Noi/NOTES/2014-6-27: Difference between revisions

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Line 34: Line 34:
| align="center" style="width:70px;background:#f0f0f0;"|'''Yield in 400ul (ug)'''
| align="center" style="width:70px;background:#f0f0f0;"|'''Yield in 400ul (ug)'''
|-
|-
| 6-T_1||434||ng/mL||2||100||43.40||400.00||17.36
| 6-T-1||434||ng/mL||2||100||43.40||400.00||17.36
|-
|-
| 6-T_2||316||ng/mL||2||100||31.60||400.00||12.64
| 6-T-2||316||ng/mL||2||100||31.60||400.00||12.64
|-
|-
| 6-T_3||315||ng/mL||2||100||31.50||400.00||12.60
| 6-T-3||315||ng/mL||2||100||31.50||400.00||12.60
|-
|-
| 6-T_4||417||ng/mL||2||100||41.70||400.00||16.68
| 6-T-4||417||ng/mL||2||100||41.70||400.00||16.68
|-
|-
| 6-T_5||305||ng/mL||2||100||30.50||400.00||12.20
| 6-T-5||305||ng/mL||2||100||30.50||400.00||12.20
|-
|-
| 7-T_1||307||ng/mL||2||100||30.70||400.00||12.28
| 7-T-1||307||ng/mL||2||100||30.70||400.00||12.28
|-
|-
| 7-T_2||446||ng/mL||2||100||44.60||400.00||17.84
| 7-T-2||446||ng/mL||2||100||44.60||400.00||17.84
|-
|-
| 7-T_3||359||ng/mL||2||100||35.90||400.00||14.36
| 7-T-3||359||ng/mL||2||100||35.90||400.00||14.36
|-
|-
| 7-T_4||338||ng/mL||2||100||33.80||400.00||13.52
| 7-T-4||338||ng/mL||2||100||33.80||400.00||13.52
|-
|-
| 7-T_5||204||ng/mL||2||100||20.40||400.00||8.16
| 7-T-5||204||ng/mL||2||100||20.40||400.00||8.16
|}
|}
* I also measured with ND to determined DNA extraction quality and compare measurement by Qubit and ND
* I also measured with ND to determined DNA extraction quality and compare measurement by Qubit and ND
Line 83: Line 83:
* The concentrations from both Qubit and ND are not too much different. However the ratio of 260/230 is quite low in most samples. I am not sure if this because I reloaded column with double amount of lysed cells.
* The concentrations from both Qubit and ND are not too much different. However the ratio of 260/230 is quite low in most samples. I am not sure if this because I reloaded column with double amount of lysed cells.
* The total of gDNA extracted from tumor tissue is not very high compare to the size of tissue. I think the majority of the tissue in more fibers and the components of connective tissue.
* The total of gDNA extracted from tumor tissue is not very high compare to the size of tissue. I think the majority of the tissue in more fibers and the components of connective tissue.
==== 2014-06-28 ====
