TR_04
Mus musculus
Protocols: Fresh tumors and healthy brain tissue were dissected from Nestin-Tv-a RCAS mice. Animals were sacrificed according to institutional ethical guidelines, and brains were rapidly dissected. Tumor and control brain regions were embedded in OCT on dry ice and snap-frozen in isopentane. Samples were stored at –80 °C until cryosectioning.  For RNA quality control, 10 × 5 µm tissue sections from each tumor block were collected into microtubes and processed with the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. RNA concentration and integrity were assessed on an Agilent Bioanalyzer. Only samples with RIN > 8.8 were advanced to Visium library preparation.  Frozen tissue was cryosectioned at 10 µm on a pre-cooled cryostat and mounted onto 10x Genomics Visium Spatial Gene Expression Slides. Sections were fixed in ice-cold methanol, stained with hematoxylin and eosin (H&E), and imaged using a 10× objective including the fiducial frame. Permeabilization was performed for 21 minutes, based on prior optimization for this tissue type. Subsequent steps — second-strand synthesis, cDNA amplification, and library construction — were performed using the Visium Spatial Gene Expression Reagent Kit (10x Genomics, CG000239 Rev G) according to the manufacturer's protocol.
ENA first public
2026-03-29
INSDC center name
Dpt of Translational Cancer Research Lund University
INSDC status
public
Submitter Id
E-MTAB-16421:TR_04
broker name
ArrayExpress
collection date
not collected
common name
house mouse
developmental stage
adult
fastq_id
R423
geographic location (country and/or sea)
not collected
individual
M423
isolate
not applicable
organism part
brain
sample name
E-MTAB-16421:TR_04
sample_type
Recurrent
scientific_name
Mus musculus
sex
male
strain
mixed