Reproducibility Test Lab
[http: LabName] representative.
Round N. ID=[http: DesignID].
Score = NN.
The Reproducibilty Test Lab is a special lab that is (will be) synthesized in each synthesis round. The objectives for this lab are:
- Provide a consistent measure of the reproducibilty of the cloud lab synthesis results, for long term quality control,
- Determine how much of the variation in synthesis results is captured by the error estimates reported for each synthesized base,
- Provide some guidance as to where the synthesis process might be improved, in order to increase reproducibility, and
- Give those analysing the synthesis data a better understanding of the variation to expect when comparing data from different synthesis rounds.
Initial Sequences
| Sequence | Description or rationale for inclusion |
Original SHAPE data, or expected folding |
|
AGUCAUCUAC UACGAAAAAC ACAUUCUAUU CGAAAACGAA UAGAAUGUGU CGUAGUAGAU GAC |
Cloud Lab 1 representative. Round 1. ID=2366937. |
 |
| GCAAGGACGA AUAAGCCAUA ACCGCAGGGA AACACUGAAC GGAGCCGAAA GAGCAAGCAA UAA |
Cloud Lab 4 representative. Round 2. ID=2655773. |
 |
| GAGAUGGGUA ACGAAAGUUG CGCUGCCGAA UGAAAGUUCU GGAUGAAAGU CUGGUGGCCU AUC | Cloud Lab 9 representative. Round 2. ID=2588792. Score = 78. High GU content. |
|
| AGAGUGAAGG ACGGAGAAUC UCCGUCGUCG CGAAGCGGCC CUGGGCUUCC CAGGCUUCAC UCA | Cloud Lab 15 representative. Round 1. ID=2337872. Score = 96. |
|
| GAGAUAUUAU AAUAUUAUAA UAUGCAAAGA AAUAAGAAGC AUAUUAUAAU AUUAUAAUAU CAA | Cloud Lab 18 representative. Round 2. ID=2596919. Score = 98. High AU count. |
|
| GCGGAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAC CGC | Clouud Lab 19 representative. Round 1. ID=2339041. Score = 92. Big loop of all A. |
|
|
GCGGCGGCAA AGGCGGCGCA ACGCGGCGGA AAAUCGGCGG CGACGCGGCG GAAAUCGGCG GCG |
Cloud Lab 20 representative. Round 1. ID=2335964. Score = 91. Lab has lots of 1-1 loops. Sequence is Christmas tree that scored well. |
|
|
GUACAAAUCC UCGAAAACUC GAGGAUAUAU CAAAAGAUAG AAGGCGAGAA AAAAAGGAGG UAC |
Hair Trigger representative. ID=2433439. From switch lab, with a similar estimated MFE between the two states (without aptamer.) | |
|
AAAAAGCUCC AUGAGGAUAU AGAGCAGAAA AUAUGCCUAG AAGGCAUGGU AAAAUAGCAA AAA |
LS2 representative. ID=2435428. Switch lab. Good scores in both states. State 1 not predicted to be MFE by Eterna energy model. |
|
|
UAAGCACCAG GAGCAGGACC AGCGAAACAA AACAAACAAA GCAGGACCAG CACCAGGAGC AAA |
Ball and Chain representative. ID=2763519. Score = 96. Systematic testing of CG bases anchoring 1-1 loops with both As. |
|
|
GAGCUAGUGC UGAGGAAACU UAGCCUAGCU CAGAUUUGCC UAAUCGAAAG AUUAGUGCAG AUC |
RNA Bridge representative. ID=3006655. Score = 77. Good dot plot and melt plot, but low score. |
|
| LabName representative. Round N. ID=SOLNNNN. Score = NN. | ||
| LabName representative. Round N. ID=SOLNNNN. Score = NN. | ||
|
GACGCCGAUG GUAGCAAGGG AAACCGAGGA AACUCGCGAA AGCAAAGCGA GAGUAGGAAA GUC |
Huffman. ID=2736789. Score = 96. Sequence apperared to have stable stack including non-canconical pairs. |
|
|
AGAGUGAAGG ACGCCGUUUC GGCGUCGUGC CCUUGGCACC CUCCCGAAGG GAGGCUUCAC UCA |
Triloop Buffet. Round 2. ID=2676335. Score = 91. Sequence apperared to show tertiary bonding. | |
| AUCGAAAGAU | Very short sequence |
|
|
UAGCAGGGCUAGCUAGCUUGGCAAAAUUCGACGUAAGCAAAAUGCAAAAAACGUAUCGAUUAUAUUGAAAAAGAUCGGACUAGGCUAGG |
Maximum length (89) sequence |
|
| GCGAUGCGGAUACGAAAGUAUCGGCAUCGC
|
Project: Comparison Series: 1-1. ID=748766. Score = 86. |
<img title="aa" src="/wiki/images/2885326079.jpg" border="0" alt="aa" width="57" height="150" /> |
| GCGAUGCGGAUACGAAGUAUCGGCAUCGC
|
Project: Comparison Series: Triloop. ID=749314. Score = 93. | <img title="aa" src="/wiki/images/2666764672.jpg" border="0" alt="aa" width="58.43621399177" height="150" /> |
| GCGAUGCGGAUACGAAAAGUAUCGGCAUCGC
|
Project: Comparison Series: Pentaloop. ID=749321. Score = 96. | <img title="aa" src="/wiki/images/2095200291.jpg" border="0" alt="aa" width="60.762032085561" height="150" /> |
| GCGAUGCGGAUACGAAAAAGUAUCGGCAUCGC | Project: Comparison Series: Hexaloop. ID=749326. Score = 100. | <img title="aa" src="/wiki/images/1634789777.jpg" border="0" alt="aa" width="59.019607843137" height="150" /> |
Omei → rhiju: Will do. Am I correct in thinking that can refine the set over time, if we decide we would benefit from different sequences?
rhiju → Omei: yes of course. I think we're granting you (and the players you represent) a 'standing order' of 40 sequences over each cycle to characterize errors and to make suggestions to us devs for viewing & experimental improvements. I'm excited to see what you find!
