ONLINE. Online supplementary information S1 (Box) Method. Supplementary data. Online links

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Margery Stokes
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1 ONLINE Online supplementary information S1 (Box) Method The of the human or mouse genomes were downloaded from the UCSC Genome Browser using the Tables feature. The d component of each genome was comprehensively sampled using the cytogenetic bands track for the human genome or the GC content track for the mouse genome. FASTA files were downloaded, with the repetitive fraction represented by nucleotides in lower case. A Perl program was written to count the number of motifs in upper-, lower- or either case (on rare occasions the motif spanned a transition between and repetitive s). The motifs contained within low complexity and simple repeats were quantified by limiting the lower-case annotation for each repeat class and repeating the quantification. Our goal was to precisely reproduce a previous study that quantified motif frequencies in transposable-element-derived s 27.The data were compiled using Excel (Microsoft). Supplementary data Perl program for counting motifs. A summary of CpG, HpaII and NotI frequencies in and repetitive s in the human and mouse genomes (see Figure 1 for diagrammatic representation of the data). Online links Genetic Information Research Institute (Girinst): The Human Epigenome Project: The UCSC Genome Browser:

2 #!/usr/bin/perl -w # Determining frequency of motifs, NRG review study. # Get the DNA data print "Please type the filename of the DNA data: "; $dna_filename = <STDIN>; chomp $dna_filename; # Does the file exist? unless ( -e $dna_filename) { print "File \"$dna_filename\" doesn\'t seem to exist!!\n"; print "Running analysis, please wait\n\n"; # Can we open the file? unless ( open(dnafile, $dna_filename) ) { print "Cannot open file = <DNAFILE>; close DNAFILE; $DNA = join( # Remove whitespace $DNA =~ s/\s//g; # Initialize the counts. # Notice that we can use scalar variables to hold numbers. $cg = 0; $CG = 0; $ccgg = 0; $CCGG = 0; $cg=0; $ccgg=0; $noti=0; $NOTI=0; $NotItotal=0; $C=0; $G=0; $A=0; $T=0; # Use a regular expression "trick", and five while loops, # to find the counts of the four bases plus errors while($dna =~ /cg/g){$cg++ while($dna =~ /CG/g){$CG++ while($dna =~ /ccgg/g){$ccgg++ while($dna =~ /CCGG/g){$CCGG++ while($dna =~ /CG/ig){$cG++ while($dna =~ /CCGG/ig){$ccGG++ while($dna =~ /gcggccgc/g){$noti++ while($dna =~ /GCGGCCGC/g){$NOTI++ while($dna =~ /GCGGCCGC/ig){$NotItotal++ while($dna =~ /C/ig){$C++ while($dna =~ /G/ig){$G++ while($dna =~ /A/ig){$A++ while($dna =~ /T/ig){$T++

3 print "cg\tcg\tccgg\tccgg\tcgtotal\tccggtotal\tnoti\tnoti\tnotitotal\tctotal\tgtotal\ tatotal\tttotal\n "; print "$cg\t$cg\t$ccgg\t$ccgg\t$cg\t$ccgg\t$noti\t$noti\t$notitotal\t$c\t$g\t$a\t$t\n \n "; # Also write the results to a file called "countbase" $outputfile = "countbase"; unless ( open(countbase, ">$outputfile") ) { print "Cannot open file \"$outputfile\" to write to!!\n\n"; print COUNTBASE "cg\tcg\tccgg\tccgg\tcgtotal\tccggtotal\tnoti\tnoti\tnotitotal\tctotal\tgtotal\ tatotal\tttotal\n "; print COUNTBASE "$cg\t$cg\t$ccgg\t$ccgg\t$cg\t$ccgg\t$noti\t$noti\t$notitotal\t$c\t$g\t$a\t$t\n \n "; close(countbase); # exit the program

