Comment[GEAAccession]	E-GEAD-883
MAGE-TAB Version	1.1
Investigation Title	Exploratory study for stratification marker of immune checkpoint inhibitor in patients with advanced or recurrent non-small cell lung cancer
Experiment Description	Gene counts and TPMs calculated from RNAseq gene expression data.
Experimental Design	case control design	disease state design	translational bias design	reference design
Experimental Factor Name	disease
Experimental Factor Type	disease
Person Last Name	Kasajima
Person First Name	Rika
Person Affiliation	Molecular Pathology and Genetics Division, Kanagawa Cancer Center Resarch Institute
Person Roles	submitter
Public Release Date	2024-12-06
Protocol Name	P-GEAD-3405	P-GEAD-3406	P-GEAD-3407	P-GEAD-3408	P-GEAD-3409	P-GEAD-3410
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	formalin-fixed paraffin-embedded (FFPE) specimen of cancer tissue obtained before administering anti-PD-1/PD-L1 antibody treatment	Total RNA was extracted from FFPE tumor tissue of each patient (RNeasy Mini)	nucleic acid library construction protocol: A library for RNA sequencing was prepared using the Smart Seq Stranded kit (Takara-bio).	nucleic acid sequencing protocol: The constructed library was run on the Illumina Novaseq 6000 using the 2x150 bp paired-end protocol to obtain the primary sequence data.	dummy	read count calculated by HTSeq: hg19, TPM caluclated by salmon: GRCh38
SDRF File	E-GEAD-883.sdrf.txt
Comment[Number of channel]	single-channel
Comment[DBCLS]	The Data Access Committee of the Database Center for Life Science (DBCLS) approved that this personal data was made published according to the NBDC Guidelines for Human Data Sharing (https://humandbs.dbcls.jp/en/guidelines/data-sharing-guidelines) as the NBDC Research ID hum0442 and the application ID J-DS001050-002.
Comment[Array Design REF]	A-GEAD-11
Comment[AEExperimentType]	transcription profiling by array
Comment[BioProject]	PRJDB18865
Comment[Related study]	JGA:JGAS000675	NBDC:hum0442
Comment[Last Update Date]	2024-12-06