T-cell receptor repertoire alterations drive pathological gut immunological and microbial signatures in humans and mice with hypomorphic RAG deficiency
RNA-seq (gene expression) · mouse · 18 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
- 18 samples: 18 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
- Immunopathological and microbial signatures of inflammatory bowel disease in partial RAG deficiencyThe Journal of experimental medicine · 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 GSE277151_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 PRJNA1160874 and SRA study SRP532555. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 18 sample titles: 18 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.
- GSM8515118 lamina_propria_CD4_Tcells_rep1_HTO
- GSM8515119 lamina_propria_CD4_Tcells_rep1_mRNA
- GSM8515120 lamina_propria_CD4_Tcells_rep1_VDJ
- GSM8515121 lamina_propria_CD4_Tcells_rep2_HTO
- GSM8515122 lamina_propria_CD4_Tcells_rep2_mRNA
- GSM8515123 lamina_propria_CD4_Tcells_rep2_VDJ
- GSM8515124 lamina_propria_CD4_Tcells_rep3_HTO
- GSM8515125 lamina_propria_CD4_Tcells_rep3_mRNA
- GSM8515126 lamina_propria_CD4_Tcells_rep3_VDJ
- GSM8515127 lamina_propria_CD4_Tcells_rep4_HTO
- GSM8515128 lamina_propria_CD4_Tcells_rep4_mRNA
- GSM8515129 lamina_propria_CD4_Tcells_rep4_VDJ
- GSM8515130 lamina_propria_CD4_Tcells_rep5_HTO
- GSM8515131 lamina_propria_CD4_Tcells_rep5_mRNA
- GSM8515132 lamina_propria_CD4_Tcells_rep5_VDJ
- GSM8515133 lamina_propria_CD4_Tcells_rep6_HTO
- GSM8515134 lamina_propria_CD4_Tcells_rep6_mRNA
- GSM8515135 lamina_propria_CD4_Tcells_rep6_VDJ
- GSE325852 Translatome profiling reveals opposing alterations in inhibitory and excitatory neurons of Fragile X mice and identifies EPAC2 as a therapeutic target 69 samples shares rag, alterations
- GSE190231 Assessing the impact of TET2 and TET3 deletion in TCRa and TCRb expression and repertoire in murine CD4 T cells in physiological and pathological conditions 22 samples shares pathological, repertoire
- GSE190229 Assessing the impact of TET2 and TET3 deletion in TCRa and TCRb expression and repertoire in murine CD4 T cells in physiological and pathological conditions [TCR-SEQ] 18 samples shares pathological, repertoire
- GSE225173 Predicting age in single cells and low coverage DNA methylation data 250 samples shares rag
- GSE302715 A tumor-associated macrophage-targeted immunocytokine leveraging T and NK cell synergy for potent cancer immunotherapy [scRNA-seq] 187 samples shares rag
- GSE242568 Role of tRNA-derived fragments in the cross-talk between immune cells and beta cells during type 1 diabetes pathogenesis 52 samples shares rag
- GSE240635 Lysosomal control of type I interferon induction via Ragulator-Rag complex 48 samples shares rag
- GSE235109 Ensembles of genome-coverage single-cell histone modifications reveal epigenetic lineages during mouse preimplantation development 47 samples shares rag
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.