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===Dinh's Projects=== * ''' MONOD ''' June2015_MONOD_Efficiencies [[File:June2015_MONOD_ProbesEfficiencies.txt]] BSPP & SeqCap Mapping statistics: [[File:150209_SN216_mapping_summary_statistics.xlsx]] Plasma DNA purification [[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2015/NOTES/2015-9-14]] Test 1 ng RRBS protocol [[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2015/NOTES/2015-9-15]] Need to get results from the test protocol first!: Generating RRBS libraries from 1.5 ng plasma DNA [[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2015/NOTES/2015-9-30]] Generating RRBS libraries from 10ng normal plasma DNA [[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2016/NOTES/2016-3-23]] Noi's WGBS and BSPP capture experiment on cfDNA from Illumina [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-12-5]],[[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-12-8]] * ''' 5hmC Experiments ''' Samples Processing and Tracking: [[Dinh:5hmC_Quantification_Samples_Tracking]] Protocol and notes for Lambda controls: [[Dinh:5hmC_Lambda_Controls_Protocol]] Protocol and notes for oxBS-seq (true 5mC quantification): [[Dinh:OxBS_Protocol]] H1 ESC (p48 from Sergio): [[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2015/NOTES/2015-9-20]] Protocol and notes for TAB-seq (true 5hmC quantification): [[Dinh:TAB_Protocol]] Failed trial 1: H1 ESC (p48 from Sergio): [[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2015/NOTES/2015-9-19]] Trial 2: H1 ESC (p48 from Sergio: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2015/NOTES/2015-9-28]] Protocol and notes for MAB-seq (5fC and 5caC quantification): [[Dinh:MAB_Protocol]] * ''' Probes preparation ''' Protocol and notes for preparing probes: [[Dinh:Probes_Prep]] Protocol and notes for preparing probes: [[Dinh:Probes_Prep_May2015]] * '''Stoffel production''' Design Plasmid construction - first failed attempt: http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2014/NOTES/2014-5-12 - I repeated Sanger sequencing twice but was unable to get the Stoffel gene in the sequences. - One big issue was my plasmid prep (no column) have too much genomic DNA background which M13 primers can amplify. - For PCR/Sequencing, I need to use column to purify my plasmids. Plasmid construction - try again: http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2014/NOTES/2014-6-23 - I now use NheI digestion site in the middle of the Stoffel gene to screen for my insert. This is much faster than sequencing. * '''Cancer biomarker''' Analysis of GP1 padlock probes capture Analysis of MONOD padlock probes capture Analysis of RRBS - [[Dinh:RRBS_MONOD_Analysis/Mapping]] * '''Genome segmentation''' WGBS data segmentation using N37, Heyn et al (blood), Xie et al (developmental), and Ziller et al (whole tissues, different individuals). Mouse WGBS data segmentation using linear regression model and MOABS Salk WGBS tissues data : http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2015/NOTES/2015-10-12 * '''5hmC capture and sequencing''' HOTSPOTS460K capture experiments optimization [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2014/NOTES/2014-3-11] HOTSPOTS460K experiments summary [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2014/NOTES/2014-3-12] * '''bisReadMapper''' Developments: CpG/ChG/Chh position calling bugs fixed. New version of code will use Bowtie2. NGS Mapper ROC curves: http://lh3lh3.users.sourceforge.net/alnROC.shtml Run notes: [[dinh:COMPUTATIONAL/bisReadMapper]] UMI procedure: [[dinh:COMPUTATIONAL/umi_procedure]] * '''DMR330K probes''' re-normalization: [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-10-29] Specificity measures, [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-1] Probes efficiency measures, [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-12-21] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-12-27] Resubsetting strategy, 9 Technical Replicates: [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-1-11] QC values, [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-2-1] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-2-6] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-2-17] Simulation of STDEV, Random tagging of probes: [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-7-5] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-8-1] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-8-30] Design new probes: [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-1-26] HMM to determine UMR, LMR, and HMR *'''Protocol optimizations:''' [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-1-4] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-1-7] Capture with 30K, [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-1-11] Capture with 97KA/B [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-7-7] Multiplexing tests [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-7-9] Multivariate capture with DMR220K [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-8-19] N2-adapter [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-8-22] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-8-23] BSPP [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-10-26] Training [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-9-23] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-10-25] Normalization capture [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-10-21] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-7-18] DMR220K + EXP1-3 Supressor oligos [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-8-31] Design Probes for Single-End sequencing [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-9-1] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-9-2] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-9-21] Circularization of probes *'''Genemapster/Meangenemachine''' Updates [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-5-18] Cuda EC [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-11-15] Sanger methylation validation [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-7-13] Installed upgrades [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-7-28] New CUDA installation [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-12-7#SOAP3_.28latest_version.29] Test SOAP3 -- doesn't work on our GPU :( * '''Bisulfite Patch PCR''' (w/Michelle) [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-4] Design [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-2-10] Consider SNPs
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