GSM8973626: Mouse sagittal brain, Control + UCC; Mus musculus; OTHER
Animals were euthanized on day 6 (post-ICH / sham), and brain tissues were extracted and snap-frozen in isopentane prechilled in liquid nitrogen in Tissue-Tek OCT and transferred to a -80°C freezer for storage. Cryosections were cut sagittally at a thickness of 10 μm on a Leica CM1860 cryostat. Sections were matched to include equivalent regions of olfactory bulb, striatum, lateral and 4th ventricles, thalamus, midbrain, and cerebellum. Stereo-seq experiments followed STOmics stereo-seq chip-on-a-slide (1cm * 1cm) v1.3 kit. Libraries were constructed and barcoded using STOmics barcode library preparation kit v1.0. We fragmented amplified 300ng cDNA with 10uL of KMB in a total reaction volume of 45 μL, and incubated in a thermocycler 95°C – 5 min, 40°C – 3 min. Reaction was stopped by adding 5 μL of KME, then incubated at 37C for 10min. Fragmented DNA was cleaned up using AMPure beads with a ratio of 1:0.8 beads following manufacturer's protocol. DNA was eluted in 25 uL of 1X TE, and combined with 25 μL of a unique barcode mix, and 50 μL of 2X PCR master mix, and amplified using the following program: 95°C 5 min, 13 cycles of : 98°C – 20 sec, 58°C – 20 sec, 72°C – 30 sec, followed by 72°C   – 5 min. Final product was cleaned up using a double sided AMPure bead cleanup with a 1:0.55 bead ratio following manufacturer's protocol. Libraries were eluted in 20uL of 1X TE. Prepared libraries were then sequenced using a DBSEQ-T7RS sequencer at the Stanford Genomics core, targeting 1.5 billion 75bp PE reads per sample.