|
| Status |
Public on Jan 02, 2016 |
| Title |
Rsp-KO 1 |
| Sample type |
SRA |
| |
|
| Source name |
S. aureus
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: MRSA BD02-25
incubation time: mid-logarithmic growth phase (4h)
genotype/variation: delta-Rsp
|
| Treatment protocol |
The same bacterial CFU cultures were then collected, the cells were washed twice in 10 mM sodium phosphate buffer (pH 6.5).
|
| Growth protocol |
Overnight cultures were diluted 1:100 into 50 ml of TSB and incubated at 37°C with shaking at 200 rpm until grown to an OD600 nm of 1.5-2.0 (mid-logarithmic growth phase).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using an RNeasy Mini Kit (Qiagen) as recommended in a standard protocol as described before. A total of 10 μg of each RNA sample was subjected to further purification to enrich the mRNA using a MICROBExpress Kit (Ambion) according to the manufacturer's instructions.
An Illumina Paired End Sample Prep kit was used to prepare RNA-seq library according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: MUTANT.Gene.rpkm.txt
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then aligned to S. aureus USA300_FPR3757 (RefSeq accession number NC_007793.1 ) using BWA. Based on the above standard, the QC of alignment was produced.
The commonly used fragments per kilobase of transcript per million mapped fragments (RPKM) incorporate normalization steps to ensure that expression levels for different genes and transcripts can be compared across runs.
Based on RPKM normalization, we performed analyses of differentially expressed genes. Genes with an adjusted P value < 0.05, FDR < 0.001 and fold change > 2 were identified as being differentially expressed.
Genome_build: S. aureus USA300_FPR3757 (RefSeq accession number NC_007793.1; ASM1346v1)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each 2 Samples
|
| |
|
| Submission date |
Mar 27, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Otto |
| E-mail(s) |
MOtto@niaid.nih.gov
|
| Phone |
301 443 5209
|
| Organization name |
NIH
|
| Department |
NIAID
|
| Lab |
LHBP
|
| Street address |
9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL17452 |
| Series (1) |
| GSE67344 |
Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and △Rsp MRSA Transcriptomes |
|
| Relations |
| BioSample |
SAMN03449800 |
| SRA |
SRX970852 |
