Batf3-dendritic cells and 4-1BB/4-1BB ligand axis are required at the effector phase within the tumor microenvironment for PD-1/PD-L1 blockade efficacy
RNA-seq (gene expression) · human · 10 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
- Homo sapiens (human)
- Samples
- 10 samples: 10 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.
- Paper
- Batf3(+) DCs and the 4-1BB/4-1BBL axis are required at the effector phase in the tumor microenvironment for PD-1/PD-L1 blockade efficacyCell reports · 2024
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 GSE238145_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 PRJNA998045 and SRA study SRP451208. 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 10 sample titles: 10 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.
- GSM7659430 Bladder tumor, patient 10 sample 1
- GSM7659431 Bladder tumor, patient 1 sample 1
- GSM8171241 Bladder tumor, patient 2 CytAssist
- GSM8171242 Bladder tumor, patient 3 CytAssist
- GSM8171243 Bladder tumor, patient 4 CytAssist
- GSM8171244 Bladder tumor, patient 5 and patient 6 CytAssist
- GSM8171245 Bladder tumor, patient 7 CytAssist
- GSM8171246 Bladder tumor, patient 8 CytAssist
- GSM8171247 Bladder tumor, patient 9 CytAssist
- GSM8171248 Bladder tumor, patient 10 sample 2, and patient 1 sample 2 (CytAssist)
- GSE286827 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy 87 samples shares 4-1bb, pd-l1
- GSE295042 The Role of PD-1/PD-L1 in Overshooting Osteoclastogenesis in Periprosthetic Joint Infections 12 samples shares pd-l1, pd-1
- GSE225063 Blockade of LAG-3 and PD-1 leads to co-expression of cytotoxic and exhaustion gene modules in CD8+ T cells to promote antitumor immunity 256 samples shares pd-1, blockade
- GSE169246 PD-L1 blockade-induced temporal single cell dynamics in triple negative breast cancer 83 samples shares pd-l1, blockade
- GSE320212 Identifying Senescence and Immune Biomarkers Predictive of Benefit to Combined CDK4/6 and PD-1 Blockade in Dedifferentiated Liposarcoma: Single-Cell RNA-seq of Serial Tumor Biopsies 23 samples shares pd-1, blockade
- GSE279750 ACE2 Enhances Sensitivity to PD-L1 Blockade by Inhibiting Macrophage-Induced Immunosuppression and Angiogenesis [RNA-seq, anti-PD-L1 therapy] 10 samples shares pd-l1, blockade
- GSE293752 IL4Ra blockade inhibits proliferation of malignant lymphocytes and the immunosuppressive tumor microenvironment of mycosis fungoides 23 samples shares microenvironment, blockade
- GSE272993 Combination anti-PD-1 and anti-CTLA-4 therapy generates waves of clonal responses that include progenitor-exhausted CD8 T cells [dataset 1] 360 samples shares pd-1
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.