GSM8229742: control; Mus musculus; OTHER
The hearts from Collagen1α1-GFP 8-12 weeks old, healthy or infarcted mice (3 and 5 dpi) were excised and washed in PBS, embedded in OCT compound, frozen in dry ice and sectioned in a cryostat at a thickness of 10 μm at -20 °C following the manufacturer's recommendations. The RNA quality of the tissues was checked by extracting RNA from tissue sections with the Qiagen RNeasy extraction kit (Qiagen) according to the manufacturer's instructions. RNA quality was assessed with a 4200 TapeStation (Agilent Technologies), and all the samples had a RIN between 7.2 and 7.7. In the final experiment, the mRNA capture was performed following instructions of the Visium Spatial Gene Expression Reagent Kits User Guide (10x Genomics). For optimization of the tissue permeabilization, seven sections from the 3 dpi sample were collected onto a -20 °C pre-equilibrated Visium tissue optimization slide (10X Genomics) and the manufacturer's recommendations were followed. Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's instructions. Libraries were loaded at 650 pM and sequenced on a Nextseq 2000 System (Illumina) using a Nextseq2000 P3 Reagent Kit (100 cycles, Illumina), at an average sequencing depth of approximately 100,000 reads per spot (25-35% of the 5,000 total spots on the slide were used). Sequencing was performed using the following read protocol: Read1, 28 cycles; i7 index, 10 cycles; i5 index, 10 cycles; Read2, 91 cycles.