Repurposing Large-Format Microarrays for Scalable Spatial Transcriptomics - Bulk RNA-seq
Spatial transcriptomics · mouse · 180 samples
- What it is
- Spatial transcriptomicsGene activity measured with its position in a tissue section.
- Organism
- Mus musculus (mouse)
- Samples
- 180 samples: 180 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.
- Paper
- Repurposing large-format microarrays for scalable spatial transcriptomicsNature methods · 2025
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 GSE266246_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 PRJNA1106443 and SRA study SRP504999. 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 180 sample titles: 180 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.
- GSM8243030 Liver, CTRL, m1, d0.5
- GSM8243031 Liver, CTRL, m2, d0.5
- GSM8243032 Liver, CTRL, m3, d0.5
- GSM8243033 Liver, CTRL, m4, d0.5
- GSM8243034 Liver, 5mg-kg LPS, m5, d0.5
- GSM8243035 Liver, 5mg-kg LPS, m6, d0.5
- GSM8243036 Liver, 5mg-kg LPS, m7, d0.5
- GSM8243037 Liver, 5mg-kg LPS, m8, d0.5
- GSM8243038 Liver, TNFKO + 5mg-kg LPS, m9, d0.5
- GSM8243039 Liver, TNFKO + 5mg-kg LPS, m10, d0.5
- GSM8243040 Liver, TNFKO + 5mg-kg LPS, m11, d0.5
- GSM8243041 Liver, TNFKO + 5mg-kg LPS, m12, d0.5
- GSM8243042 Spleen, CTRL, m1, d0.5
- GSM8243043 Spleen, CTRL, m2, d0.5
- GSM8243044 Spleen, CTRL, m3, d0.5
- GSM8243045 Spleen, CTRL, m4, d0.5
- GSM8243046 Spleen, 5mg-kg LPS, m5, d0.5
- GSM8243047 Spleen, 5mg-kg LPS, m6, d0.5
- GSM8243048 Spleen, 5mg-kg LPS, m7, d0.5
- GSM8243049 Spleen, 5mg-kg LPS, m8, d0.5
- GSM8243050 Spleen, TNFKO + 5mg-kg LPS, m9, d0.5
- GSM8243051 Spleen, TNFKO + 5mg-kg LPS, m10, d0.5
- GSM8243052 Spleen, TNFKO + 5mg-kg LPS, m11, d0.5
- GSM8243053 Spleen, TNFKO + 5mg-kg LPS, m12, d0.5
- GSM8243054 Colon, CTRL, m1, d0.5
- GSM8243055 Colon, CTRL, m2, d0.5
- GSM8243056 Colon, CTRL, m3, d0.5
- GSM8243057 Colon, CTRL, m4, d0.5
- GSM8243058 Colon, 5mg-kg LPS, m5, d0.5
- GSM8243059 Colon, 5mg-kg LPS, m6, d0.5
- GSM8243060 Colon, 5mg-kg LPS, m7, d0.5
- GSM8243061 Colon, 5mg-kg LPS, m8, d0.5
- GSM8243062 Colon, TNFKO + 5mg-kg LPS, m9, d0.5
- GSM8243063 Colon, TNFKO + 5mg-kg LPS, m10, d0.5
- GSM8243064 Colon, TNFKO + 5mg-kg LPS, m11, d0.5
- GSM8243065 Colon, TNFKO + 5mg-kg LPS, m12, d0.5
- GSM8243066 Thymus, CTRL, m1, d0.5
- GSM8243067 Thymus, CTRL, m2, d0.5
- GSM8243068 Thymus, CTRL, m3, d0.5
- GSM8243069 Thymus, CTRL, m4, d0.5
+ 140 more — browse all 180 samples with per-sample file links →
- GSE238217 A combination treatment based on drug repurposing demonstrates mutation agnostic efficacy in pre-clinical retinopathy models. [RNA-seq: Rd10] 24 samples shares repurposing, rna-seq
- GSE238216 A combination treatment based on drug repurposing demonstrates mutation agnostic efficacy in pre-clinical retinopathy models. [RNA-seq: RPE65-KO] 13 samples shares repurposing, rna-seq
- GSE302163 Repurposing Zafirlukast Confers Renal Protection in Ischemia-Reperfusion Injury via Suppressing Macrophage METosis [RNA-Seq] 6 samples shares repurposing, rna-seq
- GSE263877 A combination treatment based on drug repurposing demonstrates mutation-agnostic efficacy in pre-clinical retinopathy models [scRNA-seq: Rpe65-KO] 3 samples shares repurposing, rna-seq
- GSE234797 A combination treatment based on drug repurposing demonstrates mutation-agnostic efficacy in pre-clinical retinopathy models [scRNA-seq: Rd10] 3 samples shares repurposing, rna-seq
- GSE238218 A combination treatment based on drug repurposing demonstrates mutation agnostic efficacy in pre-clinical retinopathy models. 40 samples shares repurposing
- GSE295746 Repurposing the Memory-promoting Meclofenoxate Hydrochloride as a Treatment for Parkinson’s Disease through Integrative Multi-omics analysis 28 samples shares repurposing
- GSE279117 HIF1α deletion promotes mitochondrial repurposing in bone marrow-derived macrophages, but not in tissue-resident alveolar macrophages 24 samples shares repurposing
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.