Comment[GEAAccession]	E-GEAD-403
MAGE-TAB Version	1.1
Investigation Title	Drop-Seq analysis of hemocytes of kuruma shrimp
Experiment Description	Single cell analysis of hemocytes of Marsupenaeus japonicus for clustering cell types.
Experimental Design	cell type comparison design
Experimental Factor Name	biological_replicate
Experimental Factor Type	biological_replicate
Person Last Name	Koiwai
Person First Name	Keiichiro
Person Affiliation	Tokyo University of Agriculture and Technology
Person Roles	submitter
Public Release Date	2021-02-03
Protocol Name	P-GEAD-680	P-GEAD-681	P-GEAD-682	P-GEAD-683	P-GEAD-684	P-GEAD-685
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	high throughput sequence alignment protocol	normalization data transformation protocol
Protocol Description	Hemolymph was collected using anti-coagulant solution, then hemoytes were collected by centrifugation 800g 10min.	Single cell and mRNA hybridyzation beads containing microdroplets were constructed by microfluidic device. Cells were lysis by lysis solution in microdroplets, then mRNA were captured by hybridyzation beads.	Followed Drop-seq procedure.	Constructed libraries were read by Illumina Nextseq with basecolling option --minimum-trimmed-read-length 20 and --mask-short-adapter-reads 1.	Cell and molecular barcords tagging and filtering polyA tail were conducted by Drop-seq tools-2.3.0, then reads were aligned against De novo assembled kuruma shrimp hemocyte mRNA sequences by Bowtie2 v. 2.4.1.	Aligned reads were imported as digital expression by Seurat v. 3.1. Extract single cell data by filtering with nFeature_RNA > 100 & nFeature_RNA < 2500. Data were merged and normalized by SCTransform function with variable.features.n = 3000 in Seurat. Merged and integrated digital expression data of 3 shrimps were stored.
SDRF File	E-GEAD-403.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA from single cells
Comment[BioProject]	PRJDB10658
Comment[Last Update Date]	2021-02-03