Comment[GEAAccession]	E-GEAD-619
MAGE-TAB Version	1.1
Investigation Title	Elucidation of genetic alterations in colorectal carcinogenesis and establishment of clinical significance of interstitial
Experiment Description	Recently, single cell RNA sequencing has been used to analyze cell-cell interactions between colon cancer cells and stromal cells. However, the important cancer microenvironment during early cancer development from adenomas, especially the mechanism of immune tolerance acquisition, is unclear. In this study, we investigated immune tolerance and the formation of the tumor microenvironment at the adenoma-cancer interface by integrating single-cell and spatial transcriptome analyses obtained from public databases. By integrating scRNA-seq of colorectal cancer and spatial transcriptome analysis in carcinoma in adenoma tissues, we investigated immune tolerance and tumor microenvironment formation at the adenoma-tumor interface, 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	disease_stage	isolate
Experimental Factor Type	disease_stage	isolate
Person Last Name	Mimori	Hashimoto	Ozato	Sequence
Person First Name	Koshi	Masahiro	Yuki	Kashiwa
Person Affiliation	Department of Surgery, Kyushu University Beppu Hospital			
Person Roles	submitter	submitter	submitter	submitter
Public Release Date	2024-04-18
PubMed ID	38614865
Protocol Name	P-GEAD-1844	P-GEAD-1845	P-GEAD-1846	P-GEAD-1847	P-GEAD-1848
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	Specimen collection_After consulting with the pathologist, the excess specimens were immediately placed on OCT and frozen in liquid nitrogen. Specimens were then stored at -80?C until use. Tissue processing and reverse transcription: Specimens were cut according to the capture area and sectioned into 10-um sections using a cryostat. The specimens were placed on Visium Spatial slides and stored at -80 ?C until use. Tissues were permeabilized with permeabilization enzyme (10x Genomics: 2000214) for 50 min, washed with 0.1 x SSC buffer (Sigma-Aldrich), and imaged. All steps were performed according to the manufacturer's protocol (CG000240 Rev D, CG000160 Rev A).	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).	Sequenced reads were mapped to genome assembly by GRCh38: GCF_000001405.39, using spaceranger v1.2.1(10x Genomics). Slide information; 1_A_kyudai_Beppu_RSK_210624:slide=V10L27-299,area=A1, 2_C_cancer_20210520_upper:slide=V10L27-299,area=C1,
SDRF File	E-GEAD-619.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
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-DS000637-002.
Comment[BioProject]	PRJDB16055
Comment[Last Update Date]	2024-04-18