Comment[GEAAccession]	E-GEAD-759
MAGE-TAB Version	1.1
Investigation Title	Japan COVID-19 Task Force
Experiment Description	RNA and protein expression matrices from 1,405 humans
Experimental Design	population based design
Experimental Factor Name	individual
Experimental Factor Type	individual
Person Last Name	Fukunaga	Wang
Person First Name	Koichi	Qingbo
Person Affiliation	Department of Medicine, Pulmonary Division, Keio University School of Medicine	
Person Roles	submitter	submitter
Public Release Date	2024-06-28
Protocol Name	P-GEAD-2669	P-GEAD-2670	P-GEAD-2671	P-GEAD-2672	P-GEAD-2673	P-GEAD-2674
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	We enrolled participants diagnosed as COVID-19 positive by physicians using the clinical manifestation and PCR test results at one of the >100 the affiliated hospitals participating to Japan COVID-19 Task Force. Any subjects with obtained informed consent were included without further biases. Due to the nature of COVID-19 susceptibility, the number of male participants were larger than that of females (997 / 1,405 = 70.1% male).	Whole blood samples were extracted from each participants. Isolation of RNA from the peripheral blood of the COVID-19 patients was conducted using RNeasy Mini Kit (Qiagen).	nucleic acid library construction protocol: Libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs). For protein we followed the standard protocol in Olink Explore 3072 platform.	nucleic acid sequencing protocol: RNA-seq was performed using the NovaSeq6000 platform (Illumina, CA, USA) with paired end reads (read length of 100 bp), using S4 Reagent kit (200 cycles). Plasma protein expression was measured using the Olink Explore 3072 platform.	dummy	For RNA-seq, we followed the eQTL call pipeline in GTEx. To quantify the mRNA expression, RNA-seq data was first aligned to the hg38 human reference genome using STAR v2.5.3a. Transcript amounts were quantified using RSEM v1.3.0. Since the protein measurement was separated into three batches for logistical reasons, we bridge-normalized the NPX values using the OlinkAnalyze R package64, using 16 intersecting samples as bridging samples. Then inverse-normal transformation was applied to both RNA and protein expression matrix separately.
SDRF File	E-GEAD-759.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 hum0343 and the application ID J-DS000628-003.
Comment[Array Design REF]	A-GEAD-11
Comment[AEExperimentType]	transcription profiling by array
Comment[BioProject]	PRJDB18101
Comment[Related study]	NBDC:hum0343
Comment[Last Update Date]	2024-06-28