GSM8972445: Nac tissue, HSV-ZFP189WT; Mus musculus; RNA-Seq
Nuclei were  isolated following the 10X Genomics protocol on nuclei isolation of adult mouse brain tissue for single nuclei RNA sequencing. Briefly, tissue lysis and nuclei washing, myelin removal, and density gradient centrifugation were performed for nuclei isolation. Once nuclei were successfully isolated, we followed the 10x Genomics Chromium single cell 3' gene expression pipeline. The nuclei suspension was loaded into a Chromium Chip B with partitioning oil, reverse transcription reagents, and gel beads containing 10X Genomics barcodes. Barcoded cDNA was generated for each sample then pooled together. Library construction and sequencing on an Illumina HiSeq series sequencer was performed at a depth of approximately 30,000 reads per nuclei. To incorporate three different viral constructs into the reference genome for single-nucleus RNA sequencing analysis, we generated custom reference genomes for each viral construct (ZFP189VPR, ZFP189WT, and ZFP189NFD), following steps recommended by 10X Genomics. In brief, for each viral construct the viral construct sequence was added to the mouse reference genome (mm39) to create a combined fasta file. A corresponding gene annotation in GTF format was also created. The length of each viral sequence was calculated, and an exon annotation was added to the existing GENCODE vM32 annotation file to produce a comprehensive annotation file.
GEO
GSM8972445_r1