|
| Status |
Public on May 17, 2024 |
| Title |
A549 cells, primary, REP3 |
| Sample type |
RNA |
| |
|
| Source name |
primary
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549 (ATCC CCL-185)
cell type: lung carcinoma epithelial cells
infection: primary infection
|
| Growth protocol |
The human alveolar epithelial cell line A549 (ATCC CCL-185) were cultured in F-12K culture medium (Gibco™ 21127030) supplemented with 10% fetal calf serum (FCS) and 1% L-glutamine and incubated at 37 °C in a humidified atmosphere with 5% CO2. Bacteria (pneumococcus) were diluted in serum-low cell culture medium (0,25% FCS) to get a multiplicity of infection of 20:1 (MOI 20). After 3h of infection (primary), cells were washed twice with PBS to remove the unattached bacteria, and then either collected for analysis, or cultured in medium with penicillin-streptomycin (10 microg /ml) and gentamicin (200 microg /ml) during 4 days for later time point. At 7 days post infection (PI), the cells were no infected or a second infection (secondary) is performed during 3 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cells using RNeasy Mini Kit (Qiagen, 74104) and protocol followed according to manufacturers’ instructions. Chloroform extraction/Na-Acetate 3M (pH 5.5), isopropanol precipitated and washed 3 times in 70% ethanol prior to being suspended in molecular grade water. Extracted RNA quality was assessed and quantified with RNA 6000 Nano kit (Agilent, 5067-1511) using 2100 Bioanalyzer instrument (Agilent).
|
| Label |
biotin
|
| Label protocol |
The Affymetrix Human Gene array 2.1 microarrays was performed by Eurofins Genomics (France).
|
| |
|
| Hybridization protocol |
Affymetrix protocol
|
| Scan protocol |
Affymetrix protocol
|
| Description |
Gene expression data for primary infection
|
| Data processing |
Expression signal was normalized using the Robust Multichip Average (RMA) method, from the affy R package. Control and lowly express probes were filtered out and the replicate effect was removed using the ComBat approach implemented in the sva R package.
|
| |
|
| Submission date |
Apr 20, 2023 |
| Last update date |
May 17, 2024 |
| Contact name |
Claudia Chica |
| Organization name |
Institut Pasteur
|
| Lab |
Biostatistics and Bioinformatics Hub
|
| Street address |
25-28 Rue du Dr Roux
|
| City |
Paris |
| ZIP/Postal code |
75015 |
| Country |
France |
| |
|
| Platform ID |
GPL17692 |
| Series (2) |
| GSE230138 |
Epithelial cells maintain memory of prior infection with Streptococcus pneumoniae through di-methylation of histone H3 [Affymetrix] |
| GSE230142 |
Epithelial cells maintain memory of prior infection with Streptococcus pneumoniae through di-methylation of histone H3 |
|
