Nongluk (Noi) Plongthongkum: Difference between revisions
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== Current Projects == | === [[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:LabNotes/CpG sequences | | == [[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)
- Parkinson's disease (PD) data set from Burnham Institute
- 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
- Geographic Astrophy (GA) (UCSD, Kang Zhang) Note: most of the data analysis was performed by Dr. Zhang and Dinh
- BSPP capture: [[28]] --> note: this experiment failed in amplification step [[29]]
- Mapping to hg19: File:BSPP AMD-mapping-summary 2011 10 12.xlsx
- Regression analysis by Dr. Zhang: [[30]]
- Overlapping of Illumina 450k methylation array and BSPP: [[31]]
- 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: [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
- 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: [[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
- Post-CoRE fragmentation library construction, started April2013
- epMotion testing
Protocols[edit]
- Probe preparation
- DMR330k probe synthesized by Agilent:
- Original protocol (DMR220k) by Dr. Zhang: [[96]]
- 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)