Immunogen-Sponge Hydrogel Reverses TIM-3–Mediated Dendritic-Cell Exhaustion in Alveolar Echinococcosis
RNA-seq (gene expression) · mouse · 12 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
- 12 samples: 3 × BMDC_Saline vs 3 × BMDC_PSA vs 3 × BMDC_F127 vs 3 × BMDC_SHIFTGroups 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 GSE334769_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 PRJNA1476314 and SRA study SRP707874. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM9796843 BMDC_Saline_1 BMDC_Saline
- GSM9796844 BMDC_Saline_2 BMDC_Saline
- GSM9796845 BMDC_Saline_3 BMDC_Saline
- GSM9796846 BMDC_PSA_1 BMDC_PSA
- GSM9796847 BMDC_PSA_2 BMDC_PSA
- GSM9796848 BMDC_PSA_3 BMDC_PSA
- GSM9796849 BMDC_F127_1 BMDC_F127
- GSM9796850 BMDC_F127_2 BMDC_F127
- GSM9796851 BMDC_F127_3 BMDC_F127
- GSM9796852 BMDC_SHIFT_1 BMDC_SHIFT
- GSM9796853 BMDC_SHIFT_2 BMDC_SHIFT
- GSM9796854 BMDC_SHIFT_3 BMDC_SHIFT
- GSE223424 Immune checkpoint TIM-3 regulates microglia and Alzheimer’s disease 57 samples shares tim-3
- GSE296837 IFN-γ-induced PD-L1+ and MHC II+ macrophages and Tim-3+ tumor-reactive CD8+ T cells predict a positive response to anti-PD-1 therapy in tumor-bearing mice 28 samples shares tim-3
- GSE223420 Immune checkpoint TIM-3 regulates microglia and Alzheimer’s disease [BulkRNAseq_Dataset1_Batch1_3M] 22 samples shares tim-3
- GSE254211 Analysis of different mouse P14 CD8+T cell subset gene signatures in presence and absence of Tim-3+ Treg during LCMV CL13 infection 18 samples shares tim-3
- GSE223422 Immune checkpoint TIM-3 regulates microglia and Alzheimer’s disease [BulkRNAseq_Dataset3_4M] 15 samples shares tim-3
- GSE293780 Analysis of (MC38) tumor infiltrating T regulatory cells From ERT2Cre control and ERT2CreTIM-3(FLEX4) KO mouse. 12 samples shares tim-3
- GSE300892 Cell-intrinsic Tim-3 is Required for Optimal CD8 Response to Acute LCMV Infection [RNAseq] 10 samples shares tim-3
- GSE223423 Immune checkpoint TIM-3 regulates microglia and Alzheimer’s disease [snRNAseq_5M] 10 samples shares tim-3
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.