|
| Status |
Public on Jul 17, 2023 |
| Title |
24 hour sample 1 |
| Sample type |
SRA |
| |
|
| Source name |
Epithelium infected with S. pyogenes
|
| Organisms |
Mus musculus; Streptococcus pyogenes NZ131 |
| Characteristics |
tissue: Epithelium infected with S. pyogenes
treatment: Infected epithelium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Skin was excised at indicated time point after euthanizing mice. Bead beating was used to lyse both murine and bacterial cells and RNA was extracted using the Qiagen RNAeasy kit. To obtain sufficient bacterial RNA, each sample represents 5 mice treated as technical replicates.
Ribozero RNA depletion followed by Illumina stranded library preparation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
NZ bacteria 24hr results.csv
NZ mouse 24hr results.csv
|
| Data processing |
CLC Genomics Workbench V 20.0.4 was used to import and trim data. Read were sequentially aligned to first the M musculus genome, than the S pyogenes NZ131 genome.
Uniquely mapped mouse or bacterial transcripts were normalized and used for differential gene expression analysis using R (v4.2.2), Rstudio (v2022.12.0+353, RRID: SCR_000432), and DESeq2 (v1.36.0, RRID: SCR_015687)
Differentially expressed genes were filtered based on an absolute log2 fold change cutoff and Benjamini-Hochberg False Discovery Rate (FDR) cutoff.
Assembly: mm10, NC_011375.1
Supplementary files format and content: CSV files including raw counts for each sample.
Supplementary files format and content: CSV files including processed data for each sample.
|
| |
|
| Submission date |
Jul 10, 2023 |
| Last update date |
Jul 17, 2023 |
| Contact name |
Reid V Wilkening |
| E-mail(s) |
reid.wilkening@childrenscolorado.org
|
| Organization name |
University of Colorado
|
| Department |
Department of Pediatrics, Section of Critical Care Medicine
|
| Lab |
Horswill Laboratory
|
| Street address |
12800 E. 19th Ave., Rm. P18-9101
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL33562 |
| Series (1) |
| GSE237018 |
Identifying genetic determinants of Streptococcus pyogenes-host interactions in a murine intact skin infection model |
|
| Relations |
| BioSample |
SAMN36398217 |
| SRA |
SRX20970929 |
