Comment[GEAAccession]	E-GEAD-900
MAGE-TAB Version	1.1
Investigation Title	Epigenetic Landscape of ZFP91 in Myeloid Leukemia Cells: A ChIP-seq Study
Experiment Description	ChIP-seq data from ZFP91 knockout (ZFP91-KO) and control K562 cells were used to investigate the role of ZFP91 as a transcription factor in regulating EVI1 expression. The study aimed to characterize: 1) genome-wide ZFP91 binding sites and 2) histone modification changes induced by ZFP91 knockout. The data reveal that the EVI1 promoter region is one of the major binding sites for ZFP91, and that active histone modification (H3K4me3 and H3K27ac) at the EVI1 promoter is significantly reduced in ZFP91 knockout cells. These findings provide new insights into the molecular mechanisms underlying EVI1 regulation and suggest a potential role of ZFP91 as an upstream activator of EVI1, which is critical in hematopoietic malignancies, such as acute myeloid leukemia (AML).
Experimental Design	genetic modification design	all pairs	replicate design
Experimental Factor Name	genetic_modification	antibody
Experimental Factor Type	genetic_modification	antibody
Person Last Name	Hayashida	Masamoto	Kurokawa
Person First Name	Hiroki	Yosuke	Mineo
Person Affiliation	The University of Tokyo		
Person Roles	submitter	submitter	submitter
Public Release Date	2026-04-27
PubMed ID	42034869
Protocol Name	P-GEAD-3513	P-GEAD-3514	P-GEAD-3515	P-GEAD-3516	P-GEAD-3517	P-GEAD-3518	P-GEAD-3519
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol	growth protocol	high throughput sequence alignment protocol
Protocol Description	Approximately 20 million cells suspended in medium were fixed by 1% methanol-free formaldehyde for 10 minutes at room temperature, and neutralized with 200mM glycine for five minutes.	Cells were treated in lysis buffer on ice and then incubated with micrococcal nuclease for 20 minutes at 37 degrees celsius. The digestion was stopped with EDTA, and the cells are incubated with a buffer containing detergent and protease inhibitors on ice. After centrifugation, the chromatin was fragmented by sonication, and the supernatant was collected for ChIP and input samples. The following antibodies were cross-linked to Dynabeads Protein G (Invitrogen #10004D) by overnight rotation at 4 degrees celsius and then incubated with the samples overnight at 4 degrees celsius: anti-ZFP91 rabbit polyclonal antibody (Bethyl Laboratories #A303-245A), anti-histone H3 (tri-methyl K4) rabbit monoclonal antibody (Cell Signaling Technology #9751), anti-histone H3 (acetyl K27) rabbit polyclonal antibody (abcaz #ab4729), and normal rabbit IgG (Cell Signaling Technology #2729). The samples were washed with RIPA wash buffer and then incubated with an elution buffer containing 10 mM EDTA with 1% SDS for 20 minutes at 65 degrees celsius. After centrifugation, the supernatant was incubated at 65 degrees celsius for 6 hours to reverse the cross-linking. The samples were then treated with RNaseA for 2 hour at 37 degrees celsius, followed by proteinase K for 2 hours at 50 degrees celsius. DNA was extracted using NucleoSpin Gel and PCR clean-up (Takara Bio #740609).	Each transposed sample was amplified by PCR using NEBNext Ultra II Q5 (New England Biolabs #M0544) and primers with uniquely attached index sequences.	Sequencing  was performed on Illumina NextSeq 2000 sequencing with 2x36 bp read length, generating 30-40 million paired-end reads per sample.	Peak calling was performed using the MACS3 v3.0.1 callpeak command with the options with the options -f BAMPE -c $input -g hs -B -q 0.01, followed by the MACS3 bdgcmp command with the -m FE option (fold enrichment).	Cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL penicillin and 100 microgram/mL streptomycin in a 5% CO2 incubator at 37 degrees celsius.	Reads were alligned to the human genome hg38 using Bowtie2 v2.5.2 with the default options. Concordantly and uniquely mapped reads were retained using SAMtools v1.20 view command with the options -f 0x2 -q 20. Duplicated reads were removed using Picard v3.2.0 MarkDuplicates.
SDRF File	E-GEAD-900.sdrf.txt
Comment[AEExperimentType]	ChIP-seq
Comment[BioProject]	PRJDB19903
Comment[Last Update Date]	2026-04-27