Comment[GEAAccession]	E-GEAD-637
MAGE-TAB Version	1.1
Investigation Title	AR binding ChIP in HEC50B cells
Experiment Description	Flag-tagged androgen receptor was overexpressed in HEC50B cells. After DHT treatment, Chromatin was immunoprecipitated by anti-FLAG antibody. Precipitated DNA was analyzed by NGS.
Experimental Design	species design	stimulus or stress design	binding site identification design
Experimental Factor Name	Dose+transfection
Experimental Factor Type	Dose+transfection
Person Last Name	Kohno
Person First Name	Susumu
Person Affiliation	Division of Oncology and Molecular Biology, Cancer Research Institiute, Kanazawa University
Person Roles	submitter
Public Release Date	2024-05-07
Protocol Name	P-GEAD-1942	P-GEAD-1943	P-GEAD-1944	P-GEAD-1945	P-GEAD-1946
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	Cells were harvested with NP40 buffer after washing cells with PBS. Cells were centrifuged and resuspended with SDS lysis buffer. The resuspended nuclear pellet was sonicated and centrifuged to remove debris. The supernatant was diluted with ChIP dilution buffer.	After pulldown with magnetic beads and washing step, beads were incubated with elution buffer overnight at 55 degrees. After elution, beads were treated with RNase and proteinase-K. DNA was purified by QIA Quick PCRPpurification Kit.	Sequencing libraries were prepared from the ChIP and Input DNAs using SMARTer ThruPLEX Tag-seq Kit (Clontech) according to the manufacturers protocol. Mononucleosomal DNA fragments of about 170 bp in length, for which the concentration can be determined using the Agilent Bioanalyzer. Real-time PCR-based approaches quantify the library molecules that carry the Illumina adapter sequences on both ends and, therefore, reflect the quantity of the clustering competent library molecules.	Single-read sequencing (150bp) were performed on the Illumina Hi-seq sequencer. Trimming adaptor sequence and 7-17bp of 5 prime end of reads after removing duplicate reads were conducted by using the Seqkit.	Trimmed reads were mapped to the mm10 reference sequence using Burrows-Wheeler Aligner, and duplicate reads were removed with Picard. Peak calling was performed using PePr, MACS2 and epic2 with default parameters respectively. Peak annotation were conducted by HOMER with default settings.
SDRF File	E-GEAD-637.sdrf.txt
Comment[AEExperimentType]	ChIP-seq
Comment[BioProject]	PRJDB16447
Comment[Last Update Date]	2024-05-07