Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [Data Record 2: qPCR validations]

DESCRIPTION
qPCR was used to validate the integrity of sequencing libraries of different ChIP-seq samples, as well as validate particular differentially methylated genes

FILES
Validation of ChIP-seq library enrichment:
20130426-CA1-1h-K27ac-K79me3-K4me3-H3-lib_qPCR.xlsx – this file contains tables with qPCR values from validations of ChIP-seq libraries for samples from CA1 neuronal or non-neuronal cells (+ or -, respectively) taken 1 hour (1h) after naïve (N), context (Ct) or context-shock (FC) and immunoprecipitated for H3K27ac, H3K79me3, H3K4me3 or H3. The target genes were NeuN, Chd4, GAPDH, InterG and cFOS.
20130715-ACCnaiveK76me3K27ac_qPCR.xlsx – this file contains tables with qPCR values from validations of ChIP-seq libraries for naïve (N) samples from ACC neuronal or non-neuronal cells (+ or -, respectively) and immunoprecipitated for H3K79me3 or H3K27ac. The target genes were NeuN, Chd4 and GAPDH.
20131125-CA1-Naive_qPCR.xlsx – this file contains tables with qPCR values from validations of ChIP-seq libraries for naïve (N) samples from CA1 neuronal or non-neuronal cells (+ or -, respectively) and immunoprecipitated for H3K27ac, H3K27me3, H3K79me3, H3K4me3, H3 or H3K4me1. The target genes were TFF1, GAPDH, InterG and NeuN.
20150122-CA1-K9ac_qPCR.xlsx – this file contains tables with qPCR values from validations of ChIP-seq libraries for samples from ACC neuronal or non-neuronal cells (+ or -, respectively) taken 1 hour (1h) after naïve (N), context (Ct) or context-shock (FC) and immunoprecipitated for H3K9ac. The target genes were cFosF2R2, cFosF3R3, GAPDH, InterG and NeuN.

Validation of differentially methylated genes:
20150729-MeDIP-LIB-ACC_qPCR.xlsx – this file contains tables with qPCR values for samples taken from ACC tissue 1 hour (1h) after naïve (N), context (Ct) or context-shock (CS). The target genes were Loxhd1, Vrk1, GAPDH(-) and Cobl.
20150802-ACC-lib_qPCR.xlsx – this file contains tables with qPCR values for samples taken from ACC tissue 1 hour (1h) or 4 weeks (4w) after naïve (N), context (C) or context-shock (CS). The target genes were Fgfr2, Nova1 and Reelin.

DATA GENERATION
qPCR experiments were run on Roche LightCycler 480, and the machine was used to export the Ct values. The resulting output was imported into pyQPCR (version 0.10dev) using dilutions of inputs as standards, along with the following parameters:
Calculation type: Absolute quantification
Confidence interval: 90.00%
Machine: Roche LightCycler 480
Maximum E(Ct): 0.30
Minimum Ct: 35.00