Quantitative Analysis of hippocampal transcriptomes form wild-type, control and Kdm5c mutant mice (KO and ifKO) through Next Generation Sequencing (RNA-Seq)

ABSTRACT: RNA preparation for sequencing was performed as described in (Fiorenza et al., 2016). Hippocampi derived from three different animals were pooled together for each sample and three independent samples were sequenced. RNA-seq datasets from Kdm5c null mice and control littermates at their home cages (HC) and after 1 h of novelty exploration (NE) were generated by next-generation sequencing (RNA-seq) using Illumina HiSeq 2500 apparatus, where the configuration was in conditional samples paired-end and in conventional samples single-end. RNA-Seq libraries were prepared from total RNA using poly(A) enrichment of the mRNA (mRNA-Seq). The libraries were stranded and multiplexed. Quality control of the raw data was performed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Library sizes can be found in Suppl Table 9 of the manuscript. RNA-Seq libraries were mapped to reference genome (Ensembl GRCm38) using STAR v2.5.0c (Dobin A. et al. 2013), and with corresponding gene model annotation (Mus_musculus.GRCm38.83.gtf). Samtools (v1.3) was used to further process 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) at gene level and count tables were analysed using DeSeq2 (v1.10.0) R-package (Love et al., 2014) and bioconductor v3.2. For consideration of differentially regulated genes between conditions, we used adjusted p-value < 0.1 as indicated in the manuscript.

ORGANISM(S): Mus musculus

PROVIDER: GSE85874 | GEO | 2017/08/18

SECONDARY ACCESSION(S): PRJNA339616

REPOSITORIES: GEO