Noi/NOTES/2013-2-27: Difference between revisions
Jump to navigation
Jump to search
>Noi (Created page with "* http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes '''Link to calendar''' == Plan for probe preparation for Matt's project == * I will be preparing prob...") |
>Noi mNo edit summary |
||
(7 intermediate revisions by the same user not shown) | |||
Line 1: | Line 1: | ||
* [[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes '''Link to calendar''']] | * [[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes '''Link to calendar''']] | ||
== Plan for probe preparation for Matt's project == | == Plan for probe preparation for Matt's project == | ||
* I will be preparing probes using the same method as I did for LC Sciences oligoes, [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-10-6 | * I will be preparing probes using the same method as I did for LC Sciences oligoes, [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-10-6]] | ||
* Check reagents to make sure I have all reagents ready for probe prep and padlock capture | * Check reagents to make sure I have all reagents ready for probe prep and padlock capture | ||
'''Probe prep''' | '''Probe prep''' | ||
- Waiting for seed | - Waiting for seed oligos: expected to come next Wednesday (March6, 2013) | ||
- eMIP_CA1_F and eMIP_CA1_R primer for expansion PCR and production PCR | - eMIP_CA1_F and eMIP_CA1_R primer for expansion PCR and production PCR (very little left, ordered 2/28/2013) | ||
; arrived 3/04/2013 -> resuspend 100uM | |||
- 2x KAPA SYBG FAST qPCR MM | - 2x KAPA SYBG FAST qPCR MM | ||
- Nt.AlwI (NEB) and Nb.BsrDI (NEB) -> ordered | - Nt.AlwI (NEB) and Nb.BsrDI (NEB) -> ordered 2/26/2013 ; arrived 3/04/2013 | ||
- Qiaquick | - Qiaquick columns, TBU gel, Nanosep columns | ||
'''Padlock capture''' | '''Padlock capture''' | ||
Note: There is no gap for this capture, so only need Ampligase | Note: There is no gap for this capture, so only need Ampligase | ||
- Ampligase and buffer | - Ampligase and buffer: yes | ||
- ExoI/ExoIII | - ExoI/ExoIII: yes | ||
- Amplification primer ( | - Amplification primers (Matt) | ||
* Look at the probe design (primer region), it's pretty much the same as the probes synthesized by LC Sciences oligoes. Start at '''AGGACCGGATCAACT''' | |||
* Need to check with Dr. Zhang about the gDNA, RNA and cDNA amount in capture. The expected size of citcularized DNA (no gap --> 170bp plus length of Illumina adapter = XX bp? look at primer design) | |||
* Continued on: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-3-6 |
Latest revision as of 22:50, 6 March 2013
Plan for probe preparation for Matt's project[edit]
- I will be preparing probes using the same method as I did for LC Sciences oligoes, [[1]]
- Check reagents to make sure I have all reagents ready for probe prep and padlock capture
Probe prep - Waiting for seed oligos: expected to come next Wednesday (March6, 2013) - eMIP_CA1_F and eMIP_CA1_R primer for expansion PCR and production PCR (very little left, ordered 2/28/2013) ; arrived 3/04/2013 -> resuspend 100uM - 2x KAPA SYBG FAST qPCR MM - Nt.AlwI (NEB) and Nb.BsrDI (NEB) -> ordered 2/26/2013 ; arrived 3/04/2013 - Qiaquick columns, TBU gel, Nanosep columns Padlock capture Note: There is no gap for this capture, so only need Ampligase - Ampligase and buffer: yes - ExoI/ExoIII: yes - Amplification primers (Matt)
- Look at the probe design (primer region), it's pretty much the same as the probes synthesized by LC Sciences oligoes. Start at AGGACCGGATCAACT
- Need to check with Dr. Zhang about the gDNA, RNA and cDNA amount in capture. The expected size of citcularized DNA (no gap --> 170bp plus length of Illumina adapter = XX bp? look at primer design)
- Continued on: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-3-6