Nongluk (Noi) Plongthongkum: Difference between revisions
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== 2014 Projects == | == 2014 Projects == | ||
== BSPP capture of Human DMR 460k set == | == BSPP capture of Human DMR 460k set == | ||
== MONOD's | == MONOD's project == | ||
=== BSPP capture === | === 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]] | * 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]] | ||
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** Sample info: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-2-28#2014-03-04]] | ** 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]] | ** 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]] | |||
==== | == 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 == | |||
* '''DNA methylation technology comparison (loci-specific, Blueprint project)''' | * '''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]] | ** 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]] |
Revision as of 01:15, 27 May 2014
Quick&Useful links
Labnote
Sample tracking
Current Projects
Targeted bisulfite sequencing
2014 Projects
BSPP capture of Human DMR 460k set
MONOD's project
BSPP capture
- GP1V4 or MONOD V1 and GP1V6 capture on 5 cancer samples and 3 blood samples (UCLA, SZ 96 sample set): [[1]]
- MONOD V2 BSPP capture: [[2]]
- MONOD V3 BSPP capture: [[3]]
- Amplified DNA from Illumina captured with GP1V4 using Stoffel Fragment and Illumina's polymerase (no positive control, PC): [[4]]
- 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: [[5]]
DNA (cell/cell-free) isolation
- Comparison of DNA isolation from plasma, serum and buffer coat (3 samples from cancer center)
- 30 normal plasma samples from Kang Zhang's lab: [[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
2013 Projects
- DNA methylation technology comparison (loci-specific, Blueprint project)
- Parkinson's disease (PD) data set from Burnham Institute
- Schizophrenia (UCLA, Roel Ophoff):
- BSPP capture: [[24]]
- 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
- Geographic Astrophy (GA) (UCSD, Kang Zhang) Note: most of the data analysis was performed by Dr. Zhang and Dinh
- BSPP capture: [[45]] --> note: this experiment failed in amplification step [[46]]
- Mapping to hg19: File:BSPP AMD-mapping-summary 2011 10 12.xlsx
- Regression analysis by Dr. Zhang: [[47]]
- Overlapping of Illumina 450k methylation array and BSPP: [[48]]
- HAPMAP project (HAPMAP PT01, two families, 1362 and 1464)
- Randomly tagging primers (with Athurva and Dinh)
- BSPP capture with probes synthesized by LC Sciences (Nature Methods 2012 paper)
- 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: [70]
- Mapping to separate out the reads based on different chromosomes by Dinh: [[71]] --> 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
- Probe production for Hi-resolution chromosome painting project (probe production part)
- PNAS revision_May2012 (I work on 330k BSPP capture)
- ASM and ASCM in human cells project (I work on 330k BSPP capture)
- N37 sample (10 tissues from Dr. Billy Jin, Stanford)
- LGH-Project, collaboration with Guanghui, Salk Institute
Mapping data: /home/nplongth/Noi_scratch/GL.project1-2.20120918/LGH-projectB/hg19.mapping
- Skin microbiome project, started Jan2013
- Sample information: [[96]]
- Library preparation rehearsal: [[97]]
- 72 Library prep (Library ID: NP-SkinMB_N2_Ind17-88_Feb07.2013). The libraries were light sequenced in HL144 lane1 [[98]], [[99]]
- Select the top 20 libraires from the 72 libraries for Hiseq run [[100]]. Library ID : CW-SkinMB-20SAG-Mar20.2013
- Prepare sequencing library of low DNA input (1ng): [[101]], [[102]]. Ligation after using CGI protocol to fragment DNA and A-tailing: [[103]]
- In Situ sequencing, started Mar2013
- Post-CoRE fragmentation library construction, started April2013
- epMotion testing
Protocols
- Probe preparation
- DMR330k probe synthesized by Agilent:
- Original protocol (DMR220k) by Dr. Zhang: [[113]]
- DMR330k probe production_very details version
- [Agilent_probe_preparation]
- [LC_Sciences_probe_preparation]
- Probe synthesized by LC Sciences
- DMR330k probe synthesized by Agilent:
- Library construction (BSPP)