Noi/NOTES/2014-6-9: Difference between revisions
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>Noi (Created page with "= DNA extraction of 10 plasma samples and 5 matched pair solid tumor tissue samples from Cancer Center = * [[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNot...") |
>Noi mNo edit summary |
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* I measured volume of the first tube serum during DNA extraction and adjust volume to 400ul with 1X PBS as ChargeSwitch kit required different volume of reagent for different sample volume. | * I measured volume of the first tube serum during DNA extraction and adjust volume to 400ul with 1X PBS as ChargeSwitch kit required different volume of reagent for different sample volume. | ||
=== <span style="color: | === <span style="color:blue"><u>Part 1: DNA extraction from plasma samples</u></span> === | ||
* There are <u>three tubes</u> of plasma for each sample. Dr. Zhang suggested to use 2 tubes for DNA extraction. | * There are <u>three tubes</u> of plasma for each sample. Dr. Zhang suggested to use 2 tubes for DNA extraction. | ||
* Note that the measurement could be +-5ul error since serum is viscous and I needed to adjust the pipette volume after aspiration to measure the volume | * Note that the measurement could be +-5ul error since serum is viscous and I needed to adjust the pipette volume after aspiration to measure the volume | ||
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{| {{table}} class = wikitable | {| {{table}} class = wikitable | ||
| align="center" style="width:120px;background:#f0f0f0;"|'''Sample''' | | align="center" style="width:120px;background:#f0f0f0;"|'''Sample''' | ||
| align="center" style="width:100px;background:#f0f0f0;"|''' | | align="center" style="width:100px;background:#f0f0f0;"|'''Conc. in the Qubit''' | ||
| align="center" style="width:80px;background:#f0f0f0;"|'''Unit''' | | align="center" style="width:80px;background:#f0f0f0;"|'''Unit''' | ||
| align="center" style="width:80px;background:#f0f0f0;"|'''uL used''' | | align="center" style="width:80px;background:#f0f0f0;"|'''uL used''' | ||
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|- | |- | ||
| PC-P_10||11.10||440||25.23 | | PC-P_10||11.10||440||25.23 | ||
|} | |||
=== <span style="color:blue"><u>Part /: DNA extraction from solid tumor tissue samples</u></span> === | |||
* The size of tissue samples are varied. Sharmeela noted that they should be ~25mg. | |||
* I used DNeasy Blood and Tissue kit from QIAGEN and followed the instruction of the manufacturer. | |||
==== Procedures ==== | |||
* Will be added | |||
* Eluted 1st time with 200ul AE Buffer | |||
* Eluted 2nd time with 50ul AE Buffer (total each column ~250ul | |||
* Pooled two tubes together --> total volume left ~480ul | |||
* Measure concentration with Qubit dsDNA HS assay using 2ul of extracted DNA in 200ul reaction (100x dilution). Samples PC-T_1 has very high concentration. I repeated measurement and reduced volume to 1ul. | |||
==== Qubit dsDNA HS assay result ==== | |||
{| {{table}} class = wikitable | |||
| align="center" style="width:120px;background:#f0f0f0;"|'''Sample''' | |||
| align="center" style="width:100px;background:#f0f0f0;"|'''Conc. In the Qubit''' | |||
| align="center" style="width:80px;background:#f0f0f0;"|'''Unit''' | |||
| align="center" style="width:00px;background:#f0f0f0;"|'''uL used''' | |||
| align="center" style="width:100px;background:#f0f0f0;"|'''Dilution''' | |||
| align="center" style="width:100px;background:#f0f0f0;"|'''Sample conc. (ng/ul)''' | |||
| align="center" style="width:100px;background:#f0f0f0;"|'''Volume (ul)''' | |||
| align="center" style="width:100px;background:#f0f0f0;"|'''Yield in 480ul (ug)''' | |||
|- | |||
| PC-T-1||413||ng/mL||1||200||82.7||480||39.70 | |||
|- | |||
| PC-T-2||358||ng/mL||2||100||35.8||480||17.18 | |||
|- | |||
| PC-T-4||428||ng/mL||2||100||42.8||480||20.54 | |||
|- | |||
| PC-T-6||152||ng/mL||2||100||15.2||480||7.30 | |||
|- | |||
| PC-C-7||163||ng/mL||2||100||16.3||480||7.82 | |||
|} | |} |
Revision as of 15:44, 15 June 2014
DNA extraction of 10 plasma samples and 5 matched pair solid tumor tissue samples from Cancer Center
- [Link to calendar]
- Part 1: I extract 10 plasma DNA samples from cancer patients received on 2014-06-05
- Part 2: I extract 5 matched pair solid tumor tissue samples from cancer patients received on 2014-05-27
- I assigned new sample codes to be more convenient for sample handling. --> In the future, I may only use the last 3 digit of project ID, so I don't need to rerun sample code and prevent confusion.
