title: GSM2108037: AML_MLLAF9_4.2_RNA_PE; Homo sapiens; RNA-Seq
library_construction_protocol: Chromatin from cell lines was harvested and ChIPs were performed as described (Mandoli A, GDATA, 2014). Total RNA was extracted with TRIzol (Invitrogen) or RNAsol (GenDepot), treated with DNase on column (Qiagen) and analyzed by strand specific sequencing. ChIP-seq libraries were prepared from precipitated DNA of 5 million cells (5-8 pooled biological replicas) for MLL, AF9, AF4, and RUNX1, or from 1 million cells for the histone tail modifications. End repair was performed using Klenow and T4 PNK. A 3’ protruding A base was generated using Taq polymerase and adaptors were ligated. The DNA was loaded on E-gel and a band corresponding to ~300 bp (ChIP fragment + adaptors) was excised. The DNA was isolated, amplified by PCR and used for cluster generation and sequencing on the Genome Analyzer (Illumina) or HiSeq 2000 (Illumina). For RNA-seq 250 ng of RNA was used for ribosomal RNA depletion with RiboZero (Illumina) and subsequent strand specific (USER) library preparation. 4C-seq libraries were prepared as previously described (Van de Werken, Nat. Meth., 2012)