 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 27, 2023 |
| Title |
Staphylococcus aureus M6, replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
miccro-organism from human's cheek
|
| Organism |
Staphylococcus aureus |
| Characteristics |
cultivar: M6
cell type: miccro-organism from human's cheek
genotype: WT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
To harvest cells, cultures were centrifuged at 15,000 x g for 1 min. TRIzol™ Reagent (0.7532 mL) was added to bacterial pellets that had been stored at -80℃. RNA extraction was subsequently performed according to the manufacturer’s instructions with the following modifications. To obtain RNA from S. aureus, we added glass beads and vortexed for 1 minute, before placing the sample on ice for 1 minute and repeating this process 10 times.
Protocol for rRNA depletion using NEBNext rRNA Depletion Kit (Bacteria), TruSeq Stranded Total RNA Reference Guide (1000000040499 v00)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Target, replicate 3
|
| Data processing |
The quality of RNA sequencing raw data was checked using FastQC (v0.11.9). They were trimmed using Trimmomatic (v0.39).
The trimmed data were mapped to the whole genome sequences of each strain using bowtie2 (v2.4.5).
The mapping data were assigned read counts to each gene using HTSeq (v1.99.2).
To compare transcription levels between strains, an orthologous search was performed using OrthoFinder (v2.5.5), and the S. aureus IFM15 gene with the highest score was assigned to each gene of S. aureus M6.
Afterwards, filtering and trimmed mean of M-values (TMM) normalization were performed using the edgeR (v3.36.0) package of the R (v4.1.3) language.
Assembly: IFM15.gbf and M6.gbf as supplementary file
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: tab-delimited text file includes edgeR result for each sample.
|
| |
|
| Submission date |
Nov 24, 2023 |
| Last update date |
Nov 27, 2023 |
| Contact name |
Sung Ho Yoon |
| Organization name |
Konkuk University
|
| Department |
Department of Bioscience and Biotechnology
|
| Street address |
120 Neungdong-ro, Gwangjin-gu
|
| City |
Seoul |
| ZIP/Postal code |
05029 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL25144 |
| Series (1) |
| GSE248604 |
Facemask acne attenuation through modulation of indirect microbiome interactions |
|
| Relations |
| BioSample |
SAMN38414202 |
| SRA |
SRX22637296 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7917861_M6_3_raw_count.txt.gz |
11.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
