BMDMs were transfected with RFP or U1 and then infected with HSV-1 or not
Single-nucleus RNA-seq · mouse · 20 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). 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
- 20 samples: 9 conditions, mostly in duplicateGroups 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 GSE229274_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 PRJNA953941 and SRA study SRP431714. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 9 replicated groups read from 20 sample titles; they account for 18 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.
- GSM7157870 RFP mock rep1 RFP mock
- GSM7157871 U1 mock rep1 U1 mock
- GSM7157872 RFP HSV(MOI=1) 4h rep1 RFP HSV(MOI=1) 4h
- GSM7157873 U1 HSV(MOI=1) 4h rep1
- GSM7157874 RFP HSV(MOI=1) 8h rep1 RFP HSV(MOI=1) 8h
- GSM7157875 U1 HSV(MOI=1) 8h rep1 U1 HSV(MOI=1) 8h
- GSM7157876 RFP HSV(MOI=0.1) 4h rep1 RFP HSV(MOI=0.1) 4h
- GSM7157877 U1 HSV(MOI=0.1) 4h rep1 U1 HSV(MOI=0.1) 4h
- GSM7157878 RFP HSV(MOI=0.1) 8h rep1 RFP HSV(MOI=0.1) 8h
- GSM7157879 U1 HSV(MOI=0.1) 8h rep1 U1 HSV(MOI=0.1) 8h
- GSM7157880 RFP mock rep2 RFP mock
- GSM7157881 U1 mock rep2 U1 mock
- GSM7157882 RFP HSV(MOI=1) 4h rep2 RFP HSV(MOI=1) 4h
- GSM7157883 U1 HSV(MOI=1) 4h rep2
- GSM7157884 RFP HSV(MOI=1) 8h rep2 RFP HSV(MOI=1) 8h
- GSM7157885 U1 HSV(MOI=1) 8h rep2 U1 HSV(MOI=1) 8h
- GSM7157886 RFP HSV(MOI=0.1) 4h rep2 RFP HSV(MOI=0.1) 4h
- GSM7157887 U1 HSV(MOI=0.1) 4h rep2 U1 HSV(MOI=0.1) 4h
- GSM7157888 RFP HSV(MOI=0.1) 8h rep2 RFP HSV(MOI=0.1) 8h
- GSM7157889 U1 HSV(MOI=0.1) 8h rep2 U1 HSV(MOI=0.1) 8h
- GSE328236 Transcriptomic profiling of Carfilzomib (CFZ) treatment in HSV-1 infected BV2 microglial cells 12 samples shares hsv-1, infected
- GSE233794 PMs were infected with HSV-1 or not 9 samples shares hsv-1, infected
- GSE233795 WT or Usp5 knockout (KO) PMs were infected with HSV-1 or not 6 samples shares hsv-1, infected
- GSE289356 Effects of type I IFN signaling on gene expression of Mycobacterium tuberculosis-infected bone marrow-derived macrophages (BMDMs) 34 samples shares infected, bmdms
- GSE239543 RNA-seq data from mouse BMDMs infected with Salmonella enterica serovar Typhimurium 6 samples shares infected, bmdms
- GSE299440 Subclinical Neonatal HSV-1 Infection Triggers Immune Responses and Modulates Neurological Pathways Leading to Long-Term Sequelae 20 samples shares hsv-1
- GSE237796 Bulk RNAseq REX-1 RFP mESC 2019 15 samples shares rfp
- 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
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.