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 ( | 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- | [[Noi/NOTES/2014-11-4|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) | 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]
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