title: GSM5752982: LN-2, ATAC; Mus musculus; ATAC-seq
library_construction_protocol: Cervical lymph nodes draining the ear skin were homogenized and ILCs were enriched by depleting T cells, B cells and granulocytes using negative magnetic-activated cell sorting with anti-CD3, CD19, and CD11b antibodies. Remaining cells were collected and frozen. Later, samples from multiple mice (3 in vehicle control, 3 in calcipotriol treatment groups) were thawed, pooled, and processed to obtain single nuclei suspensions that were further processed using the 10X Genomics multiome pipeline. Multiome 3v3.1 GEX and ATAC libraries were prepared as recommended by the 10x Genomics ChromiumNextGEM Multiome_ATAC_GEX_User_Guide_RevD (CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User Guide_RevD.pdf).  For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 16 rxns PN-1000283, Chromium Next GEM Chip J Single Cell Kit, 48 rxns PN-1000234, Single Index Kit N Set A, 96 rxns PN-1000212 (ATAC), Dual Index Kit TT Set A, 96 rxns PN-1000215 (3v3.1 GEX), were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  GEX libraries were pooled and run over 0.05 of a NovaSeq6000 S4 flow cell using the XP workflow and running a 28x10x10x150 sequencing recipe in accordance with manufacturer's protocol.  Target coverage was 500M reads per sample.  ATAC libraries were pooled and run over 0.167 of a NovaSeq6000 S1 flow cell using the XP workflow and running a 51x8x16x51 sequencing recipe in accordance with manufacturer's protocol.  Target coverage was 250M reads per sample.