A lentiviral fast-UTR reporter library containing native human 3′ UTR fragments, natural alleles, and designed ARE/CDE/other motif mutations was assayed in an engineered Jurkat T-cell line. 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:0367
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
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Visible columns (42 of 42)
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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 · 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: 33,123 of 41,255 source rows, including 30,253 with both T0 and T4 scores and 2,870 with steady-state score only.
Curation notes
The manuscript refers to Jurkat T cells and the supplementary methods mention Jurkat E6 cells, but do not give a Cellosaurus accession; CVCL:0367 (Jurkat E6.1) is the best-match mapping and should be treated as an inferred cell-line resolution. 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 22 clones per segment at t0 and 18 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.