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)
  2014-12-08                  LMS + CRC BSPP capture on WGBS libraries prepared from ctDNA
  2014-12-08                  LMS + CRC BSPP capture on WGBS libraries prepared from ctDNA
                               of CRC patient (Illumina)
                               of CRC patient, Illumina (with Li Liu)
  2014-12-05                  WGBS library prep and BSPP capture of cfDNA from 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  
                               ctDNA of colorectal cancer (CRC) patients from Illumina  
                               (samples from Kansas University)
                               (samples from Kansas University)
  2014-12-04                  SeqCap Epi probe pool (UMR v1) hybridization capture on cancer patient
  2014-12-04                  SeqCap Epi probe pool (UMR v1) hybridization capture on cancer patient
                               WGBS libraries (plasma/tumor tissue DNA, )
                               WGBS libraries (plasma/tumor tissue DNA, )
Line 17: 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)
                               <u>Also included</u>  
                               <u>Also included</u>  
Line 25: Line 30:
  '''October 2014'''
  '''October 2014'''
  2014-10-31                  Repeating of BIS/DNA SMART ChIP-Seq protocol
  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  
  2014-10-29                  Generation of sequencing library of a customized SeqCap EZ Epi Probe Pool  
                               to decode the sequences of LMS SeqCap probe pool
                               to decode the sequences of LMS SeqCap probe pool
                               Library generated by DNA SMART ChIP Seq Kit
                               Library generated by DNA SMART ChIP Seq Kit
  2014-10-24                  Preparation of WGBS of cfDNA from plasma using KAPA Hyper Prep kit &  
  2014-10-24                  Preparation of WGBS of cfDNA from plasma using KAPA Hyper Prep kit &  
                               NEXTflex Cell Free DNA-Seq kit
                               NEXTflex Cell Free DNA-Seq kit
                               To compare the efficiency between the two commercial kits
                               To compare the efficiency between the two commercial kits
                               Repeated experiment of 14-1022
                               Repeated experiment of 14-1022
  2014-10-22                  Preparation of WGBS of cfDNA from plasma using KAPA Hyper Prep kit
  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)
  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  
                               Bad oligos. Got re-synthesized of the new oligos by CustomArrays  
                               The new tube was amplified by [[Rui:LabNotes/Haplotyping/2014-11-12| Rui on 14-11-12]]
                               The new tube was amplified by [[Rui:LabNotes/Haplotyping/2014-11-12| Rui on 14-11-12]]
  2014-10-08                  Integration of DNA SMART ChIP-Seq protocol with RRBS for low input DNA methylation assay
  2014-10-08                  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
                              <u>Need to finish labnote</u> 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

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