Tetracycline-responsive Twister riboswitch screen
High-throughput identification of synthetic riboswitches by barcode-free amplicon-sequencing in human cellsNine synthetic Twister sublibraries (2N3N, 3N2N, 3N3N and CG/noCG variants; 18,432 constructs total) were screened in HEK-293H cells. Self-barcoding cDNA amplicon counts were measured after 3 h untreated, 12.5 µM, 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, 12.5 µM, 25 µM, or 50 µM tetracycline for 3 h
Transient episomal CMV-eGFP reporter with nine Twister ribozyme communication-module libraries in the eGFP 3′ UTR. Sequence-defined construct identities were quantified by cDNA amplicon sequencing on an Illumina NextSeq 500; published edgeR log2 fold changes and FDRs are joined to the corresponding motif keys from source-data sheet 5b.
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 · 54 definitions
- variant_id
- Unique identifier combining the Twister sublibrary pattern and the two variable sequence parts.
- pattern_name
- Twister sublibrary name encoded in the amplicon sequence pattern.
- 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 32 screen samples.
- min_detected_replicates_per_condition
- Smallest number of nonzero-count replicates among the four tetracycline conditions.
- count_untreated_rep1
- Raw cDNA amplicon count for untreated biological replicate 1 (GSM4259933).
- count_untreated_rep2
- Raw cDNA amplicon count for untreated biological replicate 2 (GSM4259934).
- count_untreated_rep3
- Raw cDNA amplicon count for untreated biological replicate 3 (GSM4259935).
- count_untreated_rep4
- Raw cDNA amplicon count for untreated biological replicate 4 (GSM4259936).
- count_untreated_rep5
- Raw cDNA amplicon count for untreated biological replicate 5 (GSM4259937).
- count_untreated_rep6
- Raw cDNA amplicon count for untreated biological replicate 6 (GSM4259938).
- count_untreated_rep7
- Raw cDNA amplicon count for untreated biological replicate 7 (GSM4259939).
- count_untreated_rep8
- Raw cDNA amplicon count for untreated biological replicate 8 (GSM4259940).
- count_tet_12_5uM_rep1
- Raw cDNA amplicon count for 12.5 µM tetracycline biological replicate 1 (GSM4259941).
- count_tet_12_5uM_rep2
- Raw cDNA amplicon count for 12.5 µM tetracycline biological replicate 2 (GSM4259942).
- count_tet_12_5uM_rep3
- Raw cDNA amplicon count for 12.5 µM tetracycline biological replicate 3 (GSM4259943).
- count_tet_12_5uM_rep4
- Raw cDNA amplicon count for 12.5 µM tetracycline biological replicate 4 (GSM4259944).
- count_tet_12_5uM_rep5
- Raw cDNA amplicon count for 12.5 µM tetracycline biological replicate 5 (GSM4259945).
- count_tet_12_5uM_rep6
- Raw cDNA amplicon count for 12.5 µM tetracycline biological replicate 6 (GSM4259946).
- count_tet_12_5uM_rep7
- Raw cDNA amplicon count for 12.5 µM tetracycline biological replicate 7 (GSM4259947).
- count_tet_12_5uM_rep8
- Raw cDNA amplicon count for 12.5 µM tetracycline biological replicate 8 (GSM4259948).
- count_tet_25uM_rep1
- Raw cDNA amplicon count for 25 µM tetracycline biological replicate 1 (GSM4259949).
- count_tet_25uM_rep2
- Raw cDNA amplicon count for 25 µM tetracycline biological replicate 2 (GSM4259950).
- count_tet_25uM_rep3
- Raw cDNA amplicon count for 25 µM tetracycline biological replicate 3 (GSM4259951).
- count_tet_25uM_rep4
- Raw cDNA amplicon count for 25 µM tetracycline biological replicate 4 (GSM4259952).
- count_tet_25uM_rep5
- Raw cDNA amplicon count for 25 µM tetracycline biological replicate 5 (GSM4259953).
- count_tet_25uM_rep6
- Raw cDNA amplicon count for 25 µM tetracycline biological replicate 6 (GSM4259954).
- count_tet_25uM_rep7
- Raw cDNA amplicon count for 25 µM tetracycline biological replicate 7 (GSM4259955).
- count_tet_25uM_rep8
- Raw cDNA amplicon count for 25 µM tetracycline biological replicate 8 (GSM4259956).
- count_tet_50uM_rep1
- Raw cDNA amplicon count for 50 µM tetracycline biological replicate 1 (GSM4259957).
- count_tet_50uM_rep2
- Raw cDNA amplicon count for 50 µM tetracycline biological replicate 2 (GSM4259958).
- count_tet_50uM_rep3
- Raw cDNA amplicon count for 50 µM tetracycline biological replicate 3 (GSM4259959).
- count_tet_50uM_rep4
- Raw cDNA amplicon count for 50 µM tetracycline biological replicate 4 (GSM4259960).
- count_tet_50uM_rep5
- Raw cDNA amplicon count for 50 µM tetracycline biological replicate 5 (GSM4259961).
- count_tet_50uM_rep6
- Raw cDNA amplicon count for 50 µM tetracycline biological replicate 6 (GSM4259962).
- count_tet_50uM_rep7
- Raw cDNA amplicon count for 50 µM tetracycline biological replicate 7 (GSM4259963).
- count_tet_50uM_rep8
- Raw cDNA amplicon count for 50 µM tetracycline biological replicate 8 (GSM4259964).
- mean_cpm_untreated
- Mean per-sample counts-per-million for untreated replicates, normalized within each Twister sublibrary.
- mean_cpm_tet_12_5uM
- Mean per-sample counts-per-million for 12.5 µM tetracycline replicates, normalized within each Twister sublibrary.
- mean_cpm_tet_25uM
- Mean per-sample counts-per-million for 25 µM tetracycline replicates, normalized within each Twister sublibrary.
- mean_cpm_tet_50uM
- Mean per-sample counts-per-million for 50 µM tetracycline replicates, normalized within each Twister sublibrary.
- log2fc_tet_12_5uM_vs_untreated
- Published edgeR log2 fold change for 12.5 µM tetracycline versus untreated.
- fdr_tet_12_5uM_vs_untreated
- Published Benjamini–Hochberg FDR for the 12.5 µM versus untreated comparison.
- significant_tet_12_5uM_vs_untreated_fdr_0_05
- True when the published FDR for 12.5 µM versus untreated is ≤ 0.05.
- 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; 5b.
- source_stats_available
- Indicates that published log2FC and FDR values are available for the row.
Quality control
The authors evaluated library abundance, replicate concordance, GC dependence, and low-abundance behavior. 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 all three tetracycline contrasts. All 18,432 input constructs passed these filters.
Curation notes
The nine sublibraries are represented as the pattern_name column so they remain analyzable in one table. The raw GEO archive also contains library-QC samples outside this experiment’s 32 screen samples; those inputs are preserved in raw_data but not mixed into the table. The library is fully synthetic, so no reference genome or genomic interval applies.