tissue: bone marrow cell type: macrophages genotype: WT
Treatment protocol
BMDM that had been exposed only to standard culture medium for 7 days were designated as M0, and basal expression levels were determined using RNA from these cells. For post-infection transcriptional analysis, M0 cells were exposed to P. aeruginosa strain K at an MOI of 5:1 for 1 h, after which infection media was aspirated, and cells were rinsed twice with PBS. The cells were then cultured in medium containing 75 μg/ml gentamicin, 100 IU/ml penicillin, and 100 μg/ml streptomycin, until RNA was collected at 6 h or 24 h after the end of the infection period.
Growth protocol
Bone marrow cells were differentiated to macrophages by 7 days of culture in RPMI media supplemented with 10% FBS and 20% conditioned media from L929 cells.
Extracted molecule
total RNA
Extraction protocol
TRIzol extraction followed by cleanup with RNeasy Mini Kit (Qiagen, Valencia, CA)
Label
Biotin
Label protocol
Affymetrix standard protocol
Hybridization protocol
Affymetrix standard protocol
Scan protocol
GeneChip Operating System (GCOS)
Data processing
RMA algorithm with quantile normalization and background correction
