The Chromium Single Cell ATAC chemistry is shown here. Oligo sequence information is taken from Chromium Single Cell ATAC Reagent Kits. The cell barcodes used in this method is slightly different from those used in the 3' gene expression assay, although the number of the cell barcodes is the same (737,280). You can find out all the cell barcodes (16 bp) here: 737K-cratac-v1.txt. This file is copied from Cell Ranger ATAC (using Cell Ranger ATAC v1.0.0 as an example) /path/to/cellranger-atac-1.0.0/1.0.0/lib/python/barcodes/.
According to Amini et al., 2014, the Tn5 transposase-mediated tagmentation contains two stages: (1) a tagging stage where the Tn5 transposome binds to DNA, and (2) a fragmentation stage where the Tn5 transposase is released from DNA using heat or denaturing agents, such as sodium dodecyl sulfate (SDS). Since the Tn5 tagging does not fragment DNA, the nuclei would remain intact after incubation with the Tn5 transposome. This provides an opportunity to perform a bulk Tn5 tagging reaction upfront, then each invididual tagged nuclei are captured in the droplet for barcoding and amplification. This is basically how 10x Single Cell ATAC works.
Beads-oligo: |--5'-
SI-PCR Primer B (PN-2000128): 5'-
i7 Sample Index Plate N, Set A (PN-3000262): 5'-
Nextera left primer entry point (s5): 5'-
Nextera right primer entry point (s7): 5'-
Illumina Nextera Read 1 primer: 5'-
Illumina Nextera Read 2 primer: 5'-
Sample index sequencing primer (index1): 5'-
Cell barcode sequencing primer (index2): 5'-
Illumina P5 adapter: 5'-
Illumina P7 adapter: 5'-
Product 1 (s5 at both ends, not amplifiable due to semi-suppressiev PCR): 5'- TCGTCGGCAGCGTC AGATGTGTATAAGAGACAG XXXXXXXXXXXX...XXXCTGTCTCTTATACACATCT TCTACACATATTCTCTGTC XXX...XXXXXXXXXXXXGACAGAGAATATGTGTAGA CTGCGACGGCTGCT -5' Product 2 (s7 at both ends, not amplifiable due to semi-suppressiev PCR): 5'-GTCTCGTGGGCTCGG AGATGTGTATAAGAGACAG XXXXXXXXXXXX...XXXCTGTCTCTTATACACATCT TCTACACATATTCTCTGTC XXX...XXXXXXXXXXXXGACAGAGAATATGTGTAGA GGCTCGGGTGCTCTG -5' Product 3 (different ends, amplifiable): 5'-TCGTCGGCAGCGTC AGATGTGTATAAGAGACAG XXXXXXXXXXXX...XXXCTGTCTCTTATACACATCT TCTACACATATTCTCTGTC XXX...XXXXXXXXXXXXGACAGAGAATATGTGTAGA GGCTCGGGTGCTCTG -5'
|--5'- AATGATACGGCGACCACCGAGATCTACAC [16-bp cell barcode] TCGTCGGCAGCGTC --------------> 5'-TCGTCGGCAGCGTC AGATGTGTATAAGAGACAG XXXXXXXXXXXX...XXXXXXXXXXXXCTGTCTCTTATACACATCT CCGAGCCCACGAGAC AGCAGCCGTCGCAG TCTACACATATTCTCTGTC XXXXXXXXXXXX...XXXXXXXXXXXXGACAGAGAATATGTGTAGA GGCTCGGGTGCTCTG -5'
5'- AATGATACGGCGACCACCGAGATCTACAC [16-bp cell barcode] TCGTCGGCAGCGTC AGATGTGTATAAGAGACAG XXXXXXXXXXXX...XXXXXXXXXXXXCTGTCTCTTATACACATCT CCGAGCCCACGAGAC TTACTATGCCGCTGGTGGCTCTAGATGTG [16-bp cell barcode] AGCAGCCGTCGCAG TCTACACATATTCTCTGTC XXXXXXXXXXXX...XXXXXXXXXXXXGACAGAGAATATGTGTAGA GGCTCGGGTGCTCTG -5'
5'- AATGATACGGCGACCACCGAGA ----------------> 5'-AATGATACGGCGACCACCGAGATCTACAC [16-bp cell barcode] TCGTCGGCAGCGTC AGATGTGTATAAGAGACAG XXX...XXXCTGTCTCTTATACACATCT CCGAGCCCACGAGAC TTACTATGCCGCTGGTGGCTCTAGATGTG [16-bp cell barcode] AGCAGCCGTCGCAG TCTACACATATTCTCTGTC XXX...XXXGACAGAGAATATGTGTAGA GGCTCGGGTGCTCTG -5' <----------------GGCTCGGGTGCTCTG [8-bp sample index]TAGAGCATACGGCAGAAGACGAAC -5'
5'- AATGATACGGCGACCACCGAGATCTACAC NNNNNNNNNNNNNNNN TCGTCGGCAGCGTC AGATGTGTATAAGAGACAG XXX...XXXCTGTCTCTTATACACATCT CCGAGCCCACGAGAC NNNNNNNNATCTCGTATGCCGTCTTCTGCTTG -3' 3'-TTACTATGCCGCTGGTGGCTCTAGATGTG NNNNNNNNNNNNNNNN AGCAGCCGTCGCAG TCTACACATATTCTCTGTC XXX...XXXGACAGAGAATATGTGTAGA GGCTCGGGTGCTCTG NNNNNNNNTAGAGCATACGGCAGAAGACGAAC -5'Illumina P5 16-bp cell s5 ME gDNAME s7 8-bpIllumina P7 barcode sample index
5'- TCGTCGGCAGCGTC AGATGTGTATAAGAGACAG -------> 3'-TTACTATGCCGCTGGTGGCTCTAGATGTG NNNNNNNNNNNNNNNN AGCAGCCGTCGCAG TCTACACATATTCTCTGTC XXX...XXXGACAGAGAATATGTGTAGA GGCTCGGGTGCTCTG NNNNNNNNTAGAGCATACGGCAGAAGACGAAC -5'
5'- CTGTCTCTTATACACATCT CCGAGCCCACGAGAC -------> 3'-TTACTATGCCGCTGGTGGCTCTAGATGTG NNNNNNNNNNNNNNNN AGCAGCCGTCGCAG TCTACACATATTCTCTGTC XXX...XXXGACAGAGAATATGTGTAGA GGCTCGGGTGCTCTG NNNNNNNNTAGAGCATACGGCAGAAGACGAAC -5'
5'- AATGATACGGCGACCACCGAGATCTACAC NNNNNNNNNNNNNNNN TCGTCGGCAGCGTC AGATGTGTATAAGAGACAG XXX...XXXCTGTCTCTTATACACATCT CCGAGCCCACGAGAC NNNNNNNNATCTCGTATGCCGTCTTCTGCTTG -3' <---------------AGCAGCCGTCGCAG TCTACACATATTCTCTGTC -5'
5'- AATGATACGGCGACCACCGAGATCTACAC NNNNNNNNNNNNNNNN TCGTCGGCAGCGTC AGATGTGTATAAGAGACAG XXX...XXXCTGTCTCTTATACACATCT CCGAGCCCACGAGAC NNNNNNNNATCTCGTATGCCGTCTTCTGCTTG -3' <------GACAGAGAATATGTGTAGA GGCTCGGGTGCTCTG -5'