GEO series

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

GSE252959 Homo sapiens (human) Single-cell RNA-seq 152 samples Submitted 2024/04/16 Platform GPL30173

At a glance

Single-cell RNA-seq · human · 152 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: 152 samples: 144 distinct titles, 4 of them repeatedGroups 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 GSE252959 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 GSE252959_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 PRJNA1063318 and SRA study SRP482991. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38755157) ↗

Study design

144 distinct titles, 4 of them repeated

GEX-Seq, BNT/BNT/BNT d7, dono ×3 CITE-Seq, BNT/BNT/BNT d7, dono ×3 BCR-Seq, BNT/BNT/BNT d7, dono ×3 TCR-Seq, BNT/BNT/BNT d7, dono ×3

How we read this: Read from 152 sample titles: 144 distinct titles with little repetition. 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

GSM8010964 GEX-Seq, BNT d14, donor 11, 12, 14 and 15
GSM8010965 CITE-Seq, BNT d14, donor 11, 12, 14 and 15
GSM8010966 BCR-Seq, BNT d14, donor 11, 12, 14 and 15
GSM8010967 TCR-Seq, BNT d14, donor 11, 12, 14 and 15
GSM8010968 GEX-Seq, BNT d14, donor 13, 16 and 17
GSM8010969 CITE-Seq, BNT d14, donor 13, 16 and 17
GSM8010970 BCR-Seq, BNT d14, donor 13, 16 and 17
GSM8010971 TCR-Seq, BNT d14, donor 13, 16 and 17
GSM8010972 GEX-Seq, BNT/BNT d7, donor 12, 13, 15 and 16
GSM8010973 CITE-Seq, BNT/BNT d7, donor 12, 13, 15 and 16
GSM8010974 BCR-Seq, BNT/BNT d7, donor 12, 13, 15 and 16
GSM8010975 TCR-Seq, BNT/BNT d7, donor 12, 13, 15 and 16
GSM8010976 GEX-Seq, BNT d7, donor 11, 12 and 13
GSM8010977 CITE-Seq, BNT d7, donor 11, 12 and 13
GSM8010978 BCR-Seq, BNT d7, donor 11, 12 and 13
GSM8010979 TCR-Seq, BNT d7, donor 11, 12 and 13
GSM8010980 GEX-Seq, BNT d7, donor 14, 15, 16 and 17
GSM8010981 CITE-Seq, BNT d7, donor 14, 15, 16 and 17
GSM8010982 BCR-Seq, BNT d7, donor 14, 15, 16 and 17
GSM8010983 TCR-Seq, BNT d7, donor 14, 15, 16 and 17
GSM8010984 GEX-Seq, BNT d14, donor 21, 22, 23 and 24
GSM8010985 CITE-Seq, BNT d14, donor 21, 22, 23 and 24
GSM8010986 BCR-Seq, BNT d14, donor 21, 22, 23 and 24
GSM8010987 TCR-Seq, BNT d14, donor 21, 22, 23 and 24
GSM8010988 GEX-Seq, BNT d14, donor 25, 26, 27 and 28
GSM8010989 CITE-Seq, BNT d14, donor 25, 26, 27 and 28
GSM8010990 BCR-Seq, BNT d14, donor 25, 26, 27 and 28
GSM8010991 TCR-Seq, BNT d14, donor 25, 26, 27 and 28
GSM8010992 GEX-Seq, BNT/BNT d7, donor 21, 22, 23 and 24
GSM8010993 CITE-Seq, BNT/BNT d7, donor 21, 22, 23 and 24
GSM8010994 BCR-Seq, BNT/BNT d7, donor 21, 22, 23 and 24
GSM8010995 TCR-Seq, BNT/BNT d7, donor 21, 22, 23 and 24
GSM8010996 GEX-Seq, BNT/BNT d7, donor 25, 26, 27 and 28
GSM8010997 CITE-Seq, BNT/BNT d7, donor 25, 26, 27 and 28
GSM8010998 BCR-Seq, BNT/BNT d7, donor 25, 26, 27 and 28
GSM8010999 TCR-Seq, BNT/BNT d7, donor 25, 26, 27 and 28
GSM8011000 GEX-Seq, BNT d7, donor 21, 22, 23 and 24
GSM8011001 CITE-Seq, BNT d7, donor 21, 22, 23 and 24
GSM8011002 BCR-Seq, BNT d7, donor 21, 22, 23 and 24
GSM8011003 TCR-Seq, BNT d7, donor 21, 22, 23 and 24

+ 112 more — browse all 152 samples with per-sample file links →

Datasets on a similar topic

GSE253862 Recruitment of plasma cells from follicular and extrafollicular immune reactions to the bone marrow 212 samples shares extrafollicular, recruitment, follicular, reactions, plasma, marrow, bone
GSE253857 Recruitment of plasma cells from follicular and extrafollicular immune reactions to the bone marrow II 60 samples shares extrafollicular, recruitment, follicular, reactions, plasma, marrow, bone
GSE271618 Glioblastoma induces the recruitment and differentiation of hybrid neutrophils from skull bone marrow 2 samples shares recruitment, marrow, bone
GSE299256 Positionally distinct interferon-stimulated dermal immune-acting fibroblasts promote neutrophil recruitment in Sweet's syndrome. 116 samples shares recruitment
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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