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Table 2 Summary of information about the different experiments

From: Targeted Chromatin Capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements

Type Genome assembly version Coordinates oligo-nucleotide positions Size of area of interest (Mb) Median resolution (kbp) Raw paired reads (n) Paired reads that could be mapped to the whole genome (n) Mapped paired reads between the region of interest and the whole genome (n) Uniquely mapped paired-reads in the whole genome without self-ligation and and non-digestion (n) Uniquely mapped paired-reads between the region of interest and the whole genome without self-ligation and non-digestion (n) Uniquely mapped paired-reads inside the region of interest without self-ligation and non-digestion (n) ‘Interactions’ inside the region of interest (n) Average number of reads/interaction in the region of interest (n)
Mouse fetal liver mm9 chr7: 109876329-111966581 2.1 2 65,165,916 9,300,108 5,716,401 4,559,952 2,723,515 557,763 4,057 137
Mouse fetal brain mm9 chr7: 109876329-111966581 2.1 2 84,977,143 6,380,256 3,191,360 3,018,169 1,414,128 271,177 2,369 114
HB2 hg18 chr11: 1100646 - 3173091 2.1 4.1 51,952,969 13,813,662 12,127,051 5,503,770 4,745,779 1,929,245 8,989 215
  1. Columns from left to right: Tissue type or cells; genome assembly version; summary of the positions of oligonucleotides (region of interest); the size and the median resolution of the area under investigation; the number of the raw paired-reads (before alignment, that is, all reads from the sequenator); the number of mapped paired reads that could be mapped back to the whole genome; the number of paired reads between the region of interest (fragments with oligonucleotides) and the whole genome; the number of uniquely mapped paired-reads in the whole genome after removal of the self-ligation and non-digestion events (See Methods); the number of uniquely mapped paired-reads between the region of interest (fragments with oligonucleotides) and the whole genome after removal of the self-ligation and non-digestion events; the number of uniquely mapped paired-reads inside the region of interest after removal of the self-ligation and non-digestion events; the number of ‘interactions’ between fragments in the region of interest; average number reads per interaction. The capture efficiency and purification (enrichment) by hybridization is high (that is, how many reads from the region of interest (‘specific’ reads) are found when compared to total reads, that is, the reads that are from other areas of the genome and not containing a sequence from the area of interest (‘non-specific’ reads)). We find that the ‘specific’ reads represent 61%, 50%, and 88% of total reads (‘specific’ plus ‘non-specific’) for mouse primary erythroid cells, mouse fetal brain cells, and HB2, respectively, including the self-ligation and non-digestion events. By removing those events those numbers change to 60%, 47%, and 86%, respectively. This means for example that 60% of the fetal liver reads (2,723,515) represent 2.1 × 106 bases (the region of interest) while the remaining 40% of reads represents 3.109 bases (the whole genome), numbers that indicate a high level of enrichment by the hybridization step.