Lab

This article is an overview of the RNA lab process.

Labs are type of puzzle in Eterna where player solutions are synthesized and scored based on experimental data. In each lab, players vote on their peers' designs to determine which are synthesized.

A player must complete the progression puzzles to submit and vote on lab designs.

Lab Steps Overview

Scheduled Rounds

Labs are organized and scheduled into rounds. Each round may last from a week to several months. A lab may continue for many rounds until a goal has been achieved. Alhough synthesis and voting has stopped on old labs, players may continue to review old lab data and work on old lab puzzles.

Analysis

The lab archive is a treasure trove of data on what RNA designs were most successful in the labs. Review successful past designs to find winning strategies that get you more points! Select a lab which has the "Results Posted" indicator then scroll down to the conclusions section. Most labs have a leaderboard which helps to find the best designs. The Forum is a great place to find suggestions made by other players and to ask questions. Each round of a lab usually has its own Forum topic.

Design

In lab puzzles, players are presented with a goal which varies by lab. In the early labs, the goal was always to design a RNA which would fold into the target structure. Later, Eterna moved to the design of aptamers and riboswitches. More recently, goals have varied and may involve designing RNA with the lowest degradation or the best activity. The goals of a lab are described in the Lab Details. Ask questions in the Discussion area or in the Forum.

Submission

The number of designs which a player may submit varies by lab. This is given in the lab info to the right of the lab details.

Voting

All designs are reviewed by other players, and votes are placed. Players may vote on their own designs, but may only vote once on a given sequence. Voting is usually simultaneous with submission. Votes may be withdrawn and changed up until the deadline.

Laboratory Synthesis

The Eterna team of scientists at various laboratories then synthesizes the most popular designs in a real laboratory. This is where the real science happens!

Design Scoring

The synthesized designs for the labs are given Lab scores as follows:

If the lab result is a SHAPE score, then the Lab score is the SHAPE score, which ranges from 0-100. If the lab results give another attribute, such as iSAT, degradation, or protein expression, then the researchers determine how to convert the measured value(s) to Lab score. The range should remain 0 – 100.

After the lab is complete, the Lab score of a synthesized design is included in Design Details when the design is opened.

All designs which were not synthesized are given a Lab score equal to that of the closest synthesized design. Closeness is determined by the number of matching bases between the two designs. These Lab scores are not included in the Design Details since they are only approximations but are used in awarding points.

Player Rewards

Points are awarded as follows:

Design points are awarded for a player’s highest scoring design for each puzzle of a lab (whether synthesized or not). A player will receive points for only 1 design per puzzle.
Design points = 4 x Lab score
Voting points are awarded for the highest scoring synthesized design for which a player voted. A player will receive points for only 1 design per puzzle.
Voting points = 2 x Lab score
A player may find their awarded points as follows: Click on Latest Activity (Bell Icon), then on the Open (square with arrow) icon, Click on Labs on the menu on the right. A player’s lab points will be listed.

Reward History: On Mar 22, 2013 a "News Item on new scoring method" in Eterna news announced a new scoring system due to the large increase in synthesized solutions allowed by Cloud Lab. The new Design reward = lab_score*4, and Vote_reward = lab_score*2. Prior to that the rewards calculation was Design reward = lab_score*20, and Vote_reward = lab_score*10.

Cooperation and Etiquette

Most experienced players are eager to help others design sequences. Design strategies are openly discussed in chat, and on the forum. The use of other players' designs as starting points is common. Newcomers to lab may find it especially helpful to modify an existing design rather than start from scratch. Players are encouraged to acknowledge the original designer the sequence being modified. Asking for votes is considered impolite.

Types of Labs

Classic Eterna - Early labs without barcodes
FMN Aptamers - Early FMN aptamer labs
Player Projects - Cloud lab beta
Switches - Early switch labs
Cloud Labs - Labs with barcodes
OpenCRISPR - Discover design patterns for guide RNAs to make gene editing more precisely controllable
OpenTB - Design RNA sensors to detect active TB
OpenRibosome - Generate customized ribosomes able to synthesize diverse polymers and materials (launched 2019)
OpenVaccine - Improve the stability of mRNA vaccines (launched 2020)

Strategies for Labs

These strategies are for labs where the goal is to design a RNA which folds into a target structure, analyzed by SHAPE data.

Main Article: Lab Strategies

Player-Created guides: Lab Guides

Boosting

The value of boosting in lab is unclear. Previous winners have included both boosted and unboosted designs. Certain special loop sequences with very low free energy appear strongly base paired, however.

GC/AU/GU Ratio

GC pairs are more stable than AU or GU pairs; however, designs with very high GC content are difficult to synthesize and likely to misfold. Designs contining exclusively GC pairs are unlikely to be voted for or synthesized. Likewise, designs that are very rich in AU or GU pairs are unlikely to be selected for synthesis.

Computational Tools

The EteRNA lab interface contains two computational tools that provide insight into the stability of the RNA being designed: the dot plot and the melt plot. Additionally, many secondary structure prediction programs are available on the web. The utility of these tools remains unclear.

Overview of Lab Rounds (prior to 2015?)

Here is a table for showing which batch a lab belongs to. It is useful knowing which round a lab belongs to because of the error rates of the lab data.

Each synthesis round will have its own characteristics with respect to error rates. Each round is different. Sometimes, this is on purpose, as the lab tries to improve their process, and some times it is accidental, such as having reagents go bad for an unknown reason. Unlike the SHAPE values, the reported error rates are not normalized between rounds. So when comparing error rates between labs, it's important to know what rounds each of the labs were synthesized in. (Omei)

Each round number is connected to an rdat file and most rounds have spreadsheets with extracted data. The data is taken from RMDB (RNA Mapping Database).

