GSM2522445: PolyA RNA-seq BmalKO KLA0h; Mus musculus; RNA-Seq
ChIP-Seq: Sequencing libraries were prepared from collected DNA by using NEB next Ultra DNA library prep kit for Illumina. Libraries were PCR-amplified for 12-15 cycles and sequenced on a Hi-Seq 1500 (Illumina) for 51 cycles. RNA-Seq: PolyA-tagged RNA was pulled down with oligo-dT magnetic beads from total RNA.  RNA-seq libraries were multiplexed and prepared according to the manufacturer's protocol (NEB cat#E7530, Ipswich, MA).  Libraries were paired-ended sequenced on a HiSeq 2000 sequencer (Illumina, San Diego, CA) Reads were aligned to mm9 genome using default parameter for RNA-star.  Aligned reads read files were analyzed with HOMER (http://homer.salk.edu/homer/) to calculate RPKM from the gene bodies of RefSeq genes, perform motif analysis in the study. Reads counts were normalized using DESeq2.