title: GSM6805174: Upf2fl/fl NPCs, GFP lentivirus treatment, 72 hours [GFP_10x_1]; Mus musculus; RNA-Seq
library_construction_protocol: 72 hours after the infection, NPCs were dissociated with 1x TrypLE Express and resuspended in 1x PBS with 0.04% BSA. NPCs were loading the single cell chip with a target recovery of 10k cells into the 10x Genomic Chromium machine, as the GFP group was loaded with 23.6 µl NPCs with 19.6 µl H2O and Cre group had 33 µl NPCs with 10.2 µl H2O. After the 10x program finished, 100 µl GEMs per sample were recovered for GEM-RT incubation. GEM-RT cDNA was further cleaned up and amplified with 12 cycles. Samples were determined as passing the QC with fragments ranging from 300 bp to 9,000 bp, and the concentration for GFP was 15.17 ng/µl while Cre was 14.27 ng/µl. 20 µl cDNA per sample was used as input for library generation. After the cDNA fragmentation and end repair & A-tailing, the adapter was ligated for amplification. Different sample indices (indices from 10x index plate or indices synthesized by IDT)  were used for additional 14 PCR cycles. PCR products were cleaned up and size selected, and samples were determined to pass the QC with a size range from 300 to 600 bp. Samples with the same mass were multiplexed and sent for sequencing.