GEO series

Single-cell transcriptional profiling of Th17 cells, differentiated in vitro for 48h [IL1B_IL6_IL23-48h-IL-17A/GFP+]

GSE75109 Mus musculus (mouse) Single-cell RNA-seq 139 samples Submitted 2015/11/20 Platform GPL9250

At a glance

Single-cell RNA-seq · mouse · 139 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: 139 samples
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)

Extensive cellular heterogeneity exists within specific immune-cell subtypes classified as a single lineage, but its molecular underpinnings are rarely characterized at a genomic scale. Here, we use single-cell RNA-seq to investigate the molecular mechanisms governing heterogeneity and pathogenicity of Th17 cells isolated from the central nervous system (CNS) and lymph nodes (LN) at the peak of autoimmune encephalomyelitis (EAE) or polarized in vitro under either pathogenic or non-pathogenic differentiation conditions.

Read the full summary ↓

Computational analysis reveals a spectrum of cellular states in vivo, including a self-renewal state, Th1-like effector/memory states and a dysfunctional/senescent state. Relating these states to in vitro differentiated Th17 cells, unveils genes governing pathogenicity and disease susceptibility. Using knockout mice, we validate four novel genes: Gpr65, Plzp, Toso and Cd5l (in a companion paper). Cellular heterogeneity thus informs Th17 function in autoimmunity, and can identify targets for selective suppression of pathogenic Th17 cells while sparing non-pathogenic tissue-protective ones.

This dataset

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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 GSE75109_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 PRJNA302459 and SRA study SRP066320. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 26607794) ↗

Samples in this study

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+ 139 more — browse all 139 samples with per-sample file links →

Datasets on a similar topic

GSE75111 Single-cell transcriptional profiling of Th17 cells, differentiated in vitro for 48h [TGFB1_IL6-48h-IL-17A/GFP+] 151 samples shares th17, il6, gfp, differentiated, single-cell, vitro
GSE75110 Single-cell transcriptional profiling of Th17 cells, differentiated in vitro for 48h [TGFB1_IL6-48h] 130 samples shares th17, il6, differentiated, single-cell, vitro
GSE290297 Population RNA-seq from Th17 cells differentiated in vitro under pathogenic (Th17p) and non-pathogenic (Th17n) conditions with DHEA or EGCG 79 samples shares th17, differentiated, vitro
GSE239946 Signatures of IL1b, IL6 and TNFa in immune cell-types 209 samples shares il1b, il6
GSE254602 Effect of deletion of SPTLC1 on gene expression and differentiation of mouse Th17 cells in vitro 24 samples shares th17, vitro
GSE92865 Single-cell RNA-seq of Lgr5-eGFP+ intestinal stem cells upon Wnt and R-spondin modulation in vivo 14 samples shares gfp, single-cell
GSE338857 Single-cell transcriptomic analysis of GFP-positive and GFP-negative CD45-positive and CD45-negative cardiac cells isolated from TAC-operated REFLEX mice 2 samples shares gfp, single-cell
GSE303699 Autoimmune Disease Risk Gene ANKRD55 Promotes Th17 Effector Function Through Metabolic Modulation [RNA-Seq] 60 samples shares th17

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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.