single cell RNA sequecing of Gene epxressions and TCR clones in late-onset EAE
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.
- Organism
- Mus musculus (mouse)
- Samples
- 12 samples: 12 samples, each with a distinct title — no replicated groupsGroups 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 GSE182747_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 PRJNA757703 and SRA study SRP334065. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 12 sample titles: 12 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.
- GSM5536157 Y1 [GEX]
- GSM5536158 O1 [GEX]
- GSM5536159 Y2 [GEX]
- GSM5536160 O2 [GEX]
- GSM5536161 Y3 [GEX]
- GSM5536162 O3 [GEX]
- GSM5536163 Y1 [VDJ]
- GSM5536164 O1 [VDJ]
- GSM5536165 Y2 [VDJ]
- GSM5536166 O2 [VDJ]
- GSM5536167 Y3 [VDJ]
- GSM5536168 O3 [VDJ]
- GSE285414 Functional memory T cells are derived from exhausted clones and expanded by checkpoint blockade [scRNATCR_rechallenge] 21 samples shares tcr, clones
- GSE285411 Functional memory T cells are derived from exhausted clones and expanded by checkpoint blockade [scRNATCR_Atlas] 21 samples shares tcr, clones
- GSE285412 Functional memory T cells are derived from exhausted clones and expanded by checkpoint blockade [scRNATCR_aPDL1] 9 samples shares tcr, clones
- GSE278804 Single cell RNA sequencing of TCF-1+ precursor cells reacting to LCMV gp33 vs np396 multimers sorted 30 days after infection with LCMV Armstrong [scRNA-Seq + TCR 10x] 12 samples shares tcr
- GSE278812 Gene expression profile at single cell level of immune cells from the dura mater of naïve C57BL6/N mice and during different phases of EAE. 10 samples shares eae
- GSE243972 Gene expression profile at single cell level of lymphocytes extracted from the mesenteric lymph nodes of TCRMOG animals colonized with either Salmonella expressing MOG or OVA 6 samples shares tcr
- GSE302856 Atomistic TCR-ligand interactions instruct memory T-cell differentiation and crossreactivity 28 samples shares tcr
- GSE267603 Tra2b's Ultraconserved Poison Exon relays TCR stimulation to shape T cell fate [Tra2bKO] 18 samples shares tcr
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.