GSM8169891: ScRNA, cKO; Mus musculus; RNA-Seq
Single-cell RNA-seq libraries were prepared following the protocols outlined in the Chromium Single Cell 3ʹ Reagent Kits v3 (10x Genomics) in accordance with the manufacturer's instructions. For the isolation of nuclei required for single cell ATAC Sequencing (scATAC-seq), the 10x Genomics Nuclei Isolation protocol (CG000169) was followed. Subsequently, scATAC-seq library construction and sequencing were initiated by incubating the prepared nuclei with Tn5 transposase. The nuclei suspension was then loaded into the Chromium microfluidic chip E, using 10x reagents, and barcoded through the 10x Chromium Controller (10x Genomics, Pleasanton, CA). DNA fragments from the barcoded cells were subsequently amplified, and sequencing libraries were constructed employing reagents from a Chromium Single Cell ATAC reagent kit (10x Genomics; PN-1000110, PN-1000156, PN-1000084), following the manufacturer's instructions as outlined in the Chromium Single Cell ATAC Reagent Kits User Guide (10x Genomics). DNA fragments from the barcoded cells were subsequently amplified, and sequencing libraries were constructed employing reagents from a Chromium Single Cell ATAC reagent kit (10x Genomics; PN-1000110, PN-1000156, PN-1000084), following the manufacturer's instructions as outlined in the Chromium Single Cell ATAC Reagent Kits User Guide (10x Genomics). Post-library construction, preliminary quantification was performed using Qubit 2.0, followed by quality inspection of the Insert DNA of the library using the Fragment Analyzer (FA). Once the Insert size met the expected criteria, qPCR was employed to accurately quantify the effective library concentration at 2 nM. Subsequently, the libraries were pooled and loaded onto an Illumina NovaSeq platform for sequencing.