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==DIP-seq for 5caC and 5fC in mouse ESC== * Followup from http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-22 * After removing other rodent repeats and keeping only the mouse repeats, I blasted the hits again to the repeat database (keeping the best hit for each multiple mapping reads) * I need to make these numbers into pie-charts. {| {{table}} border=1 | align="center" style="background:#f0f0f0;"|'''Repeat type''' | align="center" style="background:#f0f0f0;"|'''Input''' | align="center" style="background:#f0f0f0;"|'''IgG''' | align="center" style="background:#f0f0f0;"|'''5caC''' | align="center" style="background:#f0f0f0;"|'''5fC''' |- | C573||0||0||1||0 |- | Mariner/Tc1||1||2||0||0 |- | Repeat||2||0||0||0 |- | Simple||2||0||0||0 |- | MCMREP||4||8||0||0 |- | RMER1A||4||1||0||0 |- | Nonautonomous||5||3||0||1 |- | RMER1||5||1||0||2 |- | RMER1B||5||6||0||0 |- | PMR||7||0||1||0 |- | Y||15||10||6||5 |- | hAT||27||14||9||2 |- | DNA||57||60||75||19 |- | Internal||93||61||55||18 |- | Transposable||106||59||0||25 |- | Satellite||170||129||246||58 |- | Endogenous||416||346||227||85 |- | SINE||676||358||478||159 |- | LTR||686||490||859||209 |- | ERV1||1174||944||983||404 |- | SINE2/tRNA||2532||1236||1148||443 |- | SINE1/7SL||2649||1520||2007||693 |- | ERV3||5596||3435||1927||912 |- | ERV2||7762||5921||5909||2027 |- | L1||32292||28783||24410||9819 |- | SAT||45714||56613||'''61659'''||'''85119''' |} * 5caC and 5fC are definitely enriched at SATELLITE repeat elements. * Here are Dr. Zhang's repeat analysis {| {{table}} border=1 | align="center" style="background:#f0f0f0;"|'''Data_file''' | align="center" style="background:#f0f0f0;"|'''Libraries''' | align="center" style="background:#f0f0f0;"|'''% unique mappable reads''' | align="center" style="background:#f0f0f0;"|'''% non-unique mappable reads''' | align="center" style="background:#f0f0f0;"|'''# mapped to rodent repeats*''' | align="center" style="background:#f0f0f0;"|'''# mapped to GSAT*''' | align="center" style="background:#f0f0f0;"|'''% GSAT repeats''' | align="center" style="background:#f0f0f0;"|'''# mapped to L1*''' | align="center" style="background:#f0f0f0;"|'''% L1''' |- | s_1||YZ_UNC-5caC-DIP-Oct27||53.6%||40.7%||450||200||44.4%||8900.0%||19.8% |- | s_2||YZ_UNC-5caC-DIP-Oct27||53.1%||41.4%||427||170||39.8%||8300.0%||19.4% |- | s_5||YZ_UNC-5fC-DIP-Oct27||44.0%||44.6%||709||643||90.7%||2800.0%||3.9% |- | s_4||YZ_UNC-IgG-DIP-Oct27||64.1%||27.3%||459||284||61.9%||9500.0%||20.7% |- | s_3||YZ_UNC-INPUT-Oct27||65.5%||19.7%||582||256||44.0%||16000.0%||27.5% |}
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