title: GSM1545046: Kdm5b_KD_ H3K4me3; Mus musculus; ChIP-Seq
library_construction_protocol: 3 million cells crosslinked in 1% formaldehyde were lysed with Farnham and RIPA cold lysis buffers. Following collection, the crude nuclear preparation was processed in a Bioruptor at the high setting for a total of 30 minutes, in cycles of 30 seconds on/30 seconds off. The chromatin was collected by centrifugation and incubated with 5 µg of H3K4me3 antibody overnight. The immunoprecipitated samples were end-filled using a combination of  T4 DNA polymerase and T4  polynucleotide kinase , 3’ -terminal-A extended with Klenow 5'-3' exo minus, and ligated to pre-annealed TruSeq indexed Illumina adapters. Libraries were amplified using Illumina primers and gel extracted for size selection and primer-dimer removal.  Before sequencing, libraries were tested using the BioAnalyzer to test quality in terms of size and primer-dimer depletion.