Lack of TREM2 during anti-PD-1 therapy reprograms intestinal macrophages and microbiota to enhance tumor rejection
RNA-seq (gene expression) · mouse · 32 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
- 32 samples: 24 distinct titles, 7 of them repeatedGroups 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
- TREM2 deficiency reprograms intestinal macrophages and microbiota to enhance anti-PD-1 tumor immunotherapyScience immunology · 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 GSE262811_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 PRJNA1093426 and SRA study SRP498664. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 32 sample titles: 24 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.
- GSM8179684 MCA1956_CD45_CTRL_1
- GSM8179685 MCA1956_CD45_CTRL_1_2
- GSM8179686 MCA1956_CD45_CTRL_2_1
- GSM8179687 MCA1956_CD45_CTRL_2_2
- GSM8179688 MCA1956_CD45_Rg_3_1
- GSM8179689 MCA1956_CD45_Rg_3_2
- GSM8179690 MCA1956_CD45_Rg_4_1
- GSM8179691 MCA1956_CD45_Rg_4_2
- GSM8179692 MCA1956_CD45_Rg_4_3
- GSM8179693 ColonLP_myeloid_WT_1
- GSM8179694 ColonLP_myeloid_WT_2
- GSM8179695 ColonLP_myeloid_KO_1
- GSM8179696 ColonLP_myeloid_KO_2
- GSM8179697 ColonLP_myeloid_WT_aPD1_1
- GSM8179698 ColonLP_myeloid_WT_aPD1_2
- GSM8179699 ColonLP_myeloid_KO_aPD1_1
- GSM8179700 ColonLP_myeloid_KO_aPD1_2
- GSM8179701 sample.3_Colon_bulk_WT_3
- GSM8179702 sample.4_Colon_bulk_WT_4
- GSM8179703 sample.5_Colon_bulk_WT_5
- GSM8179704 sample.6_Colon_bulk_WT_6
- GSM8179705 sample.9_Colon_bulk_KO_3
- GSM8179706 sample.10_Colon_bulk_KO_4
- GSM8179707 sample.12_Colon_bulk_KO_5
- GSM8179708 sample.15_Colon_bulk_WT_aPD1_3
- GSM8179709 sample.16_Colon_bulk_WT_aPD1_4
- GSM8179710 sample.17_Colon_bulk_WT_aPD1_5
- GSM8179711 sample.18_Colon_bulk_WT_aPD1_6
- GSM8179712 sample.21_Colon_bulk_KO_aPD1_2
- GSM8179713 sample.22_Colon_bulk_KO_aPD1_3
- GSM8179714 sample.23_Colon_bulk_KO_aPD1_4
- GSM8179715 sample.24_Colon_bulk_KO_aPD1_5
- GSE291235 Effect of myeloid specific Trem2 knockout in hepatocellular carcinoma after anti-PD-1 therapy 30 samples shares anti-pd-1, trem2, therapy
- GSE314594 Cryo-thermal therapy reprograms myeloid cells into CCL5+ mature phenotype to increase T cell infiltration and potentiates anti-PD-1 therapy 18 samples shares anti-pd-1, reprograms, therapy
- GSE319035 P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease [NAFLD_time_course] 77 samples shares trem2, macrophages
- GSE292614 Loss of PTDSS1 in tumor cells improves immunogenicity and response to anti-PD-1 therapy [scRNAseq] 24 samples shares anti-pd-1, therapy
- GSE318801 P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease. 20 samples shares trem2, macrophages
- GSE318804 P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease. [macro_senescence] 12 samples shares trem2, macrophages
- GSE318651 P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease [RNAseq_sgCMPK2] 12 samples shares trem2, macrophages
- GSE327494 Localized PD-1 CAR T therapy reprograms neuroinflammation - mouse CAR T data. 302 samples shares reprograms, 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.