GSM8069361: Bone marrow of naive mice replicate 1 (scATAC-seq); Mus musculus; ATAC-seq
Mouse: myeloid cells were sorted from respective tissues (Lung/BM/blood) based on markers described in Methods section. For scRNA-seq, cells were encapsulated following 10x Genomics Chromium Next GEM Single Cell 3ʹ v3.1 protocol. For scATAC-seq, cells were subjected to nuclei isolation following 10x Genomics Chromium Next GEM Single Cell ATAC v1.1 protocol. Nuclei quality was verified by brightfield microscopy prior to loading. A target recovery number of 8000~10000 nuclei or cells were loaded onto each lane of a 10X Chromium chip according to manufacturer's instructions. Human: CD45positive cells after sorting or bead-based enrichment were subjected to nuclei isolation following 10x Genomics Chromium Next GEM Single Cell ATAC Kit v1.1 or Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol. In case of low-input samples (with <100,000 cells), we utilized 0.2 ml PCR tubes and centrifuged at 4C using swinging rotor buckets to maximize nuclear recovery. For human NSCLC sample multiome assays, cells were subjected to nuclei isolation following 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol in the presence of RNAse inhibitor (Sigma) and DTT (Sigma) to prevent RNA degradation. Nuclei quality was verified by brightfield microscopy prior to loading. A target recovery number of 8000~10000 nuclei were loaded onto each lane of a 10X Chromium chip according to manufacturer's instructions. Mouse: Libraries were prepared according to manufacturer's instructions. All libraries were quantified via Agilent 2100 hsDNA Bioanalyzer. scRNA-seq libraries were sequenced at a targeted depth of minimum 25,000 read pairs per cell pooled on the Illumina NovaSeq 6000 S2 100 cycle kit. scATAC-seq libraries were sequenced at a targeted depth of minimum 25,000 read pairs per cell using the Illumina NovaSeq 6000 S2 100 cycle kit. Human: Libraries were prepared according to manufacturer's instructions. All libraries were quantified via Agilent 2100 hsDNA Bioanalyzer. Libraries were sequenced at a targeted depth of minimum 25,000 read pairs per cell using the Illumina NovaSeq 6000 S2 100 cycle kit.