Enhancing tumor response to adoptive T cell therapy by targeting PHD2/3 in CD8 T cells
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: 6 conditions, mostly in triplicateGroups 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
- Enhanced tumor response to adoptive T cell therapy with PHD2/3-deficient CD8 T cellsNature communications · 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 GSE271367_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 PRJNA1130998 and SRA study SRP521699. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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.
- GSM8375580 SCR NORM 1 SCR NORM
- GSM8375581 SCR NORM 2 SCR NORM
- GSM8375582 SCR NORM 3 SCR NORM
- GSM8375583 HIF1A KO NORM 1 HIF1A KO NORM
- GSM8375584 HIF1A KO NORM 2 HIF1A KO NORM
- GSM8375585 HIF1A KO NORM 3 HIF1A KO NORM
- GSM8375586 PHD2/3 KO NORM 1 PHD2/3 KO NORM
- GSM8375587 PHD2/3 KO NORM 2 PHD2/3 KO NORM
- GSM8375588 PHD2/3 KO NORM 3 PHD2/3 KO NORM
- GSM8375589 SCR HYP 1 SCR HYP
- GSM8375590 SCR HYP 2 SCR HYP
- GSM8375591 SCR HYP 3 SCR HYP
- GSM8375592 HIF1A KO HYP 1 HIF1A KO HYP
- GSM8375593 HIF1A KO HYP 2 HIF1A KO HYP
- GSM8375594 HIF1A KO HYP 3 HIF1A KO HYP
- GSM8375595 PHD2/3 KO HYP 1 PHD2/3 KO HYP
- GSM8375596 PHD2/3 KO HYP 2 PHD2/3 KO HYP
- GSM8375597 PHD2/3 KO HYP 3 PHD2/3 KO HYP
- GSE269347 Daunorubicin-induced T cell remodeling facilitates a high antitumor response to PD-1 blockade therapy by promoting the expansion and effector function of CD8+ prolifeating T cells [scRNA-Seq] 16 samples shares cd8, therapy
- GSE304763 A pan-immunotherapy signature to predict intratumoral CD8+ T cell expansions [scTCR_immunotherapies] 91 samples shares cd8, therapy
- GSE274865 Epigenetic regulators of clonal hematopoiesis control CD8 T cell stemness during immunotherapy [CUT&Tag] 36 samples shares cd8, therapy
- GSE281467 Coactivation of innate immune suppressive cells induces acquired resistance against cancer immunotherapy targeting the innate immune system [TIICs RNA-seq] 30 samples shares targeting, therapy
- GSE298751 Prussian blue nanoparticles targeting multiple PANoptosome-mediated PANoptosis for myocardial ischemia-reperfusion injury therapy 15 samples shares targeting, therapy
- GSE334845 Discovery of Tcf7 regulators with clonally-resolved CRISPR screens identifies Trim28 as a mediator of CD8 T cell differentiation in tumors [RNA-Seq] 86 samples shares cd8
- GSE302682 Sleeping Beauty mutagenesis identifies BACH2 and other regulators promoting CD8+ T cell persistence and effector function under tumor-associated chronic antigen stimulation - RNAseq 66 samples shares cd8
- GSE316541 α2,6-Sialoglycan-regulated anti-tumor immunity of tumor-infiltrating CD8+ T cells in the tumor microenvironment [CD8+T] 27 samples shares cd8
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.