Noi:MONOD's project: Difference between revisions

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** RRBS library preparation of 1ng input DNA from plasma samples: [[Noi/NOTES/2014-6-20]]
** RRBS library preparation of 1ng input DNA from plasma samples: [[Noi/NOTES/2014-6-20]]
* <u>'''[[noi:Samples_from_Moores_Cancer_Center#2014-06-26| 2014-06-26]]:'''</u> Received 10 colon cancer specimens (3 plasma aliquots/case) from Cancer Center (Sharmeela Kaushal).
* <u>'''[[noi:Samples_from_Moores_Cancer_Center#2014-06-26| 2014-06-26]]:'''</u> Received 10 colon cancer specimens (3 plasma aliquots/case) from Cancer Center (Sharmeela Kaushal).
** Project ID: UCSD-006
** Project ID: UCSD-006-P
** [[Noi/NOTES/2014-6-27#Part_2:_DNA_extraction_from_plasma_samples|DNA extraction result]]
** [[Noi/NOTES/2014-6-27#Part_2:_DNA_extraction_from_plasma_samples|DNA extraction result]]
** RRBS library preparation of 1ng input DNA from plasma sample: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-6-29]]
** RRBS library preparation of 1ng input DNA from plasma sample: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-6-29]]
* <u>'''[[noi:Samples_from_Moores_Cancer_Center#2014-06-26| 2014-06-26]]:'''</u> Received 10 Lung cancer specimens (3 plasma aliquots/case) from Cancer Center (Sharmeela Kaushal).
* <u>'''[[noi:Samples_from_Moores_Cancer_Center#2014-06-26| 2014-06-26]]:'''</u> Received 10 Lung cancer specimens (3 plasma aliquots/case) from Cancer Center (Sharmeela Kaushal).
** Project ID: UCSD-007
** Project ID: UCSD-007-P
** [[Noi/NOTES/2014-6-27#Part_2:_DNA_extraction_from_plasma_samples|DNA extraction result]]
** [[Noi/NOTES/2014-6-27#Part_2:_DNA_extraction_from_plasma_samples|DNA extraction result]]
** RRBS library preparation of 1ng input DNA from plasma sample: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-6-29]]
** RRBS library preparation of 1ng input DNA from plasma sample: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-6-29]]
* <u>'''[[noi:Samples_from_Moores_Cancer_Center#2014-06-27|2014-06-27:]]'''</u> Received 5 colon solid tumor tissue samples (20mg/case) from Cancer Center. Matched pairs samples with plasma samples of colon project  (Sharmeela Kaushal).
* <u>'''[[noi:Samples_from_Moores_Cancer_Center#2014-06-27|2014-06-27:]]'''</u> Received 5 colon solid tumor tissue samples (20mg/case) from Cancer Center. Matched pairs samples with plasma samples of colon project  (Sharmeela Kaushal).
** Project ID: UCSD-006
** Project ID: UCSD-006-T
** [[DNA extraction result]]
** [[Noi/NOTES/2014-6-27#Part_1:_DNA_extraction_from_solid_tumor_tissue_samples|DNA extraction result]]
** RRBS library preparation of 100ng input DNA from tumor tissue: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-6-28]]
* <u>'''[[noi:Samples_from_Moores_Cancer_Center#2014-06-27|2014-06-27:]]'''</u> Received 5 lung solid tumor tissue samples (20mg/case) from Cancer Center. Matched pairs samples with plasma samples of lung project (Sharmeela Kaushal).
* <u>'''[[noi:Samples_from_Moores_Cancer_Center#2014-06-27|2014-06-27:]]'''</u> Received 5 lung solid tumor tissue samples (20mg/case) from Cancer Center. Matched pairs samples with plasma samples of lung project (Sharmeela Kaushal).
 
** Project ID: UCSD-007-T
** [[Noi/NOTES/2014-6-27#Part_1:_DNA_extraction_from_solid_tumor_tissue_samples|DNA extraction result]]
** RRBS library preparation of 100ng input DNA from tumor tissue: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-6-28]]
<br>
==== Samples from Kang Zhang's lab ====
==== Samples from Kang Zhang's lab ====
* <u>'''2014-05-22:'''</u> Received 30 plasma samples from Kang Zhang's lab
* <u>'''2014-05-22:'''</u> Received 30 plasma samples from Kang Zhang's lab
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** 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]]
** DNA extraction results: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-5-30]]
 
<br>
==== 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 22:20, 4 July 2014

MONOD's Project (March, 2014)

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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.
    • The samples were used for DNA isolation comparison using four different kits
      • Experimental design & results: [[1]], [[2]], [[3]]
  • 2014-05-27: Received 10 pancreatic adenocarcinoma specimens (2 serum aliquots/case) from Cancer Center (Sharmeela Kaushal).
  • 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).
  • 2014-06-26: Received 10 colon cancer specimens (3 plasma aliquots/case) from Cancer Center (Sharmeela Kaushal).
  • 2014-06-26: Received 10 Lung cancer specimens (3 plasma aliquots/case) from Cancer Center (Sharmeela Kaushal).
  • 2014-06-27: Received 5 colon solid tumor tissue samples (20mg/case) from Cancer Center. Matched pairs samples with plasma samples of colon project (Sharmeela Kaushal).
  • 2014-06-27: Received 5 lung solid tumor tissue samples (20mg/case) from Cancer Center. Matched pairs samples with plasma samples of lung project (Sharmeela Kaushal).


Samples from Kang Zhang's lab

  • 2014-05-22: Received 30 plasma samples from Kang Zhang's lab
    • Sample info.: [[8]].
    • They are all from normal samples with no cancer history
    • DNA extraction results: [[9]]


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: Matched 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 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
    • RRBS library preparation of 5ng input DNA: [[10]]
    • RRBS library preparation of 100ng input DNA: [[11]]

BSPP capture

  • GP1V4 or MONOD V1 and GP1V6 capture on 5 cancer samples and 3 blood samples (UCLA, SZ 96 sample set): [[12]]
  • MONOD V2 BSPP capture: [[13]]
  • MONOD V3 BSPP capture: [[14]]
  • Amplified DNA from Illumina captured with GP1V4 using Stoffel Fragment and Illumina's polymerase (no positive control, PC): [[15]]
  • 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: [[16]]