Illumina HiSeq 2000 paired end sequencing; ATAC-seq on endothelial cells from E11.5 mouse hearts
ATAC-seq on endothelial cells from E11.5 mouse hearts
Hearts were harvested in icecold PBS with 0.5 mM EDTA and dissociated as described (Van Handel et al. 2012), using collagenase (10 mg/ml; Worthington) and dispase (10 mg/mL, Invitrogen). Cells were stained for 30 minutes, 4',6-diamidino-2-phenylindole (DAPI, 1:1000) was used to label dead cells. Tie2Cre lineage cells, negative for blood markers CD41, CD45 and Ter119, were sorted on an InfluxTM cell sorter (BD Biosciences) and collected in RNA lysis buffer (Agilent) or TRIzol reagent (Ambion) for RNA extraction, or PBS/5% serum for ATAC-Seq (Buenrostro et al. 2013).   Van Handel B, Montel-Hagen A, Sasidharan R, Nakano H, Ferrari R, Boogerd CJ, Schredelseker J, Wang Y, Hunter S, Org T, et al. 2012. Scl represses cardiomyogenesis in prospective hemogenic endothelium and endocardium. Cell 150: 590605.  Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. 2013. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10: 12138. We performed ATAC-seq according to Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. 2013. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10: 12138.
Experimental Factor: 1
replicate
Experimental Factor: 2014-09-26
date