- I measured volume of the first tube serum during DNA extraction and adjust volume to 400ul with 1X PBS as ChargeSwitch kit required different volume of reagent for different sample volume.
Part 1: DNA extraction from plasma samples
- There are three tubes of plasma for each sample. Dr. Zhang suggested to use 2 tubes for DNA extraction.
- Note that the measurement could be +-5ul error since serum is viscous and I needed to adjust the pipette volume after aspiration to measure the volume
Project ID # Zhang lab ID Volume 2 tubes PBS to 600ul UCSD-004-04 PC-P_1 560 40 UCSD-004-05 PC-P_2 475 125 UCSD-004-06 PC-P_3 475 125 UCSD-004-07 PC-P_4 330 270 UCSD-004-08 PC-P_5 475 125 UCSD-004-09 PC-P_6 480 120 UCSD-004-10 PC-P_7 480 120 UCSD-004-11 PC-P_8 450 150 UCSD-004-12 PC-P_9 600 0 UCSD-004-13 PC-P_10 440 160
- I followed instruction of ChargeSwith gDNA 1 ml Serum kit as described in [[1]] for 600ul sample volume
Prep
- Eluted 30ul with Elution Buffer
- Measure concentration with Qubit dsDNA HS assay using 2ul of extracted DNA in 200ul reaction (100x dilution)
Qubit dsDNA HS assay result
Sample | Conc. in the Qubit | Unit | uL used | Dilution | Sample conc. (ng/uL) | Volume (ul) | Yields (ng) |
PC-P_1 | 4.73 | ng/mL | 2 | 100 | 0.473 | 30.00 | 14.19 |
PC-P_2 | 8.52 | ng/mL | 2 | 100 | 0.852 | 30.00 | 25.56 |
PC-P_3 | 13.6 | ng/mL | 2 | 100 | 1.360 | 30.00 | 40.80 |
PC-P_4 | 3.4 | ng/mL | 2 | 100 | 0.340 | 30.00 | 10.20 |
PC-P_5 | 8.13 | ng/mL | 2 | 100 | 0.813 | 30.00 | 24.39 |
PC-P_6 | 7.67 | ng/mL | 2 | 100 | 0.767 | 30.00 | 23.01 |
PC-P_7 | 6.44 | ng/mL | 2 | 100 | 0.644 | 30.00 | 19.32 |
PC-P_8 | 5.24 | ng/mL | 2 | 100 | 0.524 | 30.00 | 15.72 |
PC-P_9 | 2.38 | ng/mL | 2 | 100 | 0.238 | 30.00 | 7.14 |
PC-P_10 | 3.7 | ng/mL | 2 | 100 | 0.370 | 30.00 | 11.10 |
Normalize DNA yield to 1mL serum volume
Sample | Yields (ng) | Plasma volume (ul) | Normalized yield to 1mL (ng) |
PC-P_1 | 14.19 | 560 | 25.34 |
PC-P_2 | 25.56 | 475 | 53.81 |
PC-P_3 | 40.80 | 475 | 85.89 |
PC-P_4 | 10.20 | 330 | 30.91 |
PC-P_5 | 24.39 | 475 | 51.35 |
PC-P_6 | 23.01 | 480 | 47.94 |
PC-P_7 | 19.32 | 480 | 40.25 |
PC-P_8 | 15.72 | 450 | 34.93 |
PC-P_9 | 7.14 | 600 | 11.90 |
PC-P_10 | 11.10 | 440 | 25.23 |
Part /: DNA extraction from solid tumor tissue samples
- The size of tissue samples are varied. Sharmeela noted that they should be ~25mg.
- I used DNeasy Blood and Tissue kit from QIAGEN and followed the instruction of the manufacturer.
Procedures
- Will be added
- Eluted 1st time with 200ul AE Buffer
- Eluted 2nd time with 50ul AE Buffer (total each column ~250ul
- Pooled two tubes together --> total volume left ~480ul
- Measure concentration with Qubit dsDNA HS assay using 2ul of extracted DNA in 200ul reaction (100x dilution). Samples PC-T_1 has very high concentration. I repeated measurement and reduced volume to 1ul.
Qubit dsDNA HS assay result
Sample | Conc. In the Qubit | Unit | uL used | Dilution | Sample conc. (ng/ul) | Volume (ul) | Yield in 480ul (ug) |
PC-T-1 | 413 | ng/mL | 1 | 200 | 82.7 | 480 | 39.70 |
PC-T-2 | 358 | ng/mL | 2 | 100 | 35.8 | 480 | 17.18 |
PC-T-4 | 428 | ng/mL | 2 | 100 | 42.8 | 480 | 20.54 |
PC-T-6 | 152 | ng/mL | 2 | 100 | 15.2 | 480 | 7.30 |
PC-C-7 | 163 | ng/mL | 2 | 100 | 16.3 | 480 | 7.82 |