RNA sequencing of antigen specific CD4+ T cells induced by high vs low doses of MHC-II restricted neoantigens
RNA-seq (gene expression) · mouse · 18 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 18 samples: 3 × (CD4+ CD25+)Tregs vs 3 × (CD4+ CD25- CD200-CD39+) vs 3 × (CD4+ CD25- CD200+)Groups 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
- Neoantigen-specific cytotoxic Tr1 CD4 T cells suppress cancer immunotherapyNature · 2024
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 GSE268302_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1116134 and SRA study SRP509779. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 9 samples.
How we read this: 3 replicated groups read from 18 sample titles; they account for 9 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.
- GSM8289307 (CD4+ CD25+)Tregs 1 (CD4+ CD25+)Tregs
- GSM8289308 (CD4+ CD25+)Tregs 2 (CD4+ CD25+)Tregs
- GSM8289309 (CD4+ CD25+)Tregs 3 (CD4+ CD25+)Tregs
- GSM8289310 (CD4+ CD25- CD200-CD39+) 1 (CD4+ CD25- CD200-CD39+)
- GSM8289311 (CD4+ CD25- CD200-CD39+) 2 (CD4+ CD25- CD200-CD39+)
- GSM8289312 (CD4+ CD25- CD200-CD39+) 3 (CD4+ CD25- CD200-CD39+)
- GSM8289313 (CD4+ CD25- CD200+) 1 (CD4+ CD25- CD200+)
- GSM8289314 (CD4+ CD25- CD200+) 2 (CD4+ CD25- CD200+)
- GSM8289315 (CD4+ CD25- CD200+) 3 (CD4+ CD25- CD200+)
- GSM8289316 PBS (PBS treated CD4+ T cells from T3 TILs)
- GSM8289317 PBS (PBS treated CD4+ T cells from T3 TILs) TCR
- GSM8289318 PBS (PBS treated CD4+ T cells from T3 TILs) FBC
- GSM8289319 LD (LDVax treated CD4+ T cells from T3 TILs)
- GSM8289320 LD (LDVax treated CD4+ T cells from T3 TILs) TCR
- GSM8289321 LD (LDVax treated CD4+ T cells from T3 TILs) FBC
- GSM8289322 HD (HDVax treated CD4+ T cells from T3 TILs)
- GSM8289323 HD (HDVax treated CD4+ T cells from T3 TILs) TCR
- GSM8289324 HD (HDVax treated CD4+ T cells from T3 TILs) FBC
- GSE304995 HIV-1 reprograms CD4 T cell responses by impairing antigen-specific communication with dendritic cells 8 samples shares cd4, specific, antigen
- GSE317035 Tissue-specific clonal selection and differentiation of CD4⁺ T cells during infection. 23 samples shares cd4, specific
- GSE325803 CD40-induced humoral immunity 18 samples shares cd4, induced
- GSE293728 IFN-γ-STAT1 Axis Drives MHC-II Antigen Presentation Potentiation in Tumor Associated Macrophages 18 samples shares mhc-ii, antigen
- GSE287681 IFN-γ induced the formation of foamy macrophages by CD40 signaling control during Mycobacterium abscessus pulmonary infection 17 samples shares cd4, induced
- GSE300922 Xin-Zi-Sheng-Wan Decoction Alleviates Hyperuricemia-Induced Renal Injury by Modulating SPP1-CD44-Mediated Macrophage Infiltration and SRC/FAK/β-Catenin Signaling Pathway 12 samples shares cd4, induced
- GSE318778 Ligature-induced periodontitis in mice potentially accelerates CD4+ T cells senescence and exacerbates rheumatoid arthritis 12 samples shares cd4, induced
- GSE325580 NEMO lysine mutant mice reveal ROS-RelA signaling required for optimal CD40-induced humoral immunity [NEMODK_CUTTAG] 60 samples shares cd4, induced
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.