSE148024 |
Molecular reprogramming and phenotype switching in Staphylococcus aureus lead to high antibiotic persistence and affect therapy success |
|
| Relations |
| BioSample |
SAMN14530243 |
| SRA |
SRX8049158 |
