Comment[GEAAccession]	E-GEAD-414
MAGE-TAB Version	1.1
Investigation Title	RNA sequencing 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 transcriptomic landscapes 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-737	P-GEAD-738	P-GEAD-739	P-GEAD-740	P-GEAD-741	P-GEAD-742
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).	Total RNA from harvested organoids was extracted using RNeasy Mini Kit (Qiagen).	Library was prepared using TruSeq RNA sample Preparation KitV2 (Illumina) or TruSeq Stranded mRNA LT Sample Prep Kit (Illumina).	The libraries were sequenced using HiSeq2500 (Illumina) with paired-end 100 bp reads or NovaSeq6000 (Illumina) with paired-end 150 bp reads.	dummy	Fastq files were preprocessed using fastp (version 0.20.0) and reads were mapped onto hg19 by HISAT2 (version version 2.1.0). Mapped reads were counted using featureCounts (version 1.5.2). Reads were normalized to transcripts per million (TPM).
SDRF File	E-GEAD-414.sdrf.txt
Comment[Number of channel]	single-channel
Comment[Array Design REF]	A-GEAD-11
Comment[AEExperimentType]	transcription profiling 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:JGAS000263
Comment[Last Update Date]	2022-06-10