Nongluk (Noi) Plongthongkum: Difference between revisions
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** Sample info.: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-5-22]]. | ** Sample info.: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-5-22]]. | ||
** They are all from normal samples with no cancer history | ** They are all from normal samples with no cancer history | ||
** DNA extraction results: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-5-30]] | |||
==== FFPE and Frozen Matched Pair Genomic DNA:Human Tumor Tissue: Colon ==== | ==== FFPE and Frozen Matched Pair Genomic DNA:Human Tumor Tissue: Colon ==== | ||
*<u>'''2014-05-23:'''</u> Received two tubes of FFPE and frozen matched pair gDNA from Biochain | *<u>'''2014-05-23:'''</u> Received two tubes of FFPE and frozen matched pair gDNA from Biochain |
Revision as of 18:44, 7 June 2014
Quick&Useful links
Labnote
Sample tracking
Current Projects
Targeted bisulfite sequencing
2014 Projects
BSPP capture of Human DMR 460k set
MONOD's project
Sample record
Samples from Moores Cancer Center
- 2014-03-04: Received 4 aliquots of plasma, serum, and buffy coat from 3 cases from Cancer Center.
- 2014-05-27: Received 10 pancreatic adenocarcinoma specimens (2 serum aliquots/case) from Cancer Center (Sharmeela Kaushal).
- DNA extraction result: [[4]]
- 2014-06-05: Received 10 pancreatic adenocarcinoma specimens (3 plasma aliquots/case) and 5 tumor tissues from the same patient from cancer center (Sharmeela Kaushal).
- These samples were derived from the same patients in 2014-05-27
Samples from Kang Zhang's lab
- 2014-05-22: Received 30 plasma samples from Kang Zhang's lab
FFPE and Frozen Matched Pair Genomic DNA:Human Tumor Tissue: Colon
- 2014-05-23: Received two tubes of FFPE and frozen matched pair gDNA from Biochain
- Sample info.
- Catalog number: D8235090-FP, lot. B609045
- Tube1: Matched pair - gDNA - human primary tissue: colon. Conc.: 0.58ug/ul or 580ng/ul, amount: 2ug --> expected volume ~3.44ul
- Tube2: Match pair - gDNA - human primary tissue: colon. Conc.: 0.076ug/ul or 76ng/ul, amount: 2ug --> expected volumed ~26.31ul
- (2014-06-01) I added TE buffer to make conc. to 50ng/ul (total volume 40ul) based on original conc. and re-measured conc. with Qubit dsDNA HS assay again (1ul).
- Sample info.
Sample Original conc. (ng/ul) Estimate volume (ul) Dilute to 50ng/ul (total volume) Add TE buffer (ul) Qubit conc. (ng/ul) CTT-Frozen 580.00 3.45 40.00 36.55 52.3 CTT-FFPE 76.00 26.32 40.00 13.68 64.8
- - CTT = colon tumor tissue
BSPP capture
- GP1V4 or MONOD V1 and GP1V6 capture on 5 cancer samples and 3 blood samples (UCLA, SZ 96 sample set): [[7]]
- MONOD V2 BSPP capture: [[8]]
- MONOD V3 BSPP capture: [[9]]
- Amplified DNA from Illumina captured with GP1V4 using Stoffel Fragment and Illumina's polymerase (no positive control, PC): [[10]]
- 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: [[11]]
scRRBS
- Experimental design: [[12]]
- 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: [[26]]
- 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: [[47]] --> note: this experiment failed in amplification step [[48]]
- Mapping to hg19: File:BSPP AMD-mapping-summary 2011 10 12.xlsx
- Regression analysis by Dr. Zhang: [[49]]
- Overlapping of Illumina 450k methylation array and BSPP: [[50]]
- 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: [72]
- Mapping to separate out the reads based on different chromosomes by Dinh: [[73]] --> 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: [[98]]
- Library preparation rehearsal: [[99]]
- 72 Library prep (Library ID: NP-SkinMB_N2_Ind17-88_Feb07.2013). The libraries were light sequenced in HL144 lane1 [[100]], [[101]]
- Select the top 20 libraires from the 72 libraries for Hiseq run [[102]]. Library ID : CW-SkinMB-20SAG-Mar20.2013
- Prepare sequencing library of low DNA input (1ng): [[103]], [[104]]. Ligation after using CGI protocol to fragment DNA and A-tailing: [[105]]
- 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: [[115]]
- 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)