Dinh Diep
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Daily Lab Notebook[edit]
Tools[edit]
- RnBeads resources: http://rnbeads.mpi-inf.mpg.de/methylomes.php
- Note on how to set up passwordless login (linux): http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2015/NOTES/2015-5-7
- Note on how to download fastq file from BaseSpace account without using Web-based GUI: http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2015/NOTES/2015-3-25
- Convert oligos grams to pmol: http://www.promega.com/a/apps/biomath/index.html?calc=ugmlpmolul
- Quickly check DMRs methylation in WGBS data: http://bioinfo2.ugr.es/NGSmethDB/NGSmethDBviewer.php?assembly=hg19
- Venn Diagram plotter, http://bioinformatics.psb.ugent.be/webtools/Venn/
- "Sushi.R : flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures"
- Dual booting guide for Linux-Os X: http://www.rodsbooks.com/ubuntu-efi/
- WGET command (useful for downloading from other lab's servers via web server or FTP):
wget --user=USERNAME --password='PASSWORD' -c -nH --cut-dirs=2 -U mozilla -r -np --convert-links --reject="index.html*" -e robots=off http://enhancer.sdsc.edu/bli/brandon/Data/
- Demultiplexing Mi-Seq runs on genome-miner:
Make a new directory & go into this directory first. Then type the following commands (change MiSeq output folder and date!): ln -s /media/LTS_60T/SeqStore2016/MiSeqAnalysis/160419_M00159_0174_000000000-ANULK/Data Data cp /media/LTS_60T/SeqStore2016/MiSeqAnalysis/160419_M00159_0174_000000000-ANULK/SampleSheet.csv . cp /media/LTS_60T/SeqStore2016/MiSeqAnalysis/160419_M00159_0174_000000000-ANULK/RunInfo.xml . bcl2fastq -o 160419_MiSeq --sample-sheet SampleSheet.csv --barcode-mismatches 0
- Derek's instructions for MiSeq
Notes from August 24th 2016: http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2016/NOTES/2016-8-24
Methylation Sequencing Data Repetiore[edit]
- All methylation data to be stored on genome-miner
- Data from a publication will be stored under [FirstAuthorLastName][Year]
- Data from a project will be stored under the project name
- WGBS (/media/LTS_33T/WGBS_LTS33)
- Hg19/Ziller2013 - Ziller et al 2013 ( re-analyzed data )
- Hg19/Heyn2013 - Heyn et al 2013 ( primary data, re-map )
- Hg19/Xie2013 - Xie et al 2013 ( primary data, re-map )
- Hg19/NIHRoadMap
- Hg19/BlueprintProject
- Hg19/McGillEMC
- Mm9/
- RRBS
- BSPP
Records of all Zhang Lab Methylation data[edit]
Dinh:Methylation_Data_Records Dinh:MONOD_Data_Records
Most recent meeting notes[edit]
- [1] Current project meeting notes (Updated May 22, 2015)
- [2] Current project meeting notes
- [3] Cancer detection project (Updated April 10, 2014)
- [4] Senate Exam Meeting (Updated February 28th, 2014)
- [5] Genome partitioning project (Updated January 16, 2013)
- [6] 5hmC (CIRM) project (Updated January 3, 2013)
Current Projects and Progress[edit]
- Notes on meangenemachine: Dinh:Meangenemachine_Upgrades
- Notes on genome-miner: Dinh:Genome_Miner_Upgrades
- Current works - Overview Dinh:Thesis_Overview
Dinh's Projects[edit]
- MONOD
June2015_MONOD_Efficiencies File:June2015 MONOD ProbesEfficiencies.txt BSPP & SeqCap Mapping statistics: File:150209 SN216 mapping summary statistics.xlsx Plasma DNA purification [[7]] Test 1 ng RRBS protocol [[8]] Need to get results from the test protocol first!: Generating RRBS libraries from 1.5 ng plasma DNA [[9]] Generating RRBS libraries from 10ng normal plasma DNA [[10]] Noi's WGBS and BSPP capture experiment on cfDNA from Illumina [[11]],[[12]]
- 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): [[13]] Protocol and notes for TAB-seq (true 5hmC quantification): Dinh:TAB_Protocol Failed trial 1: H1 ESC (p48 from Sergio): [[14]] Trial 2: H1 ESC (p48 from Sergio: [[15]] 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 [16] HOTSPOTS460K experiments summary [17]
- 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: [18] Specificity measures, [19] Probes efficiency measures, [20] [21] Resubsetting strategy, 9 Technical Replicates: [22] QC values, [23] [24] [25] Simulation of STDEV, Random tagging of probes: [26] [27] [28] Design new probes: [29] HMM to determine UMR, LMR, and HMR
- Protocol optimizations:
[30] [31] Capture with 30K, [32] Capture with 97KA/B [33] Multiplexing tests [34] Multivariate capture with DMR220K [35] N2-adapter [36] [37] BSPP [38] Training [39] [40] Normalization capture [41] [42] DMR220K + EXP1-3 Supressor oligos [43] Design Probes for Single-End sequencing [44] [45] [46] Circularization of probes
- Genemapster/Meangenemachine Updates
[47] Cuda EC [48] Sanger methylation validation [49] Installed upgrades [50] New CUDA installation [51] Test SOAP3 -- doesn't work on our GPU :(
- Bisulfite Patch PCR (w/Michelle)
[52] Design [53] Consider SNPs
Projects with Collaborators[edit]
- 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 - [[54]]
- Ovarian cancer (Dana Tsui, Cambridge)
Samples information Dinh:Projects/OvarianCancer Screening tumor samples and buffy coat from Cambridge: [[55]]
- 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):[56] 1st batch
[57] Genic methylation and expression levels
- HAPMAP Study (Zhang lab, on grant proposal)
- BSPP (Noi): [58]
- WGBS (Alan): ask Alan
Dealing with WGBS data [59] GM12878 Sequence dependent ASM [60] Binomial test and T-test
- GA - (Glaucoma and optic atrophy?) (Kang Zhang lab)
- BSPP (Noi): [61] Noi did the experiment while also training two postdocs from Kang's lab.