==== 2014-06-28 ====
=== <span style="color:blue"><u>Part 2: DNA extraction from plasma samples</u></span> ===
=== <span style="color:blue"><u>Part 2: DNA extraction from plasma samples</u></span> ===
Line 96: Line 97:
| align="center" style="width:80px;background:#f0f0f0;"|'''PBS to 700ul (ul)'''
| align="center" style="width:80px;background:#f0f0f0;"|'''PBS to 700ul (ul)'''
|-
|-
| UCSD-006.1||6-P_1||430.00||270.00
| UCSD-006.1||6-P-1||430.00||270.00
|-
|-
| UCSD-006.2||6-P_2||540.00||160.00
| UCSD-006.2||6-P-2||540.00||160.00
|-
|-
| UCSD-006.3||6-P_3||220.00||480.00
| UCSD-006.3||6-P-3||220.00||480.00
|-
|-
| UCSD-006.4||6-P_4||550.00||150.00
| UCSD-006.4||6-P-4||550.00||150.00
|-
|-
| UCSD-006.5||6-P_5||665.00||35.00
| UCSD-006.5||6-P-5||665.00||35.00
|-
|-
| UCSD-006.6||6-P_6||650.00||50.00
| UCSD-006.6||6-P-6||650.00||50.00
|-
|-
| UCSD-006.7||6-P_7||700.00||0.00
| UCSD-006.7||6-P-7||700.00||0.00
|-
|-
| UCSD-006.8||6-P_8||690.00||10.00
| UCSD-006.8||6-P-8||690.00||10.00
|-
|-
| UCSD-006.9||6-P_9||520.00||180.00
| UCSD-006.9||6-P-9||520.00||180.00
|-
|-
| UCSD-006.10||6-P_10||700.00||0.00
| UCSD-006.10||6-P-10||700.00||0.00
|}
|}
:
:
Line 124: Line 125:
| align="center" style="width:80px;background:#f0f0f0;"|'''PBS to 500ul (ul)'''
| align="center" style="width:80px;background:#f0f0f0;"|'''PBS to 500ul (ul)'''
|-
|-
| UCSD-007.1||7-P_1||475.00||25.00
| UCSD-007.1||7-P-1||475.00||25.00
|-
|-
| UCSD-007.2||7-P_2||350.00||150.00
| UCSD-007.2||7-P-2||350.00||150.00
|-
|-
| UCSD-007.3||7-P_3||400.00||100.00
| UCSD-007.3||7-P-3||400.00||100.00
|-
|-
| UCSD-007.4||7-P_4||325.00||175.00
| UCSD-007.4||7-P-4||325.00||175.00
|-
|-
| UCSD-007.5||7-P_5||440.00||60.00
| UCSD-007.5||7-P-5||440.00||60.00
|-
|-
| UCSD-007.6||7-P_6||345.00||155.00
| UCSD-007.6||7-P-6||345.00||155.00
|-
|-
| UCSD-007.7||7-P_7||320.00||180.00
| UCSD-007.7||7-P-7||320.00||180.00
|-
|-
| UCSD-007.8||7-P_8||303.00||197.00
| UCSD-007.8||7-P-8||303.00||197.00
|-
|-
| UCSD-007.9||7-P_9||330.00||170.00
| UCSD-007.9||7-P-9||330.00||170.00
|-
|-
| UCSD-007.10||7-P_10||500.00||0.00
| UCSD-007.10||7-P-10||500.00||0.00
|}
|}
'''''<span style="color:crimson"><u>Prep (for 500ul sample volume)</u></span>'''''<br>
'''''<span style="color:crimson"><u>Prep (for 500ul sample volume)</u></span>'''''<br>
Line 158: Line 159:
| align="center" style="width:70px;background:#f0f0f0;"|'''Yield (ng)'''
