|
| Status |
Public on Nov 19, 2018 |
| Title |
SM1_S4 |
| Sample type |
SRA |
| |
|
| Source name |
NsaS A208E_exponentially-growing culture
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain background: SH1000
genotype/variation: NsaS A208E
growth stage: Exponentially-growing culture from tryptic soya broth
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAprotect (Qiagen) was added to cultures of each organism at 2x culture volume to stabilise RNA. Total RNA was extracted using the RNAeasy midi kit (Qiagen) according to manufacturer's instructions, with the exception that cells were first treated with lysostaphin (200 ug/ml) and proteinase K (40 ug/ml) for 90 and 10 minutes, respectively. Illumina TruSeq RNA Sample Prep Kit v2 was used for library creation with 1 ug of total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptors and based on quality score, then mapped to the S. aureus 8325 sequence using CLC genomics workbench version 8
Genome_build: Staphylococcus aureus NCTC 8325
Supplementary_files_format_and_content: Tab delimited text files provide raw counts of sequencing reads to features of interest
|
| |
|
| Submission date |
May 21, 2018 |
| Last update date |
Nov 19, 2018 |
| Contact name |
Christopher Paul Randall |
| E-mail(s) |
C.P.Randall@leeds.ac.uk
|
| Phone |
0113 343 5592
|
| Organization name |
University of Leeds
|
| Department |
Faculty of Biological Sciences
|
| Lab |
Antimicrobial Research Centre
|
| Street address |
Clarendon Way
|
| City |
Leeds |
| State/province |
West Yorkshire |
| ZIP/Postal code |
LS2 9JT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24034 |
| Series (1) |
| GSE114706 |
Changes in the transcriptome of S. aureus SH1000 containing a nisin resistance mutation in nsaS |
|
| Relations |
| BioSample |
SAMN09231666 |
| SRA |
SRX4106208 |
