GSM5493577: Mouse retina E11 (scATAC-seq); Mus musculus; ATAC-seq
Dissociated cells were resuspended in ice-cold PBS containing 0.04% bovine serum albumin (BSA). Cell count and viability were assessed by Trypan blue staining.Trypan blue staining. ScATAC-seq was performed using the 10x Genomic single cell ATAC reagent v1.1 kit following the manufacturer's instruction. Briefly, dissociated cells were centrifuged at 300xg for 5 min at 4oC. Cell pellet was resuspended in 100 μl of Lysis buffer, mixed 10x by pipetting and incubated on ice for 3 min. Wash buffer (1 ml) was added to the lysed cells, and cell nuclei were centrifuged at 500xg for 5 min at 40C. Nuclei pellet was re-suspended in 250 μl of 1x Nuclei buffer. Cell nuclei were then counted using Trypan blue. Re-suspended cell nuclei (10-15k) were used for transposition and loaded into the 10x Genomics Chromium Single Cell system. Libraries were amplified with 10 PCR cycles and were sequenced on Illumina NextSeq or NovaSeq with ~200 million reads per library. Sequencing data was processed through the Cell Ranger ATAC 1.1.0 pipeline (10x Genomics) using default parameters.