|
| Status |
Public on Nov 06, 2023 |
| Title |
∆mptD in mannose_biol rep3 [MNEDEL3_S11] |
| Sample type |
SRA |
| |
|
| Source name |
OG1RF
|
| Organism |
Enterococcus faecalis |
| Characteristics |
strain: OG1RF
genotype: mptD deletion
treatment: with mannose
|
| Treatment protocol |
OG1RF and ∆mptD were grown in TSBd with and without mannose supplementation.
|
| Growth protocol |
Overnight cultures of OG1RF and ∆mptD were sub-cultured to OD600 of 0.01 in a 24-well microtiter plate with containing 1 mL of TSBd supplemented with or without mannose at 37ᵒC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacteria were harvested at late log/early stationary phase in RNAprotect™ Bacteria Reagent and incubated at room temperature for 5 min before centrifuging at 10,000 g for 10 min. The supernatant was decanted and bacteria pellets collected were subjected to total RNA extraction using Qiagen RNeasy® Mini Kit with slight modifications. Briefly, cell pellets were resuspended in TE buffer containing 20 mg/mL lysozyme, further supplemented with 20 µL proteinase K and incubated at 37 °C for 1 h. Subsequent RNA extraction steps were performed according to manufacturer’s protocol. The extracted RNA samples were treated with DNase for removal of genome DNA before it was purified using Monarch® RNA cleanup kit.
The total RNA was converted to double stranded cDNA and made into libraries using the TruSeq Stranded mRNA Sample Preparation as per manufacturer's instructions but without the oligo dT purification.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
rawcounts_withMannose.txt
normalisedCountsCPM_mannose.txt
|
| Data processing |
Raw reads were quality and adapter trimmed using bbduk from BBMap tools (Version 39.79).
Trimmed reads were then mapped using bwa-mem of BWA (Version 0.7.17-r1188) with default options against E. faecalis OG1RF (NCBI accession: CP002621) reference genomes.
Reads mapped to predicted open reading frames were quantified using htseq-count of HTSeq (Version 0.12.4) with option “-m intersection-strict”.
Ribosomal sequences were manually removed from all data sets.
Differential gene expression analysis was performed in R using edgeR (Version 3.28.1).
Assembly: E. faecalis OG1RF (NCBI accession: CP002621)
Supplementary files format and content: Raw counts from HTSeq in .txt format.
Supplementary files format and content: Normalized counts using edgeR for every comparsion made in .txt format.
Supplementary files format and content: Sample metadata csv file used in DGE analysis in edgeR.
|
| |
|
| Submission date |
Jun 23, 2022 |
| Last update date |
Nov 06, 2023 |
| Contact name |
Casandra Tan |
| E-mail(s) |
casandra.tan.ai.zhu@gmail.com
|
| Phone |
90305694
|
| Organization name |
SCELSE
|
| Street address |
60 Nanyang Drive
|
| City |
Singapore |
| ZIP/Postal code |
637551 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL23172 |
| Series (2) |
| GSE206750 |
Purine and carbohydrate availability drive Enterococcus faecalis fitness in wound infections [dataset 2] |
| GSE206751 |
Purine and carbohydrate availability drive Enterococcus faecalis fitness in wound infections. |
|
| Relations |
| BioSample |
SAMN29260322 |
| SRA |
SRX15836796 |
