The human fast-UTR reporter library of native 3′ UTR fragments, natural alleles, and designed ARE/CDE/other motif mutations was assayed in engineered BEAS-2B airway epithelial cells. Reporter RNA and genomic-DNA barcode counts were collected before doxycycline and after 4 h of transcriptional shutoff to quantify steady-state expression and an RNA-stability score.
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
Human
Taxonomy ID
NCBITaxon:9606
Biosample
CVCL:0168
Reference genome
hg19
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Untreated baseline (t0) and doxycycline 1 µg/mL for 4 h (t4) to inhibit reporter transcription
The fast-UTR BTV construct is a tetracycline-regulated lentiviral reporter with a variable 3′ UTR test fragment and a random 8-mer clone barcode. The same 41,288-segment design targeted human RefSeq 3′ UTRs and included ARE/CDE motif-containing fragments, natural alleles, and designed mutations. RNA and genomic DNA were sequenced from t0 and t4 samples; source exports also contain exploratory t2 and t6 stability scores. The stability field is ratios_T4T0 = ratio_t4/(ratio_t4 + ratio_t0), rather than a directly fitted half-life.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (42 of 42)
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 · 42 definitions
element_id
Unique source identifier for the tested 3′ UTR sequence element.
parent_element_id
Identifier of the reference element used by the source to calculate an alternate or mutant effect; reference rows point to themselves.
gene
Gene symbol parsed from the source region field.
chromosome
Chromosome parsed from the source region field and normalized with a chr prefix.
region_start
Start coordinate parsed from the source region field.
region_end
End coordinate parsed from the source region field.
genomic_region
Source region label in the form GENE|chromosome:start-end.
sequence
DNA sequence of the tested 3′ UTR fragment or allele as supplied by the authors.
sequence_length_nt
Number of nucleotides in the stored sequence.
snp_ids
SNP identifier(s) associated with the sequence, when present.
haplotype
Source haplotype/construct label; 0 and 1 encode reference/alternate alleles and mutation labels identify designed changes.
sequence_kind
Derived class: reference_control, natural_SNP_or_allele, designed_mutation, or other_variant.
is_reference_control
Source iscontrol field: 1 for a reference sequence and 0 for a deliberate mutation or alternate allele.
is_snp
Source issnp flag indicating a natural SNP/allelic sequence.
overlap_with
Source annotation of regulatory elements overlapped by the sequence.
overlap_with_snp_inside
Source annotation of overlapped elements containing a SNP inside the oligo.
gc_fraction
Fraction of G/C nucleotides in the sequence.
steady_state_ratio_t0
Source ratios_T0 value: RNA/(RNA + DNA) before doxycycline.
steady_state_ratio_t0_gc_residual
GC-residualized source ratios_T0 value; the preferred steady-state expression score.
Source effect_size_T0: alternate/mutant minus parent-reference steady-state ratio.
effect_steady_state_t0_gc_residual
GC-residualized alternate/mutant minus parent-reference steady-state effect.
effect_stability_t2
Source alternate/mutant minus parent-reference T2/T0 stability effect.
effect_stability_t2_gc_residual
GC-residualized alternate/mutant minus parent-reference T2/T0 stability effect.
effect_stability_t4
Source alternate/mutant minus parent-reference T4/T0 stability effect.
effect_stability_t4_gc_residual
GC-residualized alternate/mutant minus parent-reference T4/T0 stability effect.
effect_stability_t6
Source alternate/mutant minus parent-reference T6/T0 stability effect.
effect_stability_t6_gc_residual
GC-residualized alternate/mutant minus parent-reference T6/T0 stability effect.
one_are_deleted
Source flag: exactly one ARE was deliberately mutated.
longest_are_deleted
Source flag: the deliberately mutated ARE was the longest ARE in the fragment.
are_cluster_bakheet_plus
Source ARED-Plus/Bakheet ARE cluster annotation; -1 indicates no ARE and 0 a subcluster motif.
parent_are_cluster_bakheet_plus
Source ARED-Plus/Bakheet ARE cluster annotation for the parent reference of a mutated ARE.
are_registration_nt
Starting registration of a perfect AUUUA-repeat ARE, in nucleotides; blank when no such ARE is present.
are_length_nt
Length in nucleotides of the longest perfect AUUUA-repeat ARE.
cde_lower_stem_length_nt
Length of the lower CDE stem; -1 indicates no CDE and 0/1 indicates no or minimal lower stem.
parent_cde_lower_stem_length_nt
Parent-reference lower CDE stem length for a mutated CDE construct.
measurement_status
Derived availability flag: steady_state_and_t4_stability or steady_state_only (t4_stability_only if encountered).
Quality control
The source methods required each sequence to have at least 5 clones with more than 5 DNA counts each and at least 1 RNA count in at least 1 clone; barcode pairs at Hamming distance 1 were collapsed, and steady-state/stability values were residualized against GC content with fifth-order polynomial fits. The processed table uses the author-provided sequence-level values and retains a row only when the ID is unique, the sequence is nonempty A/C/G/T, and at least one GC-residualized primary score (ratios_T0_GC_resid or ratios_T4T0_GC_resid) is finite. Rows with neither score were removed; missing individual timepoint scores were not imputed. Retained: 17,135 of 41,255 source rows, including 7,613 with both T0 and T4 scores and 9,522 with steady-state score only.
Curation notes
The publication names the line BEAS2B/Beas2B; CVCL:0168 is the Cellosaurus mapping for BEAS-2B. The paper does not explicitly label the reference assembly; hg19 is inferred from the RefSeq v68/UCSC source coordinates. Cells were not stimulated. The study reports approximately 9 clones per segment at t0 and 7 clones per segment for the t4 stability measurement. The authors state that the two cell types did not have technical replicates, so the Jurkat/BEAS-2B difference may include batch effects. The table keeps source-provided t2/t6 fields but uses t0/t4 as the primary stability comparison.