Comment[GEAAccession]	E-GEAD-318
MAGE-TAB Version	1.1
Investigation Title	ChIP-seq analysis of the HB1119 cell line
Experiment Description	Chromaitn immunoprecipitation of HB1119 cells was performed using Fractionation-assisted native chromatin immunoprecipitation (fanChIP) method.Specific antibodies for MLL, AF4, TAF1C, and RNAP2 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	2020-10-08
PubMed ID	26593443
Protocol Name	P-GEAD-226	P-GEAD-227	P-GEAD-228	P-GEAD-229	P-GEAD-230
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	HB1119 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 HB1119 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 (Illumina) following the manufacturer's instructions.	The libraries were sequenced for 36 cycles on an Illumina GAIIx sequencer with 36-bp single-end reads.	Sequenced reads were mapped to human genome assembly hg19 using CASAVA 1.8.2. The BAM alignment was converted to the bBigWig coverage files using bam2wig 1.6 and wigToBigWig.
SDRF File	E-GEAD-318.sdrf.txt
Comment[AEExperimentType]	ChIP-seq
Comment[BioProject]	PRJDB3379
Comment[Last Update Date]	2020-10-08