Comment[GEAAccession]	E-GEAD-865
MAGE-TAB Version	1.1
Investigation Title	Single-cell gene expression profiling of human iPSCs-derived cerebral cortical organoids
Experiment Description	To investigate the relationships between morphological features and cellular composition in cerebral cortical organoids, we classified human iPSC-derived cortical organoids based on their morphology. Subsequently, we analyzed the cellular composition associated with each morphological feature using single-cell gene expression profiling. *** Related raw data are to be made available through the controlled-access database JGA (study accession JGAS000726). ***
Experimental Design	development or differentiation design
Experimental Factor Name	organoid type
Experimental Factor Type	organoid type
Person Last Name	Ebise
Person First Name	Hayao
Person Affiliation	Sumitomo Pharma Co., Ltd.
Person Roles	submitter
Public Release Date	2024-09-20
Protocol Name	P-GEAD-3311	P-GEAD-3312	P-GEAD-3313	P-GEAD-3314	P-GEAD-3315	P-GEAD-3316
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	Organoids were dissociated into single cells with Neuron Dissociation Solutions (FUJIFILM Wako Pure Chemical Corporation). Dissociated cells were re-suspended with HBSS supplemented with 10% (v/v) KSR (Thermofisher Scientific) and 10 micro M Y-27632 (FUJIFILM Wako Pure Chemicals) at the density of 1,000 cells/micro L.	mRNAs were captured by barcoded gel beads in single-cell droplets using Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics) and Chromium Controller (10x Genomics) according to the manufacturer's protocols.	Nucleic acid library construction protocol: Single-cell gene expression libraries were constructed using Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics) according to the manufacturer's protocols.	Nucleic acid sequencing protocol: Sequencing of single-cell gene expression libraries were performed using NoveSeq 6000 sequencer (Illumina) according to the manufacturer's protocols.	dummy	Raw sequence data was transformed to single-cell RNA count data using Cell Ranger 6.1.1 software (10x Genomics) and GRCh38-based 2020-A transcriptome reference package (10x Genomics). Single-cell RNA counts were represented in gene-cell barcode matrices in Market Exchange Format (MEX). Each element of the matrix is the number of RNA molecules associated with a gene (row) and a cell barcode (column).
SDRF File	E-GEAD-865.sdrf.txt
Comment[Number of channel]	single-channel
Comment[Array Design REF]	A-GEAD-11
Comment[AEExperimentType]	transcription profiling by array
Comment[BioProject]	PRJDB18142
Comment[Related study]	JGA:JGAS000726
Comment[Last Update Date]	2024-09-20