5′-UTR uORF translation by polysome fractionation and FACS gating
Decoding mRNA translatability and stability from the 5′ UTRA synthetic mRNA MPRA library containing randomized 10-nt 5′ UTR sequences was tested in HEK293-Kb cells with a functional m7G-capped reporter and a non-functional ApppG-capped control. The table integrates input-library, ribosome-fractionation, ApppG fractionation, and 25D1/GFP FACS-gate sequence counts with RPM-normalized and transparent ratio-based measures.
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.
Perturbation & assay details
Basal / Untreated; functional m7G-capped reporter and non-functional ApppG-capped control arms
Randomized 10-nt inserts were placed in a β-globin 5′ UTR context upstream of an SIINFEKL uORF and downstream GFP, transcribed as capped polyadenylated mRNA, and transfected into HEK293-Kb cells. Functional m7G libraries were measured by in-vivo sucrose-gradient monosome/polysome/ribosome-free fractionation and by 25D1/GFP FACS gates; the ApppG arm provides cap-dependent versus cap-independent ribosome-association controls. GEO deposition provides gate/fraction sequence counts and RPM rather than the gate mean-fluorescence values used in the paper's weighted FACS score.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (55 of 55)
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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 · 55 definitions
- variant_id
- Stable package identifier in the form R10_<10-mer>.
- sequence
- The tested randomized 10-nt 5′ UTR sequence; only A/C/G/T sequences passed QC.
- sequence_length_bp
- Sequence length in base pairs; all retained sequences are 10.
- input_library_count_rep1
- Integer sequence read count in the randomized input library, replicate 1 (GSM4305122).
- input_library_rpm_rep1
- Input-library replicate 1 reads per million, recomputed from the deposited count and file total.
- input_library_count_rep2
- Integer sequence read count in the randomized input library, replicate 2 (GSM4546416).
- input_library_rpm_rep2
- Input-library replicate 2 reads per million, recomputed from the deposited count and file total.
- m7g_monosome_count_rep1
- Read count in the functional m7G-capped in-vivo monosome fraction, replicate 1 (GSM4305123).
- m7g_monosome_rpm_rep1
- RPM in the functional m7G-capped in-vivo monosome fraction, replicate 1.
- m7g_polysome_count_rep1
- Read count in the functional m7G-capped in-vivo polysome fraction, replicate 1 (GSM4305124).
- m7g_polysome_rpm_rep1
- RPM in the functional m7G-capped in-vivo polysome fraction, replicate 1.
- m7g_monosome_count_rep2
- Read count in the functional m7G-capped in-vivo monosome fraction, replicate 2 (GSM4305125).
- m7g_monosome_rpm_rep2
- RPM in the functional m7G-capped in-vivo monosome fraction, replicate 2.
- m7g_polysome_count_rep2
- Read count in the functional m7G-capped in-vivo polysome fraction, replicate 2 (GSM4305126).
- m7g_polysome_rpm_rep2
- RPM in the functional m7G-capped in-vivo polysome fraction, replicate 2.
- m7g_ribosome_free_count_rep1
- Read count in the functional m7G-capped in-vivo ribosome-free fraction, replicate 1 (GSM4305127).
- m7g_ribosome_free_rpm_rep1
- RPM in the functional m7G-capped in-vivo ribosome-free fraction, replicate 1.
- m7g_ribosome_free_count_rep2
- Read count in the functional m7G-capped in-vivo ribosome-free fraction, replicate 2 (GSM4305128).
- m7g_ribosome_free_rpm_rep2
- RPM in the functional m7G-capped in-vivo ribosome-free fraction, replicate 2.
- appg_ribosome_free_count
- Read count in the non-functional ApppG-capped ribosome-free fraction (GSM4305129).
- appg_ribosome_free_rpm
- RPM in the non-functional ApppG-capped ribosome-free fraction.
- appg_ribosome_bound_count
- Read count in the non-functional ApppG-capped ribosome-bound fraction (GSM4305130).
- appg_ribosome_bound_rpm
- RPM in the non-functional ApppG-capped ribosome-bound fraction.
- facs_25d1_low_count_rep1
- Read count from the 25D1 low/negative FACS gate, replicate 1 (GSM4305131).
- facs_25d1_low_rpm_rep1
- RPM from the 25D1 low/negative FACS gate, replicate 1.
- facs_25d1_high_count_rep1
- Read count from the 25D1 high FACS gate, replicate 1 (GSM4305132).
- facs_25d1_high_rpm_rep1
- RPM from the 25D1 high FACS gate, replicate 1.
