A pooled episomal CMV-EGFP reporter library containing 6,555 matched wild-type/mutant human UTR variant pairs was transiently transfected into HEK293T cells. Three dated biological batches were fractionated into MS/monosome, PSL/light-polysome, and PSH/heavy-polysome RNA, which was quantified by targeted amplicon sequencing.
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:0063
Reference genome
GRCh38
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated; cycloheximide 100 µg/ml for 5 min before harvest (technical polysome preservation)
The assay used episomal CMV-driven constructs in which approximately 115-nt native UTR fragments centered on disease-relevant variants were fused upstream (5′ UTR) or downstream (3′ UTR) of EGFP; each pair contained reference and alternative alleles. HEK293T lysates were separated on a 5–50% sucrose gradient, fractions were pooled into MS (monosome), PSL (light polysome; 2–5 ribosomes), and PSH (heavy polysome; ≥6 ribosomes), and UTR amplicons were sequenced. The processed table treats the pooled 5′ and 3′ libraries as one assay and retains the UTR arm in `utr_type`.
Processed data
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Visible columns (83 of 83)
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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 · 83 definitions
group_id
Study identifier for one matched reference/mutant UTR pair.
confidence_class
Author-provided Supplemental Table S2 class: HC_sig or HC_nonsig.
polysome_profile_status
Plain-language description of the author’s genotype×fraction result.
utr_type
UTR arm of the construct: 5′UTR or 3′UTR.
gene_symbol
Gene symbol supplied for HC_sig records or parsed from the construct name when available.
variant_label
Variant description from Supplemental Table S3 for HC_sig records, otherwise the source construct’s variant/transcript descriptor.
chromosome
Human chromosome for the variant, using the source annotation or construct identifier.
variant_start
Source genomic start coordinate for the tested variant.
variant_stop
Source genomic stop coordinate for the tested variant.
strand
Source strand annotation; blank when not available.
variant_type
Source variant type, such as single nucleotide variant or deletion.
reference_allele
Reference allele represented by the WT construct; blank when not resolvable from the source.
alternate_allele
Alternate allele represented by the mutant construct; blank when not resolvable from the source.
dbsnp
dbSNP identifier from Supplemental Table S3; blank when unavailable.
hgmd_id
HGMD identifier from Supplemental Table S3; blank when unavailable.
clinical_significance
Source clinical-significance annotation; blank when unavailable.
cs_level
Source clinical-significance level from Supplemental Table S3.
phenotype_list
Source phenotype or disease list from Supplemental Table S3.
phenotype_ids
Source phenotype identifiers from Supplemental Table S3.
other_ids
Other source identifiers from Supplemental Table S3.
ref_construct_id
Exact WT/reference construct identifier used as the row key in the source count matrix.
mut_construct_id
Exact mutant/alternate construct identifier used as the row key in the source count matrix.
wt_rep1_ctrl
WT read count in batch 181228 source Ctrl sample; retained for provenance and not used in the three-fraction GLM.
wt_rep1_mono
WT read count in batch 181228 MS/monosome fraction.
wt_rep1_light
WT read count in batch 181228 PSL/light-polysome fraction.
wt_rep1_heavy
WT read count in batch 181228 PSH/heavy-polysome fraction.
wt_rep2_ctrl
WT read count in batch 190305 source Ctrl sample; retained for provenance and not used in the three-fraction GLM.
wt_rep2_mono
WT read count in batch 190305 MS/monosome fraction.
wt_rep2_light
WT read count in batch 190305 PSL/light-polysome fraction.
wt_rep2_heavy
WT read count in batch 190305 PSH/heavy-polysome fraction.
wt_rep3_ctrl
WT read count in batch 190313 source Ctrl sample; retained for provenance and not used in the three-fraction GLM.
wt_rep3_mono
WT read count in batch 190313 MS/monosome fraction.
wt_rep3_light
WT read count in batch 190313 PSL/light-polysome fraction.
wt_rep3_heavy
WT read count in batch 190313 PSH/heavy-polysome fraction.
mut_rep1_ctrl
Mutant read count in batch 181228 source Ctrl sample; retained for provenance and not used in the three-fraction GLM.
mut_rep1_mono
Mutant read count in batch 181228 MS/monosome fraction.
mut_rep1_light
Mutant read count in batch 181228 PSL/light-polysome fraction.
mut_rep1_heavy
Mutant read count in batch 181228 PSH/heavy-polysome fraction.
mut_rep2_ctrl
Mutant read count in batch 190305 source Ctrl sample; retained for provenance and not used in the three-fraction GLM.
mut_rep2_mono
Mutant read count in batch 190305 MS/monosome fraction.
mut_rep2_light
Mutant read count in batch 190305 PSL/light-polysome fraction.
mut_rep2_heavy
Mutant read count in batch 190305 PSH/heavy-polysome fraction.
mut_rep3_ctrl
Mutant read count in batch 190313 source Ctrl sample; retained for provenance and not used in the three-fraction GLM.
mut_rep3_mono
Mutant read count in batch 190313 MS/monosome fraction.
mut_rep3_light
Mutant read count in batch 190313 PSL/light-polysome fraction.
mut_rep3_heavy
Mutant read count in batch 190313 PSH/heavy-polysome fraction.
