Proof-of-concept uASPIre 17-nt randomized RBS library
Large-scale DNA-based phenotypic recording and deep learning enable highly accurate sequence-function mappingA fully randomized 17-nt 5′-UTR RBS library controlling Bxb1-sfGFP translation in Escherichia coli TOP10 ΔrhaA was sampled at 18 time points after rhamnose induction. The packaged table contains 10,427 high-coverage profiles from the two public 10k uASPIre source runs, with fraction-flipped kinetics and trapezoidal 0–480-min summaries.
Processed tables are specific to each experiment. Column names, units, measurements, and table structure are not standardized across the database. Check this experiment’s column definitions and quality-control notes before comparing or combining data.
Perturbation & assay details
2 g/L L-rhamnose induction at OD600 approximately 0.5
Escherichia coli TOP10 ΔrhaA; 18 sampling time points (0, 10, 30, 40, 50, 60, 75, 90, 105, 120, 150, 180, 241, 360, 481, 720, 1124, and 1440 min); sample-specific indexed adapter ligation; Illumina NextSeq 500 paired-end sequencing. The 17-nt RBS is retrieved immediately upstream of the bxb1 start codon. The public 10k_r1 and 10k_r2 tables are treated as source runs; the table uses 10k_r2 as the canonical 10,427-profile run and joins 10k_r1 when available. The package-derived IFP summary uses trapezoidal integration of fraction-flipped values, linearly interpolating the 481-min observation to 480 min.
Plasmid-based uASPIre DNA phenotypic recording: each synthetic 17-nt RBS controls translation of a Bxb1-sfGFP modifier on the same pASPIre3 plasmid as an attP/attB discriminator. Rhamnose-induced recombination converts the discriminator to an attR state; paired-end sequencing of plasmid fragments reports the fraction flipped for each RBS, rather than an RNA/DNA barcode ratio.
Processed data
50 rows per page. Click a cell to inspect its full value.
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Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 45 definitions
- element_id
- Stable package identifier for the retained RBS row.
- rbs_sequence
- The tested 17-nucleotide RBS sequence immediately upstream of the bxb1 start codon.
- r2_fraction_flipped_0min
- Fraction of discriminator molecules in the flipped state at 0 minutes in public 10k_r2.
- r2_fraction_flipped_10min
- Fraction of discriminator molecules in the flipped state at 10 minutes in public 10k_r2.
- r2_fraction_flipped_30min
- Fraction of discriminator molecules in the flipped state at 30 minutes in public 10k_r2.
- r2_fraction_flipped_40min
- Fraction of discriminator molecules in the flipped state at 40 minutes in public 10k_r2.
- r2_fraction_flipped_50min
- Fraction of discriminator molecules in the flipped state at 50 minutes in public 10k_r2.
- r2_fraction_flipped_60min
- Fraction of discriminator molecules in the flipped state at 60 minutes in public 10k_r2.
- r2_fraction_flipped_75min
- Fraction of discriminator molecules in the flipped state at 75 minutes in public 10k_r2.
- r2_fraction_flipped_90min
- Fraction of discriminator molecules in the flipped state at 90 minutes in public 10k_r2.
- r2_fraction_flipped_105min
- Fraction of discriminator molecules in the flipped state at 105 minutes in public 10k_r2.
- r2_fraction_flipped_120min
- Fraction of discriminator molecules in the flipped state at 120 minutes in public 10k_r2.
- r2_fraction_flipped_150min
- Fraction of discriminator molecules in the flipped state at 150 minutes in public 10k_r2.
- r2_fraction_flipped_180min
- Fraction of discriminator molecules in the flipped state at 180 minutes in public 10k_r2.
- r2_fraction_flipped_241min
- Fraction of discriminator molecules in the flipped state at 241 minutes in public 10k_r2.
- r2_fraction_flipped_360min
- Fraction of discriminator molecules in the flipped state at 360 minutes in public 10k_r2.
- r2_fraction_flipped_481min
- Fraction of discriminator molecules in the flipped state at 481 minutes in public 10k_r2.
- r2_fraction_flipped_720min
- Fraction of discriminator molecules in the flipped state at 720 minutes in public 10k_r2.
- r2_fraction_flipped_1124min
- Fraction of discriminator molecules in the flipped state at 1124 minutes in public 10k_r2.
- r2_fraction_flipped_1440min
- Fraction of discriminator molecules in the flipped state at 1440 minutes in public 10k_r2.
- r2_ifp_0_480_min_trapezoid
- Package-derived mean fraction flipped from 0 to 480 minutes, computed by trapezoidal integration after linear interpolation of the 481-minute value to 480 minutes in 10k_r2.
- r2_total_reads
- Aggregate flipped plus non-flipped read count across the public 10k_r2 sampling points.
