Atomistic TCR-ligand interactions instruct memory T-cell differentiation and crossreactivity
Single-cell RNA-seq · mouse · 10 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
- 10 samples: 8 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.
- Paper
- Atomistic TCR-ligand interactions instruct memory T-cell differentiationbioRxiv : the preprint server for biology · 2025
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 GSE302680_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 PRJNA1291718 and SRA study SRP600928. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 10 sample titles: 8 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.
- GSM9108718 NP Lymph Node Gene Expression R1
- GSM9108719 NP Lymph Node VDJ R1
- GSM9108720 NP Lymph Node Gene Expression R2
- GSM9108721 NP Lymph Node VDJ R2
- GSM9108722 D2 Lymph Node Gene Expression
- GSM9108723 D2 Lymph Node VDJ
- GSM9108724 D4 Lymph Node Gene Expression
- GSM9108725 D4 Lymph Node VDJ
- GSM9108726 Non Selected Lymph Node Gene Expression
- GSM9108727 Non Selected Lymph Node VDJ
- GSE302856 Atomistic TCR-ligand interactions instruct memory T-cell differentiation and crossreactivity 28 samples shares crossreactivity, interactions, tcr-ligand, atomistic, instruct, memory, t-cell
- GSE313272 Atomistic TCR-ligand interactions instruct memory T-cell differentiation and crossreactivity [RNA-seq] 12 samples shares crossreactivity, interactions, tcr-ligand, atomistic, instruct, memory, t-cell
- GSE267441 Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation [RNA-seq] 35 samples shares interactions
- GSE268719 Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation 169 samples shares interactions
- GSE262290 Metabolic modeling reveals the aging-associated decline of host–microbiome metabolic interactions in mice 156 samples shares interactions
- GSE278548 Metabolic modeling reveals the aging-associated decline of host-microbiome metabolic interactions in mice 119 samples shares interactions
- GSE269897 Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation [ChIP-Seq] 96 samples shares interactions
- GSE261066 Transient promoter interactions modulate developmental gene activation [RNA-Seq] 79 samples shares interactions
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.