Experiment / E278QCM1POther

Composite 300k uASPIre RBS library, three biological replicates

Large-scale DNA-based phenotypic recording and deep learning enable highly accurate sequence-function mapping

A pooled plasmid library of 303,503 17-nt RBS variants, comprising the fully randomized N17 library and High1–High3 sublibraries enriched for stronger predicted RBSs, controlled Bxb1-sfGFP translation in Escherichia coli TOP10 ΔrhaA. Nine time points after rhamnose induction were sequenced in three independent biological replicates; the packaged table retains the canonical R1 variant set and joins R2/R3 data where the same sequence was observed.

Download processed table (CSV)Raw source data API documentation

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.

Organism: NCBITaxon:562
Taxonomy ID: NCBITaxon:562
Biosample: UNMAPPED:Escherichia_coli_TOP10_delta_rhaA
Reference genome: Not reported / not applicable
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

2 g/L L-rhamnose induction at OD600 approximately 0.5

Escherichia coli TOP10 ΔrhaA carrying pASPIre3; pooled N17, High1, High2, and High3 synthetic RBS sublibraries plus 31 internal-standard RBSs; nine sampling times (0, 50, 95, 155, 225, 290, 360, 480, and 720 min); target fragments were 308 bp and were read by Illumina NextSeq 500 paired-end sequencing. The R2 and R3 public source tables include IFP480_fittor1, the authors' nonlinear normalization to R1; those normalized values are used for the cross-replicate mean and standard deviation in the packaged table.

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.

Search table valuesFilter columnOperatorValue

Visible columns (40 of 40)

Row
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50

Page 1 · 50 rows · More results available

Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.

