|
| Status |
Public on Nov 29, 2022 |
| Title |
PR8 + MRSA #8 (P+M8) |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lung
strain: C57BL/6J
gender: Male
|
| Treatment protocol |
Mice were intranasally (IN) administered with saline or PR8 (30k FFU). 10 days (D10) post-IN administration, mice were intratracheally (IT) administered saline or MRSA (1*10^8 CFU/30uL) and were left to recover for 24 hours.
|
| Growth protocol |
USA300 was cultured in TSB from frozen stock for 18-24 hours. Overnight culture was diluted 1:50 and was incubated for 2.5 hours. Samples were centrifuged for 15 min at 4°C, then the pellet was resuspended in PBS, centrifuged for 3 min at room temperature, and resuspended in saline. The opitical density of the bacterial suspension was measured and diluted three times to ensure bacterial samples were at desired optical density and bacterial concentration (1*10^8 CFU/30uL). Serial dilutions of the bacterial suspension was plated on TSB plates in triplicate and incubated for 24 hours at 37°C to confirm bacterial concentration.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lungs were removed, snap frozen, homogenized, and RNA isolated using Qiagen RNeasy Midi Kit (Cat#75144).
RNA libraries were prepared using Zymo-Seq RiboFree Total RNA Library Kit (Cat#R3000) with 1 ug of total RNA for the construction of sequencing libraries. Invitrogen ERCC spike in controls (Cat#4456740) were added to all samples
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Gene expression data from total lungs treated with IN PR8 on D0 and IT MRSA on D10
|
| Data processing |
Illumina reads were trimmed for adaptor sequence and for quality in CLC Genomics Workbench (v.21.0.5)
Trimmed sequences were mapped to to the reference genome sequence of Mus musculus assembly mm10, with the parameters: mismatch cost, 2; insertion and deletion cost, 3; length and similarity fraction, 0.8.
Uniquely mapped transcripts from each sample were exported from CLC Genomics Workbench and used for normalization and differential gene expression analysis with an R package, DESeq2 version 1.32.0
Assembly: mm10
Supplementary files format and content: MRSA_gene_exp_diff contains differential gene expression between MRSA vs Control treatment. PR8_gene_exp_diff contains differential gene expression between PR8 vs Control treatment. PR8MRSA_gene_exp_diff contains differential gene expression between PR8+MRSA vs Control treatment. All files includes mouse gene names, baseMean, log2FoldChange, IfcSE, stat, pvalue, padj. Raw_gene_counts_matrix contains uniquely mapped transcripts for each sample with gene name and ENSEMBL ID.
|
| |
|
| Submission date |
Mar 29, 2022 |
| Last update date |
Nov 29, 2022 |
| Contact name |
Christophe Langouët-Astrié |
| E-mail(s) |
christophe.langouetastrie@cuanschutz.edu
|
| Organization name |
University of Colorado Denver, Anschutz
|
| Department |
Pulmonary Sciences and Critical Care
|
| Lab |
Eric Schmidt
|
| Street address |
12700 E 19th Ave
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE199707 |
RNA-sequencing of primary and secondary bacterial pneumonia |
|
| Relations |
| BioSample |
SAMN27062184 |
| SRA |
SRX14651192 |