4 cg CG CG total ccgg CCGG CCGG noti NOTI NotI total C total G total A total T total Total size (G+C)% CpG O/E CpG fraction (%) CpG fraction (%) HpaII fraction (%) HpaII fraction (%) HpaII/CpG total (%) HpaII/CpG total (%) NotI/CpG total (%) NotI/CpG total (%) repetitive repetitive total repetitive GENOME total total repetitive repetitive repetitive repetitive chr1 1,139,194 1,078,771 2,226,782 96,687 90, , ,169,649 46,160,728 64,558,181 64,675, ,564, chr2 1,066,548 1,077,591 2,152,372 86,160 78, , ,745,067 47,806,555 70,908,939 71,082, ,542, chr3 867, ,682 1,619,040 69,852 50, , ,582,987 38,597,439 58,625,984 58,668, ,474, chr4 796, ,045 1,457,580 61,002 41, , ,687,423 35,698,035 57,716,055 57,741, ,842, chr5 782, ,552 1,508,459 61,670 49, , ,077,244 35,119,552 53,609,359 53,747, ,553, chr6 757, ,102 1,472,287 61,595 47, , ,103,083 33,127,112 50,523,694 50,503, ,257, chr7 791, ,166 1,552,107 65,580 59, , ,497,915 31,473,153 45,821,860 45,884, ,677, chr8 649, ,246 1,301,222 50,847 46,741 98, ,578,739 28,581,187 42,618,835 42,569, ,348, chr9 588, ,956 1,171,502 48,990 48,168 97, ,890,796 23,868,278 33,942,349 33,923, ,624, chr10 646, ,659 1,349,199 53,235 55, , ,272,024 27,264,607 38,296,908 38,340, ,173, chr11 628, ,693 1,287,302 51,165 56, , ,187,673 27,220,932 38,245,140 38,255, ,909, chr12 679, ,554 1,262,367 56,830 44, , ,464,613 26,453,283 38,439,928 38,469, ,826, chr13 404, , ,544 31,741 25,350 57, ,407,057 18,402,969 29,335,975 29,414,591 95,560, chr14 428, , ,635 35,392 33,171 69, ,798,515 17,846,563 25,670,458 25,876,224 87,191, chr15 430, , ,482 36,695 35,177 72, ,158,606 17,137,512 23,495,764 23,468,318 81,260, chr16 524, ,060 1,109,706 46,023 54, , ,850,782 17,921,938 22,017,803 22,142,331 79,932, chr17 555, ,134 1,151,192 52,198 58, , ,697,811 17,666,031 21,134,814 21,179,496 77,678, chr18 323, , ,183 25,598 24,113 50, ,838,392 14,862,842 22,464,643 22,488,504 74,654, chr19 544, ,551 1,057,112 53,880 56, , ,473,831 13,506,669 14,383,178 14,422,296 55,785, chr20 340, , ,998 29,615 33,486 63, ,087,664 13,127,877 16,503,881 16,705,908 59,425, chr21 168, , ,735 13,852 16,395 30, ,939,139 6,928,364 10,062,475 9,994,567 33,924, chr22 255, , ,205 23,858 32,028 56, ,223,628 8,218,016 8,978,130 8,932,549 34,352, chrx 744, ,481 1,218,870 55,599 31,586 87, ,411,910 29,448,629 45,105,588 45,249, ,216, chry 123,397 75, ,782 8,920 5,208 14, ,884,812 4,907,704 7,374,991 7,482,235 24,649, GENOME 14,240,674 13,592,835 27,942,663 1,176,984 1,075,053 2,270,194 2,300 7,130 9, ,029, ,345, ,834, ,217,890 2,843,428, Within Simple repeats 226,664 7, ,943 9, , ,303,533 5,755,970 12,222,587 10,238,026 33,520, Within Low complexity repeats 184, ,730 28, ,414 1, ,245 3,175,664 3,165,688 9,206,321 7,343,495 22,891, Minus simple/low complexity repeats (transposable element only) 13,829,280 13,585,556 27,523,990 1,138,983 1,074,790 2,231, ,130 7, ,550, ,424, ,406, ,636,369 2,787,016, Within CpG islands 155,784 1,903,247 2,061,289 23, , ,079 1,213 5,207 6,483 7,349,427 7,414,202 3,505,038 3,330,753 21,599, Motif proportion islands of HpaII sites within 0.47 of islands 0.22 of NotI sites within 0.75 of NotI sites islands 0.73

