5pseq 5′ terminal-sequence lentiMPRA in HeLa cells
mRNA 5′ terminal sequences drive 200-fold differences in expression through effects on synthesis, translation and decayA synthetic reporter library containing the possible 7-nucleotide 5′ terminal sequences was packaged into lentivirus and used to stably infect HeLa cells. Direct sequencing of the reporter 5′ ends measured basal expression, actinomycin-D decay responses, and polysome/subpolysome translation distributions in DMSO vehicle and Torin 1 conditions; the table joins these readouts by 7-mer.
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
DMSO vehicle or 250 nM Torin 1 for 2 h; stability arm followed by 2 μg/mL actinomycin D for 2 h; translation arm separated into polysome and subpolysome fractions
The 5pseq vector is a CMV-promoter reporter based on pCT3-TE2, a lentiviral pLJC1-derived plasmid, with a randomized 7-nt cassette immediately after the promoter, Renilla luciferase coding sequence, and constant 3′ UTR. The library was packaged into lentivirus for stable HeLa delivery. Sequenced reporter 5′ ends were counted directly rather than through designed barcodes. The processed table combines S1 basal expression (reporter RPM divided by plasmid RPM), S2 actinomycin-D stability contrasts in DMSO and Torin 1, and S3 polysome/subpolysome translation contrasts in DMSO and Torin 1. Raw count columns are the corresponding GEO sample counts.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (35 of 35)
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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 · 35 definitions
- sequence
- Unique synthetic 7-nucleotide 5′ terminal sequence tested in the reporter library.
- initial_base
- The +1 nucleotide of the synthetic 7-mer.
- first_3mer
- The first three nucleotides of the synthetic 7-mer.
- top_like_cyyyy
- Derived TRUE when the sequence matches the CYYYYNN TOP-like pattern, with Y meaning C or T.
- tct_like_ctytyy
- Derived TRUE when the first six nucleotides match CTYTYY, the 5′ sequence form used for the TCT-like class, with Y meaning C or T.
- plasmid_count
- Raw input plasmid-library count for the 7-mer, from GEO GSM5827705.
- control_rna_rep1
- Raw reporter RNA count after 2 h DMSO vehicle treatment, replicate 1, GEO GSM5827689.
- control_rna_rep2
- Raw reporter RNA count after 2 h DMSO vehicle treatment, replicate 2, GEO GSM5827690.
- actd_control_rna_rep1
- Raw reporter RNA count after 2 h DMSO followed by 2 h actinomycin D, replicate 1, GEO GSM5827691.
- actd_control_rna_rep2
- Raw reporter RNA count after 2 h DMSO followed by 2 h actinomycin D, replicate 2, GEO GSM5827692.
- torin_rna_rep1
- Raw reporter RNA count after 2 h Torin 1 treatment, replicate 1, GEO GSM5827693.
- torin_rna_rep2
- Raw reporter RNA count after 2 h Torin 1 treatment, replicate 2, GEO GSM5827694.
- actd_torin_rna_rep1
- Raw reporter RNA count after 2 h Torin 1 followed by 2 h actinomycin D, replicate 1, GEO GSM5827695.
- actd_torin_rna_rep2
- Raw reporter RNA count after 2 h Torin 1 followed by 2 h actinomycin D, replicate 2, GEO GSM5827696.
- dmso_polysome_rep1
- Raw reporter RNA count in the DMSO polysome fraction, replicate 1, GEO GSM5827697.
- dmso_subpolysome_rep1
- Raw reporter RNA count in the DMSO subpolysome fraction, replicate 1, GEO GSM5827698.
- dmso_polysome_rep2
- Raw reporter RNA count in the DMSO polysome fraction, replicate 2, GEO GSM5827699.
- dmso_subpolysome_rep2
- Raw reporter RNA count in the DMSO subpolysome fraction, replicate 2, GEO GSM5827700.
- torin_polysome_rep1
- Raw reporter RNA count in the Torin 1 polysome fraction, replicate 1, GEO GSM5827701.
- torin_subpolysome_rep1
- Raw reporter RNA count in the Torin 1 subpolysome fraction, replicate 1, GEO GSM5827702.
- torin_polysome_rep2
- Raw reporter RNA count in the Torin 1 polysome fraction, replicate 2, GEO GSM5827703.
- torin_subpolysome_rep2
- Raw reporter RNA count in the Torin 1 subpolysome fraction, replicate 2, GEO GSM5827704.
- expression_normalized_rpm
- Published S1 normalized expression: mean control reporter reads per million divided by plasmid-library reads per million.
- stability_control_log2fc
- Published S2 DESeq2 log2 fold change for actinomycin-D-treated versus untreated reporter RNA under DMSO control conditions.
- stability_control_padj
- Published S2 adjusted p-value for the DMSO control stability contrast.
- stability_torin_log2fc
- Published S2 DESeq2 log2 fold change for actinomycin-D-treated versus untreated reporter RNA after Torin 1 treatment.
- stability_torin_padj
- Published S2 adjusted p-value for the Torin 1 stability contrast.
- stability_control_vs_torin_log2fc
- Published S2 log2 fold-change contrast comparing the stability response between DMSO control and Torin 1 conditions.
- stability_control_vs_torin_padj
- Published S2 adjusted p-value for the control-versus-Torin 1 stability contrast.
- translation_control_log2fc
- Published S3 DESeq2 log2 fold change for polysome versus subpolysome reporter RNA under DMSO control conditions.
- translation_control_padj
- Published S3 adjusted p-value for the DMSO control translation contrast.
- translation_torin_log2fc
- Published S3 DESeq2 log2 fold change for polysome versus subpolysome reporter RNA after Torin 1 treatment.
- translation_torin_padj
- Published S3 adjusted p-value for the Torin 1 translation contrast.
- translation_control_vs_torin_log2fc
- Published S3 log2 fold-change contrast comparing polysome/subpolysome translation between DMSO control and Torin 1 conditions.
- translation_control_vs_torin_padj
- Published S3 adjusted p-value for the control-versus-Torin 1 translation contrast.
Quality control
The authors reported 16,359 of 16,384 plasmid-library 7-mers with more than 20 reads and excluded +1-G reporter sequences because non-templated reverse-transcription G additions could not be distinguished from genuine +1-G initiation. For this package, the published S1, S2, and S3 tables were joined by exact 7-mer; only valid unique A/C/G/T 7-mers present in all three tables were eligible. Rows were retained only when the S1 plasmid count was at least 20 and both basal reporter replicates had at least 10 reads, retaining 12,247 of 12,270 joined rows. This package threshold is a conservative approximation to the paper’s >20-read plasmid-complexity criterion and avoids near-zero basal reporter ratios. Published DESeq2 log2 fold changes and adjusted p-values were retained as reported; supplement values marked NA remain NA, and non-significant rows were not removed.
Curation notes
The table represents the shared combinatorial 5pseq library and does not include the six targeted KARS1/SNHG1 promoter TSS reporter samples also deposited in GEO. Because +1-G reads are intrinsically ambiguous in this protocol, the final table covers the measurable A/C/T-starting subset rather than all 16,384 possible 7-mers. Raw GEO count entries absent for a retained sequence are represented as 0; missing published DESeq2 adjusted p-values are represented as NA. The library is synthetic, so no reference genome or genomic region is assigned.