Guanine-responsive HDV-ribozyme and hammerhead riboswitch screen
High-throughput identification of synthetic riboswitches by barcode-free amplicon-sequencing in human cellsA pooled guanine-responsive library tested 4,096 hepatitis-delta-virus ribozyme constructs and 16,384 hammerhead ribozyme constructs in the CMV-eGFP 3′ UTR of transiently transfected HEK-293H cells. Self-barcoding cDNA amplicon counts were measured after 3 h untreated, 30 µM, 100 µM, or 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 two pooled synthetic ribozyme libraries in the eGFP 3′ UTR: lib1 (HDV ribozyme) and lib2 (hammerhead ribozyme). Sequence-defined construct identities were quantified by cDNA amplicon sequencing on an Illumina NextSeq 500; published edgeR log2 fold changes and FDRs are joined from source-data sheets 3c and 4c.
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 pooled library pattern and the two variable sequence parts.
- pattern_name
- Pooled amplicon library pattern: lib1 is HDV ribozyme and lib2 is hammerhead ribozyme.
- 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 untreated, 30 µM, 100 µM, and 300 µM guanine conditions.
- count_untreated_rep1
- Raw cDNA amplicon count for untreated biological replicate 1 (GSM4259965).
- count_untreated_rep2
- Raw cDNA amplicon count for untreated biological replicate 2 (GSM4259966).
- count_untreated_rep3
- Raw cDNA amplicon count for untreated biological replicate 3 (GSM4259967).
- count_untreated_rep4
- Raw cDNA amplicon count for untreated biological replicate 4 (GSM4259968).
- count_untreated_rep5
- Raw cDNA amplicon count for untreated biological replicate 5 (GSM4259969).
- count_untreated_rep6
- Raw cDNA amplicon count for untreated biological replicate 6 (GSM4259970).
- count_untreated_rep7
- Raw cDNA amplicon count for untreated biological replicate 7 (GSM4259971).
- count_untreated_rep8
- Raw cDNA amplicon count for untreated biological replicate 8 (GSM4259972).
- count_gua_30uM_rep1
- Raw cDNA amplicon count for 30 µM guanine biological replicate 1 (GSM4259973).
- count_gua_30uM_rep2
- Raw cDNA amplicon count for 30 µM guanine biological replicate 2 (GSM4259974).
- count_gua_30uM_rep3
- Raw cDNA amplicon count for 30 µM guanine biological replicate 3 (GSM4259975).
- count_gua_30uM_rep4
- Raw cDNA amplicon count for 30 µM guanine biological replicate 4 (GSM4259976).
- count_gua_30uM_rep5
- Raw cDNA amplicon count for 30 µM guanine biological replicate 5 (GSM4259977).
- count_gua_30uM_rep6
- Raw cDNA amplicon count for 30 µM guanine biological replicate 6 (GSM4259978).
- count_gua_30uM_rep7
- Raw cDNA amplicon count for 30 µM guanine biological replicate 7 (GSM4259979).
- count_gua_30uM_rep8
- Raw cDNA amplicon count for 30 µM guanine biological replicate 8 (GSM4259980).
- count_gua_100uM_rep1
- Raw cDNA amplicon count for 100 µM guanine biological replicate 1 (GSM4259981).
- count_gua_100uM_rep2
- Raw cDNA amplicon count for 100 µM guanine biological replicate 2 (GSM4259982).
- count_gua_100uM_rep3
- Raw cDNA amplicon count for 100 µM guanine biological replicate 3 (GSM4259983).
- count_gua_100uM_rep4
- Raw cDNA amplicon count for 100 µM guanine biological replicate 4 (GSM4259984).
- count_gua_100uM_rep5
- Raw cDNA amplicon count for 100 µM guanine biological replicate 5 (GSM4259985).
- count_gua_100uM_rep6
- Raw cDNA amplicon count for 100 µM guanine biological replicate 6 (GSM4259986).
- count_gua_100uM_rep7
- Raw cDNA amplicon count for 100 µM guanine biological replicate 7 (GSM4259987).
- count_gua_100uM_rep8
- Raw cDNA amplicon count for 100 µM guanine biological replicate 8 (GSM4259988).
- count_gua_300uM_rep1
- Raw cDNA amplicon count for 300 µM guanine biological replicate 1 (GSM4259989).
- count_gua_300uM_rep2
- Raw cDNA amplicon count for 300 µM guanine biological replicate 2 (GSM4259990).
- count_gua_300uM_rep3
- Raw cDNA amplicon count for 300 µM guanine biological replicate 3 (GSM4259991).
- count_gua_300uM_rep4
- Raw cDNA amplicon count for 300 µM guanine biological replicate 4 (GSM4259992).
- count_gua_300uM_rep5
- Raw cDNA amplicon count for 300 µM guanine biological replicate 5 (GSM4259993).
- count_gua_300uM_rep6
- Raw cDNA amplicon count for 300 µM guanine biological replicate 6 (GSM4259994).
- count_gua_300uM_rep7
- Raw cDNA amplicon count for 300 µM guanine biological replicate 7 (GSM4259995).
- count_gua_300uM_rep8
- Raw cDNA amplicon count for 300 µM guanine biological replicate 8 (GSM4259996).
- mean_cpm_untreated
- Mean per-sample counts-per-million for untreated replicates, normalized within each pooled library pattern.
- mean_cpm_gua_30uM
- Mean per-sample counts-per-million for 30 µM guanine replicates, normalized within each pooled library pattern.
- mean_cpm_gua_100uM
- Mean per-sample counts-per-million for 100 µM guanine replicates, normalized within each pooled library pattern.
- mean_cpm_gua_300uM
- Mean per-sample counts-per-million for 300 µM guanine replicates, normalized within each pooled library pattern.
- 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 sheets supplying the published statistics: 3c for lib1/HDV and 4c for lib2/hammerhead (combined here as 3c/4c).
- 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 guanine contrasts. Of 20,480 input constructs, 20,478 passed; one construct failed the replicate-detection filter and one lacked a complete published statistic.
Curation notes
Both libraries were intentionally kept in one pooled experiment table and are distinguishable by pattern_name. Missing raw count rows were represented as zero before QC. The library is fully synthetic, so no reference genome or genomic interval applies.