GSM3144562: scATAC-seq_MM087_Sox10KD_48hr_Cell_15; Homo sapiens; OTHER
Cells were trysinised, spun down (1000 RPM, 5 min), medium was removed and cells were resuspended in fresh medium and passed through a 40 um filter, counted and diluted till 200,000 cells per mL. Cells were loaded (using a 40:60 ratio of RGT:cells) on a primed Open App IFC (10-17 um) and scATAC-seq was performed using the Fluidigm C1 system as described before [Buenrostro et al., 2015] (the protocol for ATAC-seq from the C1 Script Hub was used). After cell loading, the plate was visually checked under a microscope and the number of cells in each of the capture chambers was noted. Next, the “Sample prep” was performed on the Fluidigm C1 during which the cells underwent lysis and ATAC-seq fragments were prepared. Library prep was performed as described before [Buenrostro et al., 2015]. After the first steps of the library construction by the “Sample prep” on the Fluidigm C1, the libraries were harvested into a 96-well plate and were amplified in a 25 uL PCR reaction. The PCR products were pooled and purified on a single MinElute PCR purification column for a final library volume of 15 uL. Quality checks were performed using the Bioanalyzed high sensitivity chips. Fragments under 150 bp were removed by bead-cleanup using AMPure XP beads (1.2x bead ratio) (Beckman Coulter).
GEO Accession
GSM3144562