The sci-ATAC-seq uses the combinatorial indexing to identify single cells without single cell isolation. Cells can be identified by the unique combination of the Tn5 barcodes and i5/i7 indices (see below). In Cusanovich et al., 2015 and Cusanovich et al., 2018, they refer the exact method to an early study that was published in Nature Genetics (Amini et al., 2014). The sequences described here are taken from their Supplementary Table 4 from the Nature Genetics paper. Note the Tn5 sequences here are different from the Illumina Nextera Kit.
Barcoded Tn5 sequence s5: 5'-
Barcoded Tn5 sequence s7: 5'-
Tn5 binding site 19-bp Mosaic End (ME) bottom: 5'- /Phos/
P5 index primer entry point (s5): 5'-
P7 index primer entry point (s7): 5'-
P5 index primer: 5'-
P7 index primer: 5'-
Read 1 sequencing primer: 5'- GCGATCGAGGACGGC
Index 1 sequencing primer (i7): 5'-
Index 2 sequencing primer (i5): 5'-
Read 2 seuquencing primer: 5'- CACCGTCTCCGCCTC
Product 1 (s5 at both ends, not amplifiable due to semi-suppressive PCR: 5'- TCGTCGGCAGCGTCTCCACGC [8-bp Tn5 index] GCGATCGAGGACGGCAGATGTGTATAAGAGACAG XXXXXXXXXXXX...XXXCTGTCTCTTATACACATCT TCTACACATATTCTCTGTC XXX...XXXXXXXXXXXXGACAGAGAATATGTGTAGA CGGCAGGAGCTAGCG[8-bp Tn5 index] CGCACCTCTGCGACGGCTGCT -5' Product 2 (s7 at both ends, not amplifiable due to semi-suppressiev PCR): 5'-GTCTCGTGGGCTCGGCTGTCCCTGTCC [8-bp Tn5 index] CACCGTCTCCGCCTCAGATGTGTATAAGAGACAG XXXXXXXXXXXX...XXXCTGTCTCTTATACACATCT TCTACACATATTCTCTGTC XXX...XXXXXXXXXXXXGACAGAGAATATGTGTAGA CTCCGCCTCTGCCAC[8-bp Tn5 index] CCTGTCCCTGTCGGCTCGGGTGCTCTG -5' Product 3 (different ends, amplifiable): 5'-TCGTCGGCAGCGTCTCCACGC [8-bp Tn5 index] GCGATCGAGGACGGCAGATGTGTATAAGAGACAG XXXXXXXXXXXX...XXXCTGTCTCTTATACACATCT TCTACACATATTCTCTGTC XXX...XXXXXXXXXXXXGACAGAGAATATGTGTAGA CTCCGCCTCTGCCAC[8-bp Tn5 index] CCTGTCCCTGTCGGCTCGGGTGCTCTG -5'
5'- AATGATACGGCGACCACCGAGATCTACAC NNNNNNNNTCGTCGGCAGCGTCTCCACGC ------> 5'-TCGTCGGCAGCGTCTCCACGC [8-bp Tn5 index] GCGATCGAGGACGGCAGATGTGTATAAGAGACAG XXXXXXXXXXXX...XXXCTGTCTCTTATACACATCT TCTACACATATTCTCTGTC XXX...XXXXXXXXXXXXGACAGAGAATATGTGTAGA CTCCGCCTCTGCCAC[8-bp Tn5 index] CCTGTCCCTGTCGGCTCGGGTGCTCTG -5' <------CCTGTCCCTGTCGGCTCGGGTGCTCTG NNNNNNNNTAGAGCATACGGCAGAAGACGAAC -5'
5'- AATGATACGGCGACCACCGAGATCTACAC NNNNNNNNTCGTCGGCAGCGTCTCCACGC NNNNNNNN GCGATCGAGGACGGCAGATGTGTATAAGAGACAG XXXXXX...XXXXXXCTGTCTCTTATACACATCT GAGGCGGAGACGGTGNNNNNNNN GGACAGGGACAGCCGAGCCCACGAGAC NNNNNNNNATCTCGTATGCCGTCTTCTGCTTG -3' 3'-TTACTATGCCGCTGGTGGCTCTAGATGTG NNNNNNNNAGCAGCCGTCGCAGAGGTGCG NNNNNNNN CGCTAGCTCCTGCCGTCTACACATATTCTCTGTC XXXXXX...XXXXXXGACAGAGAATATGTGTAGA CTCCGCCTCTGCCACNNNNNNNN CCTGTCCCTGTCGGCTCGGGTGCTCTG NNNNNNNNTAGAGCATACGGCAGAAGACGAAC -5'Illumina P5 i5s5 8 bp ME gDNAME 8 bp s7 i7Illumina P7 Tn5 barcode Tn5 barcode
5'- GCGATCGAGGACGGC AGATGTGTATAAGAGACAG -------------> 3'-TTACTATGCCGCTGGTGGCTCTAGATGTG NNNNNNNNAGCAGCCGTCGCAGAGGTGCG NNNNNNNN CGCTAGCTCCTGCCGTCTACACATATTCTCTGTC XXXXXX...XXXXXXGACAGAGAATATGTGTAGA CTCCGCCTCTGCCACNNNNNNNN CCTGTCCCTGTCGGCTCGGGTGCTCTG NNNNNNNNTAGAGCATACGGCAGAAGACGAAC -5'
5'- CTGTCTCTTATACACATCT GAGGCGGAGACGGTG------------------------------------------> 3'-TTACTATGCCGCTGGTGGCTCTAGATGTG NNNNNNNNAGCAGCCGTCGCAGAGGTGCG NNNNNNNN CGCTAGCTCCTGCCGTCTACACATATTCTCTGTC XXXXXX...XXXXXXGACAGAGAATATGTGTAGA CTCCGCCTCTGCCACNNNNNNNN CCTGTCCCTGTCGGCTCGGGTGCTCTG NNNNNNNNTAGAGCATACGGCAGAAGACGAAC -5'
5'- AATGATACGGCGACCACCGAGATCTACAC NNNNNNNNTCGTCGGCAGCGTCTCCACGC NNNNNNNN GCGATCGAGGACGGCAGATGTGTATAAGAGACAG XXXXXX...XXXXXXCTGTCTCTTATACACATCT GAGGCGGAGACGGTGNNNNNNNN GGACAGGGACAGCCGAGCCCACGAGAC NNNNNNNNATCTCGTATGCCGTCTTCTGCTTG -3' <------------------------------------CGCTAGCTCCTGCCGTCTACACATATTCTCTGTC -5'
5'- AATGATACGGCGACCACCGAGATCTACAC NNNNNNNNTCGTCGGCAGCGTCTCCACGC NNNNNNNN GCGATCGAGGACGGCAGATGTGTATAAGAGACAG XXXXXX...XXXXXXCTGTCTCTTATACACATCT GAGGCGGAGACGGTGNNNNNNNN GGACAGGGACAGCCGAGCCCACGAGAC NNNNNNNNATCTCGTATGCCGTCTTCTGCTTG -3' <-------------GACAGAGAATATGTGTAGA CTCCGCCTCTGCCAC -5'