TP_1083
Mus musculus
Protocols: Mouse brain tissue (one healthy and one RCAS-derived glioma) was collected and post-fixed in 4% paraformaldehyde for 24 hours, dehydrated, and embedded in paraffin. Sections of 3 µm thickness were cut from the FFPE blocks and mounted onto standard glass slides for histological preparation and subsequent spatial transcriptomic processing.  RNA quality was assessed from each FFPE block by processing ten 5 µm sections using the RNeasy FFPE Kit (Qiagen 73504). Extracted RNA was analyzed on an Agilent Bioanalyzer to determine DV200 values and confirm that they met the recommended threshold for Visium HD spatial transcriptomics.  Tissue sections mounted on glass slides were H&E stained prior to hybridization. Probe hybridization was performed using the Visium Mouse Transcriptome Probe Set v2.0 (mm10-2020-A), supplemented with custom-designed probes targeting RCAS-derived transgenes (one probe for human PDGFB and two probes for RFP). Following hybridization, slides were processed using the Visium CytAssist instrument to transfer probe-labeled tissue onto Visium HD slides.
ENA first public
2026-03-29
INSDC center name
Dpt of Translational Cancer Research Lund University
INSDC status
public
Submitter Id
E-MTAB-16420:TP_1083
broker name
ArrayExpress
collection date
not collected
common name
house mouse
developmental stage
adult
disease
tumor
fastq_id
7
geographic location (country and/or sea)
not collected
individual
1083
isolate
not applicable
organism part
brain
sample name
E-MTAB-16420:TP_1083
sample_type
Primary
scientific_name
Mus musculus
sex
male
spaceranger_id
TP_1083
strain
mixed