Round	Comments	Labs	Signal-to-noise average
R0 12/21/2012	First batch of Player Projects R0.xlsx R0.googlesheet	Project : Thicker Zigzag Project : Test of RNAfold (5) Project : Test of RNAfold (4) Project : Test of RNAfold (3) Project : Test of RNAfold (2) Project : Test of RNAfold (1) Project : Multiloop: Two Pairs of Adjacent Stacks Project : Testing various loop designs Project : Hard Lab Fragments: Kudzu Arm Project : Hard Lab Fragments: Kudzu Neck Project : Hard Lab Fragments: Making it Up As I Go Multiloop Project : Hard Lab Fragments: Water Strider Arm Project : Neck Length 2 - 4 branch multiloop Project : Bulge Sampler: 4-nt Project : Bulge Sampler: 3-nt Project : Bulge Sampler: 2-nt Project : Bulge Sampler: 1-nt Project : 3 single nucleotide bulges Project : Isolated Base Pairs: 2-2 Loops Adjacent to Multiloop Project : Isolated Base Pairs: Adjacent 2-1 Loops (1) Project : Isolated Base Pairs: Adjacent 2-1 Loops (3) Project : Isolated Base Pairs: Adjacent 2-1-Loops (4) Project : Zigzag: 1-Nucleotide Bulge (4) Project : Zigzag: 1-Nucleotide Bulge (3) Project : Zigzag: 1-Nucleotide Bulge (2) Project : Zigzag: 1-Nucleotide Bulge (1) Project : GU-pin shape test Project : comparison series: 2-10 Project : comparison series: 2-9 Project : comparison series: 2-8 Project : Crossroads test Project : comparison series: 2-7 Project : comparison series: 2-6 Project : comparison series: 2-5 Project : comparison series: 2-4 Project : comparison series: 2-3 Project : Fisker - 2-2 loop energy challenge Project : comparison series: 10-2 Project : comparison series: 9-2 Project : comparison series: 8-2 Project : comparison series: 7-2 Project : comparison series: 6-2 Project : comparison series: 5-2 Project : comparison series: 4-2 Project : Mat - comparison series: 3-2 - D1 Project : comparison series: Hairpin loop with 15 nts Project : comparison series: Hairpin loop with 14 nts Project : comparison series: Hairpin loop with 13 nts Project : comparison series: Hairpin loop with 12 nts Project : comparison series: Hairpin loop with 11 nts Project : Mat - comparison series: Hairpin loop with 10 nts Project : Mat - comparison series: Hairpin loop with 9 nts- D1 Project : Five Branch Multiloop Project : comparison series: Octaloops Project : comparison series: Heptaloop Project : comparison series: Hexaloop Project : comparison series: Pentaloop Project : comparison series: Triloop Project : Multiloop: 4 Branches Separated by Single Unpaired Bases Project : Multiloop: 3 Branches Unevenly Spaced (2) Project : Multiloop: 3 Branches Unevenly Spaced (1) Project : Multiloop: 3 Branches 12 Unpaired Bases Project : Multiloop: 3 Branches No Unpaired Bases Project : 3-4 and 1-2 loops Project : Chain length and loop size series 1-10 Project : chain lenth and loop size series 1-9 Project : chain length and loop size series 1-8 Project : chain length and loop size series 1-5 Project : chain length and loop size series 1-4 Project : chain lengh an loop size series 1-3 Project : comparison series: 1-15 Project : comparison series: 2-15 Project : comparison series: 3-15 Project : comparison series: 4-15 Project : comparison series: 5-15 Project : comparison series: 6-15 Project : comparison series: 7-15 Project : comparison series: 8-15 Project : comparison series: 9-15 Project : comparison series: 10-15 Project : comparison series: 11-15 Project : comparison series: 12-15 Project : comparison series: 13-15 Project : comparison series: 14-15 Project : comparison series: 15-1 Project : comparison series: 15-2 Project : comparison series: 15-3 Project : comparison series: 15-4 Project : comparison series: 15-5 Project : comparison series: 15-6 Project : comparison series: 15-7 Project : comparison series: 15-8 Project : comparison series: 15-9 Project : comparison series: 15-10 Project : comparison series: 15-11 Project : comparison series: 15-12 Project : comparison series: 15-13 Project : comparison series: 15-14 Project : comparison series: 15-15 Project : comparison series: 14-14 Project : comparison series: 13-13 Project : comparison series: 12-12 Project : comparison series: 11-11 Project : comparison series: 10-10 Project : comparison series: 9-9 Project : comparison series: 8-8 Project : comparison series: 7-7 Project : comparison series: 6-6 Project : comparison series: Project : comparison series: 4-4 Project : comparison series: Project : comparison series: 2-2 Project : comparison series: 1-1 Project : Two stacks Project : Lab design for newer players Project : Sample puzzle for lab Project : Pseudoknot 2: Biotin-Binding Pseudoknot Project : Pseudoknot 1: Minimal Project : Half of The Branches Project : Saccharomyces Cerevisiae Loop Structure Project : 30 Nucleotide Loop 3 - Bulge Internal Loop Project : Two bulges and a 1-2 loop (reverse) Project : 30 Nucleotide Loop 2 - Asymmetric Internal Loop Project : 30 Nucleotide Loop 1 - Symmetric Internal Loop Project : Sharklike V-2 (SHAPE data Exp-2) Project : Sharklike V-1 (SHAPE data Exp-1) Project : S&E5 Modified Project : Reshiram Zekrom Kyurem Project : All red and blue Project : Bulge test Project : Guanine Reduction Project : Uracil Reduction Project : Large Isolated Hairpin Project : Isolated Closing Pairs 3 Project : Alternative Mismatches Project : Adenine Reduction Project : Internal Loops: 5-2 Project : Internal Loops: 6-3 Project : FMN-RNA aptamer complex lab Project : Tobramycin Aptamer Project : Hairpins: Heptaloop Project : Hairpins: Hexaloop Project : Hairpins: Pentaloop Project : Hairpins: Tetraloop Project : Hairpins: Triloop Project : Chesterfield s-The Mousekateer Project : Plain Hooked Project : Nupack s Finger Revisited Project : Large Loop Project : Hooked Project : Multiloop Isolated Closing Pairs Project : Cytosine reduction Project : Loop Heavy Project : Fractal RNA Project : Isolated Closing Pairs 2 Project : Repetitive Structures Project : Isolated Closing Pairs 1 Project : 4-4 loop Project : JerryP s winning design without tetraloop boost Project : 2-2 loop Project : Example project 2 Project : Example project Shape Library 101: The Finger Project: mRNA structure Project: helix stacking Project: all non-canonical pairs Project : miRNA hairpin robustness Project: metal ion pseudoknots Project: VAI protein kinase R inhibitor Project: unbound aptamer structures Project: Parin s favorite motifs therm1	1.583
R1 4/9/2013	Second batch of Player Projects Tested with four different SHAPE reagents: NMIA DMS CMCT 1M7 Signal-to-Noise Averages not currently available
