CTRL_E14
Rattus norvegicus
Protocols: Embryos were collected from pregnant Wistar rats at gestational day 14–16 under isoflurane anesthesia, following institutional ethical approval (No. 2020PS357K, Shengjing Hospital, China Medical University). Immediately after cesarean section, embryos were rinsed in ice-cold sterile saline to remove blood and blotted dry with RNase-free gauze. Each intact embryo was embedded in pre-cooled optimal cutting temperature (OCT) compound (SAKURA, Japan) in sagittal orientation and snap-frozen in isopentane chilled with liquid nitrogen for 1 min. Samples were stored at −80 °C until sectioning. Spatially barcoded mRNA molecules were captured in situ on 10x Genomics Visium Spatial Gene Expression Slides. Tissue sections (10 µm thick) were fixed in 3.7% formaldehyde, stained with hematoxylin and eosin, and imaged before permeabilization. Permeabilization was optimized for embryonic tissue using 0.5 U/ml collagenase and 0.2 mg/ml BSA in HBSS at 37 °C for 20 min, followed by digestion in 0.1% pepsin in 0.1 M HCl for 7 min. Released mRNA hybridized to the oligo-dT primers within each spatial capture spot. Reverse transcription generated spatially barcoded cDNA molecules, which were enzymatically released using a Proteinase K/PKD buffer (Qiagen) mix at 56 °C for 1.5 h, then collected for library construction. cDNA libraries were prepared following the 10x Genomics Visium Spatial Gene Expression User Guide and previously published protocols (Salmén et al., 2018; Ståhl et al., 2016). Released cDNA underwent second-strand synthesis, in vitro transcription, adaptor ligation, and second reverse transcription to generate indexed sequencing libraries. The libraries were purified, quantified, and quality-checked before sequencing. All spatial library preparation steps were performed on an automated MBS 8000 system (Jemt et al., 2016) by Biomarker Technologies Corporation (Beijing, China).
ENA first public
2026-01-01
INSDC center name
Translational Medicine, The Hospital for Sick Children
INSDC status
public
Submitter Id
E-MTAB-16069:CTRL_E14
age
E14
broker name
ArrayExpress
collection date
not collected
common name
Norway rat
developmental stage
E14
disease
Control
genotype
wild type genotype
geographic location (country and/or sea)
not collected
individual
CTRL_E14
isolate
not applicable
organism part
embryonic structure
sample name
E-MTAB-16069:CTRL_E14
scientific_name
Rattus norvegicus
strain
Wistar IGS Rat