A two-replicate polysome-library sequencing assay measured relative ribosome loading of reporter transcripts carrying natural 5′ transcript leaders from S. cerevisiae and S. paradoxus. Polysome-gradient reads were pooled into translating and nontranslating classes and reported as the percentage of translated reads for each construct.
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
Budding yeast
Taxonomy ID
NCBITaxon:4932
Biosample
UNMAPPED:Saccharomyces_cerevisiae_BY4741
Reference genome
Not reported / not applicable
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated; unstressed log-phase growth at 30°C
Reporter-bearing yeast polysome extracts were fractionated on a 7–47% sucrose gradient. The paper groups 40S, 60S, and monosome fractions as nontranslating and disome-and-larger fractions as translating; replicate 1 was downsampled by 0.826 to balance translating and nontranslating proportions. The source PoLib table contains 15,152 wild-type constructs, including constructs not present in the final FACS/RNA companion table.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (49 of 49)
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 · 49 definitions
element_id
Original Construct identifier formatted as gene|source context;start;end|construct state.
gene_or_locus
Gene or locus label from the original element identifier.
source_context
Chromosome label for S. cerevisiae (chr...) or source-genome label for S. paradoxus (Spar_...).
source_species
Species from which the tested transcript-leader sequence was derived, inferred from source_context.
coordinate_start
Start coordinate encoded in the source element identifier; strand-specific order is preserved.
coordinate_end
End coordinate encoded in the source element identifier; strand-specific order is preserved.
construct_state
Construct state reported by the source; all retained rows are WT.
length_nt
Designed transcript-leader length in nucleotides when the element is also present in a sequence table.
uaug_count
Number of upstream AUGs in the transcript leader when reported in a companion sequence/feature table.
utr_sequence
Designed natural 5′ transcript-leader sequence when available, written 5′ to 3′.
kozak_context
Reporter start-codon Kozak context when available from a companion sequence/feature table.
feature_data_available
Whether the element occurs in the source workbook Feature Data table.
freq_a
Fraction of transcript-leader nucleotides that are A when feature data are available.
freq_t
Fraction of transcript-leader nucleotides that are T when feature data are available.
freq_g
Fraction of transcript-leader nucleotides that are G when feature data are available.
freq_c
Fraction of transcript-leader nucleotides that are C when feature data are available.
max_a_stretch
Longest consecutive A run in the transcript leader.
num_gggg_quartets
Number of GGGG quartets using the source definition.
kozak_strength
Source Kozak-strength score for the reporter start context.
ddg_median
Median predicted ΔΔG for unfolding the structure around the main start codon.
ddg_avg
Mean predicted ΔΔG for unfolding the structure around the main start codon.
g_quadruplex_count
Predicted G-quadruplex count reported by the source feature table.
cap40nt_folding_dg
Predicted folding free energy for the first 40 nt near the 5′ cap; source field Cap40ntFodling.
cap40nt_folding_abs
Absolute value of the first-40-nt cap folding energy used for modeling.
lsm_kozak_start
Adjusted Kozak score from the leaky-scanning model.
u_max
Longest homopolymeric U/T run in the transcript leader; T is used because the source sequence is DNA-encoded.
cap_proximal_a
A fraction among the first ≤20 nt near the 5′ cap.
cap_proximal_c
C fraction among the first ≤20 nt near the 5′ cap.
cap_proximal_g
G fraction among the first ≤20 nt near the 5′ cap.
cap_proximal_t
T fraction among the first ≤20 nt near the 5′ cap.
distal_a
A fraction among the last ≤30 nt near the main start codon.
distal_c
C fraction among the last ≤30 nt near the main start codon.
distal_g
G fraction among the last ≤30 nt near the main start codon.
distal_t
T fraction among the last ≤30 nt near the main start codon.
replicate_1_ncp_fraction_counts
Comma-separated counts from source R1-ncp across seven fraction positions.
replicate_1_cap_fraction_counts
Comma-separated counts from source R1-cap across seven fraction positions.
replicate_1_translated_reads
Reads pooled into the translating class for replicate 1, as supplied by the source.
replicate_1_nontranslating_reads
Reads pooled into the nontranslating class for replicate 1, as supplied by the source.
replicate_1_rrl_percent
Source R1-TEff value: relative ribosome load, reported as percent translated/total.
replicate_1_total_fraction_reads
Sum of numeric R1-ncp and R1-cap fraction counts; used in read-depth QC.
replicate_2_ncp_fraction_counts
Comma-separated counts from source R2-ncp across seven fraction positions.
replicate_2_cap_fraction_counts
Comma-separated counts from source R2-cap across seven fraction positions.
replicate_2_translated_reads
Reads pooled into the translating class for replicate 2, as supplied by the source.
replicate_2_nontranslating_reads
Reads pooled into the nontranslating class for replicate 2, as supplied by the source.
replicate_2_rrl_percent
Source R2-TEff value: relative ribosome load, reported as percent translated/total.
replicate_2_total_fraction_reads
Sum of numeric R2-ncp and R2-cap fraction counts; used in read-depth QC.
combined_fraction_reads
Total numeric fraction counts across both replicates; rows below 5,000 were excluded.
mean_rrl_percent
Arithmetic mean of the two source TEff replicate values, generated for this package.
rrl_replicate_sd_percent
Sample standard deviation of the two source TEff replicate values.
Quality control
The paper applied a 5,000-total-read cutoff across the fraction counts from replicates 1 and 2 after pooling the fraction classes described in the methods. This package sums the numeric counts in both source ncp/cap fields for both replicates, excludes LowReads/non-numeric TEff entries, and retains 10,758 of 15,152 rows with combined fraction reads ≥5,000 and numeric TEff values in both replicates. 4,394 source rows were excluded; 997 carried at least one LowReads label.
Curation notes
The assay host is S. cerevisiae BY4741 (NCBI BioSample SAMN18740588; SRA project PRJNA721222), while the tested library includes S. cerevisiae and S. paradoxus transcript-leader sequences. The source element IDs preserve strand-specific coordinate order and the paper does not state a reference assembly, so reference_genome is null. The PoLib source table has 15,152 constructs; after QC, 9,378 retained rows could be joined to the Table_1 sequence table and 9,304 to the Table_3 feature table. Blank sequence/feature fields indicate that the companion workbook did not provide that information for the retained PoLib construct, not that the PoLib measurement was discarded.