GSM7729666: HC-2; Mus musculus; ATAC-seq
snATAC-seq: Frozen hippocampal tissue was homogenized in pre-chilled lysis buffer using Dounce homogenizers. The homogenate was then transferred into pre-chilled Nuclei Isolation Columns, and the columns were centrifuged. The flowthrough was briefly vortexed, followed by centrifugation. The nuclear pellet was resuspended in Debris Removal Buffer and centrifuged. The nuclear pellet was then resuspended in Wash Buffer, centrifuged, and finally resuspended in Resuspension Buffer. SPLIT-seq: Frozen hippocampal tissue was homogenized in homogenization buffer using Dounce homogenizers. The homogenate was filtered through strainer and centrifuged. The pellet was resuspended in PBS containing BSA and centrifuged. The pellet was resuspended in PBS and passed through a cell strainer. The Single Cell ATAC-Seq protocol, comprising of the Transposition, GEM Generation, Barcoding, and Library Construction steps were carried out according to the manufacturer's protocol (Chromium Next GEM Single Cell ATAC Kit, 10x Genomics). Libraries were sequenced in paired end in Illumina Novaseq. RNA from the fixed nuclei were subjected to multiple rounds of reverse transcription barcoding and ligation barcoding in customized 96-well thermocycler plates that contain barcoded primers in each well. After the final round of thermocycling, nuclei were pooled together and distributed into 8 sublibraries. Barcoded DNA in each sublibrary was then amplified, following which Template Switching and SPRI Clean-Up steps were performed. Sublibraries were then subjected to Fragmentation, End Repair, and A-Tailing; followed by Post-Fragmentation Double sided SPRI selection, Adaptor Ligation, and Sublibrary Index PCR. Finally, Post-Amplification Double-sided size selection was performed before sequencing them on an Illumina Novaseq Sequencer.