Nongluk (Noi) Plongthongkum: Difference between revisions

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*[[Noi: Noi LabTraining|Noi Lab Training]]
=== [[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)]] ==

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]