Transcriptomic studies on ruxolitinib with or without checkpoint inhibitors as a cancer therapy
RNA-seq (gene expression) · mouse · 14 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
- 14 samples: 14 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
- JAK inhibition enhances checkpoint blockade immunotherapy in patients with Hodgkin lymphomaScience (New York, N.Y.) · 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 GSE209647_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 PRJNA861983 and SRA study SRP387932. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 3 samples read as cases, 4 as controls.
How we read this: Read from 14 sample titles: 14 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.
- GSM6381776 MC38_wt_TIC, mRNA-derived cDNA
- GSM6381777 MC38_wt_TIC, ADT- and HTO-derived cDNA
- GSM6381778 MC38_wt_BM_blood, mRNA-derived cDNA
- GSM6381779 MC38_wt_BM_blood, ADT- and HTO-derived cDNA
- GSM6381780 MC38_JAK1ko_TIC and LCMV_S, mRNA-derived cDNA
- GSM6381781 MC38_JAK1ko_TIC and LCMV_S, ADT- and HTO-derived cDNA
- GSM6381782 EL4_TIC, mRNA-derived cDNA
- GSM6381783 EL4_TIC, ADT- and HTO-derived cDNA
- GSM6381784 LLC1_TIC, mRNA-derived cDNA
- GSM6381785 LLC1_TIC, ADT- and HTO-derived cDNA
- GSM6381786 tumor-infiltrating NK cells, vehicle treated mice
- GSM6381787 tumor-infiltrating NK cells, ICB treated mice
- GSM6381788 tumor-infiltrating NK cells, ruxolitinib treated mice
- GSM6381789 tumor-infiltrating NK cells, ICB and ruxolitinib treated mice
- GSE337208 scRNA seq. of PDAC models treated with Kras inhibitors in combination with checkpoint immunotherapy 9 samples shares checkpoint, inhibitors, therapy
- GSE266971 Spatial and scRNAseq profiling of murine glioblastomas treated with and without anti-CSF-1R inhibitors 23 samples shares inhibitors, without
- GSE290464 Noncanonical role of NCOR1 as a facilitator of DNA mismatch repair and its deficiency sensitizes cancers to immune checkpoint blockade therapy 18 samples shares checkpoint, therapy
- GSE235242 Senescent cancer-associated fibroblasts in pancreatic adenocarcinoma suppress CD8+ T cell activation and inhibit response to immune checkpoint therapy [Kras_p53] 14 samples shares checkpoint, therapy
- GSE254919 Extracellular vesicles from obese visceral adipose promote pancreatic cancer development and resistance to immune checkpoint blockade therapy [ATAC-seq] 12 samples shares checkpoint, therapy
- GSE307388 Immune checkpoint blockade augments lymphodepleting chemotherapy-induced antitumor immunity by expanding effector CD8+ T cell clones in preclinical models of cancer 12 samples shares checkpoint, therapy
- GSE301138 Combining p53 mRNA nanotherapy with immune checkpoint blockade reprograms the immune microenvironment for effective cancer therapy 11 samples shares checkpoint, therapy
- GSE292854 Cytotoxic NK cells impede response to checkpoint immunotherapy in melanoma with an immune-excluded phenotype 10 samples shares checkpoint, therapy
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.