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=='''Preliminary Sequencing Results'''== *Table below summarizes results *The clonal rate is much better, averaging around 50% which is good *The mapping rate is a little low for some of these. I will use Dr. Zhang's suggestion and using the quality trimming algorithm to see if it helps the mapping rate *Some of the read numbers (unfiltered) are a little low. These will turn into good libraries if resequenced at a higher depth, and I will let Alan know which libraries to resequence *Lane 7 failed due to an instrument error and will have to be resequenced *I will focus more analysis on the Alzheimer's cortex library with enough reads {| {{table}} | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''Sample''' | align="center" style="background:#f0f0f0;"|'''Type''' | align="center" style="background:#f0f0f0;"|'''Lane''' | align="center" style="background:#f0f0f0;"|'''Index''' | align="center" style="background:#f0f0f0;"|'''# Reads''' | align="center" style="background:#f0f0f0;"|'''Mapped (%)''' | align="center" style="background:#f0f0f0;"|'''% Clonal''' | align="center" style="background:#f0f0f0;"|'''# Usable Reads''' |- | HL135||2041_059_Alzcbl_p||Neuron, alz_cerebellum||5||34||7476700||2576033 (34.35)||79.86||518850|||| |- | HL135||2041_060_alzcbl_p||Neuron, alz_cerebellum||5||37|||||||| |- | HL135||60831_061_normal_p||Neuron, norm_ctx||5||35||7522321||2325921 (30.92)||51.25||1133796 |- | HL135||60831_062_normal_p||Neuron, norm_ctx||5||36||16340952||12017029 (73.54)||61.66||4607752 |- | HL135||60831_063_normal_p||Neuron, norm_ctx||6||33||12367633||8354396 (67.55)||56.66||3621045 |- | HL135||60831_064_normal_p||Neuron, norm_ctx||6||34||3870522||2470947 (63.84)||40.74||1464367 |- | HL135||60831_065_normal_p||Neuron, norm_ctx||6||35||8175228||3443631 (42.12)||33.42||2292841 |- | HL135||60831_066_normal_p||Neuron, norm_ctx||6||36||15497464||11475535 (74.05)||60.76||4502562 |- | HL135||60831_067_normal_p||Neuron, norm_ctx||7||33|||||||| |- | HL135||60831_068_normal_p||Neuron, norm_ctx||7||34|||||||| |- | HL135||2041_069_Alzcor_p||NeuN-, alz_cortex||7||39|||||||| |- | HL135||2041_070_Alzcbl_p||Neuron, alz_cerebellum||7||32|||||||| |- | HL135||2041_071_Alzcor_p||Neuron, alz_cortex||8||25||24439820||17625790 (72.12)||52.85||8311147 |- | HL135||2041_072_Alzcor_p||Neuron alz_cortex||8||26||3553386||1878510 (52.87)||48.07||975482 |- | HL135||2041_073_Alzcor_p||Neuron, alz_cortex||8||29||7112256||3957668 (55.65)||79.62||806608 |- | HL135||2041_074_Alzcbl_p||Neuron, alz_cerebellum||8||32||2499658||504487 (20.18)||44.06||282209 |} '''2041_071_Alzcor_p| Analysis''' *This library has enough reads for a proper analysis. Unfortunately, for the other 3 ALz cortex samples, each had its own issue (1 had high clonal, 1 had low mapping rate, and 1 had too few reads/can be resequenced). *The overall plot shows a male (correct) with a lot of variation *The APP and DYKR1A are on Chr21, so I will focus on that. APP is from 27,252,860 to 27,543,445 bp and DYKR1A is from 38,739,236 to 38,887,680. *The Chr21 plot shows a few regions of high copy number. *The middle region is ~100k upstream of the APP gene on the same locus: 21q21.3. Possibly this is where the promoter to the APP gene. The CYYR1 gene is in this region as well, which has an unknown function. *I will need to sequence more Alz cortex libraries to get a better idea, and will begin to prepare more. [[File:11-13-12 allchr.jpeg|400px]] [[File:11-13-12 21chr.jpeg|400px]]
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