GSM8567509: cKO-scATAC; Mus musculus; ATAC-seq
For ATAC-seq, nuclei suspensions were prepared using the FL™ Automated Fluorescence Cell Counter (Logos Biosystems) and incubated in a transposition mix, following the 10x Chromium Multiome ATAC+ Gene Expression protocol (CG000338).  For scRNA-seq, single-cell suspensions were diluted to ~10,000 cells and processed using the Next GEM 3' v3.1 protocol (CG000315). For scATAC seq transposed nuclei were mixed with master mix, loaded into a Chromium chip, and processed in the Chromium Controller. Post-transposition, samples were amplified, indexed with P7 and sample indices, and qualified using the Agilent 4200 TapeStation. scATAC seq libraries were sequenced on an Illumina HiSeq platform. Single cell ATAC data was analyzed by Cell Ranger ARC v2.0.0 (10x Genomics) was used to generate FASTQ files from raw data. For scRNA-seq, single-cell suspensions were diluted to ~10,000 cells and processed using the Next GEM 3' v3.1 protocol (CG000315). Cells were loaded into a Chromium Next GEM Chip G, barcoded, reverse transcribed, and the resulting cDNA was enriched via PCR. Final cDNA libraries were quantified and qualified using qPCR (KAPA) and Agilent 4200 TapeStation before sequencing on the Illumina HiSeq platform. Single cell gene expression data was analyzed using Cell Ranger v7.0.1 (10x Genomics). Briefly, raw BCL files from Illumina HiSeqXten were demultiplexed to generate FASTQ from raw data. For scRNA seq, extracted  cells were loaded into a Chromium Next GEM Chip G, barcoded, reverse transcribed, and the resulting cDNA was enriched via PCR. Final cDNA libraries were quantified and qualified using qPCR (KAPA) and Agilent 4200 TapeStation before sequencing on the Illumina HiSeq platform. Single cell gene expression data was analyzed using Cell Ranger v7.0.1 (10x Genomics). Briefly, raw BCL files from Illumina HiSeqXten were demultiplexed to generate FASTQ from raw data.