Cell type-specific transcriptomics of esophageal adenocarcinoma as a scalable alternative for single cell transcriptomics

We developed a protocol for the separation of esophageal carcinoma tissue into leukocytes (using CD45 as a marker), epithelial cells (EpCAM), and fibroblasts (two out of PDGFRA, CD90, anti-fibroblast) by fluorescence-activated cell sorting followed by RNA-sequencing

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

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Dataset ID	Description	Technology	Samples
EGAD00001005508	3' mRNA-Seq obtained from distinct isolated cell types (epithelia cells,immune cells, fibroblasts) of endoscopically obtained esophageal adenocarcinoma tissue as well as normal esophageal mucosa. Libraries for RNA-sequencing were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina according to the low input protocol. Libraries were sequenced on a HiSeq 4000 (Illumina) by 1x 50 bases.	Illumina HiSeq 4000	31

Publications	Citations
Cell type-specific transcriptomics of esophageal adenocarcinoma as a scalable alternative for single cell transcriptomics. Krämer M, Plum PS, Velazquez Camacho O, Folz-Donahue K, Thelen M, Garcia-Marquez I, Wölwer C, Büsker S, Wittig J, Franitza M, Altmüller J, Löser H, Schlößer H, Büttner R, Schröder W, Bruns CJ, Alakus H, Quaas A, Chon SH, Hillmer AM. Mol Oncol 14: 2020 1170-1184	7