| align="center" style="width:70px;background:#f0f0f0;"|'''Yield (ng)'''
|-
|-
| 6-P_1||2||ng/mL||2||100||0.200||30.00||6.00
| 6-P-1||2||ng/mL||2||100||0.200||30.00||6.00
|-
|-
| 6-P_2||11||ng/mL||2||100||1.100||30.00||33.00
| 6-P-2||11||ng/mL||2||100||1.100||30.00||33.00
|-
|-
| 6-P_3||15.7||ng/mL||2||100||1.570||30.00||47.10
| 6-P-3||15.7||ng/mL||2||100||1.570||30.00||47.10
|-
|-
| 6-P_4||8.89||ng/mL||2||100||0.889||30.00||26.67
| 6-P-4||8.89||ng/mL||2||100||0.889||30.00||26.67
|-
|-
| 6-P_5||4.87||ng/mL||2||100||0.487||30.00||14.61
| 6-P-5||4.87||ng/mL||2||100||0.487||30.00||14.61
|-
|-
| 6-P_6||2.49||ng/mL||2||100||0.249||30.00||7.47
| 6-P-6||2.49||ng/mL||2||100||0.249||30.00||7.47
|-
|-
| 6-P_7||2.47||ng/mL||2||100||0.247||30.00||7.41
| 6-P-7||2.47||ng/mL||2||100||0.247||30.00||7.41
|-
|-
| 6-P_8||2.26||ng/mL||2||100||0.226||30.00||6.78
| 6-P-8||2.26||ng/mL||2||100||0.226||30.00||6.78
|-
|-
| 6-P_9||4.08||ng/mL||2||100||0.408||30.00||12.24
| 6-P-9||4.08||ng/mL||2||100||0.408||30.00||12.24
|-
|-
| 6-P_10||3.33||ng/mL||2||100||0.333||30.00||9.99
| 6-P-10||3.33||ng/mL||2||100||0.333||30.00||9.99
|}
|}
{| {{table}} class = wikitable
{| {{table}} class = wikitable
Line 188: Line 189:
| align="center" style="width:70px;background:#f0f0f0;"|'''Yield (ng)'''
| align="center" style="width:70px;background:#f0f0f0;"|'''Yield (ng)'''
|-
|-
| 7-P_1||6.92||ng/mL||2||100||0.692||30.00||20.76
| 7-P-1||6.92||ng/mL||2||100||0.692||30.00||20.76
|-
|-
| 7-P_2||11.4||ng/mL||2||100||1.140||30.00||34.20
| 7-P-2||11.4||ng/mL||2||100||1.140||30.00||34.20
|-
|-
| 7-P_3||2.08||ng/mL||2||100||0.208||30.00||6.24
| 7-P-3||2.08||ng/mL||2||100||0.208||30.00||6.24
|-
|-
| 7-P_4||2.02||ng/mL||2||100||0.202||30.00||6.06
| 7-P-4||2.02||ng/mL||2||100||0.202||30.00||6.06
|-
|-
| 7-P_5||11.1||ng/mL||2||100||1.110||30.00||33.30
| 7-P-5||11.1||ng/mL||2||100||1.110||30.00||33.30
|-
|-
| 7-P_6||2.33||ng/mL||2||100||0.233||30.00||6.99
| 7-P-6||2.33||ng/mL||2||100||0.233||30.00||6.99
|-
|-
| 7-P_7||2.29||ng/mL||2||100||0.229||30.00||6.87
| 7-P-7||2.29||ng/mL||2||100||0.229||30.00||6.87
|-
|-
| 7-P_8||1.67||ng/mL||2||100||0.167||30.00||5.01
| 7-P-8||1.67||ng/mL||2||100||0.167||30.00||5.01
|-
|-
| 7-P_9||2.31||ng/mL||2||100||0.231||30.00||6.93
| 7-P-9||2.31||ng/mL||2||100||0.231||30.00||6.93
|-
|-
| 7-P_10||2.03||ng/mL||2||100||0.203||30.00||6.09
| 7-P-10||2.03||ng/mL||2||100||0.203||30.00||6.09
