|
| Status |
Public on Nov 06, 2023 |
| Title |
inoculum_biol rep1 [ino1_S1] |
| Sample type |
SRA |
| |
|
| Source name |
OG1RF
|
| Organism |
Enterococcus faecalis |
| Characteristics |
strain: OG1RF
genotype: wild-type
treatment: inoculum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A 1 × 1 cm of mouse skin encompassing the wound site was excised into 2 mL of RNAlater stabilization solution and incubated overnight at 4 °C. The mouse skin was then transferred into 1 mL of TRIzol and cut into smaller pieces. The entire suspension was transferred into Lysing Matrix B 2-mL tubes and homogenized using a FastPrep-24 tissue grinder for 2 rounds of 40 s at 6.0 m/s with 2 min rest on ice in between. To each sample, 200 µL of chloroform was added, vortexed vigorously for 30 s and centrifuged at 12,000 x g for 10 min at 4 °C. The top layer (aqueous phase) containing RNA was transferred to 1.5 mL tubes containing 500 µL of ice-cold ethanol and shaken vigorously before loading into the RNeasy Mini spin columns. Subsequent RNA extraction steps were performed according to manufacturer’s protocol of the RNeasy Mini Kit. Briefly, samples were washed once with Buffer RW1, followed by 2 washes with Buffer RPE and elution of RNA with RNase-free water.
Library preparation was done using the Ribo-Zero Plus rRNA depletion kit as per manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
rawcounts_inoculum.txt
normcounts.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) |
| GSE206749 |
Purine and carbohydrate availability drive Enterococcus faecalis fitness in wound infections [dataset 1] |
| GSE206751 |
Purine and carbohydrate availability drive Enterococcus faecalis fitness in wound infections. |
|
| Relations |
| BioSample |
SAMN29260303 |
| SRA |
SRX15836500 |
