TLR9-Mediated Macrophage-ILC Activation Induces Antigen-Independent Antiviral Immune Memory in the Lung
Single-cell RNA-seq · mouse · 12 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Mus musculus (mouse)
- Samples
- 12 samples: 3 × Whole lung, day 1, PBS vs 3 × Whole lung, day 1, K3-SPG vs 3 × Whole lung, day 3 PBS vs 3 × Whole lung, day 3 K3-SPGGroups 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 GSE319693_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1424971 and SRA study SRP677803. 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.
- GSM9523830 Whole lung, day 1, PBS 1 Whole lung, day 1, PBS
- GSM9523831 Whole lung, day 1, PBS 2 Whole lung, day 1, PBS
- GSM9523832 Whole lung, day 1, PBS 3 Whole lung, day 1, PBS
- GSM9523833 Whole lung, day 1, K3-SPG 1 Whole lung, day 1, K3-S…
- GSM9523834 Whole lung, day 1, K3-SPG 2 Whole lung, day 1, K3-S…
- GSM9523835 Whole lung, day 1, K3-SPG 3 Whole lung, day 1, K3-S…
- GSM9523836 Whole lung, day 3 PBS 1 Whole lung, day 3 PBS
- GSM9523837 Whole lung, day 3 PBS 2 Whole lung, day 3 PBS
- GSM9523838 Whole lung, day 3 PBS 3 Whole lung, day 3 PBS
- GSM9523839 Whole lung, day 3 K3-SPG 1 Whole lung, day 3 K3-SPG
- GSM9523840 Whole lung, day 3 K3-SPG 2 Whole lung, day 3 K3-SPG
- GSM9523841 Whole lung, day 3 K3-SPG 3 Whole lung, day 3 K3-SPG
- GSE281467 Coactivation of innate immune suppressive cells induces acquired resistance against cancer immunotherapy targeting the innate immune system [TIICs RNA-seq] 30 samples shares activation, induces
- GSE300964 Genetic inactivation of the Translin/Trax RNase activity alters small RNAs including miRNAs, disrupts gene expression and impairs distinct forms of hippocampal synaptic plasticity and memory 18 samples shares activation, memory
- GSE342096 Distinct activation programs in naïve and memory CD8 T cells govern progeny stemness and effector persistence 37 samples shares activation, memory
- GSE255212 Transcriptomic Signatures of WNT-Driven Pathways and Granulosa Cell-Oocyte Interaction during Primordial Follicle Activation 762 samples shares activation
- GSE331176 Phagosome-mediated activation of STING by purine and pyrimidine-based bacterial cyclic dinucleotides 380 samples shares activation
- GSE243942 Spatio-temporal X-linked gene reactivation in the mouse germline reveals site-specific retention of epigenetic silencing [RNA-seq] 125 samples shares activation
- GSE297515 Piezo1-dependent activation of stromal cells ignites muscle inflammation in exercise and injury and is associated with inflammaging 90 samples shares activation
- GSE236129 Activation of RAS/MEK/ERK signaling drives biliary differentiation in primary liver cancer [112UE] 80 samples shares activation
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.