Dendritic cell effector mechanisms and tumor immune microenvironment infiltration define TLR8 modulation and PD-1 blockade
Single-cell RNA-seq · human · 12 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Homo sapiens (human)
- 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.
- Paper
- Dendritic cell effector mechanisms and tumor immune microenvironment infiltration define TLR8 modulation and PD-1 blockadebioRxiv : the preprint server for biology · 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 GSE273138_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 PRJNA1140232 and SRA study SRP522272. 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.
- GSM8422433 HPT1, Pt1_R, scRNAseq, GEX
- GSM8422434 HPT3, Pt1_R, scRNAseq, GEX
- GSM8422435 HPT4, Pt2_R, scRNAseq, GEX
- GSM8422436 HPT5, Pt2_R, scRNAseq, GEX
- GSM8422437 HPT6, Pt3_NR, scRNAseq, GEX
- GSM8422438 HPT7, Pt3_NR, scRNAseq, GEX
- GSM8422439 HPT1, Pt1_R, scRNAseq, TCR
- GSM8422440 HPT3, Pt1_R, scRNAseq, TCR
- GSM8422441 HPT4, Pt2_R, scRNAseq, TCR
- GSM8422442 HPT5, Pt2_R, scRNAseq, TCR
- GSM8422443 HPT6, Pt3_NR, scRNAseq, TCR
- GSM8422444 HPT7, Pt3_NR, scRNAseq, TCR
- GSE272176 PD-1 blockade mitigates surgery-induced immunosuppression and increases the efficacy of photodynamic therapy for malignant pleural mesothelioma 82 samples shares pd-1, 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
- 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
- GSE293752 IL4Ra blockade inhibits proliferation of malignant lymphocytes and the immunosuppressive tumor microenvironment of mycosis fungoides 23 samples shares microenvironment, blockade
- GSE308973 Localized PD-1 CAR T therapy reprograms neuroinflammation - human CSF data. 88 samples shares pd-1
- GSE289743 Cancer-induced nerve injury promotes resistance to anti-PD-1 therapy [RNA-Seq FFPE] 83 samples shares pd-1
- GSE266219 Clinical and Immunological Responses to Combined JAK Inhibition and PD-1 immunotherapy for Lung Cancer Patients 79 samples shares pd-1
- GSE202069 RNA-seq data for tumor and adjacent non-tumor tissues from hepatocellular carcinoma patients with anti-PD-1 therapy 66 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.