GEO series

Transcriptome analysis of in vitro generated plasmablasts dervied from Waldenström macroglobulinemia (WM) or heathly control B-cells

GSE139671 Homo sapiens (human) RNA-seq (gene expression) 14 samples Submitted 2020/05/13 Platform GPL18573

At a glance

RNA-seq (gene expression) · human · 14 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Topic: Waldenström macroglobulinaemiaThis series is part of our curated briefing on it.
Samples: 14 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.

Summary (written by the submitters)

The ability to model WM B-cell differentiation using an in vitro system was validated in comparison to healthy cells. The stimuli used initially were CD40L and F(ab’)2 anti-IgG/M, a combination which mimics T-cell dependent activation. Using these conditions, WM B-cells generated mature plasma cells that closely resemble those from healthy controls.

Read the full summary ↓

Since WM cells harbour the characteristic gain-of-function MYD88L265P mutation, it was also of interest to determine the impact of TLR signals on the differentiation process. In contrast to the expectation of enhanced survival, WM cells exhibited a profoundly deleterious response to R848 + F(ab’)2 anti-IgG/M stimulation, with a sharp decline in population from the initiation of culture and a failure to generate plasma cells. RNA sequencing was performed on material harvested from differentiating cells at day 6 of culture within the in vitro system to assess the underlying gene expression changes that accompanied the two types of stimulation. The samples consisted of 3 healthy controls with matched samples for both CD40L and R848 stimulation and a total of 6 WM samples. Examination of the transcriptomes revealed that WM plasmablasts exhibit elevated expression levels of genes associated with TLR and NF-κB signaling, but reduced levels of genes associated with plasma cell re-programming. This is particularly pronounced in cells treated with the TLR7 agonist R848, suggesting an uncoupling of TLR signaling from plasma cell differentiation in WM.

This dataset

Open GSE139671 in finder → Find more human RNA-seq datasets → Waldenström macroglobulinaemia landscape →

Download · which file do I need?

Direct links to NCBI and ENA, 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, or the whole study as GSE139671_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA586850 and SRA study SRP227819. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 32574366) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 14 more — browse all 14 samples with per-sample file links →

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