GEO series

Detection of occurrent somatic hypermutation and associated gene expression profile in single B cells

GSE236880 Homo sapiens (human) Single-cell RNA-seq 20 samples Submitted 2024/12/25 Platform GPL20301

At a glance

Single-cell RNA-seq · human · 20 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: 20 samples: 18 distinct titles, 2 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.

Summary (written by the submitters)

This study provided new insights into the molecular mechanisms of SHM. For the first time, SHM was detected at the single-cell level in 58% of FL samples but not in chronic lymphocytic leukemia (CLL) used as control. The occurrence of SHM at the single-cell level was correlated with higher expression of DNA repair pathways and activation-induced cytidine deaminase (AID), as well as the motifs associated with AID.

Read the full summary ↓

FL is an essential in vivo model for studying SHM due to its high rate of ongoing SHM, and the findings of this study contribute to our understanding of the molecular mechanisms involved in human B-cells.

This dataset

Open GSE236880 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 GSE236880_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 PRJNA992565 and SRA study SRP448300. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

18 distinct titles, 2 of them repeated

S8934, scRNA-seq full transcriptome ×2 S8934, scRNA-seq BCR enriched ×2

How we read this: Read from 20 sample titles: 18 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

GSM7578587 lymph node, K1B:S10000-S10971-S12282-S144-S8934, scRNA-seq full transcriptome
GSM7578588 lymph node, K1B:S10000-S10971-S12282-S144-S8934, scRNA-seq BCR enriched
GSM7578589 lymph node, K2B:S11770-S12118-S12500-S13530-S13553 , scRNA-seq full transcriptome
GSM7578590 lymph node, K2B:S11770-S12118-S12500-S13530-S13553, scRNA-seq BCR enriched
GSM7578591 lymph node, K3B:S12390-S12500-S8382-S8934, scRNA-seq full transcriptome
GSM7578592 lymph node, K3B:S12390-S12500-S8382-S8934, scRNA-seq BCR enriched
GSM7578593 lymph node, K4B:S8934, scRNA-seq full transcriptome
GSM7578594 lymph node, K4B:S8934, scRNA-seq BCR enriched
GSM7578595 lymph node, K5B:S8934, scRNA-seq full transcriptome
GSM7578596 lymph node, K5B:S8934, scRNA-seq BCR enriched
GSM7578597 lymph node, K6B:S13530, scRNA-seq full transcriptome
GSM7578598 lymph node, K6B:S13530, scRNA-seq BCR enriched
GSM7578599 lymph node, K7B:S10000, scRNA-seq full transcriptome
GSM7578600 lymph node, K7B:S10000, scRNA-seq BCR enriched
GSM7578601 lymph node, K8B:S13553, scRNA-seq full transcriptome
GSM7578602 lymph node, K8B:S13553, scRNA-seq BCR enriched
GSM7578603 lymph node, Q1:S5714-S7482, scRNA-seq full transcriptome
GSM7578604 lymph node, Q1:S5714-S7482, scRNA-seq BCR enriched
GSM7578605 lymph node, Q2:S356-S4725-S9856, scRNA-seq full transcriptome
GSM7578606 lymph node, Q2:S356-S4725-S9856, scRNA-seq BCR enriched

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GSE287613 p53 safeguards chemical reprogramming of human somatic cells towards pluripotency. 63 samples shares somatic
GSE81547 Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns. 2544 samples shares somatic
GSE294045 Co-mapping Clonal and Transcriptional Heterogeneity in Somatic Evolution via GoT-Multi. 18 samples shares somatic
GSE260944 Mutability and hypermutation antagonize immunoglobulin codon optimality; Analysis of human MLN B cells. 14 samples shares hypermutation
GSE292700 Molecular architecture of the tumor microenvironment caused by BRCA1 and BRCA2 somatic mutations in human lung adenocarcinoma 12 samples shares somatic
GSE268524 A robust circulating microRNA signature for diagnosis and early detection in pancreatobiliary cancer 1403 samples shares detection

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