Noi:Labnote tracking: Difference between revisions

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  '''December 2014'''
  '''December 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)
  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 18: Line 21:
                               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|14-12-04]]                    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>  
                               Part I: Re-amplification of WGBS libraries of normal plasma samples
                               Part I: Re-amplification of WGBS libraries of normal plasma samples
 
  '''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

Revision as of 13:05, 24 December 2014

Labnote tracking

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Date                         Description
December 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)

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
14-12-04                     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