Column dictionary · 40 definitions

element_id: Stable package identifier for the retained RBS row in the canonical 300k_r1 library set.
rbs_sequence: The tested 17-nucleotide RBS sequence immediately upstream of the bxb1 start codon.
replicate_r1_fraction_flipped_0min: Fraction of discriminator molecules in the flipped state at 0 minutes in public 300k_r1.
replicate_r1_fraction_flipped_50min: Fraction of discriminator molecules in the flipped state at 50 minutes in public 300k_r1.
replicate_r1_fraction_flipped_95min: Fraction of discriminator molecules in the flipped state at 95 minutes in public 300k_r1.
replicate_r1_fraction_flipped_155min: Fraction of discriminator molecules in the flipped state at 155 minutes in public 300k_r1.
replicate_r1_fraction_flipped_225min: Fraction of discriminator molecules in the flipped state at 225 minutes in public 300k_r1.
replicate_r1_fraction_flipped_290min: Fraction of discriminator molecules in the flipped state at 290 minutes in public 300k_r1.
replicate_r1_fraction_flipped_360min: Fraction of discriminator molecules in the flipped state at 360 minutes in public 300k_r1.
replicate_r1_fraction_flipped_480min: Fraction of discriminator molecules in the flipped state at 480 minutes in public 300k_r1.
replicate_r1_fraction_flipped_720min: Fraction of discriminator molecules in the flipped state at 720 minutes in public 300k_r1.
replicate_r1_ifp_0_480_min: Author-supplied IFP480 summary for public 300k_r1, the normalized integral of the flipping profile from 0 to 480 minutes.
replicate_r1_total_reads: Aggregate flipped plus non-flipped read count across the nine 300k_r1 sampling points.
replicate_r2_fraction_flipped_0min: Fraction of discriminator molecules in the flipped state at 0 minutes in public 300k_r2; blank when unavailable.
replicate_r2_fraction_flipped_50min: Fraction of discriminator molecules in the flipped state at 50 minutes in public 300k_r2; blank when unavailable.
replicate_r2_fraction_flipped_95min: Fraction of discriminator molecules in the flipped state at 95 minutes in public 300k_r2; blank when unavailable.
replicate_r2_fraction_flipped_155min: Fraction of discriminator molecules in the flipped state at 155 minutes in public 300k_r2; blank when unavailable.
replicate_r2_fraction_flipped_225min: Fraction of discriminator molecules in the flipped state at 225 minutes in public 300k_r2; blank when unavailable.
replicate_r2_fraction_flipped_290min: Fraction of discriminator molecules in the flipped state at 290 minutes in public 300k_r2; blank when unavailable.
replicate_r2_fraction_flipped_360min: Fraction of discriminator molecules in the flipped state at 360 minutes in public 300k_r2; blank when unavailable.
replicate_r2_fraction_flipped_480min: Fraction of discriminator molecules in the flipped state at 480 minutes in public 300k_r2; blank when unavailable.
replicate_r2_fraction_flipped_720min: Fraction of discriminator molecules in the flipped state at 720 minutes in public 300k_r2; blank when unavailable.
replicate_r2_ifp_0_480_min: Author-supplied IFP480 summary for public 300k_r2; blank when unavailable.
replicate_r2_ifp_0_480_min_fitted_to_r1: Author-supplied 300k_r2 IFP480 normalized/fitted to the 300k_r1 reference replicate; blank when unavailable.
replicate_r2_total_reads: Aggregate flipped plus non-flipped read count across the nine 300k_r2 sampling points; blank when unavailable.
replicate_r3_fraction_flipped_0min: Fraction of discriminator molecules in the flipped state at 0 minutes in public 300k_r3; blank when unavailable.
replicate_r3_fraction_flipped_50min: Fraction of discriminator molecules in the flipped state at 50 minutes in public 300k_r3; blank when unavailable.
replicate_r3_fraction_flipped_95min: Fraction of discriminator molecules in the flipped state at 95 minutes in public 300k_r3; blank when unavailable.
replicate_r3_fraction_flipped_155min: Fraction of discriminator molecules in the flipped state at 155 minutes in public 300k_r3; blank when unavailable.
replicate_r3_fraction_flipped_225min: Fraction of discriminator molecules in the flipped state at 225 minutes in public 300k_r3; blank when unavailable.
replicate_r3_fraction_flipped_290min: Fraction of discriminator molecules in the flipped state at 290 minutes in public 300k_r3; blank when unavailable.
replicate_r3_fraction_flipped_360min: Fraction of discriminator molecules in the flipped state at 360 minutes in public 300k_r3; blank when unavailable.
replicate_r3_fraction_flipped_480min: Fraction of discriminator molecules in the flipped state at 480 minutes in public 300k_r3; blank when unavailable.
replicate_r3_fraction_flipped_720min: Fraction of discriminator molecules in the flipped state at 720 minutes in public 300k_r3; blank when unavailable.
replicate_r3_ifp_0_480_min: Author-supplied IFP480 summary for public 300k_r3; blank when unavailable.
replicate_r3_ifp_0_480_min_fitted_to_r1: Author-supplied 300k_r3 IFP480 normalized/fitted to the 300k_r1 reference replicate; blank when unavailable.
replicate_r3_total_reads: Aggregate flipped plus non-flipped read count across the nine 300k_r3 sampling points; blank when unavailable.
ifp_0_480_min_mean_fitted_to_r1: Arithmetic mean of the available R1 IFP480 and R2/R3 IFP480_fittor1 values on the R1-normalized scale.
ifp_0_480_min_sd_fitted_to_r1: Sample standard deviation of the available R1-normalized IFP480 values; blank when fewer than two replicates are available.
replicates_available: Number of source replicates 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. The paper selected at least 20 reads per RBS per time point; for nine time points this corresponds to a robust aggregate minimum of 180 reads. For this package, retained rows additionally require a unique valid 17-nt A/C/G/T sequence and finite fraction-flipped and IFP values in [0,1]. The canonical 300k_r1 source retains all 303,503 profiles passing these checks. R2/R3 rows are joined only when their source row passes the same checks; missing observations are left missing rather than imputed.

Curation notes

The canonical table follows the public 300k_r1 row set and therefore contains the paper's reported 303,503 RBS variants. The public r2 and r3 tables contain different observed sequence sets; 298,601 r1 sequences have r2 observations and 153,436 have r3 observations. R2/R3 are not imputed, and the replicate summary uses the supplied IFP480_fittor1 values where available. The paper's source description reports the three large-library biological replicates under SRA BioSamples SAMN15215026, SAMN15215027, and SAMN15215028; raw reads are not included.

Row
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50

Row
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50

Row
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50