title: Demultiplexed browntop signalgrass leaf sci-ATAC-seq rep 1
design: Each plate contains nuclei from replicate 1 and replicate 2. The two replicates were tagged using Tn5 with different ME-A and ME-B barcode adapters in four 96-well plates, and can be separated during the demultiplexing step.ME-A sequence: GGCGGTAGGCGTG NNNNN AGATGTGTATAAGAGACAG;ME-B sequence: CCAACACCCGTGCG NNNNN AGATGTGTATAAGAGACAG.The 12 column ME-A barcodes used by rep 1 were: ATACG, AGCGA, CTAAG, TGTCG, GTAGT, GTATA, ATTCC, GACTT, TTACT, CAATT, CATCT, TCGCG.The 12 column ME-A barcodes used by rep 2 were: TGTTT, TCCCT, GGCAG, CAAAA, GTGAG, TGGAT, CCGAG, ACTCG, GTCCT, TAAGA, ACCCC, AAACA.The 8 row ME-B barcodes used by rep 1 were: TCGGA, GTTTC, AGCTT, TCATT, GCTCC, ACTAA, CGAGG, ACCGG.The 8 row ME-B barcodes used by rep 2 were: CGGTT, GGAAC, GATGA, AACAT, CGCAC, TGACC, CGCGT, TTCCC.After Tn5 tagmentation, nuclei from rep1 and rep2 were mixed and approximately 10 nuclei were distributed to each well of a 96-well plate. PCR was performed using 8 well-indexed forward primers (ScPCR_F) and 12 well-indexed reverse primers (scPCR_R), each containing 6 nt barcodes.ScPCR_F: ACACTCTTTCCCTACACGACGCTCTTCCGATCT NNNNNN GGCGGTAGGCGTGScPCR_R: GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT NNNNNN CCAACACCCGTGCGThe 8 forward primer barcodes used were: GATCAG, TAGCTT, GGCTAC, CTTGTA, AGTCAA, AGTTCC, ATGTCA, CCGTCC.The 12 reverse primer barcodes used were: GTAGAG, GTCCGC, GTGAAA, GTGGCC, GTTTCG, CGTACG, GAGTGG, GGTAGC, ACTGAT, ATGAGC, ATTCCT, CAAAAG.After sequencing, the data from each plate was demultiplexed using the 24x16 cell and 8x12 well barcodes. Additionally, a 7 nt plate barcode was added to the cell+well barcode before combining the data from each plate.