Comment[GEAAccession]	E-GEAD-579
MAGE-TAB Version	1.1
Investigation Title	Integration of spatial and single-cell transcriptomics for clarifying colorectal cancer intratumor heterogeneity
Experiment Description	In various publications, single cell RNA sequencing has been used to analyze intercellular communication between colon cancer cells and stromal cells in colorectal cancer patients with adenocarcinoma sequence background. However, these analyses lacked a spatial perspective. In this study, we combined public single cell and spatial-transcriptome analyses to elucidate cell-to-cell communication in the advanced invasive zone of colorectal cancer cells. This analysis was aimed at identifying the mechanism by which colon cancer cells evade immunity, and thereby searching for new therapeutic target molecules.
Experimental Design	disease state design	observational design	secreted protein identification design	validation by reverse transcription PCR design
Experimental Factor Name	sampling_site
Experimental Factor Type	sampling_site
Person Last Name	Mimori	Ozato	Sequence
Person First Name	Koshi	Yuki	Kashiwa
Person Affiliation	Department of Surgery, Kyushu University Beppu Hospital		
Person Roles	submitter	submitter	submitter
Public Release Date	2022-12-12
Protocol Name	P-GEAD-1637	P-GEAD-1638	P-GEAD-1639	P-GEAD-1640	P-GEAD-1641
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	Once the colon cancer specimen was collected, the researcher worked with the pathologist to determine any excess that would not interfere with the diagnosis. Tissue was cut out with a scalpel (dry ice chilled, sterile) so that the colon cancer tissue would fit into the cliomold. A small amount of OCT (ice-cooled) was placed in the dry ice-cooled clamold and the specimen collected earlier was placed on top of the OCT. The specimens were placed on top of the OCT, and after another OCT (ice-cold) was added to seal in the specimens, the specimens were stored at -80?C until the experiment. The Visium protocol (CG000239_VisiumSpatialGeneExpression_UserGuide_Rev_D.pdf)  was then followed.	Visium Spatial Gene Expression Reagent Kits(10x Genomics)	The sequence library was constructed using the Visium Spatial Gene Expression Reagent Kits(10x Genomics).	Sequencing was performed on the Illumina NovaSeq6000 in paired end mode; Read1:Spatial Barcode, UMI(28 bp), i7 Index:Sample Index(10 bp), i5 Index:Sample Index(10 bp), Read2:Insert(90 bp).	Sequence data was processed by Space Ranger v1.2.1(10x Genomics). Slide information; A1_colorectal_cancer_1:slide=V10Y04-068,area=A1, B1_colorectal_cancer_2:slide=V10Y04-068,area=B1, C1_colorectal_cancer_3:slide=V10Y04-068,area=C1, D1_colorectal_cancer_4:slide=V10Y04-068,area=D1
SDRF File	E-GEAD-579.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA from single cells
Comment[NBDC]	The Data Access Committee of the National Bioscience Database Center (NBDC) approved that this personal data was made published according to the NBDC Guidelines for Human Data Sharing (https://humandbs.biosciencedbc.jp/en/guidelines/data-sharing-guidelines) as the NBDC Research ID hum0356 and the application ID J-DS000637-001.
Comment[BioProject]	PRJDB14904
Comment[Related study]	NBDC:hum0356
Comment[Last Update Date]	2022-12-12