Rui:LabNotes/Collaborations/2011-10-12: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Sam Chiang
m (Created page with '==Illumina library preparation of samples for Dr. Yi Zhang lab==')
 
>Sam Chiang
 
(2 intermediate revisions by one other user not shown)
Line 1: Line 1:
==Illumina library preparation of samples for Dr. Yi Zhang lab==
==Illumina library preparation of samples for Dr. Yi Zhang lab==
===DNA shearing===
* Follow the protocol used on 7/8/11 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-7-8]
* Morries Cancer Center, lab bay 2R (Yang or Sophie to contact)
===End repair===
* Follow the protocol used on 7/11/11 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-7-11#End_repair]
* Elute in 32ul and 1ul for Qubit measurement:
===dA tailing===
* Follow the protocol used on 7/11/11 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-7-11#A_tailing]
* Elute in 20ul and 1ul for Qubit measurement:
===Adaptor ligation===
* Follow the protocol used on 7/11/11 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-7-11#Adapter_ligation]
* 20uM fresh made adaptor, ~1:20 ratio
* Calculation for adaptor input:
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''samples'''
| align="center" style="background:#f0f0f0;"|'''ng/ul'''
| align="center" style="background:#f0f0f0;"|'''volume'''
| align="center" style="background:#f0f0f0;"|'''total ng'''
| align="center" style="background:#f0f0f0;"|'''pmole'''
| align="center" style="background:#f0f0f0;"|'''adaptor'''
| align="center" style="background:#f0f0f0;"|'''ul'''
| align="center" style="background:#f0f0f0;"|'''adjusted ul'''
|-
| ||||||||||||||
|-
| 1||3.28||18||59.04||0.4542||9.0831||0.4542||0.8
|-
| ||||||||||||||
|-
| 2||3.55||18||63.9||0.4915||9.8308||0.4915||0.8
|-
| ||||||||||||||
|-
| 3||4.75||18||85.5||0.6577||13.1538||0.6577||1
|-
| ||||||||||||||
|-
| 4||5.16||18||92.88||0.7145||14.2892||0.7145||1
|-
| ||||||||||||||
|-
| 5||2.44||18||43.92||0.3378||6.7569||0.3378||0.5
|-
| ||||||||||||||
|-
| 6||0.39||18||6.93||0.0533||1.0662||0.0533||0.5
|}
===PCR amplification===
* After ligation and beads purification, 22ul EB is used to elute DNA, take 20ul into tubes, take 5ul of s1-5 for PCR, use all (20ul) of s6
* 50ul PCR reaction: 25ul Phusion, 1ul N2.F, 1ul N2.R7-15, 0.5ul 20X SYBR green; 10 cycles
* beads purification: 0.7X, elute in 15ul, take 12ul
===Concentration monitor===
{| {{table}}
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''Sample'''
| align="center" style="background:#f0f0f0;"|'''#1'''
| align="center" style="background:#f0f0f0;"|'''#2'''
| align="center" style="background:#f0f0f0;"|'''#3'''
| align="center" style="background:#f0f0f0;"|'''#4'''
| align="center" style="background:#f0f0f0;"|'''#5'''
| align="center" style="background:#f0f0f0;"|'''#6'''
|-
| pre-shearing||ng/ul||||16.7||23.6||22||11.2||1.55
|-
| ||volume||10||10||10||10||10||10
|-
| ||total ng||||167||236||220||112||15.5
|-
| after repair||ng/ul||2.78||2.7||3.63||3.98||2.16||0.3
|-
| ||volume||30||30||30||30||30||30
|-
| ||total ng||83.4||81||108.9||119.4||64.8||9.12
|-
| after A tailing||ng/ul||3.28||3.55||4.75||5.16||2.44||0.39
|-
| ||volume||18||18||18||18||18||18
|-
| ||total ng||59.04||63.9||85.5||92.88||43.92||6.93
|-
| after ligation||ng/ul||2.47||2.66||3.13||4||1.83||0.32
|-
| ||volume||20||20||20||20||20||20
|-
| ||total ng||49.4||53.2||62.6||80||36.6||6.32
|-
|
|-
| ||pre-PCR ng||12.35||13.3||15.65||20||9.15||6.32
|-
| after PCR||ng/ul||8.51||10.9||10.1||11.8||11.9||11.9
|-
| ||volume||15||15||15||15||15||15
|-
| ||total ng||127.65||163.5||151.5||177||178.5||178.5
|-
| ||fold change||10.33603239||12.29323308||9.680511182||8.85||19.50819672||28.24367089
|}

Latest revision as of 19:43, 18 October 2011

Illumina library preparation of samples for Dr. Yi Zhang lab[edit]

DNA shearing[edit]

  • Follow the protocol used on 7/8/11 [1]
  • Morries Cancer Center, lab bay 2R (Yang or Sophie to contact)

End repair[edit]

  • Follow the protocol used on 7/11/11 [2]
  • Elute in 32ul and 1ul for Qubit measurement:

dA tailing[edit]

  • Follow the protocol used on 7/11/11 [3]
  • Elute in 20ul and 1ul for Qubit measurement:

Adaptor ligation[edit]

  • Follow the protocol used on 7/11/11 [4]
  • 20uM fresh made adaptor, ~1:20 ratio
  • Calculation for adaptor input:
samples ng/ul volume total ng pmole adaptor ul adjusted ul
1 3.28 18 59.04 0.4542 9.0831 0.4542 0.8
2 3.55 18 63.9 0.4915 9.8308 0.4915 0.8
3 4.75 18 85.5 0.6577 13.1538 0.6577 1
4 5.16 18 92.88 0.7145 14.2892 0.7145 1
5 2.44 18 43.92 0.3378 6.7569 0.3378 0.5
6 0.39 18 6.93 0.0533 1.0662 0.0533 0.5

PCR amplification[edit]

  • After ligation and beads purification, 22ul EB is used to elute DNA, take 20ul into tubes, take 5ul of s1-5 for PCR, use all (20ul) of s6
  • 50ul PCR reaction: 25ul Phusion, 1ul N2.F, 1ul N2.R7-15, 0.5ul 20X SYBR green; 10 cycles
  • beads purification: 0.7X, elute in 15ul, take 12ul

Concentration monitor[edit]

' Sample #1 #2 #3 #4 #5 #6
pre-shearing ng/ul 16.7 23.6 22 11.2 1.55
volume 10 10 10 10 10 10
total ng 167 236 220 112 15.5
after repair ng/ul 2.78 2.7 3.63 3.98 2.16 0.3
volume 30 30 30 30 30 30
total ng 83.4 81 108.9 119.4 64.8 9.12
after A tailing ng/ul 3.28 3.55 4.75 5.16 2.44 0.39
volume 18 18 18 18 18 18
total ng 59.04 63.9 85.5 92.88 43.92 6.93
after ligation ng/ul 2.47 2.66 3.13 4 1.83 0.32
volume 20 20 20 20 20 20
total ng 49.4 53.2 62.6 80 36.6 6.32
pre-PCR ng 12.35 13.3 15.65 20 9.15 6.32
after PCR ng/ul 8.51 10.9 10.1 11.8 11.9 11.9
volume 15 15 15 15 15 15
total ng 127.65 163.5 151.5 177 178.5 178.5
fold change 10.33603239 12.29323308 9.680511182 8.85 19.50819672 28.24367089