Genomics

Dataset Information

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Ena-DATASET-BCCA-11-12-2019-18:47:10:446-1110 - samples

ABSTRACT: 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.

PROVIDER: EGAD00001005739 | EGA |

REPOSITORIES: EGA

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Publications

Single-Cell Transcriptome Analysis Reveals Disease-Defining T-cell Subsets in the Tumor Microenvironment of Classic Hodgkin Lymphoma.

Aoki Tomohiro T   Chong Lauren C LC   Takata Katsuyoshi K   Milne Katy K   Hav Monirath M   Colombo Anthony A   Chavez Elizabeth A EA   Nissen Michael M   Wang Xuehai X   Miyata-Takata Tomoko T   Lam Vivian V   Viganò Elena E   Woolcock Bruce W BW   Telenius Adèle A   Li Michael Y MY   Healy Shannon S   Ghesquiere Chanel C   Kos Daniel D   Goodyear Talia T   Veldman Johanna J   Zhang Allen W AW   Kim Jubin J   Saberi Saeed S   Ding Jiarui J   Farinha Pedro P   Weng Andrew P AP   Savage Kerry J KJ   Scott David W DW   Krystal Gerald G   Nelson Brad H BH   Mottok Anja A   Merchant Akil A   Shah Sohrab P SP   Steidl Christian C  

Cancer discovery 20191219 3

Hodgkin lymphoma is characterized by an extensively dominant tumor microenvironment (TME) composed of different types of noncancerous immune cells with rare malignant cells. Characterization of the cellular components and their spatial relationship is crucial to understanding cross-talk and therapeutic targeting in the TME. We performed single-cell RNA sequencing of more than 127,000 cells from 22 Hodgkin lymphoma tissue specimens and 5 reactive lymph nodes, profiling for the first time the phen  ...[more]

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