Noi:MONOD's project
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MONOD's Project (March, 2014)
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.
- 2014-05-27: Received 10 pancreatic adenocarcinoma specimens (2 serum aliquots/case) from Cancer Center (Sharmeela Kaushal).
- DNA extraction result: [[4]]
- 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).
Samples from Kang Zhang's lab
- 2014-05-22: Received 30 plasma samples from Kang Zhang's lab
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: Match 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 info.
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
BSPP capture
- GP1V4 or MONOD V1 and GP1V6 capture on 5 cancer samples and 3 blood samples (UCLA, SZ 96 sample set): [[11]]
- MONOD V2 BSPP capture: [[12]]
- MONOD V3 BSPP capture: [[13]]
- Amplified DNA from Illumina captured with GP1V4 using Stoffel Fragment and Illumina's polymerase (no positive control, PC): [[14]]
- 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: [[15]]