Nongluk (Noi) Plongthongkum: Difference between revisions
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** Library preparation rehearsal: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-1-15]] | ** 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]] | ** 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]] | ** 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]] | ** 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''' | * '''In Situ sequencing, started Mar2013''' | ||
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** Probe preparation: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-3-6]] | ** 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]] | ** 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''' | * '''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]] | ** 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]] |
Revision as of 18:12, 1 June 2013
Quick&Useful links
Labnote
Sample tracking
Current Projects
Targeted bisulfite sequencing
- Parkinson's disease (PD) data set from Burnham Institute
- 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
- Geographic Astrophy (GA) (UCSD, Kang Zhang) Note: most of the data analysis was performed by Dr. Zhang and Dinh
- BSPP capture: [[24]] --> note: this experiment failed in amplification step [[25]]
- Mapping to hg19: File:BSPP AMD-mapping-summary 2011 10 12.xlsx
- Regression analysis by Dr. Zhang: [[26]]
- Overlapping of Illumina 450k methylation array and BSPP: [[27]]
- 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: [49]
- Mapping to separate out the reads based on different chromosomes by Dinh: [[50]] --> 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: [[75]]
- Library preparation rehearsal: [[76]]
- 72 Library prep (Library ID: NP-SkinMB_N2_Ind17-88_Feb07.2013). The libraries were light sequenced in HL144 lane1 [[77]], [[78]]
- Select the top 20 libraires from the 72 libraries for Hiseq run [[79]]. Library ID : CW-SkinMB-20SAG-Mar20.2013
- Prepare sequencing library of low DNA input (1ng): [[80]], [[81]]. Ligation after using CGI protocol to fragment DNA and A-tailing: [[82]]
- 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: [[92]]
- 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)