title: Illumina HiSeq 2500 sequencing; ChIP-seq of H3K4me1, me2 and me3 on mouse salivary gland cancer cells cultured in either adherent or non-adherent conditions
design: ChIP-seq of H3K4me1, me2 and me3 on mouse salivary gland cancer cells cultured in either adherent or non-adherent conditions
library_construction_protocol: Mouse salivary gland cancer cells were isolated from salivary gland of transgenic mouse that harbor K14-Cre-induced Wnt/β-catenin gain-of-function and Bmpr1a loss-of-function mutations. For  sphere culture, 24-well cell culture plates were pre-coated with 250 μl poly-hydroxyethyl-methacrylate (PolyHEMA, 12 mg/ml in 95% ethanol, Sigma). Cells were seeded as single cells in sphere culture medium (F12:DMEM 1:1, containing 1X B-27 supplement, 20 ng/ml EGF, 20 ng/ml FGF, 5 μg/ml insulin and 0.5% methylcellulose). For adherent cells, mouse salivary gland tumor cells were cultured in DMEM/F12 medium supplemented with 20% knockout serum replacement (KSR), non-essential minimal amino acids, penicillin/streptomycin solution, L-glutamine and β-mercaptoethanol (Invitrogen). Anti-H3K4me1 (C15410194), -me2 (C15410035) and -me3 (C15410003-50) antibodies were purchased from Diagenode. ChIP-seq was performed according to the protocols provided by Diagenode using the iDeal ChIP-seq kit for histones and the iDeal library preparation kit. For mRNA-seq, mRNA was extracted according to the standard TRIzol protocol (Invitrogen) and subjected to library preparation using the TruSeq stranded mRNA library preparation kit. Anti-H3K4me1 (C15410194), -me2 (C15410035) and -me3 (C15410003-50) antibodies were purchased from Diagenode. ChIP-seq was performed according to the protocols provided by Diagenode using the iDeal ChIP-seq kit for histones and the iDeal library preparation kit. For mRNA-seq, mRNA was extracted according to the standard TRIzol protocol (Invitrogen) and subjected to library preparation using the TruSeq stranded mRNA library preparation kit.
attributes.tag: Experimental Factor: immunoprecipitate
attributes.value: anti-H3K4me3
attributes.tag: Experimental Factor: growth condition
attributes.value: 3D culture