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=== <span style="color:mediumblue">Sample record</span> === ==== [[Noi:Samples from Moores Cancer Center | Samples from Moores 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 *** 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>'''[[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 ]] * <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 ** DNA extraction result: [[Noi/NOTES/2014-6-9]] ** RRBS library preparation of 100ng input DNA from tumor tissue: [[Noi/NOTES/2014-6-16]] ** 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). ** Project ID: UCSD-006-P ** [[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]] * <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-P ** [[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]] * <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-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]] * <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 ==== * <u>'''2014-05-22:'''</u> Received 30 plasma samples from Kang Zhang's lab ** Sample info.: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-5-22]]. ** 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]] ** RRBS library preparation of 1ng input DNA from plasma samples: [[Noi/NOTES/2014-6-20]] <br> ==== 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 ** 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). ::{| {{table}} class = wikitable | align="center" style="width:120px;background:#f0f0f0;"|'''Sample''' | align="center" style="width:100px;background:#f0f0f0;"|'''Original conc. (ng/ul)''' | align="center" style="width:100px;background:#f0f0f0;"|'''Estimate volume (ul)''' | align="center" style="width:100px;background:#f0f0f0;"|'''Dilute to 50ng/ul (total volume)''' | align="center" style="width:100px;background:#f0f0f0;"|'''Add TE buffer (ul)''' | align="center" style="width:100px;background:#f0f0f0;"|'''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: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-6-3]] ** RRBS library preparation of 100ng input DNA: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-6-13]]<br> <br> ==== [[Noi:Samples from Illumina | Samples from Illumina]] ====
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