|}
|}
==== Normalize DNA yield to 1mL plasma volume ====
==== Normalize DNA yield to 1mL plasma volume ====
Line 215: Line 216:
| align="center" style="width:100px;background:#f0f0f0;"|'''Normalized yield to 1mL (ng)'''
| align="center" style="width:100px;background:#f0f0f0;"|'''Normalized yield to 1mL (ng)'''
|-
|-
| 6-P_1||6.00||430.00||13.95
| 6-P-1||6.00||430.00||13.95
|-
|-
| 6-P_2||33.00||540.00||61.11
| 6-P-2||33.00||540.00||61.11
|-
|-
| 6-P_3||47.10||220.00||214.09
| 6-P-3||47.10||220.00||214.09
|-
|-
| 6-P_4||26.67||550.00||48.49
| 6-P-4||26.67||550.00||48.49
|-
|-
| 6-P_5||14.61||665.00||21.97
| 6-P-5||14.61||665.00||21.97
|-
|-
| 6-P_6||7.47||650.00||11.49
| 6-P-6||7.47||650.00||11.49
|-
|-
| 6-P_7||7.41||700.00||10.59
| 6-P-7||7.41||700.00||10.59
|-
|-
| 6-P_8||6.78||690.00||9.83
| 6-P-8||6.78||690.00||9.83
|-
|-
| 6-P_9||12.24||520.00||23.54
| 6-P-9||12.24||520.00||23.54
|-
|-
| 6-P_10||9.99||700.00||14.27
| 6-P-10||9.99||700.00||14.27
|}
|}
'''UCSD-006 Plasma original color'''<br>
'''UCSD-006 Plasma original color'''<br>
  [[File:UCSD-006-plasma_1-10_2.jpg|500px]]
  [[File:UCSD-006-plasma_1-10_1_e.jpg|500px]]
* Based on plasma color, 6-P_3 sample had very high DNA amount due to cell lysis
* Based on plasma color, 6-P_3 sample had very high DNA amount due to cell lysis
{| {{table}} class = wikitable
{| {{table}} class = wikitable
Line 244: Line 245:
| align="center" style="width:100px;background:#f0f0f0;"|'''Normalized yield to 1mL (ng)'''
| align="center" style="width:100px;background:#f0f0f0;"|'''Normalized yield to 1mL (ng)'''
|-
|-
| 7-P_1||20.76||475.00||43.71
| 7-P-1||20.76||475.00||43.71
|-
|-
| 7-P_2||34.20||350.00||97.71
| 7-P-2||34.20||350.00||97.71
|-
|-
| 7-P_3||6.24||400.00||15.60
| 7-P-3||6.24||400.00||15.60
|-
|-
| 7-P_4||6.06||325.00||18.65
| 7-P-4||6.06||325.00||18.65
|-
|-
| 7-P_5||33.30||440.00||75.68
| 7-P-5||33.30||440.00||75.68
|-
|-
| 7-P_6||6.99||345.00||20.26
| 7-P-6||6.99||345.00||20.26
|-
|-
| 7-P_7||6.87||320.00||21.47
| 7-P-7||6.87||320.00||21.47
|-
|-
| 7-P_8||5.01||303.00||16.53
| 7-P-8||5.01||303.00||16.53
|-
|-
| 7-P_9||6.93||330.00||21.00
| 7-P-9||6.93||330.00||21.00
|-
|-
| 7-P_10||6.09||500.00||12.18
| 7-P-10||6.09||500.00||12.18
|}
|}
'''UCSD-007 Plasma original color'''<br>
'''UCSD-007 Plasma original color'''<br>
  [[File:UCSD-007-plasma_1-10_1.jpg|500px]]
  [[File:UCSD-007-plasma_1-10_1.jpg|500px]]

