Tetracycline-responsive hammerhead riboswitch screen
High-throughput identification of synthetic riboswitches by barcode-free amplicon-sequencing in human cellsAn episomal CMV-eGFP 3′-UTR library containing all 16,384 combinations of a seven-nucleotide communication module was screened in HEK-293H cells. Self-barcoding cDNA amplicon counts were measured after 3 h untreated, 25 µM, or 50 µM tetracycline 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, 25 µM tetracycline, or 50 µM tetracycline for 3 h
Transient episomal plasmid reporter with the synthetic riboswitch library in the eGFP 3′ UTR. Each construct is identified by its sequence rather than an external barcode; cDNA amplicon abundance was sequenced on an Illumina NextSeq 500, while the published log2 fold changes and FDRs were obtained from edgeR analysis of the source-data workbook.
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 · 42 definitions
- variant_id
- Unique identifier combining the amplicon pattern name and the two variable sequence parts.
- pattern_name
- Amplicon sequence pattern; Orig denotes the Tet-hammerhead library.
- variable_region_1
- First variable sequence segment of the self-barcoding amplicon.
- variable_region_2
- Second variable sequence segment of the self-barcoding amplicon.
- motif
- The two variable sequence segments joined with an underscore.
- total_count
- Sum of raw cDNA amplicon abundance counts across all 24 screen samples.
- min_detected_replicates_per_condition
- Smallest number of nonzero-count replicates among untreated, 25 µM, and 50 µM tetracycline conditions.
- count_untreated_rep1
- Raw cDNA amplicon count for untreated biological replicate 1 (GSM4259904).
- count_untreated_rep2
- Raw cDNA amplicon count for untreated biological replicate 2 (GSM4259905).
- count_untreated_rep3
- Raw cDNA amplicon count for untreated biological replicate 3 (GSM4259906).
- count_untreated_rep4
- Raw cDNA amplicon count for untreated biological replicate 4 (GSM4259907).
- count_untreated_rep5
- Raw cDNA amplicon count for untreated biological replicate 5 (GSM4259908).
- count_untreated_rep6
- Raw cDNA amplicon count for untreated biological replicate 6 (GSM4259909).
- count_untreated_rep7
- Raw cDNA amplicon count for untreated biological replicate 7 (GSM4259910).
- count_untreated_rep8
- Raw cDNA amplicon count for untreated biological replicate 8 (GSM4259911).
- count_tet_25uM_rep1
- Raw cDNA amplicon count for 25 µM tetracycline biological replicate 1 (GSM4259912).
- count_tet_25uM_rep2
- Raw cDNA amplicon count for 25 µM tetracycline biological replicate 2 (GSM4259913).
- count_tet_25uM_rep3
- Raw cDNA amplicon count for 25 µM tetracycline biological replicate 3 (GSM4259914).
- count_tet_25uM_rep4
- Raw cDNA amplicon count for 25 µM tetracycline biological replicate 4 (GSM4259915).
- count_tet_25uM_rep5
- Raw cDNA amplicon count for 25 µM tetracycline biological replicate 5 (GSM4259916).
- count_tet_25uM_rep6
- Raw cDNA amplicon count for 25 µM tetracycline biological replicate 6 (GSM4259917).
- count_tet_25uM_rep7
- Raw cDNA amplicon count for 25 µM tetracycline biological replicate 7 (GSM4259918).
- count_tet_25uM_rep8
- Raw cDNA amplicon count for 25 µM tetracycline biological replicate 8 (GSM4259919).
- count_tet_50uM_rep1
- Raw cDNA amplicon count for 50 µM tetracycline biological replicate 1 (GSM4259920).
- count_tet_50uM_rep2
- Raw cDNA amplicon count for 50 µM tetracycline biological replicate 2 (GSM4259921).
- count_tet_50uM_rep3
- Raw cDNA amplicon count for 50 µM tetracycline biological replicate 3 (GSM4259922).
- count_tet_50uM_rep4
- Raw cDNA amplicon count for 50 µM tetracycline biological replicate 4 (GSM4259923).
- count_tet_50uM_rep5
- Raw cDNA amplicon count for 50 µM tetracycline biological replicate 5 (GSM4259924).
- count_tet_50uM_rep6
- Raw cDNA amplicon count for 50 µM tetracycline biological replicate 6 (GSM4259925).
- count_tet_50uM_rep7
- Raw cDNA amplicon count for 50 µM tetracycline biological replicate 7 (GSM4259926).
- count_tet_50uM_rep8
- Raw cDNA amplicon count for 50 µM tetracycline biological replicate 8 (GSM4259927).
- mean_cpm_untreated
- Mean per-sample counts-per-million for the untreated replicates, normalized within the Orig library.
- mean_cpm_tet_25uM
- Mean per-sample counts-per-million for the 25 µM tetracycline replicates, normalized within the Orig library.
- mean_cpm_tet_50uM
- Mean per-sample counts-per-million for the 50 µM tetracycline replicates, normalized within the Orig library.
- log2fc_tet_25uM_vs_untreated
- Published edgeR log2 fold change for 25 µM tetracycline versus untreated.
- fdr_tet_25uM_vs_untreated
- Published Benjamini–Hochberg FDR for the 25 µM versus untreated comparison.
- significant_tet_25uM_vs_untreated_fdr_0_05
- True when the published FDR for 25 µM versus untreated is ≤ 0.05.
- log2fc_tet_50uM_vs_untreated
- Published edgeR log2 fold change for 50 µM tetracycline versus untreated.
- fdr_tet_50uM_vs_untreated
- Published Benjamini–Hochberg FDR for the 50 µM versus untreated comparison.
- significant_tet_50uM_vs_untreated_fdr_0_05
- True when the published FDR for 50 µM versus untreated is ≤ 0.05.
- source_stats_sheet
- Source-data workbook sheet supplying the published statistics; 2d.
- source_stats_available
- Indicates that published log2FC and FDR values are available for the row.
Quality control
The authors assessed library abundance, replicate concordance, GC dependence, and low-abundance behavior in the accompanying pipeline and supplementary information. For this package, missing construct counts were treated as zero; a construct was retained only when it had total count > 0, was detected in at least 2 of 8 replicates in every condition, and had finite published log2FC and FDR for both tetracycline contrasts. All 16,384 input constructs passed these filters.
Curation notes
The raw GEO archive includes separate library-QC samples (GSM4259928–GSM4259932); they are preserved in raw_data but intentionally excluded from this screen table. The GEO SOFT metadata contains a treatment-label inconsistency for the final eight samples; sample titles and the paper’s stated 8+8+8 design were used to assign the 50 µM condition. The library is fully synthetic, so no reference genome or genomic interval applies.