title: GSM8122343: patient 13 tumor; Homo sapiens; RNA-Seq
library_construction_protocol: Pieces of resected tumor were flash frozen in liquid nitrogen and stored at -80oC.  Frozen tumors were processed with the 10X Nuclei Isolation Kit as instructed by the manufacturer (PN-1000493). The nuclei were counted using the “dead” concentration on a Countess 3 instrument.  The concentration of the single nuclei suspension was adjusted to 1 × 105 nuclei/mL in the resuspension buffer. Single-nuclei suspension was then loaded onto a microfluidic chip (Chromium Next GEM Chip G, 10X Genomics) and snRNA-seq libraries were constructed according to the manufacturer's instructions (10X Genomics) Any libraries with a concentration of under 2000 pg/µL were concentrated using the Eppendorf 5301 Vacufuge Concentrator System. The resulting snRNA-seq libraries were pooled and sequenced on an Illumina NovaSeq instrument with 150 bp paired end reads. The demultiplexing, alignment, and gene quantification were all performed using Cell Ranger from 10X Genomics with default parameters.  The run data was demultiplexed using cellranger mkfastq and the resulting FASTQ files were aligned and counted using the 10X Genomics pre-built human reference genome refdata-gex-GRCh38-2020-A with cellranger count.