Noi:MONOD's project

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MONOD's Project (March, 2014)[edit]

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Sample record[edit]

Samples from Moores Cancer Center[edit]

  • 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[edit]

  • 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]]
    • RRBS library preparation of 1ng input DNA from plasma samples: Noi/NOTES/2014-6-20


FFPE and Frozen Matched Pair Genomic DNA:Human Tumor Tissue: Colon[edit]

  • 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]]


Samples from Illumina[edit]

BSPP capture[edit]

  • 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]]


Sequencing record[edit]

  • HiSeq Rapid run at IGM, UCSD: 2014-06-27
    • Sample summary
    • PE 100+7
    • Raw data on genome-miner: /media/SeqStore2/140627_SN1001_0363/2nd_attemp/
    • Dinh did mapping
  • MiSeq run at Palsson's lab: 2014-06-30
    • Sample summary
    • PE 150+7
    • Raw data on genome-miner: ??
    • Dinh did mapping
  • HiSeq Rapid run at IGM, UCSD: 2014-07-08
    • Sample summary
    • PE 100+7
    • Sequencing libraries of solid tumor tissue from UCSD-006-T and UCSD-007-T project
  • HiSeq Rapid run at Illumina: 2014-07-09
    • Sample summary
    • PE 100+7
    • Sequencing libraries of plasma DNA from UCSD-006-P and UCSD-007-P project and plasma sequencing libraries from UCSD-004-P (PC-P) and NC-P from previous batch.