OAC scRNASeq

Please see our related publication, 'Molecular profiling to predict immunochemotherapy outcomes in esophageal adenocarcinoma'

1 Dataset 3 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001009401	This dataset contains single-cell RNA-seq generated from the LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19) and additional donors with Barrett's oesophagus using the 5' Single Cell Gene Expression assay from 10x Genomics. Samples were generated from oesophageal tumours, Barrett's oesophagus, and normal oesophagus and gastric tissues, with the aim of generating a reference atlas for cell types found in normal and disease-associated tissue states in the upper GI tract. This reference atlas was used as the basis for a deconvolution workflow to estimate the cell composition of bulk transcriptomes from these tissues, and to assess cell type-specific expression patterns of potential predictive biomarkers for immunochemotherapy regimens in this setting.	NextSeq 500	59

Publications	Citations
Tumor monocyte content predicts immunochemotherapy outcomes in esophageal adenocarcinoma. Carroll TM, Chadwick JA, Owen RP, White MJ, Kaplinsky J, Peneva I, Frangou A, Xie PF, Chang J, Roth A, Amess B, James SA, Rei M, Fuchs HS, McCann KJ, Omiyale AO, Jacobs BA, Lord SR, Norris-Bulpitt S, Dobbie ST, Griffiths L, Ramirez KA, Ricciardi T, Macri MJ, Ryan A, Venhaus RR, Van den Eynde BJ, Karydis I, Schuster-Böckler B, Middleton MR, Lu X, LUD2015-005 Project Team. Cancer Cell 41: 2023 1222-1241.e7	30
Cell states and neighborhoods in distinct clinical stages of primary and metastatic esophageal adenocarcinoma. Yates J, Mathey-Andrews C, Park J, Garza A, Gagné A, Hoffman S, Bi K, Titchen B, Hennessey C, Remland J, Carnes M, Shannon E, Camp S, Balamurali S, Cavale SK, Li Z, Raghawan AK, Kraft A, Boland G, Aguirre AJ, Sethi NS, Boeva V, Van Allen EM. Cell Rep Med 6: 2025 102188	1
Tumour Single-Cell Bioinformatics: From Immune Profiling to Molecular Dynamics. Li JS, Ji ZZ, Zhang AQ, Ng CS, Qiao G, Zhang D, Li C, Zhang Q, To KF, Tang PM. J Cell Mol Med 29: 2025 e70783	1