raw read of Pm scATAC rep 1 plate C9
Libraries were prepared using 24 Tn5 adapters: ME-A and 16 ME-B, each containing a 5 nt cell barcode. This scATAC-seq lib were prepared using proso millet (Panicum miliaceum) nuclei with 10% spike-in nuclei from Foxtail millet (secteria italica), which should be removed after mapping to the Pm genome as cells with low mapping %.ME-A sequence: GGCGGTAGGCGTG NNNNN AGATGTGTATAAGAGACAGME-B sequence: CCAACACCCGTGCG NNNNN AGATGTGTATAAGAGACAGThe 24 column ME-A barcodes used were: ATACG, AGCGA, CTAAG, TGTCG, GTAGT, GTATA, ATTCC, GACTT, TTACT, CAATT, CATCT, TCGCG, TGTTT, TCCCT, GGCAG, CAAAA, GTGAG, TGGAT, CCGAG, ACTCG, GTCCT, TAAGA, ACCCC, AAACA.The 16 row ME-B barcodes used were: TCGGA, GTTTC, AGCTT, TCATT, GCTCC, ACTAA, CGAGG, ACCGG, CGGTT, GGAAC, GATGA, AACAT, CGCAC, TGACC, CGCGT, TTCCC.After Tn5 tagmentation, 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 6 nt plate barcode was added to the cell+well barcode before combining the data from each plate.