Early-life stromal niches orchestrate B lymphopoiesis at the brain’s borders
Single-cell RNA-seq · mouse · 12 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
- Mus musculus (mouse)
- Samples
- 12 samples: 3 × Brain vs 3 × SkullBoneMarrow vs 3 × DuralMeninges vs 3 × TibiaBoneMarrowGroups 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.
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 GSE312965_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 PRJNA1377670 and SRA study SRP653511. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM9357633 Brain_01 Brain
- GSM9357634 Brain_02 Brain
- GSM9357635 Brain_03 Brain
- GSM9357636 SkullBoneMarrow_01 SkullBoneMarrow
- GSM9357637 SkullBoneMarrow_02 SkullBoneMarrow
- GSM9357638 SkullBoneMarrow_03 SkullBoneMarrow
- GSM9357639 DuralMeninges_01 DuralMeninges
- GSM9357640 DuralMeninges_02 DuralMeninges
- GSM9357641 DuralMeninges_03 DuralMeninges
- GSM9357642 TibiaBoneMarrow_01 TibiaBoneMarrow
- GSM9357643 TibiaBoneMarrow_02 TibiaBoneMarrow
- GSM9357644 TibiaBoneMarrow_03 TibiaBoneMarrow
- GSE297816 Early-life RNA sequencing of colon stromal cells and iNKT cells 40 samples shares early-life, stromal
- GSE277668 Bone marrow niches orchestrate stem cell hierarchy and immune tolerance 12 samples shares orchestrate, niches
- GSE297515 Piezo1-dependent activation of stromal cells ignites muscle inflammation in exercise and injury and is associated with inflammaging 90 samples shares stromal
- GSE313732 Type I IFN Dynamics Orchestrate Protective ICAM1⁺ Neutrophil Heterogeneity as an Early Checkpoint for Survival in Lethal Viral Infection [RNA-Seq] 78 samples shares orchestrate
- GSE268241 HPV16-expressing tumors release multiple IL-1 ligands to orchestrate systemic immunosuppression whose disruption enables efficacy of a therapeutic vaccine. 63 samples shares orchestrate
- GSE281117 Small intestinal lymph node identity is defined by medullary stromal cells in mice 50 samples shares stromal
- GSE282129 Small intestinal lymph node identity is defined by medullary stromal cells in humans and mice [Sorted_lns_macrophages_RNAseq] 45 samples shares stromal
- GSE255061 Phosphatase-independent activity of smooth-muscle calcineurin orchestrates a gene expression program leading to arterial hypertension 40 samples shares orchestrate
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.