|
| Status |
Public on Jan 29, 2019 |
| Title |
WT + apicidin rep1 |
| Sample type |
SRA |
| |
|
| Source name |
WT + apicidin rep1
|
| Organism |
Staphylococcus aureus subsp. aureus USA300 |
| Characteristics |
strain: AH1263
genotype: wildtype
treatment: apicidin
|
| Treatment protocol |
2 min treatment with RNAprotect (Qiagen).
|
| Growth protocol |
S. aureus cultures were grown in a 48-well plate to an OD600 of 4 in tryptic soy broth supplemented with 1% DMSO (vehicle control) or 100 μM apicidin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1 h lysis step with lysostaphin followed by RNA purification using Qiagen RNeasy Mini Kit.
rRNA depleted using Ribo-Zero rRNA Removal kit for Gram positive bacteria (Illumina) and libraries prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
DMSO_vs_apicidin.csv
|
| Data processing |
Paired-end reads mapped using SeqMan NGen version 14 (DNAStar).
Reads Per Kilobase of transcript per Million mapped reads (RPKM) were calculated using ArrayStar version 14 (DNAStar).
Genome_build: CP000255.1
Supplementary_files_format_and_content: csv files containing total raw counts for each replicate and average RPKM values for each condition
|
| |
|
| Submission date |
Jan 28, 2019 |
| Last update date |
Feb 04, 2019 |
| Contact name |
Alexander Horswill |
| Organization name |
University of Colorado Anschutz Medical Campus
|
| Department |
Immunology and Microbiology
|
| Street address |
12800 E. 19th Ave., Rm. P18-9101
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL17544 |
| Series (1) |
| GSE125741 |
Effect of apicidin on gene expression in Staphylococcus aureus USA300 strain LAC |
|
| Relations |
| BioSample |
SAMN10830403 |
| SRA |
SRX5299663 |
