Noi:Labnote tracking: Difference between revisions

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  '''Date                        Description'''
  '''Date                        Description'''
  '''December 2014'''
  '''December 2014'''
2014-
  2014-12-11                  RRBS library prep, mouse hippocampus gDNA (Zhou's lab)
  2014-12-11                  RRBS library prep, mouse hippocampus gDNA (Zhou's lab)
   
   
Line 20: Line 22:
  2014-11-25                  Comparison of the efficiency between TruSeq adaptor and a customized  
  2014-11-25                  Comparison of the efficiency between TruSeq adaptor and a customized  
                               unmethylated Y-adaptor with UMI
                               unmethylated Y-adaptor with UMI
  [[Noi/NOTES/2014-11-4|14-12-04]]                    SeqCap Epi probe pool (UMR v1) hybridization capture  
  [[Noi/NOTES/2014-11-4|14-11-04]]                    SeqCap Epi probe pool (UMR v1) hybridization capture  
                               on normal and cancer patient WGBS libraries  
                               on normal and cancer patient WGBS libraries  
                               1st Experiment (used 2 tubes of LMS SeqCap probe pool)
                               1st Experiment (used 2 tubes of LMS SeqCap probe pool)
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  2014-08-03                  Preparation of WGBS libraries of small fragment DNA in cancer patient plasma samples  
  2014-08-03                  Preparation of WGBS libraries of small fragment DNA in cancer patient plasma samples  
                             (no DNA fragmentation step)
                             (no DNA fragmentation step)
                             I used dA:dC:dG for end repair. The later experiment was performed using all 4 bases for end repair
                             I used dA:dC:dG for end repair. The later experiment was performed using all 4 bases  
                            for end repair


   '''July 2014'''
   '''July 2014'''
2014-07-31                  Preparation of WGBS libraries of small fragment DNA in plasma samples (TEST)
                            Use low-input RRBS protocol, but skip DNA digestion before end repair/A-tailing
2014-07-22                  Preparation of low-input RRBS sequencing libraries with MspI/TaqI double-digestion
                            on normal plasma DNA
2014-07-20                  Mapping of MspI/TaqI double-digested RRBS libraries
2014-07-11                  Preparation of low-input RRBS sequencing libraries with MspI/TaqI double-digestion
2014-07-10                  CRC oligo pool from Illumina (BSPP)
2014-07-07                  Summary of RRBS sequencing libraries and their corresponding index
2014-07-02                  Summary of samples and their corresponding index
                            HiSeq Rapid run (HiSeq 140627_SN1001)
                            MiSeq run (MiSeq140630)
'''June 2014'''
2014-06-29                  Preparation of RRBS sequencing libraries of plasma DNA from colon and lung cancer patients
2014-06-28                  Preparation of RRBS sequencing libraries of solid tumor tissue sample from colon and
                            lung cancer patients (VERY DETAILS)
2014-06-27                  DNA extraction of plasma samples and matched pair solid tumor tissue samples from
                            Moores Cancer Center

Latest revision as of 08:21, 15 January 2015

Labnote tracking[edit]

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Date                         Description
December 2014
2014-

2014-12-11                   RRBS library prep, mouse hippocampus gDNA (Zhou's lab)

2014-12-08                   LMS + CRC BSPP capture on WGBS libraries prepared from ctDNA
                             of CRC patient, Illumina (with Li Liu)

2014-12-05                   WGBS library prep and BSPP capture of cfDNA from Illumina (with Li Liu)
                             ctDNA of colorectal cancer (CRC) patients from Illumina 
                             (samples from Kansas University)

2014-12-04                   SeqCap Epi probe pool (UMR v1) hybridization capture on cancer patient
                             WGBS libraries (plasma/tumor tissue DNA, )
                             2nd experiment (used 3 tubes of LMS SeqCap probe pool)
November 2014
2014-11-25                   Comparison of the efficiency between TruSeq adaptor and a customized 
                             unmethylated Y-adaptor with UMI
14-11-04                     SeqCap Epi probe pool (UMR v1) hybridization capture 
                              on normal and cancer patient WGBS libraries 
                             1st Experiment (used 2 tubes of LMS SeqCap probe pool)
                             Also included 
                             Part I: Re-amplification of WGBS libraries of normal plasma samples
October 2014
2014-10-31                   Repeating of BIS/DNA SMART ChIP-Seq protocol

