|
| Status |
Public on Jul 01, 2023 |
| Title |
SE_WT_2 |
| Sample type |
SRA |
| |
|
| Source name |
nHEK
|
| Organism |
Mus musculus |
| Characteristics |
cell type: nHEK
treatment: 1e7 CFU/cm2 S. epidermidis 1457 WT
time: 24h
|
| Treatment protocol |
10uM of synthetic S. epidermidis or S. aureus PSMS were applied to 70% confluent (48h 2mM CaCl2 differentiated) nHEKs for 6h.
PSM peptide dissolved in DMSO and treated at final concentraiton of 0.1% on nHEK cells.
|
| Growth protocol |
nHEK cells were maintained in Epilife medium (60uM CaCl2) supplemented with human keratnocyte growth supplement (HKGS) and antibiotic/antimycotic in humidified atmosphere with 5% CO2 at 37C. Used between passages 3-5.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
mRNA was harvested using Purelinke RNA Mini kit.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Fastqc-->STAR-->featurecounts-->Rstudio (EdgeR)
Assembly: Gencode GrCh38.p13
Supplementary files format and content: excel workbork files
|
| |
|
| Submission date |
Jul 29, 2022 |
| Last update date |
Jul 01, 2023 |
| Contact name |
Michael R Williams |
| E-mail(s) |
[email protected]
|
| Organization name |
UC San Diego
|
| Department |
Dermatology
|
| Lab |
Richard L. Gallo
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093-0869 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE210046 |
Effect of S. epidermidis phenol-soluble modulins on murine dorsal skin (24h) |
|
| Relations |
| BioSample |
SAMN30050262 |
| SRA |
SRX16730822 |
