Comment[GEAAccession] E-GEAD-383 MAGE-TAB Version 1.1 Investigation Title ChIP-seq analysis of REH cells Experiment Description Chromatin immunoprecipitation of REH cells was performed using fractionation-assisted native chromatin immunoprecipitation method.Specific antibodies for MLL, ENL, H3K27ac, MOZ, RNA2 non-p, and RNAP2 Ser5-P were used for IP. The ChIPed DNAs were analyzed by deep sequencing along with the input sample. Experimental Design binding site identification design Experimental Factor Name antibody Experimental Factor Type antibody Person Last Name Kanai Yokoyama Person First Name Akinori Akihiko Person Affiliation Tsuruoka Metabolomics Laboratory, National Cancer Center Person Roles submitter submitter Public Release Date 2020-10-10 Protocol Name P-GEAD-575 P-GEAD-576 P-GEAD-577 P-GEAD-578 P-GEAD-579 Protocol Type sample collection protocol nucleic acid extraction protocol nucleic acid library construction protocol nucleic acid sequencing protocol normalization data transformation protocol Protocol Description REH cells were cultured in RPMI 1640 medium supplemented with 10% FBS and PS. Cell culture was performed in 5% CO2 37 degree C.The cells were washed with PBS once and subjected to chromatin preparation. Chromatin fractions from REH cells were prepared using the fanChIP method as previously described (Okuda et al., 2014 Nucleic Acids Res 42, 4241-56). Cells were suspended in CSK buffer and centrifuged to remove the soluble fraction. The pellet was resuspended in MNase buffer and treated with MNase at 37 degree C for 3-6 min to obtain oligonucloesomes. The MNase reaction was stopped by adding EDTA (pH 8.0) to a final concentration of 20 mM. Lysis buffer (250 mM NaCl, 20 mM sodium phosphate [pH 7.0], 30 mM sodium pyrophosphate, 5 mM EDTA, 10 mM NaF, 0.1% NP-40, 10% glycerol, 1 mM DTT, and EDTA-free protease inhibitor cocktail) was added to increase solubility. The chromatin fraction was cleared by centrifugation and subjected to immunoprecipitation with specific antibodies and magnetic microbeads (Protein-G magnet beads [Invitrogen]). Immunoprecipitates were washed five times with washing buffer (1:1 mixture of lysis buffer and MNase buffer with 20 mM EDTA) and then eluted in elution buffer. The libralies were constructed using a TruSeq ChIP Sample Prep Kit (iIllumina) following the manufacturer's instructions. The libraries were sequenced for 51 cycles on an Illumina HiSeq 2500 sequencer with 51-bp single-end reads. Sequenced reads were mapped to human genome assembly hg19 using BWA 0.7.5. The BAM alignment was converted to the bBigWig coverage files using bam2wig 1.6. and wigToBigWig. SDRF File E-GEAD-383.sdrf.txt Comment[AEExperimentType] ChIP-seq Comment[BioProject] PRJDB10300 Comment[Last Update Date] 2020-10-10