Characterization of cuprizone mouse model at single-cell and spatial transcriptomics level[bulk RNA-seq]
Spatial transcriptomics · mouse · 13 samples
- What it is
- Spatial transcriptomicsGene activity measured with its position in a tissue section.
- Organism
- Mus musculus (mouse)
- Samples
- 13 samples: 13 samples, each with a distinct title — no replicated groupsGroups 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 GSE255368_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: Spatial studies usually ship Space Ranger style folders (count matrix plus tissue images). Look for them among the supplementary files.
Also filed as BioProject PRJNA1074759 and SRA study SRP489039. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 13 sample titles: 13 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.
- GSM8070639 control-1-1
- GSM8070640 control-2-1
- GSM8070641 control-3-1
- GSM8070642 control-4-1
- GSM8070643 control-5-1
- GSM8070644 cpz4W-1-1
- GSM8070645 cpz4W-2-1
- GSM8070646 cpz4W-3-1
- GSM8070647 cpz4W-4-1
- GSM8070648 Veh-1-1
- GSM8070649 Veh-2-1
- GSM8070650 Veh-3-1
- GSM8070651 Veh-4-1
- GSE300288 Single-cell and spatial transcriptomics analysis of tobacco-associated lung adenocarcinoma development, and in response to targeting inflammation alone or in combination with immune checkpoint blockade in precancerous phase [scRNA-seq] 31 samples shares single-cell, spatial, rna-seq
- GSE319614 Bulk RNA-seq transcriptome profiling of hippocampus across 17 autism spectrum disorder mouse models 269 samples shares rna-seq, bulk
- GSE326452 Bulk RNA-seq of mouse brain following closed head injury: role of IL-1R1 signaling 200 samples shares rna-seq, bulk
- GSE254396 Single-cell and bulk RNA sequencing of mouse atherosclerosis disease stage course [TRAP-seq] 71 samples shares single-cell, bulk
- GSE228960 Bulk RNA-Seq from kidneys of uninephrectomized db/db mice as a model of severe diabetic kidney disease 28 samples shares rna-seq, bulk
- GSE262879 Single-cell RNA-sequencing of murine pancreatic tumors derived from the orthotopic transplantation of Smad4 wild-type (WT) or Smad4 knockout (KO) pancreatic ductal adenocarcinoma (PDAC) KPC organoids in nu/nu mice. 18 samples shares single-cell, rna-seq
- GSE227108 Integrated single-cell analysis defines the epigenetic basis of castration-resistant prostate luminal cells (scRNA-seq) 18 samples shares single-cell, rna-seq
- GSE264278 TIme-cource single-cell RNA-seq analysis of bleomycin and LPS-induced lung injury and fibrosis 18 samples shares single-cell, rna-seq
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.