Comment[GEAAccession]	E-GEAD-511
MAGE-TAB Version	1.1
Investigation Title	Spatial transcriptome analysis of human oral cancer
Experiment Description	The purpose of this study is to clarify the factors related to lymph node metastasis of human oral squamous cell carcinoma. These included two primary tumor invasive lesions with lymph node metastasis, one metastatic site, and one primary tumor tissue with the absence of metastases.
Experimental Design	disease state design
Experimental Factor Name	disease
Experimental Factor Type	disease
Person Last Name	Furudate
Person First Name	Ken
Person Affiliation	Department of Oral and Maxillofacial Surgery, Hirosaki University Graduate School of Medicine
Person Roles	submitter
Public Release Date	2022-07-18
Protocol Name	P-GEAD-1248	P-GEAD-1249	P-GEAD-1250	P-GEAD-1251	P-GEAD-1252
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	Four FFPE tissues from two OSCC patients were obtained: two primary sites with lymph node metastasis and one metastatic site, and the primary site without lymph node metastasis.	The quality of FFPE mRNA was evaluated and confirmed that it had a percentage of RNA fragments of 200 bases or more of 50 percent or more.	Quality checks of the FFPE Visium libraries were performed using TapeStation High Sensitivity D5000. Library concentrations were determined using KAPA Library Quantification Kit.	A pool of indexed libraries was sequenced on the NextSeq 550 platform using a high Output Kit v2.5, 75 ? 2 bp-end, covering at least 25,000 reads per spot, according to the manufacturer's instructions.	We filtered out cells with UMI counts lower than 500 in the tumor region. For the peritumor and non-tumor regions, we filtered out cells with UMI counts lower than 100 and excluded rare genes that were only detected in two cells or fewer. Then, each cell was normalized to the total count of all genes, and we equalized the total count of each cell following normalization. Genes with total UMI counts greater than fraction 0.05 in at least one cell were considered highly expressed and excluded from the normalization calculation. We then converted the data matrix into natural logarithms.
SDRF File	E-GEAD-511.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA from single cells
Comment[BioProject]	PRJDB13905
Comment[Last Update Date]	2022-07-18