R2 3/7/2013	Third batch of Player Projects Tested with four different SHAPE reagents: NMIA DMS CMCT 1M7 Each design was tested with each reagent twice, the second time with a different barcode Signal-to-Noise Averages not currently available
R69	R69.xlsx R69.googlesheet	Cloud Lab 1 - Aires by wateronthemoon Cloud Lab 2 - Triangle of doom version 2 by dstea Cloud Lab 3 - A Simple Zigzag by janelle Cloud Lab 4 - Random by theravin Cloud Lab 5 - The Nonesuch by rnjensen45 Cloud Lab 6 - Cross by firedrake969 Cloud Lab 7 - 5 Fold Radial Asymmetrical Starfish Level 0 by Jieux Cloud Lab 8 - Stellar Crossbow by jmf028 Cloud Lab 9 - Final Countdown by Tesla sDisciple Cloud Lab 10 - Random Shape 2 by ElNando888 Cloud Lab 11 - Little bug by JR Cloud Lab 12 - Anchor by ribonucleic Cloud Lab 13 - Alien Party Glasses by Jennifer Pearl Cloud Lab 14 - Easy loop sizes by Edward Lane Cloud Lab 15 - Triloop Buffet by jandersonlee Cloud Lab 16 - Section from lab Water Strider by Brourd Cloud Lab 17 - Oryza sativa 8 Elements Part 2 by merryskies Cloud Lab 18 - Anaconda About to Poop by SpaceFolder Cloud Lab 19 - Big Hairpin Loop by Eli Fisker Cloud Lab 20 - Random4 by mat747	6.998
R70	Switch Cloud Labs	LabPuz02 by JR Bistable 3 by jnicol Hair Trigger by space_miser Will It Bind? by jmf028 Stratospheric by Dennis9600 Phase II - 1 by ElNando888 LS2 by c-quence Anchor 2.0 by ribonucleic Day 2 by wateronthemoon Alive and kicking by Eli Fisker Laydown and Jump by rnjensen45 McSwitch by Meechl Water Snake Redux by jruaya My Screw-Up Corrected? by SpaceFolder Nincompoop by hoglahoo Lines by starryjess Bound state has a zigzag by stevetclark Chirality by kcabral28 Switch Test 1 by Brourd Top Notch by jmf028
R71 5/10/2013	R71.xlsx R71.googlesheet	My Screw-Up Corrected? by SpaceFolder Cloud Lab 1 - Aires by wateronthemoon Cloud Lab 2 - Triangle of doom version 2 by dstea Cloud Lab 3 - A Simple Zigzag by janelle Cloud Lab 4 - Random by theravin Cloud Lab 5 - The Nonesuch by rnjensen45 Cloud Lab 6 - Cross by firedrake969 Cloud Lab 7 - 5 Fold Radial Asymmetrical Starfish Level 0 by Jieux Cloud Lab 8 - Stellar Crossbow by jmf028 Cloud Lab 9 - Final Countdown by Tesla sDisciple Cloud Lab 10 - Random Shape 2 by ElNando888 Cloud Lab 11 - Little bug by JR Cloud Lab 12 - Anchor by ribonucleic Cloud Lab 13 - Alien Party Glasses by Jennifer Pearl Cloud Lab 14 - Easy loop sizes by Edward Lane Cloud Lab 15 - Triloop Buffet by jandersonlee Cloud Lab 16 - Section from lab Water Strider by Brourd Cloud Lab 17 - Oryza sativa 8 Elements Part 2 by merryskies Cloud Lab 18 - Anaconda About to Poop by SpaceFolder Cloud Lab 19 - Big Hairpin Loop by Eli Fisker Cloud Lab 20 - Random4 by mat747	3.698
R72 6/11/2013	R72.xlsx R72.googlesheet	Ball & Chain by Krobar Simplify by Tesla sDisciple An Arm and a Leg 1.0 by kcabral28 Huffman by hotcreek QRNAL0 by Quxwozing Riboswitch-based by jruaya 1-X bulge testing by Omei EzFold by space_miser Thursday by DHammond TEBOWNED mutation - BH TEBOWNED mutation - U TEBOWNED mutation - B Flu Virus TEBOWNED reloaded MedLoop Ball & Chain by Krobar Simplify by Tesla sDisciple An Arm and a Leg 1.0 by kcabral28 Huffman by hotcreek QRNAL0 by Quxwozing Riboswitch-based by jruaya 1-X bulge testing by Omei EzFold by space_miser Thursday by DHammond	4.272
R73 7/30/2013	R73.xlsx R73.googlesheet	1-1-1-1-1-1 Multiloop 2-2 and 3-3 loops A-U Closing Base Pairs caulobacter_ncrna_lists Hex-a-Stripe Magic boosts in 2-2 loops Magic boosts in 2-2 loops revised thanks starry Permuted loops Probing the 3D motif atlas Quad Loop test RNA Bridge RNA Bridge (Updated) RNA Strength Short Stacks Single state - Switch state Single to Switch try 2 The GAAA loop Tighter Two Stacks for 3-way Multi-Loop testing Tribute To Satellite Kepler Two stacks Two Stacks - Triloop hairpin variation Variations on a theme of 1-0 loops and short stack hairpins	3.775
R73.0001	R73.0001.xlsx R73.0001.googlesheet		3.881
R74	R74.xlsx R74.googlesheet	A-U Closing Base Pairs 2 Tetraloops and 0-0-0-0 Multiloop Phase 1 Tetraloops and 0-0-0-0 Multiloop Phase 1 Version 2 Lonely Base Pair - 1-1: Multiloop Lonely Base Pair - 2-2: Multiloop Lonely Base Pair - 3-3: Multiloop FMN Switch 2.0 - First State with Locked Bases Can We do it in 10? - FMN Switch 2.0 Triloop with multiloop core phase 1 Two Bulge Zigzag - Variation 1 Two Bulge Zigzag - Variation 3 Two Bulge Zigzag - Variation 4 G-U Closing Base Pairs G-U Closing Base Pairs 2 Reversed G-C Multibranch Loop Closing Base Pairs Probing for tertiary structure Modeled Impossible: 31+ Nucleotide Internal Loops RNA windows pilot project - 16s rRNA (3I1M) Caulobacter ncRNA discovery Tristable RNA Hammerhead Ribozyme Wildtype Mutate and Map MedLoop V2 Hammerhead Ribozyme G12A Mutate and Map Entoplea bizarre tRNA 2D structure mt tRNA-Arg	4.442
R75	R75.xlsx R75.googlesheet	Short Stacks 2 SARS coronavirus structure test FMN Binding Site Chemical Footprint Modeled Impossible: 1 Nucleotide Bulge/Triloop Lonely base pair V1 New Frontier Frog leg - Electric ZigZag and ZagZig Chicken leg Chicken leg - Splayed Motor Protein - Step 1 Motor Protein - Step 2 Motor Protein - Step 3 Intrinsically unfolded RNA Probing the structure of poly-A loops by mutation PSTVd probing Improving the Nearest Neighbor Energy Model Using EteRNA Pilot TCF21 3 UTR MedLoop redux	5.621
R76 8/23/2013	R76.xlsx <a href="/wiki/Now I found">R76.googlesheet</a>	Find Z - Here It Is! Two Bulge Zigzag - Both Conformations Two Bulge Zigzag - Variation 2 Modeled Impossible: 1 Nucleotide Bulge/Triloop Lonely base pair V2 TinkerToy Retread Frog leg - relaxed Frog leg - Stretched toe Intersecting stacks 2 Is RNA directional 1 of 2 Semicircle - 2 bends Semicircle - 5 bends Location Dependent Chemical Footprints Part 1 Location Dependent Chemical Footprints Part 3 Location Dependent Chemical Footprints Part 4 Location Dependent Chemical Footprints Part 5 Location Dependent Chemical Footprints Part 6 Teeny tRNA P5abc Mutants to Affect Folding Transitions Testing 3D structure prediction of G/G mismatches (boosts!) Testing for crazy conformations of tandem G/A and A/G pairs A codon riboswitch	3.692
R76.0001	R76.0001.xlsx R76.0001.googlesheets		3.389
