Blocking CX3CR1+ Tumor-associated Macrophages Synergize with anti-PD-1 Therapy in Hepatocellular Carcinoma
RNA-seq (gene expression) · mouse · 16 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
- 16 samples: 4 × TAM_IgG vs 4 × TAM_PD vs 4 × TAM_C vs 4 × TAM_CPGroups 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.
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 GSE263240_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 PRJNA1096334 and SRA study SRP499846. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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.
- GSM8188316 TAM_IgG1 TAM_IgG
- GSM8188317 TAM_IgG2 TAM_IgG
- GSM8188318 TAM_IgG3 TAM_IgG
- GSM8188319 TAM_IgG4 TAM_IgG
- GSM8188320 TAM_PD1 TAM_PD
- GSM8188321 TAM_PD2 TAM_PD
- GSM8188322 TAM_PD3 TAM_PD
- GSM8188323 TAM_PD4 TAM_PD
- GSM8188324 TAM_C1 TAM_C
- GSM8188325 TAM_C2 TAM_C
- GSM8188326 TAM_C3 TAM_C
- GSM8188327 TAM_C4 TAM_C
- GSM8188328 TAM_CP1 TAM_CP
- GSM8188329 TAM_CP2 TAM_CP
- GSM8188330 TAM_CP3 TAM_CP
- GSM8188331 TAM_CP4 TAM_CP
- GSE291357 Short-term starvation boosts anti-PD-L1 therapy by reshaping tumor-associated macrophages in hepatocellular carcinoma 6 samples shares tumor-associated, hepatocellular, macrophages, therapy
- GSE266110 7aaRGD - a novel SPP1/integrin signaling-blocking peptide reverses immunosuppression and improves anti-PD-1 immunotherapy outcomes in experimental gliomas 40 samples shares anti-pd-1, blocking, therapy
- GSE273883 CX3CR1+ Synovial Macrophages for Barrier Restore in Rheumatoid Arthritis: A New Target for Mesenchymal Stem Cell-Based Therapy? 35 samples shares cx3cr1, macrophages, therapy
- GSE262811 Lack of TREM2 during anti-PD-1 therapy reprograms intestinal macrophages and microbiota to enhance tumor rejection 32 samples shares anti-pd-1, macrophages, therapy
- GSE291235 Effect of myeloid specific Trem2 knockout in hepatocellular carcinoma after anti-PD-1 therapy 30 samples shares anti-pd-1, hepatocellular, therapy
- GSE212259 Whole-course Taming of Tumor-associated Macrophages from Central to Peripheral using Engineered Outer Membrane Vesicle Nanohybrids for Improved Immunotherapy [part 1: RNA-seq] 36 samples shares tumor-associated, macrophages, therapy
- GSE240840 Tumor-associated neutrophils attenuate the immuno-sensitivity of hepatocellular carcinoma and curtail immunotherapy response 23 samples shares tumor-associated, hepatocellular, therapy
- GSE240838 Tumor-associated neutrophils attenuate the immuno-sensitivity of hepatocellular carcinoma and curtail immunotherapy response [RNA-Seq] 17 samples shares tumor-associated, hepatocellular, 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.