7 protocols
normalization data transformation protocol
Intensities of arrays have been quantile-normalized using Partek Genomic Suite (v6.6). Differential expressions were calculated using ANOVA of Partek package. ID_REF = VALUE = Log2 GC-RMA signal intensity
array scanning protocol
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
hybridization protocol
Following labeling, cDNAs were hybridized for 16 hr at 45C on Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
labelling protocol
Biotinylated cDNAs were prepared according to the standard Ambion and Affymetrix protocol from 250 ng total RNA (The Ambion WT Expression Kit and GeneChip Terminal Labeling Kit, Affymetrix).
nucleic acid extraction protocol
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
sample treatment protocol
The experiment was set up in a 6 well plates with 3 wells as control untreated cells, and 3 well SSRI treated cells. Seeding density was 50,000 cells per well.
growth protocol
MC3T3-E1 cells purchased from ATCC (Manassas, VA) were reconstituted and grown in a T-75 flask until transfer into T-175 flask. Cells were cultured in alpha minimum Eagles medium (αMEM) supplemented with penicillin/streptomycin (pen/strep) and 1% fetal bovine serum (FBS).