R77 9/23/2013	R77.xlsx R77.googlesheet	Intersecting stacks investigation Is RNA directional 2 of 2 Semicircle - 3 bends Semicircle - 4 bends Location Dependent Chemical Footprints Part 2 Could Curves Survive? Adding some sweet tetraloops Palindromes part one Dimer B Dimer A Robot serial killer 1 - Lab killer too? Robot serial killer 2 - Lab killer too? Short Stacks 3 Relaxed multiloop 2 New Frontier 2 Five Adjacent Stem Multibranch Loop crRNA tracrRNA sgRNA89_NGS sgRNA67 sgRNA48 Repeat hairpins v1 Codon riboswitch [repeat of tryptophan] Codon riboswitch [arginine] Class I ligase MedLoop resurrected Un-stable M-stable EteRNA R45-46 FMN Aptamer with Single Binding Site EteRNA R43 the Backwards C Codon riboswitch [histidine] Reproducibility Lab 1	1.714
R78	R78.xlsx R78.googlesheet	Example project.. G-U GAGA Tetraloop Boost Repetitious sequences Robot serial killer 3 - Lab killer too? FMN Shape Test- 1st State FMN Shape Test- 2nd State Wobble Quad Stability 1 SHAPE Profile - U-U Mismatch - Pilot Run SHAPE Profile - C-U Mismatch - Pilot Run SHAPE Profile - U-C Mismatch - Pilot Run SHAPE Profile - C-A Mismatch - Pilot Run SHAPE Profile - A-C Mismatch - Pilot Run SHAPE Profile - G-A Mismatch - Pilot Run SHAPE Profile - A-G Mismatch - Pilot Run Unmodified tRNA sequences Chicken Leg - Reversed Reversed motor - step 1 Double 1-3 Loop SHAPE Profile - C-C Mismatch - Pilot Run Large GU stack Neck strength analysis 3 of 3 - Weak - AUs + GUs. Hexaloop Kd and SHAPE test P5abc Mutants to Affect Folding Transitions 2 MedLoop Double Mutants - Shape 0 MedLoop delta Double Mutants - Shape 0 Bistable double mutants - Shape 0 M-stable double mutants - Shape 0 Un-stable double mutants - Shape 0 Bistable hairpin mutate and map - Shape 0 Un-stable alternative mutate-and-map - Shape 0 RPL11a Pseudouridylation Site Mutate and Map - Shape 0 TEF1 Pseudouridylation Site Mutate and Map - Shape 0 RPL11a Mutant Pseudouridylation Site Mutate and Map - Shape 0 Permuted Loops - Shape 0 Permuted Loops - Shape 1 Permuted Loops - Shape 2 Permuted Loops - Shape 3 Permuted Loops - Shape 4 Permuted Loops - Shape 5 Permuted Loops - Shape 6 Permuted Loops - Shape 7 Permuted Loops - Shape 8 Permuted Loops - Shape 9 Permuted Loops - Shape 10 Permuted Loops - Shape 11 Permuted Loops - Shape 12 Permuted Loops - Shape 13 Permuted Loops - Shape 14 Permuted Loops - Shape 15 Permuted Loops - Shape 16 Permuted Loops - Shape 17 Permuted Loops - Shape 18 Permuted Loops - Shape 19 Permuted Loops - Shape 20 Permuted Loops - Shape 21 Permuted Loops - Shape 22 Permuted Loops - Shape 23 Permuted Loops - Shape 24 Permuted Loops - Shape 25 Permuted Loops - Shape 26 Permuted Loops - Shape 27 Permuted Loops - Shape 28 Permuted Loops - Shape 29 Permuted Loops - Shape 30 Permuted Loops - Shape 31 Permuted Loops - Shape 32 Permuted Loops - Shape 33 Permuted Loops - Shape 34 Permuted Loops - Shape 35 Permuted Loops - Shape 36 Permuted Loops - Shape 37 Reproducibility Lab Another Round - Shape 0 Reproducibility Lab Another Round - Shape 1 Reproducibility Lab Another Round - Shape 2 Reproducibility Lab Another Round - Shape 3 Reproducibility Lab Another Round - Shape 4 Reproducibility Lab Another Round - Shape 5 Reproducibility Lab Another Round - Shape 6 Reproducibility Lab Another Round - Shape 7 Reproducibility Lab Another Round - Shape 8 Reproducibility Lab Another Round - Shape 9 Reproducibility Lab Another Round - Shape 10 Reproducibility Lab Another Round - Shape 11 Reproducibility Lab Another Round - Shape 12 Reproducibility Lab Another Round - Shape 13 Reproducibility Lab Another Round - Shape 14 Reproducibility Lab Another Round - Shape 15 Reproducibility Lab Another Round - Shape 16 Reproducibility Lab Another Round - Shape 17 Reproducibility Lab Another Round - Shape 18 Reproducibility Lab Another Round - Shape 19 Reproducibility Lab Another Round - Shape 20 Influenza PB2 mutant sequences - Shape 0 Influenza PB2 mutant sequences - Shape 1 Single strand barcodes - Shape 0 Single strand barcodes - Shape 1 Single strand barcodes - Shape 2 Single strand barcodes - Shape 3	2.604
R79	R79.xlsx R79.googlesheet	Test of locking loop bases in a ribozyme-like structure Relaxed multiloop 1 Relaxed multiloop 3 Reversed motor - Step 2 Reversed motor - Step 3 Reversed motor - Step 4 A-U Closing Base Pairs 3 A-U Closing Base Pairs 4 T.thermophilise16S Hammerhead Alien partial glasses - Mirror version Single to Switch try 2 - Mirror version Let s break the barcode Don Quixote Mummiebrain s M2 Impossible Folding II - The Intramolecular G-quadruplex PB2elem2_MR_syn - Shape 0 GNRA/receptor project - Shape 0 GNRA/receptor project - Shape 1 GNRA/receptor project - Shape 2 GNRA/receptor project - Shape 3 CR4-5 domain of human telomerase - Shape 0 CR4-5 domain of human telomerase - Shape 1 CR4-5 domain of human telomerase - Shape 2 CR4-5 domain of human telomerase - Shape 3 CR4-5 domain of human telomerase - Shape 4 CR4-5 domain of human telomerase - Shape 5 CR4-5 domain of human telomerase - Shape 6 CR4-5 domain of human telomerase - Shape 7 CR4-5 domain of human telomerase - Shape 8 CR4-5 domain of human telomerase - Shape 9 CR4-5 domain of human telomerase - Shape 10 CR4-5 domain of human telomerase - Shape 11 CR4-5 domain of human telomerase - Shape 12 CR4-5 domain of human telomerase - Shape 13 CR4-5 domain of human telomerase - Shape 14 CR4-5 domain of human telomerase - Shape 15 CR4-5 domain of human telomerase - Shape 16 CR4-5 domain of human telomerase - Shape 17 CR4-5 domain of human telomerase - Shape 18 CR4-5 domain of human telomerase - Shape 19 CR4-5 domain of human telomerase - Shape 20 CR4-5 domain of human telomerase - Shape 21 CR4-5 domain of human telomerase - Shape 22 CR4-5 domain of human telomerase - Shape 23 CR4-5 domain of human telomerase - Shape 24 CR4-5 domain of human telomerase - Shape 25 CR4-5 domain of human telomerase - Shape 26 CR4-5 domain of human telomerase - Shape 27 CR4-5 domain of human telomerase - Shape 28 CR4-5 domain of human telomerase - Shape 29 CR4-5 domain of human telomerase - Shape 30 CR4-5 domain of human telomerase - Shape 31 CR4-5 domain of human telomerase - 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Shape 27 RF01020 mutate-and-map - Shape 28 RF01020 mutate-and-map - Shape 29 RF01020 mutate-and-map - Shape 30 RF01020 mutate-and-map - Shape 31 RF01020 mutate-and-map - Shape 32 RF01020 mutate-and-map - Shape 33 RF01020 mutate-and-map - Shape 34 RF01020 mutate-and-map - Shape 35 RF01020 mutate-and-map - Shape 36 RF01020 mutate-and-map - Shape 37 RF01414 mutate-and-map - Shape 0 RF01414 mutate-and-map - Shape 1 RF01414 mutate-and-map - Shape 2 RF01414 mutate-and-map - Shape 3 RF01414 mutate-and-map - Shape 4 RF01414 mutate-and-map - Shape 5 RF01414 mutate-and-map - Shape 6 RF01414 mutate-and-map - Shape 7 RF01414 