sn-m3C-seq

• https://doi.org/10.1038/s41592-019-0547-z
• Single-nucleus methyl-3C sequencing (sn-m3C-seq). Specification assumes 2x151bp paired-end reads with 10bp dual indices based on snmC-seq3 and chromatin confirmation capture. Note that all reads are simultaneously bisulfite-converted gDNA containing potential 3C ligation junctions.
• methyl, hic

Final library

methyl

AATGATACGGCGACCACCGAGATCTACACNNNNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNNNHHHHHHHHHXXYAGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG

1. illumina_p5

   • region_type: illumina_p5
   • sequence_type: fixed
   • sequence:

     AATGATACGGCGACCACCGAGATCTACAC

   • min_len: 29
   • max_len: 29
   • onlist: None
   • regions:
2. I2.fastq.gz

   • region_type: fastq
   • sequence_type: joined
   • sequence:

     NNNNNNNNNNN

   • min_len: 10
   • max_len: 10
   • onlist: None
   • regions:
     1. i5_barcode

        • region_type: index5
        • sequence_type: onlist
        • sequence:

          NNNNNNNNNNN

        • min_len: 10
        • max_len: 10
        • onlist: i5_onlist.txt (md5: c36c18a6ee1603758767878b794335f1)
        • regions:
3. truseq_read1

   • region_type: truseq_read1
   • sequence_type: fixed
   • sequence:

     ACACTCTTTCCCTACACGACGCTCTTCCGATCT

   • min_len: 33
   • max_len: 33
   • onlist: None
   • regions:
4. R1.fastq.gz

   • region_type: fastq
   • sequence_type: joined
   • sequence:

     NNNNNNNNHHHHHHHHHX

   • min_len: 151
   • max_len: 151
   • onlist: None
   • regions:
     1. cellbarcode

        • region_type: barcode
        • sequence_type: onlist
        • sequence:

          NNNNNNNN

        • min_len: 8
        • max_len: 8
        • onlist: cb_onlist.txt (md5: 0691bed03feb775d9aff8b37fb4dc94b)
        • regions:
     2. primer9H

        • region_type: methyl
        • sequence_type: random
        • sequence:

          HHHHHHHHH

        • min_len: 9
        • max_len: 9
        • onlist: None
        • regions:
     3. bisulfite_gDNA-1

        • region_type: methyl
        • sequence_type: random
        • sequence:

          X

        • min_len: 1
        • max_len: 134
        • onlist: None
        • regions:
5. R2.fastq.gz

   • region_type: fastq
   • sequence_type: joined
   • sequence:

     XY

   • min_len: 151
   • max_len: 151
   • onlist: None
   • regions:
     1. bisulfite_gDNA-2

        • region_type: methyl
        • sequence_type: random
        • sequence:

          X

        • min_len: 1
        • max_len: 150
        • onlist: None
        • regions:
     2. adaptase_CTs

        • region_type: linker
        • sequence_type: fixed
        • sequence:

          Y

        • min_len: 1
        • max_len: 15
        • onlist: None
        • regions:
6. truseq_read2

   • region_type: truseq_read2
   • sequence_type: fixed
   • sequence:

     AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC

   • min_len: 34
   • max_len: 34
   • onlist: None
   • regions:
7. I1.fastq.gz

   • region_type: fastq
   • sequence_type: joined
   • sequence:

     NNNNNNNNNNNN

   • min_len: 10
   • max_len: 10
   • onlist: None
   • regions:
     1. i7_barcode

        • region_type: barcode
        • sequence_type: onlist
        • sequence:

          NNNNNNNNNNNN

        • min_len: 10
        • max_len: 10
        • onlist: i7_onlist.txt (md5: 47874d94562f3b00125385a6c60daf9d)
        • regions:
8. illumina_p7

   • region_type: illumina_p7
   • sequence_type: fixed
   • sequence:

     ATCTCGTATGCCGTCTTCTGCTTG

   • min_len: 24
   • max_len: 24
   • onlist: None
   • regions:

hic

AATGATACGGCGACCACCGAGATCTACACNNNNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNNNHHHHHHHHHXXYAGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG

1. illumina_p5

   • region_type: illumina_p5
   • sequence_type: fixed
   • sequence:

     AATGATACGGCGACCACCGAGATCTACAC

   • min_len: 29
   • max_len: 29
   • onlist: None
   • regions:
2. I2.fastq.gz

   • region_type: fastq
   • sequence_type: joined
   • sequence:

     NNNNNNNNNNN

   • min_len: 10
   • max_len: 10
   • onlist: None
   • regions:
     1. i5_barcode

        • region_type: index5
        • sequence_type: onlist
        • sequence:

          NNNNNNNNNNN

        • min_len: 10
        • max_len: 10
        • onlist: i5_onlist.txt (md5: c36c18a6ee1603758767878b794335f1)
        • regions:
3. truseq_read1

   • region_type: truseq_read1
   • sequence_type: fixed
   • sequence:

     ACACTCTTTCCCTACACGACGCTCTTCCGATCT

   • min_len: 33
   • max_len: 33
   • onlist: None
   • regions:
4. R1.fastq.gz

   • region_type: fastq
   • sequence_type: joined
   • sequence:

     NNNNNNNNHHHHHHHHHX

   • min_len: 151
   • max_len: 151
   • onlist: None
   • regions:
     1. cellbarcode

        • region_type: barcode
        • sequence_type: onlist
        • sequence:

          NNNNNNNN

        • min_len: 8
        • max_len: 8
        • onlist: cb_onlist.txt (md5: 0691bed03feb775d9aff8b37fb4dc94b)
        • regions:
     2. primer9H

        • region_type: hic
        • sequence_type: random
        • sequence:

          HHHHHHHHH

        • min_len: 9
        • max_len: 9
        • onlist: None
        • regions:
     3. chromcontact-1

        • region_type: hic
        • sequence_type: random
        • sequence:

          X

        • min_len: 1
        • max_len: 134
        • onlist: None
        • regions:
5. R2.fastq.gz

   • region_type: fastq
   • sequence_type: joined
   • sequence:

     XY

   • min_len: 151
   • max_len: 151
   • onlist: None
   • regions:
     1. chromcontact-2

        • region_type: hic
        • sequence_type: random
        • sequence:

          X

        • min_len: 1
        • max_len: 150
        • onlist: None
        • regions:
     2. adaptase_CTs

        • region_type: linker
        • sequence_type: fixed
        • sequence:

          Y

        • min_len: 1
        • max_len: 15
        • onlist: None
        • regions:
6. truseq_read2

   • region_type: truseq_read2
   • sequence_type: fixed
   • sequence:

     AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC

   • min_len: 34
   • max_len: 34
   • onlist: None
   • regions:
7. I1.fastq.gz

   • region_type: fastq
   • sequence_type: joined
   • sequence:

     NNNNNNNNNNNN

   • min_len: 10
   • max_len: 10
   • onlist: None
   • regions:
     1. i7_barcode

        • region_type: barcode
        • sequence_type: onlist
        • sequence:

          NNNNNNNNNNNN

        • min_len: 10
        • max_len: 10
        • onlist: i7_onlist.txt (md5: 47874d94562f3b00125385a6c60daf9d)
        • regions:
8. illumina_p7

   • region_type: illumina_p7
   • sequence_type: fixed
   • sequence:

     ATCTCGTATGCCGTCTTCTGCTTG

   • min_len: 24
   • max_len: 24
   • onlist: None
   • regions: