GSM5454326: RNASET2HippocampusControl5000nucleiSakib_C3_L003; Mus musculus; RNA-Seq
10X Chromium v3.1 kit (NextGEM) and 5000 nuclei out of 300000 sorted nuclei were barcoded Mice were deeply anesthetized with ketamine and medetomidine and transcardially perfused with phosphate buffered saline (PBS, pH 7.4). After cervical dislocation, the whole brain was removed from the skull and the preparation of the hippocampus and caudate putamen was performed in a petri dish filled with ice cold PBS buffer under a binocular. Tissue sample from two hemispheres of different mice were pooled and immediately frozen on liquid nitrogen and stored at -80°C until further processing. Nuclei from frozen mouse brain tissues were isolated according to previously published protocol with modifications.65 Isolated total nuclei were stained with 7AAD (Invitrogen, Cat: 00-6993-50) and single nuclei were sorted using BD FACS Aria III sorter. Sorted nuclei were counted in Countess II FL Automated Counter. Around 5000 single nuclei per sample were used for GEM generation, barcoding, and cDNA libraries according to 10X Chromium Next GEM Single Cell 3′ Reagent v3.1 protocol. Pooled libraries were sequenced in Illumina NextSeq 550 in order to achieve >50,000 reads/nuclei. 10X genomics single-cell seq