CRE multi-hit sampling MPRA in forskolin-induced and vehicle-treated HEK293T/17 cells
Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assayA multi-hit sampling library of randomized synthetic CRE variants was assayed in HEK293T/17 cells in paired forskolin-induced and DMSO vehicle states. Each variant was represented by one reporter tag and measured in two biological transfection replicates per state.
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
100 uM forskolin for 5 h (induced) versus DMSO vehicle for 5 h (uninduced)
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. Multi-hit sampling: approximately 27,000 CRE variants, one tag per variant, assayed in two induced and two uninduced libraries. Sample accessions: GSM792091-GSM792098. The source activity ratios are author-provided normalized mRNA/plasmid tag ratios for induced and uninduced states.
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 · 33 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_sequence
- The single 10-nt reporter tag associated with the variant.
- dna_count_induced_rep1
- Raw plasmid DNA count for induced replicate 1.
- rna_count_induced_rep1
- Raw reporter mRNA count for induced replicate 1.
- activity_ratio_induced_rep1
- Author-provided library-size-normalized mRNA/plasmid activity ratio for induced replicate 1.
- log2_activity_induced_rep1
- Base-2 logarithm of the induced replicate-1 activity ratio.
- dna_count_induced_rep2
- Raw plasmid DNA count for induced replicate 2.
- rna_count_induced_rep2
- Raw reporter mRNA count for induced replicate 2.
- activity_ratio_induced_rep2
- Author-provided library-size-normalized mRNA/plasmid activity ratio for induced replicate 2.
- log2_activity_induced_rep2
- Base-2 logarithm of the induced replicate-2 activity ratio.
- dna_count_uninduced_rep1
- Raw plasmid DNA count for uninduced replicate 1.
- rna_count_uninduced_rep1
- Raw reporter mRNA count for uninduced replicate 1.
- activity_ratio_uninduced_rep1
- Author-provided library-size-normalized mRNA/plasmid activity ratio for uninduced replicate 1.
- log2_activity_uninduced_rep1
- Base-2 logarithm of the uninduced replicate-1 activity ratio.
- dna_count_uninduced_rep2
- Raw plasmid DNA count for uninduced replicate 2.
- rna_count_uninduced_rep2
- Raw reporter mRNA count for uninduced replicate 2.
- activity_ratio_uninduced_rep2
- Author-provided library-size-normalized mRNA/plasmid activity ratio for uninduced replicate 2.
- log2_activity_uninduced_rep2
- Base-2 logarithm of the uninduced replicate-2 activity ratio.
- mean_log2_activity_induced
- Arithmetic mean of induced replicate log2 activity values.
- mean_log2_activity_uninduced
- Arithmetic mean of uninduced replicate log2 activity values.
- log2_inducibility
- Mean induced log2 activity minus mean uninduced log2 activity.
- induced_over_uninduced_fold_change
- 2 raised to log2_inducibility; induced-to-uninduced activity fold change.
- wt_normalized_log2_activity_induced
- Mean induced log2 activity minus the mean across synCRE_Promega wild-type controls.
- wt_normalized_log2_activity_uninduced
- Mean uninduced log2 activity minus the mean across synCRE_Promega wild-type controls.
- wt_normalized_log2_inducibility
- Variant log2 inducibility minus wild-type-control mean log2 inducibility.
- qc_pass
- True for rows present in the author ratio worksheet and passing finite positive-activity validation.
Quality control
The paper required exact tag/construct matching, discarded tags with plasmid counts below 20 in every sequenced plasmid pool, normalized mRNA/plasmid ratios by total plasmid-to-mRNA tag counts, and used permutation tests with 5% FDR for information footprints. Package QC retained 26437 of 26437 rows available in the corresponding author ratio worksheet and excluded 0 rows; the retained rows have finite positive activity ratios. This multi-hit library uses one reporter tag per variant, so no multi-tag minimum was imposed.
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.