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

<b>DESCRIPTION</b><br>qPCR was used to validate the integrity of sequencing libraries of different ChIP-seq samples, as well as validate particular differentially methylated genes<br><br><b>FILES</b><br>Validation of ChIP-seq library enrichment:<br><b>20130426-CA1-1h-K27ac-K79me3-K4me3-H3-lib_qPCR.xlsx</b> – 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.<br><b>20130715-ACCnaiveK76me3K27ac_qPCR.xlsx</b> – 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.<br><b>20131125-CA1-Naive_qPCR.xlsx</b> – 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.<br><b>20150122-CA1-K9ac_qPCR.xlsx</b> – 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.<br><br>Validation of differentially methylated genes:<br><b>20150729-MeDIP-LIB-ACC_qPCR.xlsx</b> – 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 <i>Loxhd1</i>, <i>Vrk1</i>, <i>GAPDH</i>(-) and <i>Cobl</i>.<br><b>20150802-ACC-lib_qPCR.xlsx</b> – 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 <i>Fgfr2</i>, <i>Nova1</i> and <i>Reelin</i>.<br><br><b>DATA GENERATION</b><br>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:<br>Calculation type: Absolute quantification<br>Confidence interval: 90.00%<br>Machine: Roche LightCycler 480<br>Maximum E(Ct): 0.30<br>Minimum Ct: 35.00<br><br>

<b>数据集描述</b><br>本研究采用实时定量聚合酶链式反应（quantitative Polymerase Chain Reaction，qPCR）验证不同染色质免疫共沉淀测序（Chromatin Immunoprecipitation Sequencing，ChIP-seq）样本的测序文库完整性，并对特定差异甲基化基因开展验证。<br><br><b>数据文件</b><br>##### ChIP-seq文库富集验证：<br><b>20130426-CA1-1h-K27ac-K79me3-K4me3-H3-lib_qPCR.xlsx</b> – 该文件包含qPCR数值表格，用于验证来自海马CA1区神经元或非神经元细胞（分别记为+、-）的ChIP-seq文库。此类样本在给予天然状态（N）、情境暴露（Ct）或情境-电击（FC）处理1小时（1h）后取材，分别针对H3K27ac、H3K79me3、H3K4me3或组蛋白H3进行免疫沉淀，靶基因为NeuN、Chd4、GAPDH、InterG及cFOS。<br><b>20130715-ACCnaiveK76me3K27ac_qPCR.xlsx</b> – 该文件包含qPCR数值表格，用于验证来自前扣带回皮质（Anterior Cingulate Cortex，ACC）神经元或非神经元细胞（分别记为+、-）的天然状态（N）样本的ChIP-seq文库，此类样本分别针对H3K79me3或H3K27ac进行免疫沉淀，靶基因为NeuN、Chd4及GAPDH。<br><b>20131125-CA1-Naive_qPCR.xlsx</b> – 该文件包含qPCR数值表格，用于验证来自海马CA1区神经元或非神经元细胞（分别记为+、-）的天然状态（N）样本的ChIP-seq文库，此类样本分别针对H3K27ac、H3K27me3、H3K79me3、H3K4me3、组蛋白H3或H3K4me1进行免疫沉淀，靶基因为TFF1、GAPDH、InterG及NeuN。<br><b>20150122-CA1-K9ac_qPCR.xlsx</b> – 该文件包含qPCR数值表格，用于验证来自前扣带回皮质（ACC）神经元或非神经元细胞（分别记为+、-）的ChIP-seq文库，此类样本在给予天然状态（N）、情境暴露（Ct）或情境-电击（FC）处理1小时（1h）后取材，针对H3K9ac进行免疫沉淀，靶基因为cFosF2R2、cFosF3R3、GAPDH、InterG及NeuN。<br><br>##### 差异甲基化基因验证：<br><b>20150729-MeDIP-LIB-ACC_qPCR.xlsx</b> – 该文件包含qPCR数值表格，对应在给予天然状态（N）、情境暴露（Ct）或情境-电击（CS）处理1小时（1h）后取材的前扣带回皮质（ACC）组织样本，靶基因为<i>Loxhd1</i>、<i>Vrk1</i>、<i>GAPDH</i>（阴性对照）及<i>Cobl</i>。<br><b>20150802-ACC-lib_qPCR.xlsx</b> – 该文件包含qPCR数值表格，对应在给予天然状态（N）、情境暴露（C）或情境-电击（CS）处理1小时（1h）或4周（4w）后取材的前扣带回皮质（ACC）组织样本，靶基因为<i>Fgfr2</i>、<i>Nova1</i>及<i>Reelin</i>。<br><br><b>数据生成流程</b><br>qPCR实验在Roche LightCycler 480实时荧光定量PCR仪上运行，仪器导出循环阈值（Cycle Threshold，Ct）值。将所得结果导入pyQPCR（版本0.10dev）进行分析，以梯度稀释的输入样本作为标准品，采用以下分析参数：<br>计算类型：绝对定量<br>置信区间：90.00%<br>所用仪器：Roche LightCycler 480<br>最大Ct值变化对应扩增效率（Maximum E(Ct)）：0.30<br>最小Ct值：35.00