[62] mQTL on 30 samples, SOM analysis [63] PCA and HClust
- Schizophrenia (UCLA, Tina and Dr. Roel)
- BSPP (Noi): [64] Noi did the experiment while also training Tina over the summer.
Sample identity - males versus females, [65] Family background substraction, [66] SibPair using TTest with family null data, [67] Overlap SibPair with MPO, [68] SNP Genetic distance plot, [69] Bis-SNP = more sensitive SNP calling, [70]
- African Diversity - 48 Methylomes (UPenn collaboration, Sara/Laura)
[73] Analysis with EIGENSTAT software (population structure) [74] PCA [75] mQTL [76] Cleaning and repeat PCA [77] Checking for reference genome bias [78] 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:
[79] Genes Region Enrichment analysis, Biotin-labeled dIP [80] Antibody dIP [81] [82][83] Analysis at repeats [84] 24 sets BOWTIE mapping [85] [86] [87] [88] BWA PE mapping and peak calling [89] RNA-seq - repeats mapping
- Immunogeneticity and reprogramming (Yang Xu lab)
- BSPP (Noi):[90]
[91] [92] Memory/mutation calling [93] Compare WGBS
- Breast Cancer and Diet (Richard, Moores Cancer Center UCSD)
- Experiments were done in December 2009, January 2010, and February 2010.
[94] Paired Chi-square test [95] [96] Compared resequenced datasets with old [97] [98] mQTL
- Methylation and metabolic genes
[99] Calculate DMS
- Memory/Mutation of iPSCs (Salk - Juan Carlos Lab, Sergio)
[104] Memory/mutation calling [105] CpG localization [106] [107] Localization with ChIP data
Finished/dropped projects[edit]
- [108] PGC WGBS/Rui (Updated July 19, 2012)
- [109] PNAS/Sergio (Updated 4/6/12)
- [110] BSPP Meeting (Updated March 16, 2012)
- [111] Meeting notes/work for Nature Methods paper revision
- Bisulfite Sequencing of CpG Sites (w/ Jie)
- Insertional Mutagenesis, Sequencing of HIV Insertion Site (w/ Sam & Kyle)
- bwalnGPU
- Learn sequencing
1. Perform quantification of libraries using PhiX 2. Perform Cluster Generation and Sequencing, Protocol 3. Run pipeline modules for image analysis, base calling, and sequence alignment.
Slides[edit]
most recent ones at bottom
- File:GPU Project 9-28-09.pdf 8-26-09 thru 9-28-09 Slides
- File:Dinh-Presentation October 26, 2009.pdf October 26, 2009 Slides
- File:Dinh Presentation November 23, 2009.pdf November 23, 2009 Slides
- File:Lab Meeting Jan 25 2010.pdf January 25, 2010 (short slides)
- File:March 8 2010 Lab Meeting.pdf March 8, 2010 CpG Methylation
- File:7-28-10 Lab Meeting.pdf July 28, 2010 mQTL CpG-SNP distance distribution, Epigenetic Reprogramming
- File:Lab Meeting 11 10 10.pdf November 10 2010 Lab Meeting
- File:Lab Meeting 06 21 11.pdf June 21 2011 Lab Meeting
- File:Journal Club 06 28 11.pdf June 28 2011 Journal Club
- File:Journal Club 09 13 11.pdf September 13 2011 Journal Club
- File:Differential Methylation of IPSCs by Episomal Reprogramming 8 26 2011.pdf August 21 2011 DMS of iPSCs by Episomal Reprogramming
- File:Lab Meeting 08 23 11.pdf August 23 2011 Lab Meeting
- File:African Methylome QC and Coverage.pdf August 26 2011 African Methylomes QC and Average Coverage
- File:African Methylome QC and Genetics Aug31.pdf August 31 2011 African Methylomes QC and Genetics
- File:5fC DIP-seq slides 9 22 11.pdf September 22 2011 5fC DIP-seq analysis
- File:UCLA Schizophrenia Sibpair.ppt December 5 2011 Schizophrenia Sib-pair Analysis
- File:Journal Club 12 12 11.ppt December 12 2011 Journal Club
- File:Data Progress 8 8 12 DD.ppt August 8, 2012 Data and progress
- File:Progress and update 11 19 12 DD.ppt November 19, 2012 Data and progress
- File:Progress and update 01 22 13 DD.ppt January 22, 2013 Data and progress
- File:Progress and update 03 12 13 DD.ppt March 12, 2013 Data and progress
- File:Progress and update 07 03 13 DD.ppt July 3, 2013 Data and progress
- File:Progress and update 08 28 13 DD.ppt August 28, 2013 Data and progress
- File:Progress and update 04 17 14 DD.ppt April 17, 2014 Data and progress