mutate-and-map - Shape 8 RF01414 mutate-and-map - Shape 9 RF01414 mutate-and-map - Shape 10 RF01414 mutate-and-map - Shape 11 RF01414 mutate-and-map - Shape 12 RF01414 mutate-and-map - Shape 13 RF01414 mutate-and-map - Shape 14 RF01414 mutate-and-map - Shape 15 RF01414 mutate-and-map - Shape 16 RF01414 mutate-and-map - Shape 17 RF01414 mutate-and-map - Shape 18 RF01414 mutate-and-map - Shape 19 RF01414 mutate-and-map - Shape 20 RF01414 mutate-and-map - Shape 21 RF01414 mutate-and-map - Shape 22 RF01414 mutate-and-map - Shape 23 RF01414 mutate-and-map - Shape 24 RF01414 mutate-and-map - Shape 25 RF01414 mutate-and-map - Shape 26 RF01414 mutate-and-map - Shape 27 RF01125 mutate-and-map - Shape 0 RF01125 mutate-and-map - Shape 1 RF01125 mutate-and-map - Shape 2 RF01125 mutate-and-map - Shape 3 RF01125 mutate-and-map - Shape 4 RF01125 mutate-and-map - Shape 5 RF01125 mutate-and-map - Shape 6 RF01125 mutate-and-map - Shape 7 RF01125 mutate-and-map - Shape 8 RF01125 mutate-and-map - Shape 9 RF01125 mutate-and-map - Shape 10 RF01125 mutate-and-map - Shape 11 RF01125 mutate-and-map - Shape 12 RF01125 mutate-and-map - Shape 13 RF01125 mutate-and-map - Shape 14 RF01125 mutate-and-map - Shape 15 RF01125 mutate-and-map - Shape 16 RF01125 mutate-and-map - Shape 17 RF01125 mutate-and-map - Shape 18 RF01125 mutate-and-map - Shape 19 RF01125 mutate-and-map - Shape 20 RF01125 mutate-and-map - Shape 21 RF01125 mutate-and-map - Shape 22 RF01125 mutate-and-map - Shape 23 RF01125 mutate-and-map - Shape 24 RF01125 mutate-and-map - Shape 25 RF01125 mutate-and-map - Shape 26 RF01125 mutate-and-map - Shape 27 RF01125 mutate-and-map - Shape 28 RF01125 mutate-and-map - Shape 29 RF01125 mutate-and-map - Shape 30	3.046
R80 2/5/2014	R80.xlsx R80.googlesheet	Wobble Quad Control 2 Wobble Quad Control 3 Wobble Quad Control 4 SHAPE Profile - G-G Mismatch - Pilot Run Reversed G-C Multibranch Loop Closing Base Pairs 2 SHAPE Profile - U-U Mismatch - Pilot Run 2A SHAPE Profile - U-U Mismatch - Pilot Run 2B SHAPE Profile - A-G Mismatch - Pilot Run 2A SHAPE Profile - A-G Mismatch - Pilot Run 2B Tetraloop Competition Series - GAAA Tetraloop Competition - UUCG Tetraloop Competition Series - UACG Tetraloop Competition Series - GAGA SHAPE Profile - A-A Mismatch - Pilot Run Repeatability - Melted Helix Variation 1 Repeatability - Melted Helix Variation 2 SHAPE Profile - Most Likely Base Pair C/G Really big loop coil - Classic science toy Intrinsical - Frequency 1 Intrinsical - Frequency 8 Impossible Folding I Poly (A) Structure Analysis 1 New Frontier 3 Cobalamin Riboswitches - Shape 0 Cobalamin Riboswitches - Shape 1 Cobalamin Riboswitches - Shape 2 Cobalamin Riboswitches - Shape 3 Cobalamin Riboswitches - Shape 5 Cobalamin Riboswitches - Shape 11 Cobalamin Riboswitches - Shape 12 Cobalamin Riboswitches - Shape 14 Cobalamin Riboswitches - Shape 19 Cobalamin Riboswitches - Shape 23 Motif Assembled GAAA tetraloop binders - Shape 0 The RFAM Mapping project - Shape 0 The RFAM Mapping project - Shape 1 The RFAM Mapping project - Shape 2 The RFAM Mapping project - Shape 3 The RFAM Mapping project - Shape 4 The RFAM Mapping project - Shape 5 The RFAM Mapping project - Shape 6 The RFAM Mapping project - Shape 7 The RFAM Mapping project - Shape 8 The RFAM Mapping project - Shape 9 The RFAM Mapping project - Shape 10 The RFAM Mapping project - Shape 11 The RFAM Mapping project - Shape 12 The RFAM Mapping project - Shape 13 The RFAM Mapping project - Shape 14 The RFAM Mapping project - Shape 15 The RFAM Mapping project - Shape 16 The RFAM Mapping project - Shape 17 The RFAM Mapping project - Shape 18 The RFAM Mapping project - Shape 19 The RFAM Mapping project - Shape 20 The RFAM Mapping project - Shape 21 The RFAM Mapping project - Shape 22 The RFAM Mapping project - Shape 23 The RFAM Mapping project - Shape 24 The RFAM Mapping project - Shape 25 The RFAM Mapping project - Shape 26 The RFAM Mapping project - Shape 27 The RFAM Mapping project - Shape 28 The RFAM Mapping project - Shape 29 The RFAM Mapping project - Shape 30 The RFAM Mapping project - Shape 31 The RFAM Mapping project - Shape 32 The RFAM Mapping project - Shape 33 The RFAM Mapping project - Shape 34 The RFAM Mapping project - Shape 35 The RFAM Mapping project - Shape 36 The RFAM Mapping project - Shape 37 The RFAM Mapping project - Shape 38 The RFAM Mapping project - Shape 39 The RFAM Mapping project - Shape 40 The RFAM Mapping project - Shape 41 The RFAM Mapping project - Shape 42 The RFAM Mapping project - Shape 43 The RFAM Mapping project - Shape 44 The RFAM Mapping project - Shape 45 The RFAM Mapping project - Shape 46 The RFAM Mapping project - Shape 47 The RFAM Mapping project - Shape 48 The RFAM Mapping project - Shape 49 The RFAM Mapping project - Shape 50 The RFAM Mapping project - Shape 51 The RFAM Mapping project - Shape 52 The RFAM Mapping project - Shape 53 The RFAM Mapping project - Shape 54 The RFAM Mapping project - Shape 55 The RFAM Mapping project - Shape 56 The RFAM Mapping project - Shape 57 The RFAM Mapping project - Shape 58 The RFAM Mapping project - Shape 59 The RFAM Mapping project - Shape 60 The RFAM Mapping project - Shape 61 The RFAM Mapping project - Shape 62 The RFAM Mapping project - Shape 63 The RFAM Mapping project - Shape 64 The RFAM Mapping project - Shape 65 The RFAM Mapping project - Shape 66 The RFAM Mapping project - Shape 67 The RFAM Mapping project - Shape 68 The RFAM Mapping project - Shape 69 The RFAM Mapping project - Shape 70 The RFAM Mapping project - Shape 71 The RFAM Mapping project - Shape 72 The RFAM Mapping project - Shape 73 The RFAM Mapping project - Shape 74 The RFAM Mapping project - Shape 75 The RFAM Mapping project - Shape 76 The RFAM Mapping project - Shape 77 The RFAM Mapping project - Shape 78 The RFAM Mapping project - Shape 79 The RFAM Mapping project - Shape 80 The RFAM Mapping project - Shape 81 The RFAM Mapping project - Shape 82 The RFAM Mapping project - Shape 83 The RFAM Mapping project - Shape 84 The RFAM Mapping project - Shape 85 The RFAM Mapping project - Shape 86 The RFAM Mapping project - Shape 87 The RFAM Mapping project - Shape 88 The RFAM Mapping project - Shape 89 The RFAM Mapping project - Shape 90 The RFAM Mapping project - Shape 91 The RFAM Mapping project - Shape 92 The RFAM Mapping project - Shape 93 The RFAM Mapping project - Shape 94 The RFAM Mapping project - Shape 95 The RFAM Mapping project - Shape 96 The RFAM Mapping project - Shape 97 The RFAM Mapping project - Shape 98 Nando s Zippers - Shape 0 Ambiguous Bulges - Shape 0 Ambiguous Bulges - Shape 1 Ambiguous Bulges - Shape 2 Ambiguous Bulges - Shape 3	2.217