wt_rep1_profile_total
WT batch 181228 total across MS, PSL, and PSH fractions.
wt_rep2_profile_total
WT batch 190305 total across MS, PSL, and PSH fractions.
wt_rep3_profile_total
WT batch 190313 total across MS, PSL, and PSH fractions.
mut_rep1_profile_total
Mutant batch 181228 total across MS, PSL, and PSH fractions.
mut_rep2_profile_total
Mutant batch 190305 total across MS, PSL, and PSH fractions.
mut_rep3_profile_total
Mutant batch 190313 total across MS, PSL, and PSH fractions.
min_profile_total
Minimum of the six WT/mutant analyzed-profile totals; the package QC threshold is ≥20.
wt_profile_total_mean
Mean WT analyzed-profile total across the three batches.
mut_profile_total_mean
Mean mutant analyzed-profile total across the three batches.
wt_rep1_mono_fraction
WT batch 181228 MS count divided by its WT MS+PSL+PSH total.
wt_rep1_light_fraction
WT batch 181228 PSL count divided by its WT MS+PSL+PSH total.
wt_rep1_heavy_fraction
WT batch 181228 PSH count divided by its WT MS+PSL+PSH total.
wt_rep2_mono_fraction
WT batch 190305 MS count divided by its WT MS+PSL+PSH total.
wt_rep2_light_fraction
WT batch 190305 PSL count divided by its WT MS+PSL+PSH total.
wt_rep2_heavy_fraction
WT batch 190305 PSH count divided by its WT MS+PSL+PSH total.
wt_rep3_mono_fraction
WT batch 190313 MS count divided by its WT MS+PSL+PSH total.
wt_rep3_light_fraction
WT batch 190313 PSL count divided by its WT MS+PSL+PSH total.
wt_rep3_heavy_fraction
WT batch 190313 PSH count divided by its WT MS+PSL+PSH total.
mut_rep1_mono_fraction
Mutant batch 181228 MS count divided by its mutant MS+PSL+PSH total.
mut_rep1_light_fraction
Mutant batch 181228 PSL count divided by its mutant MS+PSL+PSH total.
mut_rep1_heavy_fraction
Mutant batch 181228 PSH count divided by its mutant MS+PSL+PSH total.
mut_rep2_mono_fraction
Mutant batch 190305 MS count divided by its mutant MS+PSL+PSH total.
mut_rep2_light_fraction
Mutant batch 190305 PSL count divided by its mutant MS+PSL+PSH total.
mut_rep2_heavy_fraction
Mutant batch 190305 PSH count divided by its mutant MS+PSL+PSH total.
mut_rep3_mono_fraction
Mutant batch 190313 MS count divided by its mutant MS+PSL+PSH total.
mut_rep3_light_fraction
Mutant batch 190313 PSL count divided by its mutant MS+PSL+PSH total.
mut_rep3_heavy_fraction
Mutant batch 190313 PSH count divided by its mutant MS+PSL+PSH total.
wt_mono_fraction_mean
Mean WT MS/monosome fraction across the three batches.
wt_light_fraction_mean
Mean WT PSL/light-polysome fraction across the three batches.
wt_heavy_fraction_mean
Mean WT PSH/heavy-polysome fraction across the three batches.
mut_mono_fraction_mean
Mean mutant MS/monosome fraction across the three batches.
mut_light_fraction_mean
Mean mutant PSL/light-polysome fraction across the three batches.
mut_heavy_fraction_mean
Mean mutant PSH/heavy-polysome fraction across the three batches.
mut_minus_wt_mono_fraction
Mutant minus WT mean MS/monosome fraction.
mut_minus_wt_light_fraction
Mutant minus WT mean PSL/light-polysome fraction.
mut_minus_wt_heavy_fraction
Mutant minus WT mean PSH/heavy-polysome fraction.
profile_shift_total_variation
Package-derived half-L1 distance between the mean WT and mutant three-fraction distributions; not a published p-value or a directional translation call.
Quality control
The package follows the authors’ high-confidence classification in Supplemental Table S2. The study’s QC required at least 20 reads in the three-fraction polysome profile for each allele in each of three repeated experiments, then excluded pairs with significant batch main effects or genotype×batch effects in the negative-binomial GLM. HC_sig calls are the study’s Bonferroni-adjusted genotype×fraction interaction calls; HC_nonsig pairs are high-confidence non-significant controls. The table retains 442 of 6,555 pair groups (46 HC_sig and 396 HC_nonsig), excluding 5,085 read_filter and 1,028 non-high-confidence nonsig groups. All retained rows have a minimum analyzed-profile total of at least 20; Ctrl counts are retained for provenance but are not part of the three-fraction profile.
Curation notes
HEK293T was resolved to Cellosaurus CVCL:0063. The source GEO series is GSE229492 and was private at packaging, so the accessible author-repository count matrices and eLife supplemental tables were used. The revised manuscript text says 483 high-confidence pairs, but Supplemental Table S2 contains 396 HC_nonsig plus 46 HC_sig groups (442 total); the package follows the supplied group-level data. The study intentionally did not convert profile shifts into increased/decreased translation direction, so the table reports raw counts and normalized fraction differences only. Supplemental Table S3 annotations are available for the 46 HC_sig groups; unavailable annotations for HC_nonsig groups are blank.