Hepatocellular carcinoma specific epigenetic checkpoint bi-directionally regulates antitumor immunity of CD4+T cell
RNA-seq (gene expression) · mouse · 16 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
- 16 samples: 16 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 GSE263391_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 PRJNA1097278 and SRA study SRP500169. 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 16 sample titles: 16 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.
- GSM8190768 5DCON1, scRNAseq
- GSM8190769 5DCON2, scRNAseq
- GSM8190770 5DKO1, scRNAseq
- GSM8190771 5DKO2, scRNAseq
- GSM8190772 14DCON1, scRNAseq
- GSM8190773 14DCON2, scRNAseq
- GSM8190774 14DKO1, scRNAseq
- GSM8190775 14DKO2, scRNAseq
- GSM8190776 5DCON1, TCRseq
- GSM8190777 5DCON2, TCRseq
- GSM8190778 5DKO1, TCRseq
- GSM8190779 5DKO2, TCRseq
- GSM8190780 14DCON1, TCRseq
- GSM8190781 14DCON2, TCRseq
- GSM8190782 14DKO1, TCRseq
- GSM8190783 14DKO2, TCRseq
- GSE313761 Single-cell screens identify ADAM12 as a fibroblast checkpoint impeding anti-tumor immunity - scRNA-seq of Adam12CKO Mouse Model CD45- cells 11 samples shares cd4, checkpoint, immunity
- GSE291447 Targeting CD11b+ regulatory B cells via RAS/RAF/PI3K pathway inhibition augments response to immune checkpoint blockade or CD40 agonism in metastatic melanoma 60 samples shares cd4, checkpoint
- GSE325227 CD69 regulates the tissue dynamics of epigenetically imprinted memory CD4+ T cells [RNA-seq_ATAC-seq] 22 samples shares cd4, epigenetic
- GSE325803 CD40-induced humoral immunity 18 samples shares cd4, immunity
- GSE302620 Oncolytic virus therapy mobilizes tumor-resident CD4+ bystander T cells to restore systemic anti-microbial immunity [ATAC-seq] 16 samples shares cd4, immunity
- GSE324687 Eomes sustains progenitor CD4⁺ T helper cells to promote anti-tumor immunity during immunotherapy [scRNA] 16 samples shares cd4, immunity
- GSE283198 Combined Flt3L and CD40 agonism restores dendritic cell driven T cell immunity in mouse models and patients with pancreatic cancer [mouse] 13 samples shares cd4, immunity
- GSE304995 HIV-1 reprograms CD4 T cell responses by impairing antigen-specific communication with dendritic cells 8 samples shares cd4, specific
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.