R81 2/4/2014	R81.xlsx R81.googlesheets	Dimer A - control Small Loops- v. 1 SHAPE Profile - G-G Mismatch - Pilot Run 2A SHAPE Profile - G-G Mismatch - Pilot Run 2B SHAPE Profile - A-A Mismatch - Pilot Run 2B Simplify - Mirror version SHAPE Profile - Most Likely Base Pair G/C Early bulge Really big loop coil - control Intrinsical frequency Intrinsically Green Intrinsically Blue Very relaxed multiloop Intrinsical - Frequency 2 Intrinsical - Frequency 6 Intrinsical - Frequency 7 TrpBoundState TrpAltA TrpAltB TrpAltC GNRA/receptor project - Shape 0 GNRA/receptor project - Shape 1 GNRA/receptor project - Shape 2 GNRA/receptor project - Shape 3 GNRA/receptor project - Shape 4 GNRA/receptor project - Shape 5 GNRA/receptor project - Shape 8 GNRA/receptor project - Shape 12	2.620
R82 2/5/2014	R82.xlsx R82.googlesheet	Improving the Energy Model: Competing Tetraloops Part 1 Ziggy 25 (aka Multiloop Test) Reversed G-C Multibranch Loop Closing Base Pairs 3 SHAPE Profile - A-C Mismatch - Pilot Run 2A SHAPE Profile - G-A Mismatch - Pilot Run 2B Neck strength analysis 1 of 3 - Strong - alternating GCs. Neck strength analysis 2 of 3 - Medium - alternating AUs. SHAPE Profile - C-C Mismatch - Pilot Run 2B SHAPE Profile - A-A Mismatch - Pilot Run 2A Late bulge Late bulge control Intrinsically Red Intrinsical - Frequency 3 Intrinsical - Frequency 4 Short Neck and Split Ends Adding some sweet triloops Ribozyme 1: Hammerhead variant JR s Let s Break the Barcode - 2 nt Dangling End Gap JR s Let s Break the Barcode - 3 nt Dangling End Gap Improving the Energy Model: Favoring an Equivalent Structure Improving the Energy Model: 5-Base Hairpin Loops Reproducibility Lab Round 3 - Shape 0 Reproducibility Lab Round 3 - Shape 1 Reproducibility Lab Round 3 - Shape 2 Reproducibility Lab Round 3 - Shape 3 Reproducibility Lab Round 3 - Shape 4 Reproducibility Lab Round 3 - Shape 5 Reproducibility Lab Round 3 - Shape 6 Reproducibility Lab Round 3 - Shape 7 Reproducibility Lab Round 3 - Shape 8 Reproducibility Lab Round 3 - Shape 9 Reproducibility Lab Round 3 - Shape 10 Reproducibility Lab Round 3 - Shape 11 Reproducibility Lab Round 3 - Shape 12 Reproducibility Lab Round 3 - Shape 13 Reproducibility Lab Round 3 - Shape 14 Reproducibility Lab Round 3 - Shape 15 Reproducibility Lab Round 3 - Shape 16 Reproducibility Lab Round 3 - Shape 17 Reproducibility Lab Round 3 - Shape 18 Reproducibility Lab Round 3 - Shape 19 Reproducibility Lab Round 3 - Shape 20 Motif Assembled GAAA tetraloop binders - Shape 0 Motif Assembled GAAA tetraloop binders - Shape 1 Motif Assembled GAAA tetraloop binders - Shape 2 Motif Assembled GAAA tetraloop binders - Shape 4 Motif Assembled GAAA tetraloop binders - Shape 6 Motif Assembled GAAA tetraloop binders - Shape 7 Motif Assembled GAAA tetraloop binders - Shape 8 Motif Assembled GAAA tetraloop binders - Shape 10 Motif Assembled GAAA tetraloop binders - Shape 11 Johan s sequences	2.989
R83 3/27/2014	P4-P6 domain Tetrahymena ribozyme was also run, but only in R83, not R83.2 or R83.3 R83.xlsx R83.googlesheet	Wobble Quad Stability 2 Wobble Quad Stability 3 Wobble Quad Stability 4 Wobble Quad Control 1 SHAPE Profile - C-U Mismatch - Pilot Run 2A SHAPE Profile - C-A Mismatch - Pilot Run 2B SHAPE Profile - A-C Mismatch - Pilot Run 2B SHAPE Profile - G-A Mismatch - Pilot Run 2A SHAPE Profile - C-C Mismatch - Pilot Run 2A Early bulge control Intrinsical - Frequency 5 Triloop Hairpin and Stem Loop - Helix Stability The G Quadruplex - Round 2 New Frontier 4 SAM II Riboswitch	1.946
R83.0002 4/1/2014	R83.0002.xlsx R83.0002.googlesheet		4.907
R83.0003 4/3/2014	R83.0003.xlsx R83.0003.googlesheet		5.690
R84 4/21/2014	R84.xlsx R84.googlesheet	FMN Binding Site - Rotated SHAPE Profile - C-U Mismatch - Pilot Run 2B SHAPE Profile - Most Likely Base Pair U/A - Variation 1.1 Most Likely Base Pair U/A - Variation 1.1B SHAPE Profile - Most Likely Base Pair U/A - Variation 1.3 SHAPE Profile - Most Likely Base Pair G/C - Variation 2 SHAPE Profile - Most Likely Base Pair G/C - Variation 2B Kinky Bits JR s Let s Break the Barcode - Adjacent Barcode Version The Donkey s Tail A-U Closing Base Pairs - 4.1 A-U Closing Base Pairs - 4.2 G-U Closing Base Pairs - 4.3 G-U Closing Base Pairs - 4.4 Motif study: the S-turn Consensus Pure A GA mismatch only G14A Alternative C-C mismatch Alternative U-C mismatch Alternative U-C & A-C mismatches G12A Mad multiloop - Pentaloop 1 Pentaloop 2 Pentaloop 3 Hexaloop 1 Hexaloop 2 Hexaloop 3 Neck-Hairpin Spacing 3 Neck-Hairpin Spacing 1 Neck-Hairpin Spacing 0 Neck-Hairpin Spacing 2 Return of the boost Multibranch Loop Terminal Mismatch Stability Pilot - Strand Length 6 Multibranch Loop Terminal Mismatch Stability Pilot - Strand Length 5 Multibranch Loop Terminal Mismatch Stability Pilot - Strand Length 4 Multibranch Loop Terminal Mismatch Stability Pilot - Strand Length 3 Multibranch Loop Terminal Mismatch Stability Pilot - Strand Length 2 Multibranch Loop Terminal Mismatch Stability Pilot - Strand Length 1 Hairpin ribozyme Variant 1 Variant 2 RNA Transient Structures and pre-miRs - Shape 0 RNA Transient Structures and pre-miRs - Shape 1 RNA Transient Structures and pre-miRs - Shape 2 RNA Transient Structures and pre-miRs - Shape 3 RNA Transient Structures and pre-miRs - Shape 4 RNA Transient Structures and pre-miRs - Shape 5 RNA Transient Structures and pre-miRs - Shape 6 RNA Transient Structures and pre-miRs - Shape 7 RNA Transient Structures and pre-miRs - Shape 10	2.725
