A single-hit scanning library of variants of the human interferon-beta (IFNB) enhancer was assayed in HEK293T/17 cells after Sendai virus infection. Each variant was represented by multiple 10-nt reporter tags in one biological transfection replicate.
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Organism
Human
Taxonomy ID
NCBITaxon:9606
Biosample
CVCL:1926
Reference genome
NCBI36/hg18
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Sendai virus infection at MOI 10 for 16 h (induced state)
The library used 142-mer oligonucleotides containing an 87-nt variable enhancer sequence, a 10-nt identifying reporter tag, and invariant cloning sequences. Variants were cloned upstream of a minimal TATA-box promoter and luc2 ORF in a plasmid MPRA vector, transfected into HEK293T/17 cells, and quantified by 36-nt single-end Illumina Tag-Seq of reporter mRNA and plasmid DNA. Single-hit scanning: approximately 1,000 IFNB variants; 13 tags per variant before plasmid-count filtering; 65 wild-type enhancer-tag pairs in the deposited count files. Sample accessions: GSM792107, GSM792108. The source activity ratios are author-provided median normalized mRNA/plasmid tag ratios for the virus-induced state.
Processed data
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Visible columns (18 of 18)
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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 · 18 definitions
variant_id
Unique variant identifier assigned in the deposited library.
sequence
The 87-nt variable enhancer sequence from the deposited variant library.
variant_class
Library design class inferred from the deposited variant identifier.
design_position_0based
0-based scanning start position or split-scan offset encoded in the variant identifier; blank for controls/random variants.
designed_alt_base
Designed alternate base for single-substitution variants; blank for other designs.
sequence_length
Length of the deposited variable sequence in nucleotides; insertion variants are longer than 87 nt.
n_substitutions_vs_reference
Number of same-length nucleotide mismatches relative to the library wild-type sequence; blank for insertion variants.
changed_positions_0based
Comma-separated 0-based positions differing from the same-length wild-type sequence; blank for insertion variants.
tag_sequences
Semicolon-separated 10-nt reporter tags retained after the paper plasmid-count filter.
n_valid_tags_rep1
Number of retained reporter tags contributing to the induced activity ratio.
dna_count_sum_rep1
Sum of raw plasmid DNA tag counts over retained tags.
rna_count_sum_rep1
Sum of raw reporter mRNA tag counts over retained tags.
activity_ratio_induced_rep1
Author-provided library-size-normalized mRNA/plasmid activity ratio in the induced replicate.
log2_activity_induced_rep1
Base-2 logarithm of the induced activity ratio.
mean_log2_activity_induced
The single induced replicate log2 activity value.
wt_normalized_log2_activity_induced
Induced log2 activity minus the mean across deposited hINFB1_enhancer wild-type controls.
published_pvalue_rep1
Author-provided Mann-Whitney p-value versus wild-type for the induced replicate.
qc_pass
True for rows retained after source plasmid-count and finite-activity QC.
Quality control
The paper required exact tag/construct matching, discarded tags with plasmid counts below 20 in every relevant plasmid pool, normalized mRNA/plasmid ratios by total plasmid-to-mRNA tag counts, and used Mann-Whitney tests with 5% FDR for single-hit variant comparisons. Package QC retained 1000 of 1000 rows available in the corresponding author ratio worksheet and excluded 0 rows. Tag-level filtering leaves 4–13 valid reporter tags per variant; no arbitrary minimum tag count was imposed beyond retaining at least one source-valid tag.
Curation notes
The processed activity_ratio columns are taken from the author-provided Supplementary Table ratio worksheets so that the reported plasmid-count filtering and total-count normalization are preserved. Raw DNA/RNA count summaries and tag sequences are joined from the GEO GSE31982 count archive. WT-normalized values use the mean of the deposited wild-type-control rows (synCRE_Promega_* or hINFB1_enhancer_*). CRE is synthetic and has no genomic coordinate; the IFNB variable sequence was derived from NCBI36/hg18, but the paper does not provide an exact coordinate for this 87-nt tested fragment. The single-hit libraries contain induced-state data only; paired inducibility is available in the multi-hit tables.