GEO series

Analyzing primary Hodgkin and Reed-Sternberg cells to capture the molecular and cellular pathogenesis of classical Hodgkin lymphoma

GSE40160 Homo sapiens (human) Expression microarray 10 samples Submitted 2012/09/17 Platform GPL570

At a glance

Expression microarray · human · 10 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Topic: Hodgkin lymphomaThis series is part of our curated briefing on it.
Samples: 10 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

The pathogenesis of classical Hodgkin lymphoma (cHL), the most common lymphoma in the young, is still enigmatic, largely because its Hodgkin and Reed-Sternberg (HRS) tumor cells are rare in the involved lymph node and therefore difficult to analyze.

Read the full summary ↓

Here, by overcoming this technical challenge and performing for the first time a genome-wide transcriptional analysis of microdissected HRS cells in comparison to other B-cell lymphomas, cHL lines and normal B-cell subsets, we show that they differ extensively from the usually studied cHL cell lines, that the lost B-cell identity of cHLs is not linked to the acquisition of a plasma cell-like gene expression program, and that Epstein-Barr virus infection of HRS cells has a minor transcriptional influence on the established cHL clone. Moreover, although cHL appears a distinct lymphoma entity overall, HRS cells of its histological subtypes diverged in their similarity to other related lymphomas. Unexpectedly, we identified two molecular subgroups of cHL associated to differential strengths of the transcription factor activity of the NOTCH1, MYC and IRF4 proto-oncogenes. Finally, HRS cells display deregulated expression of several genes potentially highly relevant to lymphoma pathogenesis, including silencing of the apoptosis-inducer BIK and of INPP5D, an inhibitor of the PI3K-driven oncogenic pathway.

This dataset

Open GSE40160 in finder → Find more human microarray datasets → Hodgkin lymphoma landscape →

Download · which file do I need?

Direct links to NCBI, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE40160_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

What the files usually look like: For arrays the series matrix is normally the normalised expression table you want; the raw array files (CEL and similar) are in the RAW.tar.

Also filed as BioProject PRJNA172980. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 22955914) ↗

Samples in this study

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+ 10 more — browse all 10 samples with per-sample file links →

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GSE301492 Transcriptome sequencing of Hodgkin lymphoma Hodgkin and Reed-Sternberg cells reveals escape from NK cell recognition and an unfolded protein response 41 samples same disease briefing · shares reed-sternberg, lymphoma, hodgkin
GSE290026 scRNA and TCR-Seq of peripheral blood mononuclear cells (PBMC) from r/r classical Hodgkin Lymphoma patients under anti-PD1 therapy. 23 samples same disease briefing · shares classical, lymphoma, hodgkin
GSE17920 Expression data of diagnostic biopsy samples from Hodgkin lymphoma patients 130 samples same disease briefing · shares lymphoma, hodgkin
GSE305165 Redefining the Spectrum of EBV-Positive Diffuse Large B-Cell Lymphoma and EBV-Positive Classic Hodgkin Lymphoma 47 samples same disease briefing · shares lymphoma, hodgkin
GSE288623 Transcriptional profiles of the Hodgkin lymphoma tumor-associated macrophage in vitro models 24 samples same disease briefing · shares lymphoma, hodgkin
GSE289903 Gene expression profiling of HIV and EBV-associated classic Hodgkin lymphomas from Malawi 19 samples same disease briefing · shares lymphoma, hodgkin

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