5′-UTR mRNA stability time courses under functional and non-functional caps
Decoding mRNA translatability and stability from the 5′ UTRThe same synthetic randomized 10-nt 5′ UTR mRNA library was followed through functional m7G-capped in-vivo and in-vitro decay time courses, with an ApppG-capped in-vivo control arm. The table provides deposited counts/RPM, transparent time-point log2 changes, and author-reported half-life values where the source workbook reports them.
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 versus non-functional ApppG-capped stability control across time points
For in-vivo decay, transfected HEK293-Kb cells were sampled at 2 h and 5 h after the initial 1 h expression period; the in-vitro cytoplasmic-extract series was sampled at 0, 10, 30, and 60 min. The package also joins author-published FACS- and ribosome-derived half-life values from Source Data Fig. 2 where a sequence is present. Author half-life estimation used a two-step normalization and regression workflow, so the package does not substitute simple RPM ratios for those values.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (51 of 51)
| 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 |
Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 51 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_in_vivo_2h_count_rep1
- Read count in the functional m7G-capped in-vivo 2 h sample, replicate 1 (GSM4305139).
- m7g_in_vivo_2h_rpm_rep1
- RPM in the functional m7G-capped in-vivo 2 h sample, replicate 1.
- m7g_in_vivo_5h_count_rep1
- Read count in the functional m7G-capped in-vivo 5 h sample, replicate 1 (GSM4305140).
- m7g_in_vivo_5h_rpm_rep1
- RPM in the functional m7G-capped in-vivo 5 h sample, replicate 1.
- m7g_in_vivo_2h_count_rep2
- Read count in the functional m7G-capped in-vivo 2 h sample, replicate 2 (GSM4305141).
- m7g_in_vivo_2h_rpm_rep2
- RPM in the functional m7G-capped in-vivo 2 h sample, replicate 2.
- m7g_in_vivo_5h_count_rep2
- Read count in the functional m7G-capped in-vivo 5 h sample, replicate 2 (GSM4305142).
- m7g_in_vivo_5h_rpm_rep2
- RPM in the functional m7G-capped in-vivo 5 h sample, replicate 2.
- in_vitro_0min_count
- Read count in the functional m7G-capped in-vitro extract at 0 min (GSM4305143).
- in_vitro_0min_rpm
- RPM in the functional m7G-capped in-vitro extract at 0 min.
- in_vitro_10min_count
- Read count in the functional m7G-capped in-vitro extract at 10 min (GSM4305144).
- in_vitro_10min_rpm
- RPM in the functional m7G-capped in-vitro extract at 10 min.
- in_vitro_30min_count
- Read count in the functional m7G-capped in-vitro extract at 30 min (GSM4305145).
- in_vitro_30min_rpm
- RPM in the functional m7G-capped in-vitro extract at 30 min.
- in_vitro_60min_count
- Read count in the functional m7G-capped in-vitro extract at 60 min (GSM4305146).
- in_vitro_60min_rpm
- RPM in the functional m7G-capped in-vitro extract at 60 min.
- appg_in_vivo_2h_count_rep1
- Read count in the non-functional ApppG-capped in-vivo 2 h sample, replicate 1 (GSM4305147).
- appg_in_vivo_2h_rpm_rep1
- RPM in the non-functional ApppG-capped in-vivo 2 h sample, replicate 1.
- appg_in_vivo_5h_count_rep1
- Read count in the non-functional ApppG-capped in-vivo 5 h sample, replicate 1 (GSM4305148).
- appg_in_vivo_5h_rpm_rep1
- RPM in the non-functional ApppG-capped in-vivo 5 h sample, replicate 1.
- appg_in_vivo_2h_count_rep2
- Read count in the non-functional ApppG-capped in-vivo 2 h sample, replicate 2 (GSM4305149).
- appg_in_vivo_2h_rpm_rep2
- RPM in the non-functional ApppG-capped in-vivo 2 h sample, replicate 2.
