Daniel:Notebook/RNAFISH/2014-7-7: Difference between revisions
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##Designer created by Arjun Raj, utilized by Long Cai for paper | ##Designer created by Arjun Raj, utilized by Long Cai for paper | ||
##Creates 20mer probes | ##Creates 20mer probes | ||
#Copy/paste probe sequences into .txt file | |||
#Print only sequence to the oligo file | |||
##awk '{print $2}' malat1_probes.txt > oligos_malat1.txt | |||
#Attach primer sequences before/after | |||
##VI command, forward: :%s!^!GTCATATCGGTCACTGTT! | |||
##VI command, reverse: :g/$/norm AGATCAGGATACACACTACCC | |||
##Primer sequences are AP1 and AP2 from the V6 set, used in High Resolution Chromosome Painting | |||
==Price Comparison IDT and Stellaris== | |||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | |||
|- style="background-color:#C5D9F1;font-size:12pt" | |||
| align="center" width="141" height="30" valign="bottom" | | |||
|style="font-weight:bold" width="56" align="center" valign="bottom" | IDT Primers | |||
|style="font-weight:bold" width="83" align="center" valign="bottom" | IDT Fluorophores | |||
|style="font-weight:bold" width="65" align="center" valign="bottom" | Stellaris | |||
|- style="font-size:12pt" | |||
| height="15" valign="bottom" | Length | |||
| align="center" align="center" valign="bottom" | 58 | |||
| align="center" align="center" valign="bottom" | 20 | |||
| align="center" align="center" valign="bottom" | 20 | |||
|- style="background-color:#D9D9D9;font-size:12pt" | |||
| height="15" valign="bottom" | Number of Oligos | |||
| align="center" align="center" valign="bottom" | 93 | |||
| align="center" align="center" valign="bottom" | 93 | |||
| align="center" align="center" valign="bottom" | 93 | |||
|- style="font-size:12pt" | |||
| height="15" valign="bottom" | Price/Base (100 nmol, USD) | |||
| align="center" align="center" valign="bottom" | 0.28 | |||
| align="center" align="center" valign="bottom" | 0.28 | |||
| align="center" valign="bottom" | NA | |||
|- style="background-color:#D9D9D9;font-size:12pt" | |||
| height="15" valign="bottom" | Modifications | |||
| align="center" valign="bottom" | None | |||
| align="center" valign="bottom" | Fluorophore | |||
| align="center" valign="bottom" | Fluorophore | |||
|- style="font-size:12pt" | |||
| height="15" valign="bottom" | Oligo Price | |||
| align="center" align="center" valign="bottom" | 1510.32 | |||
| align="center" align="center" valign="bottom" | 520.8 | |||
| align="center" align="center" valign="bottom" | 1725 | |||
|- style="background-color:#D9D9D9;font-size:12pt" | |||
| height="15" valign="bottom" | Modifications | |||
| align="center" align="center" valign="bottom" | 0 | |||
| align="center" align="center" valign="bottom" | 85 | |||
| align="center" align="center" valign="bottom" | 0 | |||
|- style="font-size:12pt" | |||
| height="15" valign="bottom" | Total Price | |||
|style="font-weight:bold" align="center" align="center" valign="bottom" | 1510.32 | |||
|style="font-weight:bold" align="center" align="center" valign="bottom" | 44268 | |||
|style="font-weight:bold" align="center" align="center" valign="bottom" | 1725 | |||
|} | |||
It would appear Stellaris can do this pretty cheap. However, one thing to keep in mind is that the oligos from Stellaris will not be renewable, and so once I use up all the probe I'll have to order again. Oligos from IDT with primer sequences will be renewable, but I'll have to do processing on them. |
Latest revision as of 22:25, 7 July 2014
Probe Design[edit]
Designing probes for Matt and Hosuk's rolony project. The three genes they are testing are ACTB, RAB7A, and MALAT1. I will design probe sets for these three genes.
Workflow[edit]
- Obtain transcript sequence from Genome Browser
- Use genome browser to find genes, and tables to download transcript (mRNA only)
- Use gene sequence as input for probe designer
- Designer created by Arjun Raj, utilized by Long Cai for paper
- Creates 20mer probes
- Copy/paste probe sequences into .txt file
- Print only sequence to the oligo file
- awk '{print $2}' malat1_probes.txt > oligos_malat1.txt
- Attach primer sequences before/after
- VI command, forward: :%s!^!GTCATATCGGTCACTGTT!
- VI command, reverse: :g/$/norm AGATCAGGATACACACTACCC
- Primer sequences are AP1 and AP2 from the V6 set, used in High Resolution Chromosome Painting
Price Comparison IDT and Stellaris[edit]
IDT Primers | IDT Fluorophores | Stellaris | |
Length | 58 | 20 | 20 |
Number of Oligos | 93 | 93 | 93 |
Price/Base (100 nmol, USD) | 0.28 | 0.28 | NA |
Modifications | None | Fluorophore | Fluorophore |
Oligo Price | 1510.32 | 520.8 | 1725 |
Modifications | 0 | 85 | 0 |
Total Price | 1510.32 | 44268 | 1725 |
It would appear Stellaris can do this pretty cheap. However, one thing to keep in mind is that the oligos from Stellaris will not be renewable, and so once I use up all the probe I'll have to order again. Oligos from IDT with primer sequences will be renewable, but I'll have to do processing on them.