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=== [[Noi:Quicklinks | Quick&Useful links]] === === [[Noi:DMR220k LabNotes | Labnote]] === === [[Noi:Labnote tracking | LabNote tracking]] === === [[Noi:Noi' Reagents | Noi' Reagents ]] === === [[Noi:Sample tracking | Sample tracking]] === === Current Projects === == [[Noi:Targeted bisulfite sequencing|Targeted bisulfite sequencing]] == == 2014 Projects == ==== [[Noi:MONOD's project | MONOD's project ]] ==== ==== [[Noi:scRRBS's project | scRRBS's project]] ==== == 2013 Projects == * '''DNA methylation technology comparison (loci-specific, Blueprint project)''' ** First batch of 12k probe set TEST experiment: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-5-30]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-6-6]] ** Record of samples (32 of mandatory (22) and optional (10) samples arrived June 12, 2013) : [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-6-12#DNA_methylation_assay_for_Blueprint_project]] ** Normalized probe set TEST experiment: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-7-3]] * '''Parkinson's disease (PD) data set from Burnham Institute''' ** BSPP capture: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-2-15]] ** Mapping to hg18 (CpG): [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-3-17]] ** Mapping to hg19 (CpG and non-CpG): <br> * '''Schizophrenia''' (UCLA, Roel Ophoff): ** BSPP capture: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-8-14]] ** Raw data in genome-miner (There are 4 batches of sequencing data, some of them failed in read2 '''Batch1 (HiSeq data from UCLA)''' Length: 100bp /media/SeqStore2/110920_UCLA_RO_BSPP Note: Index 94 was missing from this batch '''Batch2''' Length: 101bp /media/SeqStore2/111005_HL104/UCLA_Blood_SZ Lane: 8, PE, PE but success only 1 read (read2 failed) Note: sample s_8_1_Indx28_fixed.txt.gz sequences have been fixed '''Batch 3''' Length: 100bp /media/SeqStore2/111112_HL109/UCLA_Blood_SZ Lane: 4 – 8, PE but success only 1 read (read2 failed) Lane 1-3 are Rui’ samples and there were some overlapping index to lane 4-8 '''Batch 4: HL111''' Length: 110bp Lane 4, PE http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-1-2 /media/SeqStore2/111209_HL111/BSPP ** Mapping *** Batch4: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-1-2]] ** Sample identity check by Dinh (checked after combining three batches of sequencing data): *** Homozygous SNPs and heterozygous SNPs call for X chromosome to identify males vs. females: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-28]] *** Genetic distance: [[http://genome-tech.ucsd.edu/LabNotes/index.php/File:UCLA_GeneticDistance.pdf]] ** Mid-parent offspring (mpo) analysis *** Preliminary result by Dr. Zhang: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/CpgSeq/2011-9-27]] *** Analysis of combining data (4 batches of sequencing data): [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-3-19]] ** mQTL analysis: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-1-24]] *** Multiple test correction: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-4-11]] *** mQTL on 5M impute SNPs [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-3-26]] *** Repeated analysis on '''no CpG-SNP''' methylMatrix: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-4-26]] ** ASM analysis: *** Sequence-dependent ASM identification by TTest: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-3-21]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-3-23]] *** Plot the distance of candidate CpG SNP ASM and correspondence p-value: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-3-24]] *** Multiple test correction: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-4-12#Multiple_testing_correction]] ** Regression analysis: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-3-22]] *** PCA analysis with control of GA sample from Kang Zhang's lab: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-4-6]] *** Multiple test correction: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-4-17]] *** Repeat PCA analysis and classified with LDA: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-4-30]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-12]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-6-13]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-6-14]] ** Reports of data analysis progress: *** [[Media:UCLA_data_analysis_2012_04_28_editedbyKZ.docx| UCLA_data_analysis_2012_04_28]] *** [[Media:UCLA_SZ_ASM_analysis_2012_05_10.pptx| UCLA_SZ_ASM_analysis_2012_05_10]] *** [[Media:UCLA_SZ_regression_analysis_2012_05_10.pptx| UCLA_SZ_regression_analysis_2012_05_10]] <br> * '''Geographic Astrophy (GA)''' (UCSD, Kang Zhang) Note: most of the data analysis was performed by Dr. Zhang and Dinh ** BSPP capture: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-7-28]] --> note: this experiment failed in amplification step [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-8-9]] ** Mapping to hg19: [[File:BSPP_AMD-mapping-summary_2011_10_12.xlsx]] ** Regression analysis by Dr. Zhang: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/CpgSeq/2011-10-14]] ** Overlapping of Illumina 450k methylation array and BSPP: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-7-28]] <br> * '''HAPMAP project''' (HAPMAP PT01, two families, 1362 and 1464) ** Note: Sample IDs from HAPMAPPT01 start with '''NA (DNA product)''' whereas '''GM''' represents '''cell products''' ** BSPP capture: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-16]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-18]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-10-17#Normalization_of_libraries_from_HL104_run_.28Library_ID:_NP-BSPP-Ind1_45-Sep18.29_for_additional_sequencing_by_GAIIx_flowcell]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-11-15]] ** Mapping to hg19: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-2-2]] ** ASM analysis: *** Preliminary analysis of sequence-dependent ASM: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-2-15#On_ASM_output_data]] *** Sequence dependent test by Dinh: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-3-21]] <br> * '''Randomly tagging primers''' (with Athurva and Dinh) ** IDT spec sheets (primers used in this experiment): *** [[Media:AmpF7AUSol_Seq.pdf| AmpF7AUSol]] *** [[Media:AmpF7NUSol_Seq.pdf| AmpF7NUSol]] *** [[Media:Syb_FP5A_Seq.pdf| Syb_FP5A]] *** [[Media:Syb_RP7_Seq.pdf| Syb_RP7]] ** PCR condition optimization: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-1]] [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-2#PCR_set_up]] [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-4#Part_III]] [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-5]] ** Colony PCR and sequence verification by Sanger sequencing: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-7]] [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-13]] ** Repeat experiment for more validation by Sanger sequencing: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-6-1]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-6-3]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-6-5]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-6-6]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-6-7]] <br> * '''BSPP capture with probes synthesized by LC Sciences (Nature Methods 2012 paper)''' ** BSPP capture (1st experiment designed for SE sequencing-> read both ends at once): [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-10-6]] ** BSPP capture (2nd experiment, improved to library-free protocol and for PE sequencing): [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-4-23]] ** Summary of mapping of the data generated by library-free protocol (120426_HL118, lane5): [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-7#Mapping_to_hg19_.28on_Triton_cluster.29]] <br> * '''ASM analysis of WGBS of NA12878''' ** Concatenate fastq files as input for ASM pipeline (this step failed because less or cat command cannot print out all data into the same file: [http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-2-29] ** Mapping to separate out the reads based on different chromosomes by Dinh: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-3-5]] --> output files on genome-miner: '''/media/Ext12T/DD_Ext12T/HL_WGBS_map''' ** ASM output data on genome-miner: '''/home/nplongth/Noi_scratch/ASM_WGBS.NA12878_2012_03_14''' <br> * '''Probe production for Hi-resolution chromosome painting project (probe production part)''' ** Dr. Zhang's protocol link: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/HiResChrPaint/2012-4-4]] ** Plan: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-8]], Probe production: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-14]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-16]] ** [[Media:ARESTM_DNA_Labeling_Kits.pdf| ARES™ DNA Labeling Kits]] ** Dye coupling by Dr. Zhang: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/HiResChrPaint/2012-7-12]] <br> * '''PNAS revision_May2012''' (I work on 330k BSPP capture) ** List of samples: [[Media:List_of_prioritized_samples_5_25_2012.pdf| List_of_prioritized_samples_5_25_2012]] ** BSPP capture: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-17]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-20]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-21]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-25]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-31]] ** Mapping was performed by Dinh ** Raw reads: on genome-miner, '''/media/SeqStore2/120531_SN100_DD/NP_BSPP''' <br> * '''ASM and ASCM in human cells project''' (I work on 330k BSPP capture) ** BSPP capture: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-24]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-31]] ** Mapping to hg19: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-6-27]] ** ASM analysis: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-8-6]] <br> * '''N37 sample (10 tissues from Dr. Billy Jin, Stanford)''' ** BSPP