treatment: NAIVE tissue: Amygdala Sex: Male age: PN12 Pups
Treatment protocol
Immediately following the acute tests of shock with and without the dam, pups were euthanized, as were Controls at the same time
Extracted molecule
total RNA
Extraction protocol
Dissection storage: The infant brains were rapidly frozen (-45oC - total time from decapitation to frozen ~ 2min), amygdala dissected, stored in a (-80oC) freezer RNA processing: Total RNA (Qiagen RNeasy Micro Kit). mRNA was amplified linearly
Label
biotin
Label protocol
Affymetrix protocol
Hybridization protocol
They were hybridized to Affymetrix rat 2.0 gene arrays as specified by Affymetrix (Santa Clara, CA) and NuGEN (Pico System; San Carlos, CA).
Scan protocol
Affymetrix protocol
Description
Gene expression data from the amydala of PN12 pups in the three conditions
Data processing
Expression: Expression values were preprocessed, background-corrected, and normalized by RMA using BRAINARRAY [University of Michigan; CDF: Rat 1.0_Rn_ENTREZG] resulting in approximately 19,000 distinct genes Significant effects: Rank Products, which simulates probabilities based on pairwise comparison differences, was used to assess differential expression in each experimental condition compared to the other. GO: All genes were input with the fold change or pfp values (percentage of false positive predictions) calculated by the Rank Products analysis into ErmineJ using the gene score resampling method Networks: To define networks of related probes we input probes with fold change that exceeded ±1.25, using the direct connection option. We included up- and downregulated genes together
