Nongluk (Noi) Plongthongkum: Difference between revisions

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= [[Noi:Quicklinks | Quick&Useful links]] =
=== [[Noi:Quicklinks | Quick&Useful links]] ===
= [[Noi:DMR220k LabNotes | Labnote]] =
=== [[Noi:DMR220k LabNotes | Labnote]] ===
= [[Noi:Sample tracking | Sample tracking]] =
=== [[Noi:Labnote tracking | LabNote tracking]] ===
= Current Projects =
=== [[Noi:Noi' Reagents | Noi' Reagents ]] ===
=== [[Noi:Sample tracking | Sample tracking]] ===
=== Current Projects ===


== [[Noi:Targeted bisulfite sequencing|Targeted bisulfite sequencing]]  ==
== [[Noi:Targeted bisulfite sequencing|Targeted bisulfite sequencing]]  ==
== 2014 Projects ==
== 2014 Projects ==
== BSPP capture of Human DMR 460k set ==
==== [[Noi:MONOD's project  | MONOD's project ]] ====
== MONOD's project ==
==== [[Noi:scRRBS's project |  scRRBS's project]] ====
=== Sample record ===
==== Samples from cancer center ====
* 2014-05-27: Received 10 pancreatic adenocarcinoma specimens (2 serum aliquot s/case) from cancer center (Sharmeela Kaushal).
** Sample info. file: [[Media:2014-05-27_10Serum-samples-PANCREAS_cancercenter.pdf]]
==== Samples from Kang Zhang's lab ====


=== BSPP capture ===
* GP1V4 or MONOD V1 and GP1V6 capture on 5 cancer samples and 3 blood samples (UCLA, SZ 96 sample set): [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-12-24]]
* MONOD V2 BSPP capture: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-3-2]]
* MONOD V3 BSPP capture: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-3-30#DNA_methylation_assay_-_MONOD_Project.2C_MONOD_V3_12k_probe_set_.28BSPP_capture.29]]
* Amplified DNA from Illumina captured with GP1V4 using Stoffel Fragment and Illumina's polymerase (no positive control, PC): [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-5-13]]
* 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: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-5-23]]
=== DNA (cell/cell-free) isolation ===
* Comparison of DNA isolation from plasma, serum and buffer coat (3 samples from cancer center)
** Sample info: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-2-28#2014-03-04]]
** Experimental design & results: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-2-28]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-3-11]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-4-4]]
* 30 normal plasma samples from Kang Zhang's lab: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-5-22]]
** DNA isolation results:
== scRRBS  ==
* Experimental design: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-2-7]]
* Trial experiment with STD Illumina adaptors and methylated NEBNext adaptors
** Experiment and results: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-2-13]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-2-14]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-2-17]]
* Experiment on flow-sorted nuclei with methylated adaptor from Illumina TruSeq kit
** Apr#1 experiment: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-4-21]]
** Apr#2 experiment: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-4-23]]
** Apr#3 experiment: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-4-25]] --> continue to sequencing (HL166 run)
== 2013 Projects ==
== 2013 Projects ==
* '''DNA methylation technology comparison (loci-specific, Blueprint project)'''
* '''DNA methylation technology comparison (loci-specific, Blueprint project)'''

Latest revision as of 02:38, 7 January 2015

Quick&Useful links[edit]

Labnote[edit]

LabNote tracking[edit]

Noi' Reagents [edit]

Sample tracking[edit]

Current Projects[edit]

Targeted bisulfite sequencing[edit]

2014 Projects[edit]

MONOD's project [edit]

scRRBS's project[edit]

2013 Projects[edit]

  • DNA methylation technology comparison (loci-specific, Blueprint project)
    • First batch of 12k probe set TEST experiment: [[1]], [[2]]
    • Record of samples (32 of mandatory (22) and optional (10) samples arrived June 12, 2013) : [[3]]
    • Normalized probe set TEST experiment: [[4]]
  • Parkinson's disease (PD) data set from Burnham Institute
    • BSPP capture: [[5]]
    • Mapping to hg18 (CpG): [[6]]
    • Mapping to hg19 (CpG and non-CpG):


  • Schizophrenia (UCLA, Roel Ophoff):
    • BSPP capture: [[7]]
    • 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: [[9]]
      • Genetic distance: [[10]]
    • Mid-parent offspring (mpo) analysis
      • Preliminary result by Dr. Zhang: [[11]]
      • Analysis of combining data (4 batches of sequencing data): [[12]]
    • mQTL analysis: [[13]]
      • Multiple test correction: [[14]]
      • mQTL on 5M impute SNPs [[15]]
      • Repeated analysis on no CpG-SNP methylMatrix: [[16]]
    • ASM analysis:
      • Sequence-dependent ASM identification by TTest: [[17]], [[18]]
      • Plot the distance of candidate CpG SNP ASM and correspondence p-value: [[19]]
      • Multiple test correction: [[20]]
    • Regression analysis: [[21]]
      • PCA analysis with control of GA sample from Kang Zhang's lab: [[22]]
      • Multiple test correction: [[23]]
      • Repeat PCA analysis and classified with LDA: [[24]], [[25]], [[26]], [[27]]
    • 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: [[32]], [[33]], [[34]], [[35]]
    • Mapping to hg19: [[36]]
    • ASM analysis:
      • Preliminary analysis of sequence-dependent ASM: [[37]]
      • Sequence dependent test by Dinh: [[38]]



  • 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): [[50]]
    • BSPP capture (2nd experiment, improved to library-free protocol and for PE sequencing): [[51]]
    • Summary of mapping of the data generated by library-free protocol (120426_HL118, lane5): [[52]]


  • 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: [53]
    • Mapping to separate out the reads based on different chromosomes by Dinh: [[54]] --> 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: [[77]], [[78]]
    • 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: [[79]]
    • Library preparation rehearsal: [[80]]
    • 72 Library prep (Library ID: NP-SkinMB_N2_Ind17-88_Feb07.2013). The libraries were light sequenced in HL144 lane1 [[81]], [[82]]
    • Select the top 20 libraires from the 72 libraries for Hiseq run [[83]]. Library ID : CW-SkinMB-20SAG-Mar20.2013
    • Prepare sequencing library of low DNA input (1ng): [[84]], [[85]]. Ligation after using CGI protocol to fragment DNA and A-tailing: [[86]]
  • 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: [[87]]
    • Padlock probe capture: [[88]]
  • Post-CoRE fragmentation library construction, started April2013
    • Jeff's microwell MDA samples: [[89]]
    • Eric's MEF cell samples: [[90]]. Library IDs: EC-MEF-Dev7-1-8-May21-2013 & EC-MEF-Dev7-9-16-May21-2013
    • Eric's PGP1#1 cell samples: [[91]]. Library IDs: EC-PGP1-Dev7-1-12-May23-2013 & EC-PGP1-Dev7-13-24-May23-2013
  • epMotion testing
    • AMPure bead purification optimization: [[92]], [[93]], [[94]], [[95]]
    • Bisulfite conversion/Zymo Lightning MagPrep kit optimization:

Protocols[edit]


Library construction (with Dinh)[edit]

Lab presentation (Journal club/Progress report)[edit]