Promotion of TLR7-MyD88-dependent Inflammation and Autoimmunity through Stem-loop Changes in Lnc-Atg16l1
RNA-seq (gene expression) · mouse · 33 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
- 33 samples: 25 distinct titles, 4 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
- Promotion of TLR7-MyD88-dependent inflammation and autoimmunity in mice through stem-loop changes in Lnc-Atg16l1Nature communications · 2024
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 GSE228970_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 PRJNA952257 and SRA study SRP430900. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 33 sample titles: 25 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.
- GSM7146815 RAW264.7 cells,WT,0h-1
- GSM7146816 RAW264.7 cells,WT,0h-2
- GSM7146817 RAW264.7 cells,WT,0h-3
- GSM7146818 RAW264.7 cells,WT,4h-1
- GSM7146819 RAW264.7 cells,WT,4h-2
- GSM7146820 RAW264.7 cells,WT,4h-3
- GSM7146821 RAW264.7 cells,Lnc-Atg16l1 kd,0h-1
- GSM7146822 RAW264.7 cells,Lnc-Atg16l1 kd,0h-2
- GSM7146823 RAW264.7 cells,Lnc-Atg16l1 kd,0h-3
- GSM7146824 RAW264.7 cells,Lnc-Atg16l1 kd,4h-1
- GSM7146825 RAW264.7 cells,Lnc-Atg16l1 kd,4h-2
- GSM7146826 RAW264.7 cells,Lnc-Atg16l1 kd,4h-3
- GSM7146827 TLR7-activated-HA-iCLIP-seq
- GSM7146828 mTLR7-iCLIP-seq
- GSM7146829 Myd88-iCLIP-seq
- GSM7146830 TLR7-activated-Myd88-iCLIP-seq
- GSM7146831 Endosome RNA-seq
- GSM7146832 B6-D1 icSHAPE RNA-seq
- GSM7146833 B6-D2 icSHAPE RNA-seq
- GSM7146834 B6-N1 icSHAPE RNA-seq
- GSM7146835 B6-N2 icSHAPE RNA-seq
- GSM7146836 Yaa-D1 icSHAPE RNA-seq
- GSM7146837 Yaa-D2 icSHAPE RNA-seq
- GSM7146838 Yaa-N1 icSHAPE RNA-seq
- GSM7146839 Yaa-N2 icSHAPE RNA-seq
- GSM7146840 RAW_0h-D1 icSHAPE RNA-seq
- GSM7146841 RAW_0h-D2 icSHAPE RNA-seq
- GSM7146842 RAW_0h-N1 icSHAPE RNA-seq
- GSM7146843 RAW_0h-N2 icSHAPE RNA-seq
- GSM7146844 RAW_4h-D1 icSHAPE RNA-seq
- GSM7146845 RAW_4h-D2 icSHAPE RNA-seq
- GSM7146846 RAW_4h-N1 icSHAPE RNA-seq
- GSM7146847 RAW_4h-N2 icSHAPE RNA-seq
- GSE272723 PAC1 constrains type II inflammation through promotion of CGRP signaling in ILC2s [RNA-seq] 16 samples shares promotion
- GSE272722 PAC1 constrains type II inflammation through promotion of CGRP signaling in ILC2s [FastATAC-seq] 8 samples shares promotion
- GSE272724 PAC1 constrains type II inflammation through promotion of CGRP signaling in ILC2s [scRNA-seq] 2 samples shares promotion
- GSE293882 Tissue-resident memory CD4+ T cells sustain chronic CNS autoimmunity 8 samples shares autoimmunity
- GSE235248 Stress-Induced Glucocorticoids Exacerbate Inflammation and Autoimmunity by Promoting the Differentiation and Function of Th17 Cells [mTh17_RNAseq] 7 samples shares autoimmunity
- GSE286263 The deubiquitinase OTUD7B ameliorates central nervous system autoimmunity by inhibiting degradation of glial fibrillary acidic protein and astrocyte hyperinflammation 4 samples shares autoimmunity
- GSE235250 Stress-Induced Glucocorticoids Exacerbate Inflammation and Autoimmunity by Promoting the Differentiation and Function of Th17 Cells [ChIP-seq] 3 samples shares autoimmunity
- GSE312237 Spatial transcriptomic profiling identifies lacrimal gland epithelial cell-driven mechanisms underlying autoimmunity in Sjögren’s disease 90 samples shares autoimmunity
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.