title: GSM5216654: AML01_Alu_pool_cell_14 [i502_B2_i702_201027_AML01_Alu_pool_S4_L001]; Homo sapiens; Bisulfite-Seq
library_construction_protocol: We utilised the G&T-seq protocol to separate genomic DNA and RNA from the single-cell samples [Macaulay, I.C., et al., G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nature Methods, 2015.]. Genomic DNA from each cell was purified and bisulphite conversion was performed as described [Angermueller, C., et al., Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity. Nature methods, 2016], with minor modifications. Bisulphite conversion was carried out using the EZ-96 DNA Methylation-Direct MagPrep Kit (Integrated Sciences, catalog # D5054) with half volumes of the manufacturer's instructions. Bisulphite converted DNA was eluted directly from MagBeads into PCR-mix, and amplification of TEs was performed with MagBeads still in the well. PCR cycling conditions used were 95°C for 5 min (1 cycle), 98°C for 20 sec, 53°C for 15 sec, 72°C for 1 min (35 cycles), and 72°C for 10min (1 cycle). PCR mix used 7.5µl 1x KAPA HiFi hotStart Uracil + ReadyMix (Millennium, catalog # ROC-07959079001) and 0.3µM primer mix. Primers were designed against SINE Alu and LINE-1 consensus sequences (Supplementary Figure S2A) and are contained in Supplementary Tables S1 and S2. After amplification, plates of 96 single cell libraries purified using a 1.2x volume of AMPure XP beads (Beckman Coulter, catalog # A63881). All libraries were then quantified using the Qubit dsDNA HS kit (Life Technologies), normalised and pooled to a single tube. Pools where then added to 0.8µM NEBNext dual index oligo sets (Genesearch, catalog # E7780S) and 14.5µl 1x KAPA HiFi HotStart ReadyMix (Millennium, catalog # ROC-07958935001) for indexing and adaptor addition. PCR cycling conditions used were 98°C for 45 sec (1 cycle), 98°C for 15 sec, 65°C for 30 sec, 72°C for 30 sec (5 cycles), and 72°C for 5 min (1 cycle). Pools were then purified using 0.9x volume of Ampure XP beads, normalised and combined for sequencing.