Effect of U1 snRNA knock-in on gene expression during HSV-1 infection
Single-nucleus RNA-seq · mouse · 12 samples
- What it is
- Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue).
- Organism
- Mus musculus (mouse)
- Samples
- 12 samples: 3 × WT mock vs 3 × WT HSV-1 vs 3 × U1 mock vs 3 × U1 HSV-1Groups 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 GSE269901_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 PRJNA1124088 and SRA study SRP514013. 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.
- GSM8329879 WT mock rep1 WT mock
- GSM8329880 WT mock rep2 WT mock
- GSM8329881 WT mock rep3 WT mock
- GSM8329882 WT HSV-1 rep1 WT HSV-1
- GSM8329883 WT HSV-1 rep2 WT HSV-1
- GSM8329884 WT HSV-1 rep3 WT HSV-1
- GSM8329885 U1 mock rep1 U1 mock
- GSM8329886 U1 mock rep2 U1 mock
- GSM8329887 U1 mock rep3 U1 mock
- GSM8329888 U1 HSV-1 rep1 U1 HSV-1
- GSM8329889 U1 HSV-1 rep2 U1 HSV-1
- GSM8329890 U1 HSV-1 rep3 U1 HSV-1
- GSE270728 Analysis of striatal zinc finger protein (ZFP) repression of mutant Huntingtin (HTT) in the zQ175DN knock-in mouse model of Huntington's disease (snRNA-seq) 120 samples shares knock-in, snrna
- GSE299440 Subclinical Neonatal HSV-1 Infection Triggers Immune Responses and Modulates Neurological Pathways Leading to Long-Term Sequelae 20 samples shares hsv-1
- GSE229274 BMDMs were transfected with RFP or U1 and then infected with HSV-1 or not 20 samples shares hsv-1
- GSE276253 RNA-seq analysis of the brain of mice following recombinant HSV-1 carrying the S302A mutation in vUNG and the repaired HSV-1 strain 14 samples shares hsv-1
- GSE300560 EGR proteins mediate interferon-independent anti-HSV-1 responses through viral and host targets 12 samples shares hsv-1
- GSE328236 Transcriptomic profiling of Carfilzomib (CFZ) treatment in HSV-1 infected BV2 microglial cells 12 samples shares hsv-1
- GSE291610 Splice isoform-perturbation coupled to single cell transcriptome profiling reveals functions of microexons in neurogenesis and autism-linked pathways [snRNA-Seq] 96 samples shares snrna
- GSE272098 Elevated PKA activity at synapses and broad molecular disturbances in the striatum of Akap11 mutant mice, a genetic model of schizophrenia and bipolar disorder [snRNA-Seq] 61 samples shares snrna
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.