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====Genomic regions to target in the first probe set==== *Hox gene cluster: chr7:27.12M-27.30M. This is very small, will select barcodes that cover the region 25M-29M, 2,800 probes in total. {| {{table}} | align="center" style="background:#f0f0f0;"|'''Barcode''' | align="center" style="background:#f0f0f0;"|'''Barcode position''' | align="center" style="background:#f0f0f0;"|'''Digit offset''' | align="center" style="background:#f0f0f0;"|'''Digit ID''' | align="center" style="background:#f0f0f0;"|'''Digit position''' | align="center" style="background:#f0f0f0;"|'''Digit color''' |- | 3421234||chr7:25092383-27094188||1||85||chr7:25092383-25292367||3 |- | 3421234||chr7:25092383-27094188||2||86||chr7:25392752-25592739||4 |- | 3421234||chr7:25092383-27094188||3||87||chr7:25692908-25892831||2 |- | 3421234||chr7:25092383-27094188||4||88||chr7:25992844-26192792||1 |- | 3421234||chr7:25092383-27094188||5||89||chr7:26294006-26493909||2 |- | 3421234||chr7:25092383-27094188||6||90||chr7:26594282-26794247||3 |- | 3421234||chr7:25092383-27094188||7||91||chr7:26894433-27094188||4 |- | 3421241||chr7:27494794-29492367||1||93||chr7:27494794-27693444||3 |- | 3421241||chr7:27494794-29492367||2||94||chr7:27793569-27993512||4 |- | 3421241||chr7:27494794-29492367||3||95||chr7:28093548-28292337||2 |- | 3421241||chr7:27494794-29492367||4||96||chr7:28392552-28592526||1 |- | 3421241||chr7:27494794-29492367||5||97||chr7:28692735-28892703||2 |- | 3421241||chr7:27494794-29492367||6||98||chr7:28992787-29192364||4 |- | 3421241||chr7:27494794-29492367||7||99||chr7:29292653-29492367||1 |- | |} *Chr15 regions based on HiC data: will use whole-genome barcodes in the entire chr15 (39,160 probes); **As a backup plan, I also manually picked digits in these regions for a second probe set that has a different amplification primer pair (V4). 11,759 probes in total Domain ChrStart ChrEnd Size Digit IDs(color) A 42,252,708 42,772,708 520,000 66(1),67(1),68(1) A 44,092,708 44,852,708 760,000 72(2),73(2),74(2) B 52,532,708 53,052,708 520,000 100(3),101(3),102(3) B 58,492,708 59,212,708 720,000 119(4),120(4),121(4) A 67,172,946 68,092,946 920,000 148(1),149(2),150(1),151(2) A 76,252,945 77,212,945 960,000 179(2),180(1),181(2) B 83,202,945 84,848,996 1,646,051 200(3),201(4),202(1),203(3),204(4),205(1) B 93,598,996 94,918,996 1,320,000 234(4),235(2),236(3),237(2),238(4) ./[[Media:extractProbesInDigits.txt|extractProbesInDigits.pl]] [[Media:chr15_HiC_region_digit_info.txt|chr15_HiC_region_digit_info.txt]] chr15_probe_grouped_by_digits_200k_100k_100.txt > chr15_HiC_region_oligoPools.txt *Chr3 region that might be inverted in African: 45M-60M, 15,226 probes in total. To fill out the space of 80,000 oligos, I decided to expand the region to 20M-66M, and include 26,281 probes *Combined all the oligos and split them based on the color, I ended up getting four pools with different sizes. This is because with the way I assign the barcodes different chromosomes (or regions) have enrichment on different colors, which leads to the unbalanced distribution when design probes on a small number of chromosomal regions. 19518 Feb2012_80k_oligoPools.color_1.txt 28967 Feb2012_80k_oligoPools.color_2.txt 15400 Feb2012_80k_oligoPools.color_3.txt 16114 Feb2012_80k_oligoPools.color_4.txt Since each pool contains 20k sequences, I will have to exclude 8967 oligos in color 2. These oligos are from the end of chromosome 15. *Because the pool sizes for the other three colors are less than 20k, I decided to use the space to test additional ideas. These oligos will also be amplified with the V4 primer pairs, so that we can separate them from the whole genome set. **Different probe density: 50/digit; 200/digit; 400/digit **Different barcode size/spacing: 20kb/10kb; 40kb/20kb; 100kb/50kb; 400kb/200kb **The regions were hand-picked. [[Media:chr19_various_spacing_probe_density_barcode_info.txt]] *After including these sequences to the pools, and taking only the first 20k from the color 2 pool, I got the following four sets of oligos to order: V6 V4 19,518 [[Media:Feb2012_80k_set_1.txt.gz|Feb2012_80k_set_1.txt]] 16559 2959 20,000 [[Media:Feb2012_80k_set_2.txt.gz|Feb2012_80k_set_2.txt]] 16400 3600 18,850 [[Media:Feb2012_80k_set_3.txt.gz|Feb2012_80k_set_3.txt]] 13000 5850 19,301 [[Media:Feb2012_80k_set_4.txt.gz|Feb2012_80k_set_4.txt]] 13314 5987 Genomics regions covered: V4: chr15 HiC domain (hand-picked barcodes); chr19 variable spacing. V6: chr7 Hox cluster, chr15 HiC domain (globally assigned barcodes); chr3
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