- facs_gfp_low_count_rep1
- Read count from the GFP low FACS gate, replicate 1 (GSM4305133).
- facs_gfp_low_rpm_rep1
- RPM from the GFP low FACS gate, replicate 1.
- facs_gfp_high_count_rep1
- Read count from the GFP high FACS gate, replicate 1 (GSM4305134).
- facs_gfp_high_rpm_rep1
- RPM from the GFP high FACS gate, replicate 1.
- facs_25d1_low_count_rep2
- Read count from the 25D1 low/negative FACS gate, replicate 2 (GSM4305135).
- facs_25d1_low_rpm_rep2
- RPM from the 25D1 low/negative FACS gate, replicate 2.
- facs_25d1_high_count_rep2
- Read count from the 25D1 high FACS gate, replicate 2 (GSM4305136).
- facs_25d1_high_rpm_rep2
- RPM from the 25D1 high FACS gate, replicate 2.
- facs_gfp_low_count_rep2
- Read count from the GFP low FACS gate, replicate 2 (GSM4305137).
- facs_gfp_low_rpm_rep2
- RPM from the GFP low FACS gate, replicate 2.
- facs_gfp_high_count_rep2
- Read count from the GFP high FACS gate, replicate 2 (GSM4305138).
- facs_gfp_high_rpm_rep2
- RPM from the GFP high FACS gate, replicate 2.
- m7g_monosome_to_polysome_ratio_rep1
- Functional m7G in-vivo monosome RPM divided by polysome RPM for replicate 1.
- m7g_monosome_to_polysome_ratio_rep2
- Functional m7G in-vivo monosome RPM divided by polysome RPM for replicate 2.
- log2_m7g_monosome_to_polysome_ratio_mean
- Mean across replicates of log2(monosome RPM / polysome RPM), calculated only where both ratios are defined.
- m7g_ribosome_free_fraction_rep1
- Functional m7G ribosome-free RPM divided by the sum of ribosome-free, monosome, and polysome RPM for replicate 1.
- m7g_ribosome_free_fraction_rep2
- Functional m7G ribosome-free RPM divided by the sum of ribosome-free, monosome, and polysome RPM for replicate 2.
- appg_ribosome_bound_to_free_ratio
- Non-functional ApppG ribosome-bound RPM divided by ribosome-free RPM.
- appg_ribosome_bound_fraction
- Non-functional ApppG ribosome-bound RPM divided by the sum of bound and free RPM.
- facs_25d1_high_fraction_rep1
- 25D1 high RPM divided by 25D1 high plus low RPM for replicate 1; a gate-count proxy, not the paper's fluorescence-weighted score.
- facs_25d1_high_fraction_rep2
- 25D1 high RPM divided by 25D1 high plus low RPM for replicate 2; a gate-count proxy, not the paper's fluorescence-weighted score.
- facs_gfp_high_fraction_rep1
- GFP high RPM divided by GFP high plus low RPM for replicate 1; a gate-count proxy, not the paper's fluorescence-weighted score.
- facs_gfp_high_fraction_rep2
- GFP high RPM divided by GFP high plus low RPM for replicate 2; a gate-count proxy, not the paper's fluorescence-weighted score.
- log2_facs_25d1_high_to_low_rep1
- log2(25D1 high RPM / 25D1 low RPM) for replicate 1.
- log2_facs_25d1_high_to_low_rep2
- log2(25D1 high RPM / 25D1 low RPM) for replicate 2.
- log2_facs_gfp_high_to_low_rep1
- log2(GFP high RPM / GFP low RPM) for replicate 1.
- log2_facs_gfp_high_to_low_rep2
- log2(GFP high RPM / GFP low RPM) for replicate 2.
- qc_pass
- True for rows passing the package's sequence and input-count filters.
Quality control
The paper describes adapter trimming, exclusion of sequences whose post-trimming length was not 10 nt, read counting, and RPM normalization. For this package, an additional reproducible filter retained only exact 10-nt A/C/G/T sequences present in both input libraries with at least 5 reads in each; duplicate sequence keys were absent. This retained 866,759 variants from 1,033,228 valid common input sequences. Downstream zero counts were kept as numeric zeros, while ratios and log2 measures are blank when their denominator is zero.
Curation notes
The processed table has one row per retained synthetic 10-mer and combines deposited sequence counts with simple RPM-normalized summaries. The paper's FACS activity score uses mean fluorescence of the high and negative gates; GEO supplies only high/low sequence counts, so the table exposes high-gate fractions and high/low RPM ratios instead of claiming to reproduce that weighted score. No reference genome or genomic region applies to this synthetic library. ApppG denotes the non-functional cap control.