Single-cell RNA sequencing of 22 Hodgkin lymphoma tumors and 5 reactive lymph nodes

Study ID Alternative Stable ID Type
EGAS00001004085 Other

Study Description

Hodgkin lymphoma (HL) is characterized by an extensively dominant tumor microenvironment (TME) composed of different types of non-cancerous immune cells with rare malignant cells. Characterization of the cellular components and their spatial relationship is crucial to understanding crosstalk and therapeutic targeting in the TME. We performed single-cell RNA sequencing of more than 127,000 cells from 22 HL tissue specimens and 5 reactive lymph nodes, profiling for the first time the phenotype of the HL-specific immune microenvironment at single-cell resolution. Library preparation was performed using the 10x Genomics Chromium system, and Illumina sequencing was used to generate 3' gene expression data for every cell. Downstream analysis was performed in R to identify HL-specific microenvironment patterns and identify novel cell populations.

Study Datasets 2 dataset.

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Dataset ID Description Technology Samples
EGAD00001005739 Single-cell gene expression was profiled for 22 Hodgkin lymphoma tumors and 5 reactive lymph nodes (2 replicates were performed for RLN-1). Library preparation was performed with the 10x Chromium platform (3' version 2 assay). Sequencing was performed on an Illumina NextSeq. The BAM files were generated from the raw sequencing data using Cell Ranger (v2.1.0) mkfastq and count commands. Illumina HiSeq 2500 28
EGAD00001006221 This dataset contains merged data from the 22 Hodgkin lymphoma and 5 reactive lymph node samples, including count data and cell cluster assignments. 28

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Publications Citations
Single-Cell Transcriptome Analysis Reveals Disease-Defining T-cell Subsets in the Tumor Microenvironment of Classic Hodgkin Lymphoma.
Cancer Discov 10:2020 406-421