Three-way EEP MPRA: Ap1m1 promoter library
Large-scale analysis of the integration of enhancer-enhancer signals by promotersOne of eight promoter-specific libraries in the three-way enhancer-enhancer-promoter (EEP) MPRA, using the Ap1m1 promoter with pairs of approximately 450 bp mouse regulatory elements or synthetic controls. The library was transiently transfected separately into E14TG2a mouse embryonic stem cells, and reporter cDNA/pDNA barcode ratios were summarized across three biological replicates.
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
Basal / Untreated (2i+LIF culture)
Transient episomal downstream reporter assay. The barcoded pSMART-based GFP reporter contained an approximately 400 bp promoter and two approximately 450 bp enhancer/control fragments cloned as a random duplet after the barcode; inverse PCR linked barcodes to inserts, and normalized cDNA:pDNA barcode ratios provided activity values.
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 · 46 definitions
- combination_id
- Unique identifier for the tested two-element combination, including orientations.
- combination_class
- Element composition class derived from source labels: EE, ER, RE, or RR; E denotes a genomic enhancer and R a synthetic randomized control.
- source_combination_class
- Original class field from Supplementary Table 3, retained for provenance; its legacy E/R prefix can label shuffled controls as E.
- promoter_id
- Study identifier for the promoter used in this library.
- promoter_gene
- Promoter gene/library label.
- promoter_chrom
- mm10 chromosome for the promoter fragment from Supplementary Table 1.
- promoter_start
- 0-based mm10 start coordinate of the promoter fragment.
- promoter_end
- 0-based mm10 end coordinate of the promoter fragment.
- element1_id
- Fragment identifier in enhancer position 1.
- element1_orientation
- Cloned orientation of element 1 (+ or -).
- element1_type
- Element 1 category: Enhancer or Randomized control.
- element1_source
- Enhancer cluster/source label for element 1; Controls denotes a synthetic control.
- element1_chrom
- mm10 chromosome for element 1; NA for synthetic controls.
- element1_start
- 0-based mm10 start coordinate for element 1; NA for synthetic controls.
- element1_end
- 0-based mm10 end coordinate for element 1; NA for synthetic controls.
- element2_id
- Fragment identifier in enhancer position 2.
- element2_orientation
- Cloned orientation of element 2 (+ or -).
- element2_type
- Element 2 category: Enhancer or Randomized control.
- element2_source
- Enhancer cluster/source label for element 2; Controls denotes a synthetic control.
- element2_chrom
- mm10 chromosome for element 2; NA for synthetic controls.
- element2_start
- 0-based mm10 start coordinate for element 2; NA for synthetic controls.
- element2_end
- 0-based mm10 end coordinate for element 2; NA for synthetic controls.
- activity_rep1
- Activity ratio of normalized cDNA to pDNA barcode counts for biological replicate 1.
- activity_rep2
- Activity ratio of normalized cDNA to pDNA barcode counts for biological replicate 2.
- activity_rep3
- Activity ratio of normalized cDNA to pDNA barcode counts for biological replicate 3.
- activity_geometric_mean
- Geometric mean activity across the three biological replicates.
- library
- Promoter library name.
- promoter_baseline_activity
- Median activity across the promoter's control-control combinations.
- promoter_baseline_sd
- Standard deviation of control-control activities used with the promoter baseline.
- boost_index_log2
- Log2(activity_geometric_mean / promoter_baseline_activity).
- pair_context
- Study grouping for the pair: Controls, SingleControls, Rest, or an enhancer-cluster label.
- element1_single_activity
- Median activity estimate for element 1 from enhancer-control combinations; NA when not applicable.
- element1_single_n
- Number of enhancer-control measurements used for the element 1 estimate.
- element1_single_sd
- Standard deviation of enhancer-control activities used for element 1.
- element2_single_activity
- Median activity estimate for element 2 from enhancer-control combinations; NA when not applicable.
- element2_single_n
- Number of enhancer-control measurements used for the element 2 estimate.
- element2_single_sd
- Standard deviation of enhancer-control activities used for element 2.
- additive_expected_activity
- Expected additive activity, element1_single_activity + element2_single_activity - promoter_baseline_activity.
- additive_cooperation_log2
- Log2(observed activity / additive_expected_activity); NA when an additive expectation is unavailable.
- multiplicative_expected_activity
- Computed expected multiplicative activity, element1_single_activity * element2_single_activity / promoter_baseline_activity; NA when unavailable.
- multiplicative_cooperation_log2
- Author-provided log2 cooperation relative to the multiplicative expectation; original source header was MiltipCoop.
- element1_boost_index_log2
- Log2(element1_single_activity / promoter_baseline_activity).
- element2_boost_index_log2
- Log2(element2_single_activity / promoter_baseline_activity).
- cooperation_log2
- Author-provided cooperation value, boost_index_log2 - element1_boost_index_log2 - element2_boost_index_log2.
- element1_activity_ratio_to_baseline
- Linear element 1 activity ratio, element1_single_activity / promoter_baseline_activity.
- element2_activity_ratio_to_baseline
- Linear element 2 activity ratio, element2_single_activity / promoter_baseline_activity.
Quality control
The authors removed ambiguous barcode-to-duplet assignments, normalized cDNA and pDNA barcode counts per replicate, required at least 5 barcodes per duplet and at least 8 pDNA counts per barcode, and summarized three biological replicates using a geometric mean. The housekeeping Ap1m1 library had the lower reported replicate correlations (Pearson R=0.74–0.78). The source normalized table contributed 15868 rows for this promoter; package QC retained 15867 rows after requiring nonempty identifiers/class, finite boost index, and finite strictly positive replicate activities, aggregate activity, and promoter baseline, excluding 1 zero-activity row(s). NA values in class-specific single-element/cooperation fields are retained when those estimates are not applicable.
Curation notes
Promoter-specific split of the authors' normalized Supplementary Table 3/GEO data. GEO samples: iPCR GSM7703055; pDNA GSM7703082/GSM7703114; cDNA GSM7703083–GSM7703085 and GSM7703115–GSM7703117. Synthetic controls have no genomic coordinates and are represented as NA. The original source class field is retained as source_combination_class; combination_class and element*_type use the paper's Controls suffix label so shuffled controls are classified correctly.