|
| Status |
Public on Jun 15, 2022 |
| Title |
∆ldh1 iron unchelated, LDH_RP25 |
| Sample type |
SRA |
| |
|
| Source name |
E. faecalis ∆ldh1 macrocolonies on TSBG agar (single-species)
|
| Organism |
Enterococcus faecalis |
| Characteristics |
genotype mapped: OG1RF
growth protocol: iron replete
condition: single
e. faecalis strain: LDH1
|
| Treatment protocol |
Macrocolonies were grown in TSBG agar with or without 2 mM 2,2’ bipyridyl.
|
| Growth protocol |
Single-species (E. faecalis OG1RF, E. faecalis ∆ldh1 or P. aeruginosa PADP6) and mixed-species (PADP6+OG1RF or PADP6+∆ldh1) macrocolonies grown in TSBG agar (TSB supplemented with 10 mM glucose) at 37ᵒC for 48 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Macrocolonies were first scraped into RNAprotect™ Bacteria Reagent and bacteria pellets were then subjected to total RNA extraction using RNeasy® mini kit with slight modifications. Briefly, cell pellets were resuspended in TE buffer containing 20 mg/mL lysozyme and further supplemented with 20 µL proteinase K. Followed by incubation at 37 °C for 1 h, and subsequent extraction steps was performed according to manufacturer’s protocol. Extracted RNA samples were treated with DNase (TURBO DNA-free™ kit, Invitrogen, USA) and 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 instruction but without the oligo dT purification. The sequencing was done using the HiSeq Rapid SBS Kit V2 200 cycles.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
∆ldh1 total RNA
LDH_RP25
Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, ToOG1RF.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 options “-T 20 -k 13” against E. faecalis OG1RF (NCBI accession: CP002621) or P. aeruginosa PAO1 (NCBI accession: NC_002516) 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 filtered out from all data sets.
Differential gene expression analysis was performed in R using edgeR (Version 3.28.1).
Genome_build: E. faecalis OG1RF (NCBI accession: CP002621) and P. aeruginosa PAO1 (NCBI accession: NC_002516).
Supplementary_files_format_and_content: toOG1RF.txt, toPAO1.txt (Text files containing raw counts of sequencing reads for each sample mapped to E. faecalis OG1RF or P. aeruginosa PADP6.)
Supplementary_files_format_and_content: *VS*.txt (Normalized counts using edgeR for every comparison made. )
Supplementary_files_format_and_content: *conditions.txt (Sample metadata csv file used in DGE analysis in edgeR.)
|
| |
|
| Submission date |
Dec 03, 2021 |
| Last update date |
Jun 15, 2022 |
| 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 (1) |
| GSE190090 |
Enterococcus faecalis antagonizes Pseudomonas aeruginosa growth in mixed-species interactions |
|
| Relations |
| BioSample |
SAMN23583145 |
| SRA |
SRX13298901 |
