|
| Status |
Public on Jun 28, 2023 |
| Title |
wild type bacterium, rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Staphylococcus aureus |
| Characteristics |
cell type: bacteria
genotype: wild type bacterium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAprotect Cell Reagent was added immediately to the infected samples. RNA of bacteria or infected macrophages was prepared using RNeasy Mini Kit (Qiagen).
DNA libraries suitable for sequencing were prepared using CORALL Total RNA-Seq Library Prep protocol according to manufacturer’s recommendation.
libraries were sequenced on an Illumina NextSeq platform (1*75 bp single-end run)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Sa_WT_10h_3
RAW_COUNT_TABLE_SA.csv
|
| Data processing |
To assure high sequence quality, Illumina reads were quality and adapter-trimmed via Cutadapt v2.5
Reads were first filtered with FastQScreen and then subsequently mapped to the human and bacterial genomes
Differential Expression analysis with DESeq2 v1.24.0
Assembly: GRCh38.p13 for human and GCF_000013465.1_ASM1346v1 for bacteria
Supplementary files format and content: DESeq2_intracell_Mut_vs_RPMI_Mut_BACTERIA.xlsx - DESeq2 Comparison of S. aureus transcripts (brnQ1 mutant in infected macrophages vs growth in RPMI1640)
Supplementary files format and content: DESeq2_intracell_Mut_vs_intracell_WT_BACTERIA.xlsx - DESeq2 Comparison of S. aureus transcripts (brnQ1 mutant in infected macrophages vs JE2 WT in infected macrophages)
Supplementary files format and content: DESeq2_intracell_Mut_vs_intracell_WT_HUMAN.xlsx - DESeq2 Comparison of human transcripts (brnQ1 mutant in infected macrophages vs JE2 WT in infected macrophages)
Supplementary files format and content: DESeq2_intracell_WT_vs_RPMI_WT_BACTERIA.xlsx - DESeq2 Comparison of S. aureus transcripts (JE2 WT in infected macrophages vs growth in RPMI1640)
|
| |
|
| Submission date |
Jun 27, 2023 |
| Last update date |
Jun 28, 2023 |
| Contact name |
Martin J Fraunholz |
| E-mail(s) |
martin.fraunholz@uni-wuerzburg.de
|
| Organization name |
University of Wuerzburg
|
| Department |
Chair of Microbiolgy
|
| Street address |
Theodor-Boveri-Weg
|
| City |
Wuerzburg |
| ZIP/Postal code |
97074 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24034 |
| Series (1) |
| GSE235929 |
A new form of Staphylococcus aureus dormancy controlled by branched-chain amino acid availability in human macrophages |
|
| Relations |
| BioSample |
SAMN36001633 |
| SRA |
SRX20793372 |
