Nongluk (Noi) Plongthongkum

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Quick&Useful links

Labnote

Sample tracking

Current Projects

Targeted bisulfite sequencing

2014 Projects

BSPP capture of Human DMR 460k set

MONOD's project

Sample record

Samples from Moores Cancer Center

Samples from Kang Zhang's lab

  • 2014-05-22: Received 30 plasma samples from Kang Zhang's lab
    • Sample info.: [[5]].
    • They are all from normal samples with no cancer history

BSPP capture

  • GP1V4 or MONOD V1 and GP1V6 capture on 5 cancer samples and 3 blood samples (UCLA, SZ 96 sample set): [[6]]
  • MONOD V2 BSPP capture: [[7]]
  • MONOD V3 BSPP capture: [[8]]
  • Amplified DNA from Illumina captured with GP1V4 using Stoffel Fragment and Illumina's polymerase (no positive control, PC): [[9]]
  • Comparison of cancer DNA samples and amplified DNA from Illumina GP1V4 capture using three different DNA polymerases, Stoffel Fragment, Hemo KlenTaq and Illumina's polymerase: [[10]]

scRRBS

  • Experimental design: [[11]]
  • Trial experiment with STD Illumina adaptors and methylated NEBNext adaptors
  • Experiment on flow-sorted nuclei with methylated adaptor from Illumina TruSeq kit
    • Apr#1 experiment: [[15]]
    • Apr#2 experiment: [[16]]
    • Apr#3 experiment: [[17]] --> continue to sequencing (HL166 run)
      • Data analysis: [[18]]

2013 Projects

  • DNA methylation technology comparison (loci-specific, Blueprint project)
    • First batch of 12k probe set TEST experiment: [[19]], [[20]]
    • Record of samples (32 of mandatory (22) and optional (10) samples arrived June 12, 2013) : [[21]]
    • Normalized probe set TEST experiment: [[22]]
  • Parkinson's disease (PD) data set from Burnham Institute
    • BSPP capture: [[23]]
    • Mapping to hg18 (CpG): [[24]]
    • Mapping to hg19 (CpG and non-CpG):


  • Schizophrenia (UCLA, Roel Ophoff):
    • BSPP capture: [[25]]
    • 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
    • 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: [[27]]
      • Genetic distance: [[28]]
    • Mid-parent offspring (mpo) analysis
      • Preliminary result by Dr. Zhang: [[29]]
      • Analysis of combining data (4 batches of sequencing data): [[30]]
    • mQTL analysis: [[31]]
      • Multiple test correction: [[32]]
      • mQTL on 5M impute SNPs [[33]]
      • Repeated analysis on no CpG-SNP methylMatrix: [[34]]
    • ASM analysis:
      • Sequence-dependent ASM identification by TTest: [[35]], [[36]]
      • Plot the distance of candidate CpG SNP ASM and correspondence p-value: [[37]]
      • Multiple test correction: [[38]]
    • Regression analysis: [[39]]
      • PCA analysis with control of GA sample from Kang Zhang's lab: [[40]]
      • Multiple test correction: [[41]]
      • Repeat PCA analysis and classified with LDA: [[42]], [[43]], [[44]], [[45]]
    • Reports of data analysis progress:


  • Geographic Astrophy (GA) (UCSD, Kang Zhang) Note: most of the data analysis was performed by Dr. Zhang and Dinh


  • 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: [[50]], [[51]], [[52]], [[53]]
    • Mapping to hg19: [[54]]
    • ASM analysis:
      • Preliminary analysis of sequence-dependent ASM: [[55]]
      • Sequence dependent test by Dinh: [[56]]



  • 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): [[68]]
    • BSPP capture (2nd experiment, improved to library-free protocol and for PE sequencing): [[69]]
    • Summary of mapping of the data generated by library-free protocol (120426_HL118, lane5): [[70]]


  • 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: [71]
    • Mapping to separate out the reads based on different chromosomes by Dinh: [[72]] --> 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




  • ASM and ASCM in human cells project (I work on 330k BSPP capture)



  • WGBS of HAPMAP samples by KAPA protocol (epMotion run)


  • LGH-Project, collaboration with Guanghui, Salk Institute
    • BSPP capture: [[95]], [[96]]
    • 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: [[97]]
    • Library preparation rehearsal: [[98]]
    • 72 Library prep (Library ID: NP-SkinMB_N2_Ind17-88_Feb07.2013). The libraries were light sequenced in HL144 lane1 [[99]], [[100]]
    • Select the top 20 libraires from the 72 libraries for Hiseq run [[101]]. Library ID : CW-SkinMB-20SAG-Mar20.2013
    • Prepare sequencing library of low DNA input (1ng): [[102]], [[103]]. Ligation after using CGI protocol to fragment DNA and A-tailing: [[104]]
  • In Situ sequencing, started Mar2013
    • Matt's Project, I worked with Math on probe prep and in vitro padlock probe capture
    • Probe information: [2013 set]
    • Probe preparation: [[105]]
    • Padlock probe capture: [[106]]
  • Post-CoRE fragmentation library construction, started April2013
    • Jeff's microwell MDA samples: [[107]]
    • Eric's MEF cell samples: [[108]]. Library IDs: EC-MEF-Dev7-1-8-May21-2013 & EC-MEF-Dev7-9-16-May21-2013
    • Eric's PGP1#1 cell samples: [[109]]. Library IDs: EC-PGP1-Dev7-1-12-May23-2013 & EC-PGP1-Dev7-13-24-May23-2013
  • epMotion testing
    • AMPure bead purification optimization: [[110]], [[111]], [[112]], [[113]]
    • Bisulfite conversion/Zymo Lightning MagPrep kit optimization:

Protocols


Library construction (with Dinh)

Lab presentation (Journal club/Progress report)