Comment[GEAAccession]	E-GEAD-353
MAGE-TAB Version	1.1
Investigation Title	Deconstructing stem cell populations in intestinal adenoma by single-cell RNA-seq
Experiment Description	To analyze the heterogeneity and population-wide transcriptomic changes among candidate tumor stem cell populations in intestinal adenoma, p57-tdTomato+ cells, Lgr5-EGFP+ cells and whole cell populations from adenoma were subjected to single-cell RNA-seq analysis using CEL-seq2 platform.
Experimental Design	cell component comparison design
Experimental Factor Name	adenoma cell type
Experimental Factor Type	adenoma cell type
Person Last Name	Higa
Person First Name	Tsunaki
Person Affiliation	Department of Molecular and Cellular Biology
Person Roles	submitter
Public Release Date	2024-04-15
Protocol Name	P-GEAD-415	P-GEAD-416	P-GEAD-417	P-GEAD-418	P-GEAD-419
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	Dissociated single crypt cells from small intestine were FACS-isolated to each well of 96-well plates.	Total mRNAs in every single cell were reverse-tanscribed using oligo-dT primers with cell barcodes and unique molecular identifiers (UMIs).	UMI- and cell barcode-added cDNAs from single cells were pooled and amplified by in vitro transcription, followed by PCR amplification (15-20 cycles) to obtain complete single-cell RNA-seq libraries (CEL-seq2 protocol).	The libraries were sequenced using illumina NovaSeq 6000 sequencer at a coverage of 100,000-150,000 reads per cell.	The raw fastq files were demultiplexed, mapped and counted using celseq2 software. The gene-cell matrices were normalized and subjected to PCA/tSNE analyses using standard workflow of R software Seurat.
SDRF File	E-GEAD-353.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA from single cells
Comment[BioProject]	PRJDB9151
Comment[Last Update Date]	2024-04-15