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Quantitative analysis of chromatin occupancy (ChIP-Seq) from wild-type mice and Kdm5c KO mice in standard conditions (H3K4me3, H3K4me1, and Kdm5C) or upon novelty exposure (H3K4me3), and control mice and Kdm5c ifKO mice in basal state (H3K4me3).

ABSTRACT: Chromatin immunoprecipitation (ChIP) experiments were conducted as previously described (Ito et al, 2013) using anti-H3K4me3 (Millipore, #07-473), anti-H3K4me1 (Abcam, #ab8895), or anti-Kdm5C (Iwase et al., 2016). Hippocampi derived from two different animals were pooled together for each sample and two independent biological replicates per condition were sequenced according to manufacturer instructions in a HiSeq2500 apparatus (Illumina, Inc). Information on library preparation method, size of the libraries, and mapping to reference genome can be found in Supplementary Material accompanying the manuscript. ChIP-seq reads were aligned to the mouse genome (Mus_musculus.GRCm.38.83) using bowtie2 (v2.2.9) (Langmead and Salzberg, 2012) and further processed using samtools (v1.3.1) (Li et al., 2009). Peak calling was performed using MACS2 (v2.1.0) (Zhang et al., 2008) with default parameters except for Kdm5c that were as follows: -q 0.01 --nomodel --extsize 131 --broad --broad-cutoff 0.1. Read counts on aligned bam files were performed using Rsubread (v1.22.3) (Liao et al., 2014). Differential peak methylation analysis for H3K4me3 chromatin mark was performed using DESeq2 (v1.10.0) (Love et al., 2014) of the bioconductor suite (Huber et al., 2015) in the R (v3.3) statistical computing platform. For consideration of differentially methylated regions between conditions, we used adjusted p-value < 0.05 as indicated in the manuscript.

ORGANISM(S): Mus musculus

PROVIDER: GSE85873 | GEO | 2017/08/18

SECONDARY ACCESSION(S): PRJNA339615

REPOSITORIES: GEO

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Project description:Quantitative Analysis of cortical transcriptomes through Next Generation Sequencing (RNA-Seq) from wild-type mice, wild-type mice treated with IL1b (200 ng/mouse, 14h), IL-1R8-/- mice and IL-1R8-/- mice treated with IL1b antagonist Anakinra (25 mg/kg per day for 3 consecutive days, i.p. administration). mRNA profiles of cortical tissue from adult wild-type mice, wild-type mice treated with IL1b (200 ng/kg, 14h), IL-1R8-/- mice (Garlanda et al., 2004), and IL-1R8-/- mice treated with Anakinra (25 mg/kg per day for 3 consecutive days, i.p. administration) were generated by next-generation sequencing (RNA-seq) using Illumina HiSeq 2500 apparatus in paired-end configuration (2x125bp). Each condition was assessed in triplicate (12 mRNA-seq libraries) and, to reduce biological variability, each mRNA library was generated from pooled total RNA isolated from cortical tissue of 3 individual mice. In total, 9 mice per condition were used. Libraries were stranded and multiplexed. To increase sequencing depth, libraries were sequenced in two different lanes. All the libraries were loaded in each of the two lanes. Quality control of the raw data was performed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Libraries were trimmed for adapter removal using Trimmomatic (Bolger et al., 2014) and mapped to reference genome (Ensembl GRCm38) using TopHat2 (Kim et al., 2013) and Bowtie2 (Langmead et al., 2009). Library sizes of primary mapped reads were between 70 and 96 million reads. Samtools was used to manipulate BAM files (Li et al., 2009). For calling of differentially expressed genes (DEG), mapped reads were counted with HTSeq v0.6.1 (Anders et al., 2014) and count tables were analysed using DeSeq2 v1.10.1 R-package (Love et al., 2014) with a design of one factor with four levels (“wild-type”, “wild-type + IL1”, “IL-1R8-/-”, “IL-1R8-/- + Anakinra"), and differences between groups were tested using contrasts for wild-type + IL1b versus wild-type; IL-1R8-/- versus wild-type; IL-1R8-/- + Kineret versus wild-type. For consideration of differentially regulated genes between conditions, we used adjusted p-value < 0.1 or adjusted p-value < 0.05 as indicated in the manuscript.

Dataset Information

Quantitative analysis of chromatin occupancy (ChIP-Seq) from wild-type mice and Kdm5c KO mice in standard conditions (H3K4me3, H3K4me1, and Kdm5C) or upon novelty exposure (H3K4me3), and control mice and Kdm5c ifKO mice in basal state (H3K4me3).

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