R85 5/9/2014	R85.xlsx R85.googlesheet	SHAPE Profile - Most Likely Base Pair U/A - Variation 1.2 SHAPE Profile - Most Likely Base Pair U/A - Variation 1.4 SHAPE Profile - Most Likely Base Pair C/G - Variation 2 SHAPE Profile - Most Likely Base Pair C/G - Variation 2B GGG/UCC Wobble Closing Base Pairs - Hexaloop RE GGG/UCC Wobble Closing Base Pairs - Heptaloop 5 Hairpin Stem Part 1 - Five Base Pairs + UUCG Tetraloop Stabilise the 1-1-1-1-1 multiloop FMN in zigzag L3-9 L3-8 L3-7 L3-6 L3-5 L3-4 Helix Comparison - 4x4 Loop Helix Comparison - 5x5 Loop Helix Comparison - 6x6 Loop Helix Comparison - Four Base Pair Stem Helix Comparison - Eight Base Pair Stem Helix Comparison - Stem 2 G-U Helix Comparison - Stem 1 G-U New Frontier 5 Telephone Effect of Bulge Proximity on RNA Stability Effect of Bulge Proximity on RNA Stability: More Distance FMN Mimic Pilot - (CCUAUC/GAAGG & AGUAUA/UAACA) 1 FMN Mimic Pilot - (CCUAUC/GAAGG & AGUAUA/UAACA) 2 FMN Mimic Pilot - AGUAUA/UAACA FMN Mimic Pilot - (GUAGUA/GAAAC & AGGAUA/UAAUU) FMN Mimic Pilot - (UGUAUU/GAAGG & UGGAUA/GACGG) FMN Mimic Pilot - (CUGAAC/GACGG & CGUUAC/GGAGG) FMN Mimic Pilot - (AGGAUA/UACUG & AGGAUA/UAAGG) FMN Mimic Pilot - (CUGAGC/GACGG & CGGAUA/GACGG) Unbound Bound - Mimic CCUAUC--GAAGG Bound - Mimic GUAGUA--GAAAC Bound - Mimic UGUAUU--GAAGG Bound - Mimic AGGAUA--UAAUU Bound - Mimic UGGAUA--GACGG Bound - Mimic CUGAAC--GACGG Bound - Mimic AGUAUA--UAACA Bound - Mimic CGUUAC--GGAGG Aptamer secondary structure - Shape 2 Aptamer secondary structure - Shape 5 Aptamer secondary structure - Shape 6 Aptamer secondary structure - Shape 7 Aptamer secondary structure - Shape 8 Reproducibility Lab 2 - Shape 0 Reproducibility Lab 2 - Shape 1 Reproducibility Lab 2 - Shape 2 Reproducibility Lab 2 - Shape 3 Reproducibility Lab 2 - Shape 4 Reproducibility Lab 2 - Shape 5 Reproducibility Lab 2 - Shape 6 Reproducibility Lab 2 - Shape 7 Reproducibility Lab 2 - Shape 8 Reproducibility Lab 2 - Shape 9 Reproducibility Lab 2 - Shape 10 Reproducibility Lab 2 - Shape 11 Reproducibility Lab 2 - Shape 12 Reproducibility Lab 2 - Shape 13 Reproducibility Lab 2 - Shape 14 Reproducibility Lab 2 - Shape 15 Reproducibility Lab 2 - Shape 16 Reproducibility Lab 2 - Shape 17 Reproducibility Lab 2 - Shape 18 Reproducibility Lab 2 - Shape 19 Reproducibility Lab 2 - Shape 20 Stanford Switch Puzzle	2.295
R86 6/9/2014	R86.xlsx R86.googlesheet	20% Non Watson-Crick Base Pairs - Effortless 40% Non Watson-Crick Base Pairs - Medium 60% Non Watson-Crick Base Pairs - Heating Up 70% Non Watson-Crick Base Pairs - Hard Mode 80% Non Watson-Crick Base Pairs - Insanity Hand and Finger Remade - OFF State Hand and Finger Remade - Mimic Simple RNA Switch Remade - OFF State Simple RNA Switch Remade - Mimic Hair Trigger - Sub 2 (Stable) by Brourd: -2.51 Kcal/mol Mimic Bonus Hair Trigger - Sub 2 (Stable) by Brourd: -4.86 Kcal/mol Mimic Bonus Bistable 3 - Mod of Eli by mat747: -2.51 Kcal/mol Mimic Bonus Bistable 3 - Mod of Eli by mat747: -4.86 Kcal/mol Mimic Bonus Identify tRNA Mutants Subject to Alternative RNA Processing - Shape 0 Investigation of Alternative Human tRNA Structures - Shape 4 Investigation of Alternative Human tRNA Structures - Shape 5 Investigation of Alternative Human tRNA Structures - Shape 14 Investigation of Alternative Human tRNA Structures - Shape 15 Investigation of Alternative Human tRNA Structures - Shape 16 Investigation of Alternative Human tRNA Structures - Shape 17 Investigation of Alternative Human tRNA Structures - Shape 18 Investigation of Alternative Human tRNA Structures - Shape 19 Investigation of Alternative Human tRNA Structures - Shape 23 Investigation of Alternative Human tRNA Structures - Shape 25 Investigation of Alternative Human tRNA Structures - Shape 28 Investigation of Alternative Human tRNA Structures - Shape 36 Alternative structure space for human tRNAs - Shape 4 Alternative structure space for human tRNAs - Shape 5 Alternative structure space for human tRNAs - Shape 14 Alternative structure space for human tRNAs - Shape 15 Alternative structure space for human tRNAs - Shape 16 Alternative structure space for human tRNAs - Shape 17 Alternative structure space for human tRNAs - Shape 18 Alternative structure space for human tRNAs - Shape 19 Alternative structure space for human tRNAs - Shape 23 Alternative structure space for human tRNAs - Shape 25 Alternative structure space for human tRNAs - Shape 28 Alternative structure space for human tRNAs - Shape 36	3.217
R87 8/18/2014	R87.xlsx R87.googlesheet	Lab Entry Level 0 - The Finger lab revisited - Frozen shape with gap size 0 Lab Entry Level 0 - The Finger lab revisited - Frozen shape with gap size 4 Lab Entry Level 1 - The Finger lab revisited - Gap size 2 Lab Entry Level 2 - The Finger lab modified - Gap size 2 Poly (A) Structure Analysis 2 Multistate RNA Sequence - 2 Residues Multistate RNA Sequence - 3 Residues Multistate RNA Sequence - 4 Residues Hairpin Loop Comparison Pilot - Shape 0 Hairpin Loop Comparison Pilot - Shape 1 Hairpin Loop Comparison Pilot - Shape 2 Hairpin Loop Comparison Pilot - Shape 3 Hairpin Loop Comparison Pilot - Shape 4 Hairpin Loop Comparison Pilot - Shape 5 Hairpin Loop Comparison Pilot - Shape 6 Hairpin Loop Comparison Pilot - Stem Comparison Tests SHAPE Profile - G/A Hairpin Terminal Mismatch and Neighboring Base Pairs GNCgaaaaGNC - Shape 0 SHAPE Profile - G/A Hairpin Terminal Mismatch and Neighboring Base Pairs GNCgaaaaGNC - Shape 1 SHAPE Profile - G/A Hairpin Terminal Mismatch and Neighboring Base Pairs CNGgaaaaCNG - Shape 0 SHAPE Profile - G/A Hairpin Terminal Mismatch and Neighboring Base Pairs CNGgaaaaCNG - Shape 1 Multistate RNA - CC/G bulge - Shape 0 Cyanocobalamin (vitamin B12) RNA aptamer SHAPE profile - Shape 0 Sarcin-ricin vs boosted internal loops - Shape 0 Sarcin-ricin vs boosted internal loops - Shape 1 Sarcin-ricin vs boosted internal loops - Shape 2 Sarcin-ricin vs boosted internal loops - Shape 3 Sarcin-ricin vs boosted internal loops - Shape 4 Sarcin-ricin vs boosted internal loops - Shape 5 Sarcin-ricin vs boosted internal loops - Shape 6 2-2 Superboost Apical Loop Comparison - Dissimilar Stem Sequences - Shape 0 Apical Loop Comparison - Dissimilar Stem Sequences - Shape 1 Apical Loop Comparison - Dissimilar Stem Sequences - Shape 2 Apical Loop Comparison - Dissimilar Stem Sequences - Shape 3 Apical Loop Comparison - Dissimilar Stem Sequences - Shape 4 Apical Loop Comparison - Dissimilar Stem Sequences - Shape 5 Apical Loop Comparison - Dissimilar Stem Sequences - Shape 6 Apical Loop Comparison - Dissimilar Stem Sequences - Shape 7 Effects of Base Pair Mutations on the RNA Ensemble and Reverse Transcription - Shape 0 Effects of Base Pair Mutations on the RNA Ensemble and Reverse Transcription - Shape 1 Effects of Base Pair Mutations on the RNA Ensemble and Reverse Transcription - Shape 2 Identify tRNA Mutants Subject to Alternative RNA Processing - Shape 0 Alternative structure space for human tRNAs - Shape 4 Alternative structure space for human tRNAs - Shape 5 Alternative structure space for human tRNAs - Shape 14 Alternative structure space for human tRNAs - Shape 15 Alternative structure space for human tRNAs - Shape 16 Alternative structure space for human tRNAs - Shape 17 Alternative structure space for human tRNAs - Shape 18 Alternative structure space for human tRNAs - Shape 19 Alternative structure space for human tRNAs - Shape 23 Alternative structure space for human tRNAs - Shape 25 Alternative structure space for human tRNAs - Shape 28 Alternative structure space for human tRNAs - Shape 36	1.004