Latest revision as of 20:00, 25 November 2014

DNA extraction of plasma samples and matched pair solid tumor tissue samples from Cancer Center[edit]

Calendar

  • Part 1: I extract matched pair solid tumor tissue samples (colon & lung) from cancer patients received on 2014-06-27
  • Part 2: I extract plasma samples from cancer patients (colon & lung) received on 2014-06-26

Part 1: DNA extraction from solid tumor tissue samples[edit]

  • The size of tissue samples are varied. Sharmeela noted that they should be ~20mg.
  • I used DNeasy Blood and Tissue kit from QIAGEN and followed the instruction of the manufacturer.

Procedures[edit]

  • Followed protocol of DNeasy Blood and tissue kit: Page 28, but increase volume of reagents to 4x as the size of tissue is quite big.
  • I added RNase A to remove RNA contamination
- I added 170ul* 4 = 680ul of ATL buffer + 80ul of ProteinaseK
- Incubate at 56C for ~2-3h with shaking 900rpm/min and occasionally vigorously vortexing for every 10min.
I did not use homogenizer to homogenize tissue as it might be difficult to handle and it will generate a lot of bubbles.
- Anyway, Vortexing and shaking on thermo mixer is good enough to lyse the tissue. This time took longer to lyse the colon and lung tissues than pancreas tissue. Possibly the tissue compositions are differents.
- After the tissue is completely lysed, I add 40ul of 10mg/mL RNase A to each tub and incubate at RT for 2min (I'm supposed to add 80ul, but I do not have enough RNaseA)
- I split it into two 2mL tube (~400ul each) + added 4000ul of Buffer AL. Mix vigorously.
- Add 800ul of 100% EtOH. Mix Vigorously.
- Load cell lysis through column ~800ul (reload more 800ul --> total 1600ul of cell lysis/ column)
- Wash with 500ul AW1 Buffer
- Wash with 500ul of AW2 Buffer
- Eluted 1st time with 100ul AE Buffer
- Eluted 2nd time with 100ul AE Buffer (total each column ~200ul
- Pooled two tubes together --> total volume left ~400ul
  • Measure concentration with Qubit dsDNA HS assay using 2ul of extracted DNA in 200ul reaction (100x dilution).

Qubit dsDNA HS assay result[edit]

Sample Conc. In the Qubit Unit uL used Dilution Sample conc. (ng/ul) Volume (ul) Yield in 400ul (ug)
6-T-1 434 ng/mL 2 100 43.40 400.00 17.36
6-T-2 316 ng/mL 2 100 31.60 400.00 12.64
6-T-3 315 ng/mL 2 100 31.50 400.00 12.60
6-T-4 417 ng/mL 2 100 41.70 400.00 16.68
6-T-5 305 ng/mL 2 100 30.50 400.00 12.20
7-T-1 307 ng/mL 2 100 30.70 400.00 12.28
7-T-2 446 ng/mL 2 100 44.60 400.00 17.84
7-T-3 359 ng/mL 2 100 35.90 400.00 14.36
7-T-4 338 ng/mL 2 100 33.80 400.00 13.52
7-T-5 204 ng/mL 2 100 20.40 400.00 8.16
  • I also measured with ND to determined DNA extraction quality and compare measurement by Qubit and ND
Sample ID ND conc. (ng/ul) 260/280 260/230
6-T-1 57.51 2 1.67
6-T-2 84.83 1.99 1.54
6-T-3 42.86 1.84 1.04
6-T-4 55.42 1.69 0.96
6-T-5 36.96 1.93 1.26
7-T-1 39.44 1.51 0.89
7-T-2 66.63 1.78 1.36
7-T-3 62.39 1.83 1.37
7-T-4 49.6 1.91 1.53
7-T-5 28.74 1.68 1.07
  • The concentrations from both Qubit and ND are not too much different. However the ratio of 260/230 is quite low in most samples. I am not sure if this because I reloaded column with double amount of lysed cells.
  • The total of gDNA extracted from tumor tissue is not very high compare to the size of tissue. I think the majority of the tissue in more fibers and the components of connective tissue.

2014-06-28[edit]

Part 2: DNA extraction from plasma samples[edit]

  • There are three tubes of plasma for each sample. Dr. Zhang suggested to use 2 tubes for DNA extraction.
  • I measured volume of two tube serum during DNA extraction and adjust volume to 600ul with 1X PBS as ChargeSwitch kit required different volume of reagent for different sample 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
  • I followed instruction of ChargeSwith gDNA 1 ml Serum kit as described in [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-3-

11#3._ChargeSwitch.C2.AE_gDNA_1_ml_Serum_kit]] for 700ul sample volume

Project ID Sample ID Plasma Volumn (ul) PBS to 700ul (ul)
UCSD-006.1 6-P-1 430.00 270.00
UCSD-006.2 6-P-2 540.00 160.00
UCSD-006.3 6-P-3 220.00 480.00
UCSD-006.4 6-P-4 550.00 150.00
UCSD-006.5 6-P-5 665.00 35.00
UCSD-006.6 6-P-6 650.00 50.00
UCSD-006.7 6-P-7 700.00 0.00
UCSD-006.8 6-P-8 690.00 10.00
UCSD-006.9 6-P-9 520.00 180.00
UCSD-006.10 6-P-10 700.00 0.00

Prep (for 700ul sample volume)

