2024-09-20
ENA first public
ERC000011
ENA-CHECKLIST
INSERM U1015, Gustave Roussy Cancer Campus, Bâtiment de Médecine Moléculaire
INSDC center name
public
INSDC status
ERS20948741
SRA accession
E-MTAB-14409:Sample 8 - patient 6
Submitter Id
78
year
age
ArrayExpress
broker name
not collected
collection date
human
common name
Protocols: Samples were collected at Gustave Roussy in the routine pathology laboratory. These cohorts were previously reported in two published studies (Marhic et al., Int J Oral Maxillofac Surg, 2021 and Moya-Plana et al., Oral Oncol, 2018). These patients did not receive pre-operative therapy and were thus considered as “treatment-naïve” before the surgery. All patients gave a written informed consent. The Visium Spatial Gene Expression Slide, Visium FFPE Reagent kit, and Visium human transcriptome probe kit (10X Genomics) were used to generate sequencing libraries.  RNA quality was accessed for all samples using the DV200 method. For library construction, 5μm cryosections of 6.5 x 6.5mm, from each FFPE sample, were placed into the four capture areas of the Spatial Transcriptomics slides (10X Genomics). Samples were then deparaffinized, stained, imaged, and decross-linked. Probe hybridization and ligation to RNA were then performed, followed by the single-stranded ligation product release and extension. Libraries were then prepared following the manufacturer's instructions.
description
adult
developmental stage
squamous cell carcinoma, MGC low
disease
not collected
geographic location (country and/or sea)
not applicable
isolate
Homo sapiens
organism
Homo sapiens
organism
oral cavity
organism part
Homo sapiens
scientific_name
female
sex
Sample 8 - patient 6
title