R87.0001 8/21/2014	R87.xlsx R87.googlesheet		1.731
R87.0002 8/21/2014	R87.xlsx R87.googlesheet		1.109
R88 8/27/2014	R88.xlsx R88.googlesheet	Lab Entry Level 0 - The Cross lab revisited - Frozen shape with gap size 0 Lab Entry Level 0 - The Cross lab revisited - Frozen shape with gap size 4 Lab Entry Level 1 - The Cross lab revisited - Gap size 2 Lab Entry Level 2 - The Cross lab modified - Gap size 2	0.918
R88.0002			5.627
R89	R89.xlsx R89.googlesheet	Switch Cloud Lab: The Next Generation 4 - OFF Switch Cloud Lab: The Next Generation 4 - MIMIC Hair Trigger - Sub 2 (Stable) by Brourd: -2.51 Kcal/mol Mimic Bonus R2 Bistable 3 - Mod of Eli by mat747: -2.51 Kcal/mol Mimic Bonus R2 Bistable 3 - Double Trouble by Darkfire47: -2.51 Kcal/mol Mimic Bonus Hair Trigger - Reresub 3 (Unstable) by Brourd: -2.51 Kcal/mol Mimic Bonus Pseudo-Titration Experiment: Lines - Errazaarge by ViennaUCT Lab Entry Level 0 - Bulge Cross revisited - Frozen shape with gap size 0 Lab Entry Level 0 - Bulge Cross revisited - Frozen shape with gap size 4 Lab Entry Level 1 - Bulge Cross lab revisited - Gap size 2 Lab Entry Level 2 - Bulge Cross lab modified - Gap size 2	3.149
R90	R90.xlsx R90.googlesheet	Lab Entry Level 0 - Bend and Ends Sampler revisited - Frozen shape with gap size 0 Lab Entry Level 0 - Bend and Ends Sampler revisited - Frozen shape with gap size 4 Lab Entry Level 1 - Bend and Ends Sampler revisited - Frozen shape with gap size 2 Lab Entry Level 2 - Bends and Ends Sampler modified - Gap size 2	1.037
R91	R91.xlsx R90.googlesheet	Lab Entry Level 0 - The Asymmetry lab revisited - Frozen shape with gap size 0 Lab Entry Level 0 - The Asymmetry lab revisited - Frozen shape with gap size 4 Lab Entry Level 1 - The Asymmetry lab revisited - Gap size 2 Lab Entry Level 2 - The Asymmetry lab modified - Gap size 2 S1-KL1 S1-KL1-noGU S1-KL-negative S1-KL-1S72_423 S1-KL-new_A S1-KL-new_B S2-KL1 S2-KL1-noGU S2-KL-negative S2-KL-1S72_423 S2-KL-new_A S2-KL-new_B 4/4 Base Pairs 5 5/5 Base Pairs 5 6/6 Base Pairs 5 7/7 Base Pairs 5 4/4 Base Pairs 3 5/5 Base Pairs 3 6/6 Base Pairs 3 7/7 Base Pairs 3 Shift 4/4 Base Pairs 5 Shift 5/4 Base Pairs 5 Shift 6/4 Base Pairs 5 Shift 5/5 Base Pairs 3 Shift 6/5 Base Pairs 3 Shift 7/5 Base Pairs 3	2.364
R92	R92.xlsx R92.googlesheet	Lab Entry Level 0 - The Backwards C lab revisited - Frozen shape with gap size 0 Lab Entry Level 0 - The Backwards C lab revisited - Frozen shape with gap size 4 Lab Entry Level 1 - The Backwards C lab revisited - Gap size 2 Lab Entry Level 2 - The Backwards C lab modified - Gap size 2 4 x 4 TEP Riboswitch 5 5 x 5 TEP Riboswitch 5 6 x 6 TEP Riboswitch 5 4 x 4 TEP Riboswitch 3 5 x 5 TEP Riboswitch 3 6 x 6 TEP Riboswitch 3 Shift 5 x 5 TEP Riboswitch 5 Shift 6 x 5 TEP Riboswitch 5 Shift 7 x 5 TEP Riboswitch 5 Shift 5 x 5 TEP Riboswitch 3 Shift 6 x 5 TEP Riboswitch 3 Shift 7 x 5 TEP Riboswitch 3 Structure Competition 3x3 v1 Structure Competition 3x3 v2 Structure Competition 2x2 v1 Structure Competition 2x2 v2 Structure Competition 1x1 v1 Structure Competition 1x1 v2 Structure Competition 0x0 v1 Structure Competition 0x0 v2 TEP Aptamer Chemical Mapping Footprint TEP Aptamer Chemical Mapping Footprint 2 TEP Aptamer Chemical Mapping Footprint 3	6.407
R93	R93.googlesheet	binary capture Control II - Intermolecular KL	27.251
R94 [1]	R94.googlesheet [2]	Three Branch Junction - AAAUAAA Three Branch Junction - Sequence Mutation 1 Three Branch Junction - Sequence Mutation 2 Three Branch Junction - Sequence Mutation 3 Three Branch Junction - Structure Mutation 1 Three Branch Junction - Structure Mutation 2 External Loop Test Hairpin Loop Test Multibranch Loop Test 88-nt 72-nt Lab Entry Level 0 - Chalk Outline lab revisited - Frozen shape with gap size 0 Lab Entry Level 0 - Chalk Outline lab revisited - Frozen shape with gap size 4 Lab Entry Level 1 - Chalk Outline lab revisited - Gap size 2 Lab Entry Level 2 - Chalk Outline lab modified - Gap size 2 Design your own Kissing-Loop Control I - Parallel Crossover KL Control II - Intermolecular KL Six of One Mod Solutions Aplenty by Mayanne Pentaloop by Hyphema Rational Design by ElNando888 Mod of Jandersonlee s Flip Turn 6-4 - Mark IV (split further) by Jieux Collage by Hyphema Slip Loop 5-4 by Jandersonlee Straighten It 3 by Starryjess Branch Zipper by codygeary Can t Score This 6x6 by Jnicol Mod of Barely Score This 6x5 by Jnicol Mod of Cross Section by Starryjess Mod of 1x1 Loop Experiment by Jieux Lab Entry Level 0 - Tilted picture of running man revisited - Frozen shape with gap size 0 Lab Entry Level 0 - Tilted picture of running man revisited - Frozen shape with gap size 4 Lab Entry Level 1 - Tilted picture of running man revisited - Gap size 2 Lab Entry Level 2 - Tilted picture of running man modified - Gap size 2 GgaC/GgaC vs GagC/GagC 1 GgaC/GgaC vs GagC/GagC 2 GgaC/GgaC vs GagC/GagC 3 GgaC/GgaC vs GagC/GagC 4 GgaC/GgaC vs GagC/GagC 5 GgaC/GgaC vs GagC/GagC 6 GgaC/GgaC vs GagC/GagC 7 GgaC/GgaC vs GagC/GagC 8 GgaC/GgaC vs GagC/GagC 9 GgaC/GgaC vs GagC/GagC 10 GgaC/GgaC vs GagC/GagC 11 GgaC/GgaC vs GagC/GagC 12 GgaC/GgaC vs GagC/GagC 13 GagC/GagC vs GgaC/GgaC 1 GagC/GagC vs GgaC/GgaC 2 GagC/GagC vs GgaC/GgaC 3 GagG/CagC vs GgaG/CgaC GgaG/CgaC vs GagG/CagC GgaC/GgaC vs GagC/GagC 1B GagC/GagC vs GgaC/GgaC 1B	3.347
R95	R95.googlesheet	Lab Entry Level 0 - Water Strider revisited - Frozen shape with gap size 0 Lab Entry Level 0 - Water Strider revisited - Frozen shape with gap size 4 Lab Entry Level 1 - Water Strider revisited - Gap size 2 Lab Entry Level 2 - Water Strider modified - Gap size 2	5.067
R96	R96.googlesheet R96.fusion table	Same State 1 Same State 2 Same State NG 1 Same State NG 2 Same State NG 3 Exclusion 1 Exclusion 2 Exclusion 3 Exclusion 4 Brourd's Mod of Exclusion 4 Exclusion 5 Exclusion 6 Sensor for hsa-mir-208a Sensor v2, turn-off variant Sensor v2, turn-off variant 2 Sensor v3, turn-off variant 1 Sensor v3, turn-off variant 2
R97	R97.googlesheet R97.xlsx R97.fusion table R97ExclusionsWithDesignerAndLink.googlesheet R97.Meechl's Exclusion Plus - Fusion Table Most Recent Fusion Table for R97 (hopefully)	Brourd's Mod of Exclusion 4 Exclusion 1 Exclusion 2 Exclusion 3 Exclusion 4 Exclusion 5 Exclusion 6 Sensor, turn-off variant 1
	R98 NG Fusion Table

R100	R100 google spreadsheet
R101	R101 FMN MS2 Riboswitch Structure, with Switch Graphs
R102	[3]
R103	R103 Google spreadsheet