Comment[GEAAccession]	E-GEAD-416
MAGE-TAB Version	1.1
Investigation Title	ATAC-seq analysis of patient-derived normal pancreas and 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 ATAC-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-749	P-GEAD-750	P-GEAD-751	P-GEAD-752	P-GEAD-753	P-GEAD-754
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 gently dissociated into single cell suspension using TrypLE and DNaseI. Nuclei from 50,000 cells were used for ATAC-seq.	Library preparation was performed as previously described by Buenrostro et al. (PMID: 24097267). Breifly, cells were washed and lysed using lysis buffer followed by transposase reaction with Tagment DNA TDE1 Enzyme and Buffer Small Kit (Illumina). Transposed DNA was purified using MinElute PCR Purification kit (Qiagen) and amplified using NEBNext High-Fidelity 2X PCR Master Mix (NEB) followed by size selection with AMPure Beads (Beckman Coulter).	Libraries were sequenced using NextSeq500 (Illumina) with paired-end 50 bp + 25 bp reads.	dummy	Data were processed using PEPATAC (pipeline version:  0.8.4). Breifly, sequence reads were trimmed and aligned to the human genome (hg19) using bowtie2. PCR duplicates were removed using picard MarkDuplicates. Peaks were called using MACS2 with a parameter -q 0.01. Unless otherwise noted, all the analyses were performed only on chromosome 1-22 and X. Reads for each peak were extracted using featureCounts (version 1.5.2). Reads were normalized by log2CPM using edgeR. Bigwig files were generated  by normalizing to RPKM and smoothed by 150 bp sliding windows with 20 bp bin size using bamCoverage. Cell type merged TMM normalized bigwig files were also generated for comparison.
SDRF File	E-GEAD-416.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