GSM7574424: TBI 3 dpi mouse brain legacy; Mus musculus; RNA-Seq
Additional TBI samples (6 hours and 3 days post-injury) were independently prepared with the Legacy ST kit, an earlier version of 10x Genomics' ST platform. Mouse TBI samples were obtained as described above and prepared for ST analysis following the Library Preparation Manual Version 190219 (10x Genomics, USA). Briefly, ipsilateral brain hemisphere samples were collected at 6 hours and 3 days post-TBI and embedded in O.C.T. Next, 10 μm cryosections were collected onto the Legacy ST library preparation slide, fixed with 4% paraformaldehyde at room temperature and then stained with haematoxylin for 10 minutes, blueing buffer for 1 minute, and eosin Y for 3 minutes in an RNase-Free environment. High-resolution H&E images were again captured using the Zeiss Axio Imager. ST sequencing libraries were prepared as per the manufacturer's instructions, with pre-permeabilisation and permeabilisation performed at 20 minutes and 7 minutes, respectively. On-slide cDNA synthesis, tissue removal, probe cleavage, and final library preparation were all performed as per the manual. High-quality cDNA libraries with sizes ranging between 660-780bp were obtained and sequenced on the Illumina Nextseq500, using a 150 cycles kit with read configuration as read 1 (26 bp) and read 2 (124 bp). Spatial transcriptomics Legacy platform