Comment[GEAAccession]	E-GEAD-415
MAGE-TAB Version	1.1
Investigation Title	Hi-C 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 three-dimensional genome structure by Hi-C 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-743	P-GEAD-744	P-GEAD-745	P-GEAD-746	P-GEAD-747	P-GEAD-748
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).	Nuclei were extracted from one million cells from organoids crosslinked with 2% formaldehyde for 10 minutes at room temperature and quenched using stop solution.	Library was prepared using Arima Hi-C kit (Arima Genomics) according to the manufacturer's instructions.	Library was sequenced by NovaSeq6000 (Illumina) with paired-end 150 bp reads.	dummy	Data processing was performed using juicer pipeline.
SDRF File	E-GEAD-415.sdrf.txt
Comment[Number of channel]	single-channel
Comment[Array Design REF]	A-GEAD-11
Comment[AEExperimentType]	comparative genomic hybridization 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:JGAS000262
Comment[Last Update Date]	2022-06-10