Noi:MONOD's project: Difference between revisions

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=== Sample record ===
=== Sample record ===
==== [[Noi:Samples from Moores Cancer Center  | Samples from Moores Cancer Center]] ====
==== [[Noi:Samples from Moores Cancer Center  | Samples from Moores Cancer Center]] ====
* <u>'''2014-03-04:'''</u> Received 4 aliquots of plasma, serum, and buffy coat from 3 cases from Cancer Center.  
* <u>'''[[noi:Samples_from_Moores_Cancer_Center#2014-03-04|2014-03-04:]]'''</u> 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
** The samples were used for DNA isolation comparison using four different kits
*** Experimental design & results: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-2-28]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-3-11]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-4-4]]
*** Experimental design & results: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-2-28]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-3-11]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-4-4]]
* <u>'''2014-05-27:'''</u> Received 10 pancreatic adenocarcinoma specimens (2 serum aliquots/case) from Cancer Center (Sharmeela Kaushal).
* <u>'''[[noi:Samples_from_Moores_Cancer_Center#2014-05-27|2014-05-27:]]'''</u> Received 10 pancreatic adenocarcinoma specimens (2 serum aliquots/case) from Cancer Center (Sharmeela Kaushal).
** DNA extraction result: [[Noi/NOTES/2014-5-31#DNA_extraction_of_10_serum_samples_from_Cancer_Center|Noi/NOTES/2014-5-31 ]]
** DNA extraction result: [[Noi/NOTES/2014-5-31#DNA_extraction_of_10_serum_samples_from_Cancer_Center|Noi/NOTES/2014-5-31 ]]
* <u>'''2014-06-05:'''</u> Received 10 pancreatic adenocarcinoma specimens (3 plasma aliquots/case) and 5 tumor tissues from the same patient from cancer center (Sharmeela Kaushal).
* <u>'''[[noi:Samples_from_Moores_Cancer_Center#2014-06-05|2014-06-05:]]'''</u> Received 10 pancreatic adenocarcinoma specimens (3 plasma aliquots/case) and 5 tumor tissues from the same patient from cancer center (Sharmeela Kaushal).
** These samples were derived from the same patients in 2014-05-27
** These samples were derived from the same patients in 2014-05-27
** DNA extraction result: [[Noi/NOTES/2014-6-9]]
** DNA extraction result: [[Noi/NOTES/2014-6-9]]
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* <u>'''[[noi:Samples_from_Moores_Cancer_Center#2014-06-26| 2014-05-26]]:'''</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| 2014-05-26]]:'''</u> Received 10 Lung cancer specimens (3 plasma aliquots/case) from Cancer Center (Sharmeela Kaushal).
** Project ID: UCSD-007
** Project ID: UCSD-007
* <u>'''2014-05-27:]]'''</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|2014-05-27:]]'''</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>'''2014-05-27:'''</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|2014-05-27:]]'''</u> Received 5 lung solid tumor tissue samples (20mg/case) from Cancer Center. Matched pairs samples with plasma samples of lung project (Sharmeela Kaushal).
 
==== 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

Revision as of 20:18, 27 June 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).
  • 2014-05-26: Received 10 colon cancer specimens (3 plasma aliquots/case) from Cancer Center (Sharmeela Kaushal).
    • Project ID: UCSD-006
  • 2014-05-26: Received 10 Lung cancer specimens (3 plasma aliquots/case) from Cancer Center (Sharmeela Kaushal).
    • Project ID: UCSD-007
  • 2014-05-27: Received 5 colon solid tumor tissue samples (20mg/case) from Cancer Center. Matched pairs samples with plasma samples of colon project (Sharmeela Kaushal).
  • 2014-05-27: 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.: [[4]].
    • They are all from normal samples with no cancer history
    • DNA extraction results: [[5]]

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: [[6]]
    • RRBS library preparation of 100ng input DNA: [[7]]

BSPP capture

  • GP1V4 or MONOD V1 and GP1V6 capture on 5 cancer samples and 3 blood samples (UCLA, SZ 96 sample set): [[8]]
  • MONOD V2 BSPP capture: [[9]]
  • MONOD V3 BSPP capture: [[10]]
  • Amplified DNA from Illumina captured with GP1V4 using Stoffel Fragment and Illumina's polymerase (no positive control, PC): [[11]]
  • 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: [[12]]