Full-length single-cell BCR sequencing paired with RNA sequencing reveals convergent responses to vaccination
Single-cell RNA-seq · human · 16 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Samples
- 16 samples: 4 × PBMC_Bcell vs 4 × PBMCGroups 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
- Full-length single-cell BCR sequencing paired with RNA sequencing reveals convergent responses to pneumococcal vaccinationCommunications biology · 2024
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE266697_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1108286 and SRA study SRP505976. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 2 replicated groups read from 16 sample titles; they account for 8 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.
- GSM8253970 PBMC_Bcell_rep1 PBMC_Bcell
- GSM8253971 PBMC_Bcell_rep2 PBMC_Bcell
- GSM8253972 PBMC_Bcell_rep3 PBMC_Bcell
- GSM8253973 PBMC_Bcell_rep4 PBMC_Bcell
- GSM8253974 PBMC_rep1 PBMC
- GSM8253975 PBMC_rep2 PBMC
- GSM8253976 PBMC_rep3 PBMC
- GSM8253977 PBMC_rep4 PBMC
- GSM8253978 PBMC_Bcell_rep1_BCR
- GSM8253979 PBMC_Bcell_rep2_BCR
- GSM8253980 PBMC_Bcell_rep3_BCR
- GSM8253981 PBMC_Bcell_rep4_BCR
- GSM8253982 PBMC_rep1_BCR
- GSM8253983 PBMC_rep2_BCR
- GSM8253984 PBMC_rep3_BCR
- GSM8253985 PBMC_rep4_BCR
- GSE315534 Single-cell RNA sequencing of primary colorectal cancer, matched adjacent normal tissues, and paired liver metastases 15 samples shares single-cell, paired
- GSE305971 Integrative single-cell analysis reveals malignant archetypes and proliferative hierarchies in multiple myeloma 2105 samples shares single-cell
- GSE328048 Single-cell transcriptome reveals keratinocyte subclusters that contribute to altered differentiation and inflammatory responses in atopic dermatitis 116 samples shares single-cell
- GSE287301 Single-cell RNA-sequencing of HNSCC-infiltrating T cells 48 samples shares single-cell
- GSE269877 Single-cell RNA-sequencing of BCG naïve and recurrent non-muscle invasive bladder cancer reveals a CD6/ALCAM-mediated immune-suppressive pathway 38 samples shares single-cell
- GSE291890 Single-Cell RNA Sequencing Unveils Macrophage Involvement in Aortic Valve Stenosis Progression 33 samples shares single-cell
- GSE243013 A single-cell atlas of immune heterogeneity in anti-PD1-treated non-small cell lung cancer 243 samples shares single-cell
- GSE305078 Single-cell RNA sequencing of ICB samples from FUSCC 32 samples shares single-cell
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.