- r1_fraction_flipped_0min
- Fraction of discriminator molecules in the flipped state at 0 minutes in public 10k_r1; blank when the sequence did not pass the secondary-run filter.
- r1_fraction_flipped_10min
- Fraction of discriminator molecules in the flipped state at 10 minutes in public 10k_r1; blank when unavailable.
- r1_fraction_flipped_30min
- Fraction of discriminator molecules in the flipped state at 30 minutes in public 10k_r1; blank when unavailable.
- r1_fraction_flipped_40min
- Fraction of discriminator molecules in the flipped state at 40 minutes in public 10k_r1; blank when unavailable.
- r1_fraction_flipped_50min
- Fraction of discriminator molecules in the flipped state at 50 minutes in public 10k_r1; blank when unavailable.
- r1_fraction_flipped_60min
- Fraction of discriminator molecules in the flipped state at 60 minutes in public 10k_r1; blank when unavailable.
- r1_fraction_flipped_75min
- Fraction of discriminator molecules in the flipped state at 75 minutes in public 10k_r1; blank when unavailable.
- r1_fraction_flipped_90min
- Fraction of discriminator molecules in the flipped state at 90 minutes in public 10k_r1; blank when unavailable.
- r1_fraction_flipped_105min
- Fraction of discriminator molecules in the flipped state at 105 minutes in public 10k_r1; blank when unavailable.
- r1_fraction_flipped_120min
- Fraction of discriminator molecules in the flipped state at 120 minutes in public 10k_r1; blank when unavailable.
- r1_fraction_flipped_150min
- Fraction of discriminator molecules in the flipped state at 150 minutes in public 10k_r1; blank when unavailable.
- r1_fraction_flipped_180min
- Fraction of discriminator molecules in the flipped state at 180 minutes in public 10k_r1; blank when unavailable.
- r1_fraction_flipped_241min
- Fraction of discriminator molecules in the flipped state at 241 minutes in public 10k_r1; blank when unavailable.
- r1_fraction_flipped_360min
- Fraction of discriminator molecules in the flipped state at 360 minutes in public 10k_r1; blank when unavailable.
- r1_fraction_flipped_481min
- Fraction of discriminator molecules in the flipped state at 481 minutes in public 10k_r1; blank when unavailable.
- r1_fraction_flipped_720min
- Fraction of discriminator molecules in the flipped state at 720 minutes in public 10k_r1; blank when unavailable.
- r1_fraction_flipped_1124min
- Fraction of discriminator molecules in the flipped state at 1124 minutes in public 10k_r1; blank when unavailable.
- r1_fraction_flipped_1440min
- Fraction of discriminator molecules in the flipped state at 1440 minutes in public 10k_r1; blank when unavailable.
- r1_ifp_0_480_min_trapezoid
- Package-derived trapezoidal 0–480-minute mean fraction flipped for 10k_r1; blank when unavailable.
- r1_total_reads
- Aggregate flipped plus non-flipped read count across the public 10k_r1 sampling points; blank when unavailable.
- ifp_0_480_min_mean
- Arithmetic mean of the available package-derived 0–480-minute IFP estimates across the two public 10k runs.
- ifp_0_480_min_sd
- Sample standard deviation of the available package-derived 0–480-minute IFP estimates; blank when only one run is available.
- replicates_available
- Number of public 10k source runs contributing a QC-passing profile for the row.
Quality control
The published pipeline removed reads with more than six consecutive unidentified bases, selected target fragments by the 10-bp constant region with at most three mismatches, demultiplexed by unique paired 6-bp indices, classified attP/attR discriminator states with at most three mismatches, retrieved the 17-nt RBS sequence upstream of bxb1, and removed variants with more than 8% mismatches in the bxb1 CDS. For this package, retained canonical 10k_r2 rows also require a valid 17-nt A/C/G/T sequence, finite fraction-flipped values in [0,1], and total_reads ≥ 1,000, yielding exactly 10,427 rows, matching the paper's reported proof-of-concept profile count. The aggregate source total_reads field does not expose per-timepoint counts, so the published high-coverage profile cutoff is applied as this reproducible aggregate filter. Secondary 10k_r1 values are joined only when they pass the same checks; missing secondary observations are left missing.
Curation notes
The article describes the proof-of-concept plot as 10,427 RBS profiles from a single NextSeq run, while the public repository supplies 10k_r1 and 10k_r2 processed tables. The 10k_r2 table has exactly 10,427 rows after total_reads ≥ 1,000 and is therefore used as the canonical profile set; 10k_r1 contributes a secondary profile where the sequence also passes the same filter. The public aggregate counts do not permit direct verification of a per-timepoint read minimum. The IFP field in this child table is intentionally labelled as a package-derived trapezoidal estimate rather than an author-supplied logistic-fit IFP480.