|
| Status |
Public on Nov 07, 2022 |
| Title |
Staphylococcus aureus JE2 biofilm 48h |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Staphylococcus aureus |
| Characteristics |
cell type: bacterial cells
genotype: JE2
treatment: Biofilm culture 48h
|
| Treatment protocol |
Biofilm culture in vitro
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified using RiboPure RNA purification kit
Illumina Nextera XT library was used for sequencing library preparation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
CLC genomic benchwork
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.36.
Trimmed sequence reads were mapped to USA300_FPR3757 reference genome using STAR aligner v.2.5.2b
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: USA300_FPR3757 reference genome (GCF_000013465.1)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Oct 27, 2022 |
| Last update date |
Nov 08, 2022 |
| Contact name |
Koichi Yuki |
| E-mail(s) |
koichi.yuki@childrens.harvard.edu
|
| Organization name |
Boston Children's Hospital
|
| Street address |
300 Longwood Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL25144 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN31494363 |
| SRA |
SRX18051344 |