- appg_in_vivo_5h_count_rep2
- Read count in the non-functional ApppG-capped in-vivo 5 h sample, replicate 2 (GSM4305150).
- appg_in_vivo_5h_rpm_rep2
- RPM in the non-functional ApppG-capped in-vivo 5 h sample, replicate 2.
- m7g_in_vivo_log2_change_2h_vs_input_rep1
- log2(functional m7G in-vivo 2 h RPM / input-library RPM) for replicate 1.
- m7g_in_vivo_log2_change_5h_vs_input_rep1
- log2(functional m7G in-vivo 5 h RPM / input-library RPM) for replicate 1.
- m7g_in_vivo_log2_change_2h_vs_input_rep2
- log2(functional m7G in-vivo 2 h RPM / input-library RPM) for replicate 2.
- m7g_in_vivo_log2_change_5h_vs_input_rep2
- log2(functional m7G in-vivo 5 h RPM / input-library RPM) for replicate 2.
- m7g_in_vivo_log2_change_5h_vs_2h_rep1
- log2(functional m7G in-vivo 5 h RPM / 2 h RPM) for replicate 1; a count-based decay proxy, not a half-life.
- m7g_in_vivo_log2_change_5h_vs_2h_rep2
- log2(functional m7G in-vivo 5 h RPM / 2 h RPM) for replicate 2; a count-based decay proxy, not a half-life.
- in_vitro_log2_change_10min_vs_0min
- log2(functional m7G in-vitro 10 min RPM / 0 min RPM); a count-based decay proxy, not a half-life.
- in_vitro_log2_change_30min_vs_0min
- log2(functional m7G in-vitro 30 min RPM / 0 min RPM); a count-based decay proxy, not a half-life.
- in_vitro_log2_change_60min_vs_0min
- log2(functional m7G in-vitro 60 min RPM / 0 min RPM); a count-based decay proxy, not a half-life.
- appg_in_vivo_log2_change_5h_vs_2h_rep1
- log2(non-functional ApppG in-vivo 5 h RPM / 2 h RPM) for replicate 1; a count-based decay proxy, not a half-life.
- appg_in_vivo_log2_change_5h_vs_2h_rep2
- log2(non-functional ApppG in-vivo 5 h RPM / 2 h RPM) for replicate 2; a count-based decay proxy, not a half-life.
- published_facs_in_vivo_half_life_hours
- Author-reported in-vivo half-life in hours from FACS-based Source Data Fig. 2, when available.
- published_facs_in_vivo_group
- Author source-data grouping for the FACS-derived in-vivo half-life value.
- published_facs_in_vitro_half_life_minutes
- Author-reported in-vitro half-life in minutes from FACS-based Source Data Fig. 2, when available.
- published_facs_in_vitro_group
- Author source-data grouping for the FACS-derived in-vitro half-life value.
- published_ribosome_in_vivo_half_life_hours
- Author-reported in-vivo half-life in hours from ribosome-fractionation Source Data Fig. 2, when available.
- published_ribosome_in_vivo_group
- Author source-data grouping for the ribosome-derived in-vivo half-life value.
- published_ribosome_in_vitro_half_life_minutes
- Author-reported in-vitro half-life in minutes from ribosome-fractionation Source Data Fig. 2, when available.
- published_ribosome_in_vitro_group
- Author source-data grouping for the ribosome-derived in-vitro half-life value.
- 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; it further reports significance/R² filters for downstream half-life analyses. 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 retained, and count-based log2 changes are blank when their denominator is zero.
Curation notes
The processed table has one row per retained synthetic 10-mer. Published half-life fields are sparse because they are present only for sequences in the paper's reported downstream analyses; blank means not reported, not that the sequence failed package QC. The log2 RPM time-point changes are transparent count-based summaries and must not be interpreted as the paper's regression-derived half-life estimates. In-vivo half-life values are in hours and in-vitro values are in minutes. No reference genome or genomic region applies to this synthetic library.