Project ID Sample ID Plasma Volumn (ul) PBS to 500ul (ul)
UCSD-007.1 7-P-1 475.00 25.00
UCSD-007.2 7-P-2 350.00 150.00
UCSD-007.3 7-P-3 400.00 100.00
UCSD-007.4 7-P-4 325.00 175.00
UCSD-007.5 7-P-5 440.00 60.00
UCSD-007.6 7-P-6 345.00 155.00
UCSD-007.7 7-P-7 320.00 180.00
UCSD-007.8 7-P-8 303.00 197.00
UCSD-007.9 7-P-9 330.00 170.00
UCSD-007.10 7-P-10 500.00 0.00

Prep (for 500ul sample volume)

  • 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[edit]

Sample Conc. in the Qubit Unit uL used Dilution Sample Conc. (ng/ul) Volume Yield (ng)
6-P-1 2 ng/mL 2 100 0.200 30.00 6.00
6-P-2 11 ng/mL 2 100 1.100 30.00 33.00
6-P-3 15.7 ng/mL 2 100 1.570 30.00 47.10
6-P-4 8.89 ng/mL 2 100 0.889 30.00 26.67
6-P-5 4.87 ng/mL 2 100 0.487 30.00 14.61
6-P-6 2.49 ng/mL 2 100 0.249 30.00 7.47
6-P-7 2.47 ng/mL 2 100 0.247 30.00 7.41
6-P-8 2.26 ng/mL 2 100 0.226 30.00 6.78
6-P-9 4.08 ng/mL 2 100 0.408 30.00 12.24
6-P-10 3.33 ng/mL 2 100 0.333 30.00 9.99
Sample Conc. in the Qubit Unit uL used Dilution Sample Conc. (ng/ul) Volume Yield (ng)
7-P-1 6.92 ng/mL 2 100 0.692 30.00 20.76
7-P-2 11.4 ng/mL 2 100 1.140 30.00 34.20
7-P-3 2.08 ng/mL 2 100 0.208 30.00 6.24
7-P-4 2.02 ng/mL 2 100 0.202 30.00 6.06
7-P-5 11.1 ng/mL 2 100 1.110 30.00 33.30
7-P-6 2.33 ng/mL 2 100 0.233 30.00 6.99
7-P-7 2.29 ng/mL 2 100 0.229 30.00 6.87
7-P-8 1.67 ng/mL 2 100 0.167 30.00 5.01
7-P-9 2.31 ng/mL 2 100 0.231 30.00 6.93
7-P-10 2.03 ng/mL 2 100 0.203 30.00 6.09

Normalize DNA yield to 1mL plasma volume[edit]

Sample Yield (ng) Serum volume (ul) Normalized yield to 1mL (ng)
6-P-1 6.00 430.00 13.95
6-P-2 33.00 540.00 61.11
6-P-3 47.10 220.00 214.09
6-P-4 26.67 550.00 48.49
6-P-5 14.61 665.00 21.97
6-P-6 7.47 650.00 11.49
6-P-7 7.41 700.00 10.59
6-P-8 6.78 690.00 9.83
6-P-9 12.24 520.00 23.54
6-P-10 9.99 700.00 14.27

UCSD-006 Plasma original color

File:UCSD-006-plasma 1-10 1 e.jpg
  • Based on plasma color, 6-P_3 sample had very high DNA amount due to cell lysis
Sample Yield (ng) Serum volume (ul) Normalized yield to 1mL (ng)
7-P-1 20.76 475.00 43.71
7-P-2 34.20 350.00 97.71
7-P-3 6.24 400.00 15.60
7-P-4 6.06 325.00 18.65
7-P-5 33.30 440.00 75.68
7-P-6 6.99 345.00 20.26
7-P-7 6.87 320.00 21.47
7-P-8 5.01 303.00 16.53
7-P-9 6.93 330.00 21.00
7-P-10 6.09 500.00 12.18

UCSD-007 Plasma original color

File:UCSD-007-plasma 1-10 1.jpg