GEO series

Recruitment of plasma cells from follicular and extrafollicular immune reactions to the bone marrow II

GSE253857 Homo sapiens (human) Single-cell RNA-seq 60 samples Submitted 2024/04/16 Platform GPL30173

At a glance

Single-cell RNA-seq · human · 60 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Homo sapiens (human)
Samples: 60 samples: 15 conditions, mostly in duplicateGroups are read from the sample names, not from the paper. Check the list below.
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.
Paper: Recruitment of plasma cells from IL-21-dependent and IL-21-independent immune reactions to the bone marrowNature communications · 2024

Summary (written by the submitters)

Bone marrow plasma cells (BMPC) are the correlate of humoral immunity, consistently releasing antibodies into the bloodstream. It remains unclear if BMPC reflect different activation environments or maturation of their precursors. Here we define human BMPC heterogeneity and track the recruitment of antibody-secreting cells (ASC) from SARS-CoV-2 vaccine immune reactions to the bone marrow (BM).

Read the full summary ↓

Trajectories based on single-cell transcriptomes and repertoires of peripheral and BM ASC reveal sequential colonisation of BMPC compartments. In activated B cells, IL-21 suppresses CD19 expression, indicating that CD19low-BMPC are derived from follicular, while CD19high-BMPC originate from extrafollicular immune reactions. In primary immune reactions, both CD19low- and CD19high-BMPC compartments are populated. In secondary immune reactions, most BMPC are recruited to CD19high-BMPC compartments, reflecting their origin from extrafollicular reactivations of memory B cells. A pattern also observed in vaccinated-convalescent individuals and upon diphtheria/tetanus/pertussis recall-vaccination. Thus, BMPC diversity reflects the evolution of a given humoral immune response.

Published in

Recruitment of plasma cells from IL-21-dependent and IL-21-independent immune reactions to the bone marrow

Ferreira-Gomes M, Chen Y, Durek P et al. · Nature communications 2024 · PMID 38755157 · doi:10.1038/s41467-024-48570-0

This dataset

Open GSE253857 in finder → Find more human RNA-seq datasets →

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 GSE253857_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1067578 and SRA study SRP485204. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38755157) ↗

Study design

15 conditions, mostly in duplicate

GEX-Seq, BM PC and Bmem, dono ×5 CITE-Seq, BM PC and Bmem, dono ×5 BCR-Seq, BM PC and Bmem, dono ×5 GEX-Seq, spike-specific B cells, dono ×3 CITE-Seq, spike-specific B cells, dono ×3 BCR-Seq, spike-specific B cells, dono ×3 GEX-Seq, BM PC, dono ×2 CITE-Seq, BM PC, dono ×2 +25 more

Supports a between-group comparison across 42 samples.

