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===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
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