Guanine-responsive U1-snRNP polyadenylation-dependent RNA-device screen
High-throughput identification of synthetic riboswitches by barcode-free amplicon-sequencing in human cellsA 4,096-member synthetic library randomized six nucleotides in the P1/U1-binding communication region of a guanine-responsive aptamer-RNA device and was screened in HEK-293H cells. The processed table preserves the published source-data statistics for untreated, 30 µM, 100 µM, and 300 µM guanine stimulation, with eight biological replicates per condition.
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
Untreated, 30 µM, 100 µM, or 300 µM guanine for 3 h
Transient episomal CMV-eGFP reporter with a guanine aptamer/U1-snRNP polyadenylation-dependent RNA device in the eGFP 3′ UTR. Construct identity was quantified by self-barcoding cDNA amplicon sequencing and the published edgeR log2 fold changes and FDRs are retained from source-data sheet 6d.
Processed data
50 rows per page. Click a cell to inspect its full value.
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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 · 16 definitions
- variant_id
- Unique identifier combining lib4 and the published 3+3 motif key.
- pattern_name
- lib4, the U1-snRNP device library label in the GEO count archive.
- variable_region_1
- First three nucleotides of the published randomized 3+3 motif key.
- variable_region_2
- Second three nucleotides of the published randomized 3+3 motif key.
- motif
- Published six-nucleotide motif key, represented as three bases, underscore, three bases.
- log2fc_gua_30uM_vs_untreated
- Published edgeR log2 fold change for 30 µM guanine versus untreated.
- fdr_gua_30uM_vs_untreated
- Published Benjamini–Hochberg FDR for the 30 µM versus untreated comparison.
- significant_gua_30uM_vs_untreated_fdr_0_05
- True when the published FDR for 30 µM versus untreated is ≤ 0.05.
- log2fc_gua_100uM_vs_untreated
- Published edgeR log2 fold change for 100 µM guanine versus untreated.
- fdr_gua_100uM_vs_untreated
- Published Benjamini–Hochberg FDR for the 100 µM versus untreated comparison.
- significant_gua_100uM_vs_untreated_fdr_0_05
- True when the published FDR for 100 µM versus untreated is ≤ 0.05.
- log2fc_gua_300uM_vs_untreated
- Published edgeR log2 fold change for 300 µM guanine versus untreated.
- fdr_gua_300uM_vs_untreated
- Published Benjamini–Hochberg FDR for the 300 µM versus untreated comparison.
- significant_gua_300uM_vs_untreated_fdr_0_05
- True when the published FDR for 300 µM versus untreated is ≤ 0.05.
- source_stats_sheet
- Source-data workbook sheet supplying the published statistics; 6d.
- source_stats_only
- Indicates that this table is based on the published source statistics rather than an unverified raw-count/motif join.
Quality control
The authors evaluated library abundance, replicate concordance, GC dependence, and low-abundance behavior. The processed table retains rows with finite published log2FC and FDR values for all three guanine contrasts; all 4,096 published motif records passed this filter.
Curation notes
The GEO lib4 count files encode the variable amplicon portions as an 11-nt segment plus a 2-nt segment, whereas source-data sheet 6d reports the six randomized nucleotides as a 3+3 motif key. Because the archive encoding could not be mapped to the published keys with a defensible sequence transformation, the table retains the published 6d statistics without inventing a raw-count join; the complete GEO archive remains in raw_data. The library is fully synthetic, so no reference genome or genomic interval applies.