How we read this: 15 replicated groups read from 60 sample titles; they account for 42 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM8028802 GEX-Seq, BM PC, donor 1681 GEX-Seq, BM PC, dono
GSM8028803 CITE-Seq, BM PC, donor 1681 CITE-Seq, BM PC, dono
GSM8028804 BCR-Seq, BM PC, donor 1681 BCR-Seq, BM PC, dono
GSM8028805 GEX-Seq, BM Bmem, donor 1681 GEX-Seq, BM Bmem, dono
GSM8028806 CITE-Seq, BM Bmem, donor 1681 CITE-Seq, BM Bmem, dono
GSM8028807 BCR-Seq, BM Bmem, donor 1681 BCR-Seq, BM Bmem, dono
GSM8028808 GEX-Seq, blood Bmem, donor 1681 GEX-Seq, blood Bmem, do…
GSM8028809 CITE-Seq, blood Bmem, donor 1681 CITE-Seq, blood Bmem, d…
GSM8028810 BCR-Seq, blood Bmem, donor 1681 BCR-Seq, blood Bmem, do…
GSM8028811 GEX-Seq, BM PC, donor 1684 GEX-Seq, BM PC, dono
GSM8028812 CITE-Seq, BM PC, donor 1684 CITE-Seq, BM PC, dono
GSM8028813 BCR-Seq, BM PC, donor 1684 BCR-Seq, BM PC, dono
GSM8028814 GEX-Seq, BM Bmem, donor 1684 GEX-Seq, BM Bmem, dono
GSM8028815 CITE-Seq, BM Bmem, donor 1684 CITE-Seq, BM Bmem, dono
GSM8028816 BCR-Seq, BM Bmem, donor 1684 BCR-Seq, BM Bmem, dono
GSM8028817 GEX-Seq, blood Bmem, donor 1684 GEX-Seq, blood Bmem, do…
GSM8028818 CITE-Seq, blood Bmem, donor 1684 CITE-Seq, blood Bmem, d…
GSM8028819 BCR-Seq, blood Bmem, donor 1684 BCR-Seq, blood Bmem, do…
GSM8028820 GEX-Seq, spike-specific B cells, donor 546, 547 and 548
GSM8028821 CITE-Seq, spike-specific B cells, donor 546, 547 and 548
GSM8028822 BCR-Seq, spike-specific B cells, donor 546, 547 and 548
GSM8028823 GEX-Seq, spike-specific B cells, donor 553 GEX-Seq, spike-specific…
GSM8028824 CITE-Seq, spike-specific B cells, donor 553 CITE-Seq, spike-specifi…
GSM8028825 BCR-Seq, spike-specific B cells, donor 553 BCR-Seq, spike-specific…
GSM8028826 GEX-Seq, BM PC and Bmem, donor 553 GEX-Seq, BM PC and Bmem…
GSM8028827 CITE-Seq, BM PC and Bmem, donor 553 CITE-Seq, BM PC and Bme…
GSM8028828 BCR-Seq, BM PC and Bmem, donor 553 BCR-Seq, BM PC and Bmem…
GSM8028829 GEX-Seq, spike-specific B cells, donor 555 and 556
GSM8028830 CITE-Seq, spike-specific B cells, donor 555 and 556
GSM8028831 BCR-Seq, spike-specific B cells, donor 555 and 556
GSM8028832 GEX-Seq, tetanus-specific B cells, donor 555 and 556
GSM8028833 CITE-Seq, tetanus-specific B cells, donor 555 and 556
GSM8028834 BCR-Seq, tetanus-specific B cells, donor 555 and 556
GSM8028835 GEX-Seq, BM PC and Bmem, donor 555 GEX-Seq, BM PC and Bmem…
GSM8028836 CITE-Seq, BM PC and Bmem, donor 555 CITE-Seq, BM PC and Bme…
GSM8028837 BCR-Seq, BM PC and Bmem, donor 555 BCR-Seq, BM PC and Bmem…
GSM8028838 GEX-Seq, BM PC and Bmem, donor 556, blood Bmem, donor 555
GSM8028839 CITE-Seq, BM PC and Bmem, donor 556, blood Bmem, donor 555
GSM8028840 BCR-Seq, BM PC and Bmem, donor 556, blood Bmem, donor 555
GSM8028841 GEX-Seq, spike-specific B cells, donor 558 GEX-Seq, spike-specific…

+ 20 more — browse all 60 samples with per-sample file links →

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GSE290351 IRF4 promotes immune-evasion and shapes the Tumor Microenvironment in Follicular Lymphoma 42 samples shares follicular
GSE313660 Single-cell analysis of follicular fluid reveals dysregulation of ovulatory immune function in Polycystic Ovary Syndrome patients undergoing ovarian stimulation 16 samples shares follicular
GSE318717 Single-cell sequencing reveals dynamic immune features of paraneoplastic pemphigus in a patient with follicular lymphoma 10 samples shares follicular
GSE298908 Positionally distinct interferon-stimulated dermal immune-acting fibroblasts promote neutrophil recruitment in Sweet's syndrome [RNA-seq] 113 samples shares recruitment

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.