5 cg CG CG total ccgg CCGG CCGG total noti NOTI NotI total C total G total A total T total Total size (G+C)% CpG O/E CpG fraction CpG fraction HpaII fraction HpaII fraction HpaII/CpGtotal HpaII/CpGtotal NotI/CpG total NotI/CpG total repetitive repetitive repetitive GENOME total total repetitive repetitive repetitive repetitive chr1 559, ,621 1,479,804 47,642 58, , ,503,706 39,456,961 56,628,061 56,444, ,033, chr2 514, ,509 1,513,519 43,060 68, , ,175,380 37,197,747 51,105,064 51,171, ,649, chr3 467, ,554 1,206,164 40,223 44,070 84, ,830,070 31,877,331 46,843,662 46,935, ,487, chr4 482, ,332 1,306,697 41,121 60, , ,466,579 31,471,600 42,874,559 42,947, ,760, chr5 446, ,170 1,268,412 38,021 58,050 96, ,281,354 29,262,459 39,604,803 39,550, ,699, chr6 427, ,007 1,159,234 36,811 45,843 83, ,972,891 29,921,804 42,321,890 42,345, ,562, chr7 405, ,113 1,100,827 34,350 51,420 86, ,779,765 26,734,827 35,151,126 35,237, ,902, chr8 377, ,693 1,144,789 31,848 53,340 85, ,547,321 26,514,563 36,124,132 36,043, ,229, chr9 368, ,318 1,075,425 30,457 49,166 80, ,845,825 25,810,560 34,703,514 34,683, ,043, chr10 390, ,225 1,112,435 32,673 46,693 80, ,336,743 26,388,205 37,338,023 37,425, ,488, chr11 364, ,423 1,159,714 30,399 62,234 93, ,942,464 25,921,592 33,292,048 33,193, ,349, chr12 318, , ,480 26,852 38,559 65, ,993,296 23,034,790 32,257,810 32,541, ,827, chr13 337, , ,920 27,716 38,772 66, ,471,216 23,448,167 33,031,034 32,862, ,812, chr14 323, , ,388 27,372 35,041 62, ,161,646 23,164,803 33,279,317 33,330, ,935, chr15 286, , ,537 24,382 37,481 62, ,967,310 19,974,183 27,669,575 27,649,943 95,261, chr16 277, , ,634 23,917 29,405 53, ,449,344 19,477,246 28,101,533 28,136,885 95,165, chr17 286, , ,383 23,761 39,959 64, ,168,807 19,119,808 25,731,836 25,685,481 89,705, chr18 241, , ,176 20,291 27,450 48, ,846,604 16,880,106 23,855,456 23,889,660 81,471, chr19 163, , ,050 13,258 25,906 39, ,661,369 11,635,328 15,685,408 15,538,450 54,520, chrx 517, , ,793 48,510 21,272 70, ,880,771 29,861,009 46,315,245 46,245, ,302, chry 69,377 39, ,302 5,439 2,187 7, ,482,971 3,489,230 5,462,580 5,422,344 17,857, GENOME 7,627,246 13,157,791 20,900, , ,546 1,555,126 2,162 3,841 6, ,765, ,642, ,376, ,283,008 2,496,067, Within Simple repeats 290,976 8, ,123 5, , ,748,232 14,769,628 28,209,042 22,869,035 80,595, Within Low complexity repeats 114, ,992 12, , ,284,537 3,910,676 9,893,047 7,950,207 26,038, Minus simple/low complexity repeats (transposable element only) 7,221,278 13,149,644 20,486, , ,394 1,536,998 1,280 3,841 5, ,732, ,962, ,274, ,463,766 2,389,433, Within CpG islands 70,895 1,048,389 1,120,308 9, , , ,845 3,478 3,831,478 3,842,495 1,924,438 1,806,347 11,404, Motif proportion islands of within 0.58 of islands 0.14 of NotI sites within 0.63 of NotI sites islands 0.74

Assignment 5: Integrative epigenomics analysis

Assignment 5: Integrative epigenomics analysis Due date: Friday, 2/24 10am. Note: no late assignments will be accepted. Introduction CpG islands (CGIs) are important regulatory regions in the genome. What