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==Current Projects and Progress== * Notes on meangenemachine: [[Dinh:Meangenemachine_Upgrades]] * Notes on genome-miner: [[Dinh:Genome_Miner_Upgrades]] * Current works - Overview [[Dinh:Thesis_Overview]] ===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 ===Projects with Collaborators=== * '''BluePrint''' (Christoph Bock, CEMM - Vienna) 11/12/15 Received reference samples from Christoph - Store them in -80C, Rack id: 5B, Box labels: "BluePrint Reference samples - human gDNA" - Sample ids: Hct15p, Hct116p, 2N, 4N, 5T, 5N, 6N, 4T, 3N, 3T, 6T, Hct15, Hct116 * '''Twins WGBS''' (Brinda Rana lab, UCSD) 11/12/15 Mapping HiSeq High Output run - [[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2015/NOTES/2015-11-12]] * ''' Ovarian cancer''' (Dana Tsui, Cambridge) Samples information [[Dinh:Projects/OvarianCancer]] Screening tumor samples and buffy coat from Cambridge: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2015/NOTES/2015-8-27]] * ''' Myelodysplastic syndromes''' (Rafeal Bejar, Tiffany Tanaka, Brian Reilly, Moores Cancer Center) Samples information [[Dinh:Projects/MDS]] * '''N37 individual, multiple tissues''' (Stanford, Billy Li) **BSPP (Noi):[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:Sample_tracking#May_25.2C_2011.2C_gDNA_of_10_different_tissues_from_Billi_Li.2C_Standforf_Univ] 1st batch [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-10-3] Genic methylation and expression levels * '''HAPMAP Study''' (Zhang lab, on grant proposal) **BSPP (Noi): [http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-16] **WGBS (Alan): ask Alan Dealing with WGBS data [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-3-5] GM12878 Sequence dependent ASM [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-3-21] Binomial test and T-test * '''GA - (Glaucoma and optic atrophy?)''' (Kang Zhang lab) **BSPP (Noi): [http://genome-tech.ucsd.edu/LabNotes/index.php/noi:Sample_tracking#July_8.2C_2011.2C_gDNA_from_the_blood_samples_of_control_and_GA_patients_from_Kang_Zhang.27s_lab.2C_UCSD] Noi did the experiment while also training two postdocs from Kang's lab. [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-18] mQTL on 30 samples, SOM analysis [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-12-14] PCA and HClust * '''Schizophrenia''' (UCLA, Tina and Dr. Roel) **BSPP (Noi): [http://genome-tech.ucsd.edu/LabNotes/index.php/noi:Sample_tracking#August_1.2C_2011.2C_gDNA_of_the_blood_samples_of_schizophrenia_disorder_patients_from_Dr._Roel_Ophoff.2C_UCLA] Noi did the experiment while also training Tina over the summer. Sample identity - males versus females, [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-28] Family background substraction, [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-28] SibPair using TTest with family null data, [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-30] Overlap SibPair with MPO, [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-30] SNP Genetic distance plot, [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-30] Bis-SNP = more sensitive SNP calling, [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-9-22] * '''African Diversity - 48 Methylomes''' (UPenn collaboration, Sara/Laura) **BSPP (Noi):[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:Sample_tracking#December_7.2C_2010_.28Sarah.27s_African_gDNA.2C_UPenn_.29] 1st batch [http://genome-tech.ucsd.edu/LabNotes/index.php/noi:Sample_tracking#September16.2C_2011.2C_received_3_more_gDNA_from_UPenn_to_repeat_the_capture_of_the_samples_with_low_QC_values] 2nd batch, tried to improve QC but they were all too low compared to previously assayed samples. [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-7-20] Analysis with EIGENSTAT software (population structure) [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-8-29] PCA [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-9-29] mQTL [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-2-21] Cleaning and repeat PCA [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-2-27] Checking for reference genome bias [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-3-22] Standardized CpGs quality filter using UPenn48 as an example. * '''5fC/5caC DIP-seq''' (University of Northern Carolina Medical School , Yi/Hao/Li) **Barcoding and sequencing by Alan: [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-9-12] Genes Region Enrichment analysis, Biotin-labeled dIP [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-14] Antibody dIP [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-21] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-22][http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-12-7] Analysis at repeats [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-12-20] 24 sets BOWTIE mapping [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-12-22] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-2-2] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-2-9] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-2-13] BWA PE mapping and peak calling [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-2-18] RNA-seq - repeats mapping * '''Immunogeneticity and reprogramming''' (Yang Xu lab) **BSPP (Noi):[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:Sample_tracking#September_17.2C_2011.2C_received_3_cell_pellet_samples_from_Alice_.28sample_from_Yang_Xu.27s_lab.29] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-17] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-12-1] Memory/mutation calling [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-12-13] Compare WGBS * '''Breast Cancer and Diet''' (Richard, Moores Cancer Center UCSD) ** Experiments were done in December 2009, January 2010, and February 2010. [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-4-22] Paired Chi-square test [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-7-24] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-8-2] Compared resequenced datasets with old [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-7-27] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-8-17] mQTL * '''Methylation and metabolic genes''' [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-7-8] Calculate DMS * '''Memory/Mutation of iPSCs''' (Salk - Juan Carlos Lab, Sergio) **BSPP (Noi): [http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-5-3] 2nd batch (MSCs, hESCs) [http://genome-tech.ucsd.edu/LabNotes/index.php/noi:Sample_tracking#September16.2C_2011.2C_gDNA_from_Sergio.2C_Salk_Institute] 3rd batch, after differentiation **BSPP with N2 protocol (Dinh): [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-9-1], [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-9-6] 1st batch [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-5] Memory/mutation calling [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-9] CpG localization [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-1-4] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-1-6] Localization with ChIP data ===Finished/dropped projects=== * [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-7-18] PGC WGBS/Rui (Updated July 19, 2012) * [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-4-6] PNAS/Sergio (Updated 4/6/12) * [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-1-27] BSPP Meeting (Updated March 16, 2012) * [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-10-7] Meeting notes/work for Nature Methods paper revision * [[dinh:LAB/Bisulfite_Sequencing|Bisulfite Sequencing of CpG Sites (w/ Jie)]] * [[dinh:COMPUTATIONAL/HIV_Insertion_Site_Sequencing| Insertional Mutagenesis, Sequencing of HIV Insertion Site (w/ Sam & Kyle)]] * [[dinh:COMPUTATIONAL/GPU_Project|bwalnGPU]] * Learn sequencing 1. Perform quantification of libraries using PhiX 2. Perform Cluster Generation and Sequencing, [http://genome-tech.ucsd.edu/LabNotes/upload/7/71/Dinh_All_In_One_Cluster_Generation.doc Protocol] 3. Run pipeline modules for image analysis, base calling, and sequence alignment.
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