The miR-29-IFN-γ-JAK-STAT axis attenuates CD8+ T cell overactivation and differentiation in ulcerative colitis, and delivery of mimics in LMSH-CS hydrogel reduces colitis in mice
RNA-seq (gene expression) · mouse · 14 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
- 14 samples: 7 × C57BL/6N mice, WT vs 7 × C57BL/6N mice, miR-29ab1-/Groups 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.
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 GSE253734_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 PRJNA1066833 and SRA study SRP484762. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 14 samples.
How we read this: 2 replicated groups read from 14 sample titles; they account for 14 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.
- GSM8027133 C57BL/6N mice, WT1 C57BL/6N mice, WT
- GSM8027134 C57BL/6N mice, WT2 C57BL/6N mice, WT
- GSM8027135 C57BL/6N mice, WT3 C57BL/6N mice, WT
- GSM8027136 C57BL/6N mice, WT4 C57BL/6N mice, WT
- GSM8027137 C57BL/6N mice, miR-29ab1-/-1 C57BL/6N mice, miR-29ab…
- GSM8027138 C57BL/6N mice, miR-29ab1-/-2 C57BL/6N mice, miR-29ab…
- GSM8027139 C57BL/6N mice, miR-29ab1-/-3 C57BL/6N mice, miR-29ab…
- GSM8027140 C57BL/6N mice, miR-29ab1-/-4 C57BL/6N mice, miR-29ab…
- GSM8027141 C57BL/6N mice, WT5 C57BL/6N mice, WT
- GSM8027142 C57BL/6N mice, WT6 C57BL/6N mice, WT
- GSM8027143 C57BL/6N mice, WT7 C57BL/6N mice, WT
- GSM8027144 C57BL/6N mice, miR-29ab1-/-5 C57BL/6N mice, miR-29ab…
- GSM8027145 C57BL/6N mice, miR-29ab1-/-6 C57BL/6N mice, miR-29ab…
- GSM8027146 C57BL/6N mice, miR-29ab1-/-7 C57BL/6N mice, miR-29ab…
- GSE296763 Mitochondrial respiration is necessary for CD8 T cell proliferation and cell fate 99 samples shares cd8
- GSE334845 Discovery of Tcf7 regulators with clonally-resolved CRISPR screens identifies Trim28 as a mediator of CD8 T cell differentiation in tumors [RNA-Seq] 86 samples shares cd8
- GSE302682 Sleeping Beauty mutagenesis identifies BACH2 and other regulators promoting CD8+ T cell persistence and effector function under tumor-associated chronic antigen stimulation - RNAseq 66 samples shares cd8
- GSE337601 XCR1+ and CD11b+ migratory dendritic cells cooperate for the crosspriming of intratumoral CD8+ T cells with a tissue-resident memory phenotype [RNA-Seq] 36 samples shares cd8
- GSE306744 Pre-division TCF1 downregulation determines long-term effector and memory CD8 T cell fates [RNA-Seq] 31 samples shares cd8
- GSE338265 Smad4 and Eomes converge on a shared transcriptional program associated with inflammatory CD8 T-cell differentiation 31 samples shares cd8
- GSE248272 Therapeutically targeting perivascular macrophage effector function improves CD8+ T-cell infiltration and response to chemotherapeutic drugs in cancer 30 samples shares cd8
- GSE331107 The transcription factor AFF3 is necessary to maintain metabolic quiescence in naïve CD8 T cells and prevent premature immune aging 30 samples shares cd8
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.