Nongluk (Noi) Plongthongkum

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Revision as of 00:22, 28 February 2013 by >Noi
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Quick&Useful links

Labnote

Sample tracking

Current Projects

Targeted bisulfite sequencing

  • Parkinson's disease (PD) data set from Burnham Institute
    • BSPP capture: [[1]]
    • Mapping to hg18 (CpG): [[2]]
    • Mapping to hg19 (CpG and non-CpG):


  • Schizophrenia (UCLA, Roel Ophoff):
    • BSPP capture: [[3]]
    • 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: [[5]]
      • Genetic distance: [[6]]
    • Mid-parent offspring (mpo) analysis
      • Preliminary result by Dr. Zhang: [[7]]
      • Analysis of combining data (4 batches of sequencing data): [[8]]
    • mQTL analysis: [[9]]
      • Multiple test correction: [[10]]
      • Repeated analysis on no CpG-SNP methylMatrix: [[11]]
    • ASM analysis:
      • Sequence-dependent ASM identification by TTest: [[12]], [[13]]
      • Plot the distance of candidate CpG SNP ASM and correspondence p-value: [[14]]
      • Multiple test correction: [[15]]
    • Regression analysis: [[16]]
      • PCA analysis with control of GA sample from Kang Zhang's lab: [[17]]
      • Multiple test correction: [[18]]
      • Repeat PCA analysis and classified with LDA: [[19]], [[20]], [[21]], [[22]]
    • 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: [[27]], [[28]], [[29]], [[30]]
    • Mapping to hg19: [[31]]
    • ASM analysis:
      • Preliminary analysis of sequence-dependent ASM: [[32]]
      • Sequence dependent test by Dinh: [[33]]



  • 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): [[45]]
    • BSPP capture (2nd experiment, improved to library-free protocol and for PE sequencing): [[46]]
    • Summary of mapping of the data generated by library-free protocol (120426_HL118, lane5): [[47]]


  • 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: [48]
    • Mapping to separate out the reads based on different chromosomes by Dinh: [[49]] --> 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: [[72]], [[73]]
    • 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: [[74]]
    • Library preparation rehearsal: [[75]]
    • 72 Library prep (Library ID: NP-SkinMB_N2_Ind17-88_Feb07.2013). The libraries were light sequenced in HL144 lane1 [[76]], [[77]]
  • epMotion testing
    • AMPure bead purification optimization: [[78]], [[79]], [[80]], [[81]]
    • Bisulfite conversion/Zymo Lightning MagPrep kit optimization:

Protocols


Library construction (with Dinh)

Lab presentation (Journal club/Progress report)