Comment[GEAAccession]	E-GEAD-344
MAGE-TAB Version	1.1
Investigation Title	Single cell RNA-seq analysis of peripheral blood monocytes in systemic sclerosis.
Experiment Description	To elucidate the subpopulation of monocytes that are related to the pathophysiology of systemic sclerosis, peripheral blood monocytes from 3 systemic sclerosis patients were collected and single cell RNA-seq was performed for 984 cells.
Experimental Design	disease state design
Experimental Factor Name	patient
Experimental Factor Type	patient
Person Last Name	Nagafuchi	Fujio
Person First Name	Yasuo	Keishi
Person Affiliation	Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo	
Person Roles	submitter	submitter
Public Release Date	2020-10-10
Protocol Name	P-GEAD-369	P-GEAD-370	P-GEAD-371	P-GEAD-372	P-GEAD-373	P-GEAD-374
Protocol Type	sample collection protocol	nucleic acid extraction protocol	normalization data transformation protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol	array scanning and feature extraction protocol
Protocol Description	Peripheral blood CD14+CD3-CD19- monocytes were sorted  and suspended in STEM-CELLBANKER GMP grade (ZENOAQ) for storage at -80 degree C. After the samples thawed, they were resuspended in GT-T551 (TaKaRa).	Single cell RNA-seq analysis was performed with an ICELL8 Single-CELL System in accordance with the manufacturers protocol.	The sequencing primer, poly-A, and poly-T were trimmed by Cutadapt and low-quality ends (phred quality score < 25) were also trimmed. After trimming, the read (the length of which was < 50 bases) was also removed. Mapping was performed with STAR with the Ensembl GRCh38 reference sequence.	dummy protocol	dummy protocol	dummy protocol
SDRF File	E-GEAD-344.sdrf.txt
Comment[Number of channel]	single-channel
Comment[Array Design REF]	A-GEAD-11
Comment[AEExperimentType]	transcription profiling by array
Comment[BioProject]	PRJDB9416
Comment[Last Update Date]	2020-10-10