capture: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-5-28]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-6-6]] ** Mapping data: [[Media:N37_MappingData_July2011.xlsx| N37_MappingData_July2011.xlsx]] ** ASM analysis: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-7-20]] ** Low coverage WGBS by KAPA protocol (epMotion run): [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-7-31]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-8-26]] <br> * '''WGBS of HAPMAP samples by KAPA protocol (epMotion run)''' ** Library preparation: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-7-6]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-7-27]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-8-1]] <br> * '''LGH-Project, collaboration with Guanghui, Salk Institute''' ** BSPP capture: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-8-22]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-8-23]] ** Note: This batch of experiment also included 5 samples from Dr. Yang Xu's lab ** '''Data analysis''' *** LGH-projectB (FA-NSC, 1st priority): Data analysis was performed on both genome-miner & genemapster Mapping data: /home/nplongth/Noi_scratch/GL.project1-2.20120918/LGH-projectB/hg19.mapping * '''Skin microbiome project, started Jan2013''' ** Sample information: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-1-11]] ** Library preparation rehearsal: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-1-15]] ** 72 Library prep (Library ID: '''NP-SkinMB_N2_Ind17-88_Feb07.2013'''). The libraries were light sequenced in HL144 lane1 [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-1-31]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-10-6]] ** Select the top 20 libraires from the 72 libraries for Hiseq run [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-3-20]]. Library ID : '''CW-SkinMB-20SAG-Mar20.2013''' ** Prepare sequencing library of low DNA input (1ng): [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-4-11]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-4-16]]. Ligation after using CGI protocol to fragment DNA and A-tailing: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-4-25]] * '''In Situ sequencing, started Mar2013''' ** Matt's Project, I worked with Math on probe prep and in vitro padlock probe capture ** Probe information: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/inSituSeq#Feb. 2013 set]] ** Probe preparation: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-3-6]] ** Padlock probe capture: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-3-12]] * '''Post-CoRE fragmentation library construction, started April2013''' ** Jeff's microwell MDA samples: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-4-30]] ** Eric's MEF cell samples: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-5-22]]. Library IDs: '''EC-MEF-Dev7-1-8-May21-2013''' & '''EC-MEF-Dev7-9-16-May21-2013''' ** Eric's PGP1#1 cell samples: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-5-24]]. Library IDs: '''EC-PGP1-Dev7-1-12-May23-2013''' & '''EC-PGP1-Dev7-13-24-May23-2013''' * '''epMotion testing''' ** AMPure bead purification optimization: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-7-11]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-7-12]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-7-14]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-7-17]] ** Bisulfite conversion/Zymo Lightning MagPrep kit optimization: = Protocols = * '''Probe preparation''' ** DMR330k probe synthesized by Agilent: *** Original protocol (DMR220k) by Dr. Zhang: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/CpgSeq/2010-6-8]] *** [[Media:DMR330k probe production.doc| DMR330k probe production_very details version]] *** [[http://genome-tech.ucsd.edu/public/Gen2_BSPP/Agilent_probe_preparation_Apr2012.pdf Agilent_probe_preparation]] *** [[http://genome-tech.ucsd.edu/public/Gen2_BSPP/LC_Sciences_probe_preparation_Apr2012.pdf LC_Sciences_probe_preparation]] ** Probe synthesized by LC Sciences *** Reference protocol: [http://arep.med.harvard.edu/pdf/Porreca07.pdf] *** Adjusted protocol and related experiment: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-10-6]] <br> * '''Library construction (BSPP)''' ** N2 adapter protocol: Related experiment --> [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-3-18]] ** Library-free protocol (Agilent probes): Related experiment --> [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-5-28]] [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-6-6]] ** Library-free protocol (LC Sciences probes): *** Capture protocol: [[Media:LC_Sciences_DNA_capture_protocol_edit.pdf]] *** Related experiment -->[[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-4-22]] [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-4-23]] == [[Noi:Library construction|Library construction (with Dinh)]] == == [[Noi:Lab Presentation| Lab presentation (Journal club/Progress report)]] ==
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