Leveraging TNFR2 for antitumour immunity: Treg depletion and myeloid reprogramming versus T cell costimulation
Single-cell RNA-seq · mouse · 11 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
- Mus musculus (mouse)
- Samples
- 11 samples: 5 conditions, mostly in duplicateGroups 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 GSE330958_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 PRJNA1466296 and SRA study SRP700585. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 6 samples read as cases, 2 as controls.
How we read this: 5 replicated groups read from 11 sample titles; they account for 10 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.
- GSM9736507 Isotype control day 2 Isotype control day
- GSM9736508 TNFR2-3F10 treated day 2 TNFR2-3F10 treated day
- GSM9736509 TNFR2-5A05 treated day 2 TNFR2-5A05 treated day
- GSM9736510 anti-CTLA4 treated day 2 anti-CTLA4 treated day
- GSM9736511 anti-PD1 treated day 2 anti-PD1 treated day
- GSM9736512 Isotype control day 8 Isotype control day
- GSM9736513 TNFR2-3F10 treated day 8 TNFR2-3F10 treated day
- GSM9736514 TNFR2-5A05 treated day 8 TNFR2-5A05 treated day
- GSM9736515 anti-CTLA4 treated day 8 anti-CTLA4 treated day
- GSM9736516 anti-PD1 treated day 8 anti-PD1 treated day
- GSM9736517 anti-CTLA4 treated day 8 rep
- GSE283694 Bacterial immunotherapy leveraging IL-10R hysteresis for both phagocytosis evasion and tumor immunity revitalization [RNA-seq] 21 samples shares leveraging, immunity
- GSE263625 Microglial reprogramming enhances antitumor immunity and immunotherapy response in melanoma brain metastases 19 samples shares reprogramming, immunity
- GSE270414 Precision targeting of beta-catenin induces tumor reprogramming and immunity in hepatocellular cancers [Bulk RNA-seq CTNNB1/hMet/NFE2L2] 13 samples shares reprogramming, immunity
- GSE296733 Elevated Ozone Activates Maternal Immunity to Drive Offspring IgG-Mediated Anaphylaxis through IgG Glycosylation Reprogramming 12 samples shares reprogramming, immunity
- GSE319397 Particle Reprogramming of the TLR–Ferroptosis Axis and Immunometabolic Pathways Inhibits Myeloid Suppression to Improve Checkpoint Blockade in Prostate Cancer 9 samples shares reprogramming, myeloid
- GSE283696 Bacterial immunotherapy leveraging IL-10R hysteresis for both phagocytosis evasion and tumor immunity revitalization [CUT&Tag] 33 samples shares leveraging, immunity
- GSE333494 Hippocampal CA3 Nex+ neuronal TNFR2 alleviates chronic neuropathic pain by sex-dependently engaging opioid and endocannabinoid pathways 26 samples shares tnfr2
- GSE342477 Characterization of an Antagonistic Antibody reactive to human and mouse TNFR2 with Anti-tumor Capacity 9 samples shares tnfr2
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.