GSM6592446: StageII-Day8_ATAC; Homo sapiens; ATAC-seq
The nuclei were isolated and washed according to the methods supplied by 10x Gemomics: Nuclei Isolation for Single Cell ATAC + Gene Expression Sequencing (CG000365). Then the nuclei were resuspended in chilled Diluted Nuclei Buffer (10x Genomics, PN2000153). The volume of Diluted Nuclei Buffer used was based on the number of starting cells and the final target nuclei concentration. Nuclei were counted using Countstar (Rigel S2) and then subjected to single-cell multiome libraries construction immediately. Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide (CG000338) using Chromium Next GEM Chip J Single Cell Kit (PN-1000234) and Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (PN-1000283). Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. The transposed nuclei in bulk samples were then loaded into a microfluidic chip and run in the Chromium Controller to be partitioned into nanoliter-scale Gel Beads-in-emulsion (GEMs). A pool of ~736,000 10x Barcodes is sampled to separately and uniquely index the transposed DNA and cDNA of each individual nucleus. ATAC and gene expression (GEX) libraries were generated from the same pool of pre-amplified transposed DNA/cDNA (performed by CapitalBio Technology, Beijing). The ATAC libraries were sequenced using an Illumina Novaseq sequencer with a sequencing depth of at least 25,000 read pairs per nucleus with pair-end 50bp (PE50) reading strategy, while GEX libraries were sequenced with pair-end 150bp (PE150) reading strategy and a sequencing depth of at least 20,000 read pairs per nucleus.