Comment[GEAAccession]	E-GEAD-417
MAGE-TAB Version	1.1
Investigation Title	ChIP-seq analysis of patient-derived pancreas neoplasm organoids
Experiment Description	Pancreatic cancers arise from two different precursors; intraductal papillary mucinous neoplasms (IPMN) and pancreatic intraepithelial neoplasm (PanIN), while biological differences in cancers originated from them remain obscure. Here, we analyzed their epigenomic landscape by CTCF ChIP-seq using patient-derived organoids.
Experimental Design	cell type comparison design
Experimental Factor Name	cell_type
Experimental Factor Type	cell_type
Person Last Name	Kato	Tateishi
Person First Name	Hiroyuki	Keisuke
Person Affiliation	Department of Gastroenterology, The University of Tokyo, Graduate School of Medicine	
Person Roles	submitter	submitter
Public Release Date	2021-12-27
Protocol Name	P-GEAD-755	P-GEAD-756	P-GEAD-757	P-GEAD-758	P-GEAD-759	P-GEAD-760
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol	array scanning and feature extraction protocol	normalization data transformation protocol
Protocol Description	Patient-derived pancreas neoplasm organoids were established as described previously (PMID: 25557080).	Harvested organoids were washed, lysed and sonicated for chromatin extraction. CTCF-DNA complexes were isolated with antibody (Cell Signaling Technology, #3418). H3K27Ac-DNA complexes were isolated with antibody (Abcam, ab4729).	Library was prepared using SMARTer ThruPLEX Tag-seq 6S Kit (Takara).	Library was sequenced using NextSeq500 (Illumina) with single-end 75 bp reads.	dummy	Fastq files were mapped onto human genome (hg19) using bowtie (version 1.2.2). Duplicates were removed using picard MarkDuplicates. Peaks against input control were called using MACS2 (version 2.1.2) with a parameter -q 0.01. Reads for each peak were extracted using featureCounts (version 1.5.2). Input counts were extracted from CTCF ChIP counts with negative values being set to zero. These counts were normalized by edgeR giving log2CPM. Fold enrichment signal against input was calculated using bdgcmp command in MACS2 to create bedgraph file followed by conversion into bigwig file using bedGraphToBigwig command. Bigwig file was further adjusted using scaling factor obtained from edgeR TMM normalization.
SDRF File	E-GEAD-417.sdrf.txt
Comment[Number of channel]	single-channel
Comment[Array Design REF]	A-GEAD-11
Comment[AEExperimentType]	ChIP-chip by array
Comment[NBDC]	The Data Access Committee of the National Bioscience Database Center (NBDC) approved that this personal data was made published according to the NBDC Guidelines for Human Data Sharing (https://humandbs.biosciencedbc.jp/en/guidelines/data-sharing-guidelines) as the NBDC Research ID hum0257 and the application ID J-DS000307-005.
Comment[BioProject]	PRJDB11024
Comment[Related study]	NBDC:hum0257	JGA:JGAS000264
Comment[Last Update Date]	2022-06-10