Endogenous retroviruses promote aberrant T cell differentiation in systemic lupus erythematosus via the RIG-I pathway [SLE]
RNA-seq (gene expression) · human · 10 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
- Homo sapiens (human)
- Samples
- 10 samples: 4 × CD4+T cells, N vs 4 × CD4+T cells, SLE vs 2 × CD4+T cells, SLE_TGroups 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
- DNA demethylation mediated endogenous retroviruses transcription promotes aberrant T cell differentiation in systemic lupus erythematosus via RIG-I pathwayEBioMedicine · 2025
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 GSE297006_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 PRJNA1262359 and SRA study SRP584860. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 3 replicated groups read from 10 sample titles; they account for 10 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.
- GSM8981526 CD4+T cells, N1 CD4+T cells, N
- GSM8981527 CD4+T cells, N2 CD4+T cells, N
- GSM8981528 CD4+T cells, N3 CD4+T cells, N
- GSM8981529 CD4+T cells, N4 CD4+T cells, N
- GSM8981530 CD4+T cells, SLE1 CD4+T cells, SLE
- GSM8981531 CD4+T cells, SLE2 CD4+T cells, SLE
- GSM8981532 CD4+T cells, SLE3 CD4+T cells, SLE
- GSM8981533 CD4+T cells, SLE4 CD4+T cells, SLE
- GSM8981534 CD4+T cells, SLE_T1 CD4+T cells, SLE_T
- GSM8981535 CD4+T cells, SLE_T2 CD4+T cells, SLE_T
- GSE288271 Endogenous retroviruses promote aberrant T cell differentiation in systemic lupus erythematosus via the RIG-I pathway [whole transcriptomics] 10 samples shares rig-i, erythematosus, retroviruses, endogenous, aberrant, systemic, promote
- GSE312474 MODULATION OF VIRUS–TUMOR-STROMAL INTERACTIONS BY MINNELIDE ENHANCES SYSTEMIC DUAL TARGETED MEASLES VIROTHERAPY IN BRAF-MUTANT COLORECTAL CANCER 14 samples shares sle, systemic
- GSE250025 Impaired innate and adaptive immune responses to BNT162b2 SARS-CoV-2 vaccination in systemic lupus erythematosus 84 samples shares erythematosus, systemic
- GSE250023 Impaired innate and adaptive immune responses to BNT162b2 SARS-CoV-2 vaccination in systemic lupus erythematosus 75 samples shares erythematosus, systemic
- GSE226147 Modeling of Clinical Phenotypes in Systemic Lupus Erythematosus Based on the Platelet Transcriptome and FCGR2a Genotype 69 samples shares erythematosus, systemic
- GSE249619 Divergent Epigenetic and Transcriptomic Remodelling during Monocyte Subset Differentiation in Systemic Lupus Erythematosus [RNA-seq] 57 samples shares erythematosus, systemic
- GSE294789 Daratumumab in systemic lupus erythematosus: a phase 2 trial 56 samples shares erythematosus, systemic
- GSE278120 Interferon activation in bone marrow long-lived plasma cells in systemic lupus erythematosus 48 samples shares erythematosus, systemic
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.