|
| Status |
Public on Nov 01, 2024 |
| Title |
RAW 264.7 cells, MOI 100 (c_100X1) |
| Sample type |
SRA |
| |
|
| Source name |
RAW 264.7 macrophages infected with E. faecalis
|
| Organism |
Mus musculus |
| Characteristics |
cell line: RAW 264.7
cell type: macrophage
genotype: WT
infection: Enterococcus faecalis OG1RF
moi: 100
treatment: no LPS
|
| Treatment protocol |
Macrophages were either treated with LPS control or with E. faecalis at various MOI indicated in the presence or absence of LPS stimulation and incubated for 6 hours at 37ᵒC with 5% CO2.
|
| Growth protocol |
RAW264.7 macrophages were grown overnight in DMEM with 10% FBS supplementation at 37ᵒC with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were washed once with PBS and resuspended in 1 mL Trizol. RNA was extracted using zymo direct-zol rna miniprep kit and purified using RNA Clean & concentrator (Zymo Research) as per manufacturer's protocol.
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 |
Mouse mRNA, OG1RF total RNA
|
| Data processing |
Raw reads were quality and adapter trimmed using bbduk
Using the rsem-calculate-expression wrapper script from RSEM, the mRNA reads were mapped using bowtie2 v 2.4.1 to the GRCm39 reference genome and feature counts were obtained sequentially using with the rsem-calculate-expression wrapper
Differential expression was determined using DESeq2
Genome_build: Mus musculus GRCm39
Supplementary_files_format_and_content: counts.txt (Text file containing raw counts of sequencing reads for each sample)
Supplementary_files_format_and_content: normalizedTMM_counts.txt (Normalized abundance (using trimmed means of M values))
Supplementary_files_format_and_content: conditions.csv (Sample metadata csv file used in DGE analysis in DESeq2)
|
| |
|
| Submission date |
Nov 15, 2021 |
| Last update date |
Nov 01, 2024 |
| Contact name |
Brenda Tien |
| Organization name |
NTU
|
| Street address |
60 Nanyang Drive
|
| City |
Singapore |
| ZIP/Postal code |
637551 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE188916 |
Enterococcus faecalis-derived lactate mediated suppression of NF-κB and ERK pathways in macrophages to promote polymicrobial wound infection |
|
| Relations |
| BioSample |
SAMN23169454 |
| SRA |
SRX13144818 |