2014-10-29                   Generation of sequencing library of a customized SeqCap EZ Epi Probe Pool 
                             to decode the sequences of LMS SeqCap probe pool
                             Library generated by DNA SMART ChIP Seq Kit

2014-10-24                   Preparation of WGBS of cfDNA from plasma using KAPA Hyper Prep kit & 
                             NEXTflex Cell Free DNA-Seq kit
                             To compare the efficiency between the two commercial kits
                             Repeated experiment of 14-1022

2014-10-22                   Preparation of WGBS of cfDNA from plasma using KAPA Hyper Prep kit

2014-10-15                   Expansion PCR of new probe set from CustomArrays (90k_oligos_30Sept2014)
                             Bad oligos. Got re-synthesized of the new oligos by CustomArrays 
                             The new tube was amplified by  Rui on 14-11-12

2014-10-08                   Integration of DNA SMART ChIP-Seq protocol with RRBS for low input DNA methylation assay

2014-10-03                   Measurement of the size distribution of WGBS libraries generated from cfDNA
                             Using Bioanalyzer
 September 2014
2014-09-14                   Summary of BSPP sequencing libraries and their corresponding index
                             1) HiSeq Rapid run at Illumina (140912_D00171_0588)
                             2) HiSeq Rapid run at Illumina (140912_D00171_0589)

2014-09-10                   MONOD V5 set A + CRC BSPP capture of tumor DNA samples and ctDNA from Illumina
                             Also included some samples of WGBS libraries from normal and cancer cfDNA DNA

2014-09-08                   Preparation of WGBS libraries of ctDNA/cfDNA from Illumina (no DNA fragmentation step)
                             cfDNA, NORM1-02-P1, NORM1-03-P1, COLO2-03

2014-09-05                   MONOD V5 set A + CRC BSPP capture of tumor DNA samples
                             Also included few of WGBS libraries from normal and cancer cfDNA DNA
 August 2014
2014-08-27                   BSPP LMS cluster capture of colon cancer primary tumor DNA 
                             Need to finish labnote May not go to sequencing!

2014-08-25                   Additional cfDNA from Illumina (Nautica cfDNA) 
                             Library prep on 2014-09-08 
 
2014-08-24                   Summary of RRBS & WGBS libraries generated from plasma DNA

2014-08-21                   Expansion PCR of BSPP from CustomArrays 90K_ologos_04Aug2014 (8-20-14)
                             MONOD V5A or BSPP LMS cluster probes

2014-08-18                   Preparation of WGBS libraries of small fragment DNA in cancer patient plasma samples 
                            (no DNA fragmentation step, REPEAT with dAdGdCdT for end repair)

2014-08-15                  Preparation of WGBS libraries of small fragment DNA in normal control plasma samples 
                            (no DNA fragmentation step, with dAdGdCdT for end repair)  

2014-8-13                   Expansion PCR of new probe set from CustomArrays (90K_ologos_04Aug2014)
                            Should be MONOD V5A or BSPP LMS cluster BSPP
                            Bad oligos. Got re-synthesized of the new oligos by CustomArrays

2014-08-03                  Preparation of WGBS libraries of small fragment DNA in cancer patient plasma samples 
                            (no DNA fragmentation step)
                            I used dA:dC:dG for end repair. The later experiment was performed using all 4 bases 
                            for end repair
  July 2014
2014-07-31                  Preparation of WGBS libraries of small fragment DNA in plasma samples (TEST)
                            Use low-input RRBS protocol, but skip DNA digestion before end repair/A-tailing

2014-07-22                  Preparation of low-input RRBS sequencing libraries with MspI/TaqI double-digestion
                            on normal plasma DNA

2014-07-20                  Mapping of MspI/TaqI double-digested RRBS libraries

2014-07-11                  Preparation of low-input RRBS sequencing libraries with MspI/TaqI double-digestion

2014-07-10                  CRC oligo pool from Illumina (BSPP)

2014-07-07                  Summary of RRBS sequencing libraries and their corresponding index

2014-07-02                  Summary of samples and their corresponding index
                            HiSeq Rapid run (HiSeq 140627_SN1001)
                            MiSeq run (MiSeq140630)

June 2014
2014-06-29                  Preparation of RRBS sequencing libraries of plasma DNA from colon and lung cancer patients

2014-06-28                  Preparation of RRBS sequencing libraries of solid tumor tissue sample from colon and 
                            lung cancer patients (VERY DETAILS)

2014-06-27                  DNA extraction of plasma samples and matched pair solid tumor tissue samples from 
                            Moores Cancer Center