QuiCAT: A Scalable and Flexible Framework for Mapping Synthetic Sequences

Six bulk and five clonal primary pancreatic tumor mouse cell lines used for the single cell RNA-seq experiment. The five clonal cell lines were barcoded with Nuclear procode vector kit library (Addgene #1000000197) and isolated as single clones. All eleven cell lines were trypsinized and pooled together in equal amounts, then 5 million cells were fixed according to the protocol for Chromium Fixed RNA Profiling (10x). After fixation, a pool of 1 million cells was used for hybridization with probes, including custom probes, which lasted 19 h. For generation of GEM, 20000 cells were loaded on the chip and library was constructed as described in the guidelines (10x genomics,User guide CG000691). Quality and size analysis of cDNAs and libraries was performed on an Agilent Bioanalyzer 2100 using HS DNA Kit (Agilent). The sample was sequenced with Novaseq PE100 mode (Illumina) following the standard protocol.