Experiment / E1EPMJRADEpisomal Plasmid MPRA

Klf2 locus Downstream combinatorial MPRA

Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome

An episomal Downstream combinatorial MPRA library tested Klf2-locus cCREs downstream of reporter constructs carrying one of ten selected promoters. The clean table preserves both cCRE orientations and reports normalized reporter activity, the deposited adjusted boost statistic, and corrected cCRE-promoter boost indices across three biological replicates in E14TG2a mouse embryonic stem cells.

Download processed table (CSV)Raw source data API documentation

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.

Organism: Mouse
Taxonomy ID: NCBITaxon:10090
Biosample: CVCL:9108
Reference genome: mm10
Design focus: Region-focused
Region of interest: chr8:71885062-72761954

Perturbation & assay details

Basal / Untreated (E14TG2a mESCs cultured in 2i+LIF)

Ten selected Klf2-locus promoters were individually cloned upstream of the barcoded reporter transcription unit, and the pool of approximately 450-bp cCRE fragments was inserted downstream of the reporter, separated from the promoter by approximately 1 kb, in both orientations. The ten sublibraries were mixed for transfection. Three biological replicates were performed; barcodes were counted in cDNA and plasmid DNA, and activity was summarized as the geometric mean of normalized cDNA:pDNA ratios.

Processed data

50 rows per page. Click a cell to inspect its full value.

Visible columns (28 of 28)

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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 · 28 definitions

combination_id: Published cCRE-promoter pair identifier including cloned orientations.
combination_class: Source combination class; every retained row is EP, a cCRE-promoter pair.
enhancer_id: Study identifier for the cCRE inserted downstream of the reporter.
enhancer_orientation: Orientation of the downstream cCRE in the reporter construct (+ or -).
enhancer_chrom: mm10 chromosome for the cCRE fragment.
enhancer_start_mm10: 0-based half-open mm10 start coordinate of the cCRE fragment.
enhancer_end_mm10: 0-based half-open mm10 end coordinate of the cCRE fragment; end-start is 450 bp.
enhancer_sequence_mm10_forward: Reference forward-strand sequence of the cCRE insert from Data S1; it is not reverse-complemented when the cloned orientation is -.
promoter_id: Study identifier for the promoter cloned upstream of the reporter.
promoter_orientation: Orientation of the promoter in the reporter construct (+ or -).
promoter_chrom: mm10 chromosome for the promoter fragment.
promoter_start_mm10: 0-based half-open mm10 start coordinate of the promoter fragment.
promoter_end_mm10: 0-based half-open mm10 end coordinate of the promoter fragment; end-start is 450 bp.
promoter_sequence_mm10_forward: Reference forward-strand sequence of the promoter insert from Data S1; it is not reverse-complemented when the cloned orientation is -.
fragment_distance_bp: Distance in base pairs as deposited in the GEO source field dist.
pair_activity_rep1: Normalized cDNA:pDNA reporter activity for biological replicate 1.
pair_activity_rep2: Normalized cDNA:pDNA reporter activity for biological replicate 2.
pair_activity_rep3: Normalized cDNA:pDNA reporter activity for biological replicate 3.
pair_activity_geometric_mean: Geometric mean pair activity across the three biological replicates, as deposited in activity_all.
promoter_single_activity_rep1: Normalized activity for the promoter fragment alone in biological replicate 1, from activity_frag2_br1.
promoter_single_activity_rep2: Normalized activity for the promoter fragment alone in biological replicate 2, from activity_frag2_br2.
promoter_single_activity_rep3: Normalized activity for the promoter fragment alone in biological replicate 3, from activity_frag2_br3.
promoter_single_activity_geometric_mean: Geometric mean promoter activity across three replicates, from activity_frag2_all.
adjBoostP: Deposited Data S4/GEO field adjBoostP, copied verbatim as an adjusted boost-related statistic; the article does not define this header further and it was not used for package filtering.
promoter_baseline_median_activity: Deposited promoter-specific baseline median used in the source boost-index processing.
promoter_baseline_n: Deposited number of baseline observations used for the source baseline.
boost_index_log2: Corrected log2 cCRE-promoter boost index from Data S4/GEO, measuring pair activity relative to the promoter-specific baseline.
locus: Study locus label; Klf2 for every row in this child experiment.

Quality control

The authors aligned inverse-PCR reads to a custom fragment genome, clustered barcode sequencing errors with Starcode, removed barcodes present in multiple libraries or assigned to multiple element combinations, normalized cDNA and pDNA counts per sample, required at least 5 barcodes per singlet or combination and at least 8 pDNA counts per barcode, and calculated geometric-mean activities across three biological replicates. Downstream replicate concordance was reported as mean Pearson r=0.98 (range 0.98-0.99). Package QC restricted the deposited Data S4/GEO table to class=EP, required nonempty element identifiers and valid mm10 coordinates, and retained only finite three-replicate/aggregate pair activities and finite BoostIndex; all 1,364 of 1,364 Klf2 EP rows passed. The source adjBoostP field is retained verbatim and was not used as an additional filter.

Curation notes

The source Data S4/GEO table contains 2,364 Klf2 rows across multiple combination classes; this child keeps the 1,364 EP rows and all passed the finite-value QC. Data S1 sequences were joined by fragment identifier and locus. The source adjBoostP column is retained without assuming a threshold or a more specific interpretation than its deposited name. The table keeps orientation-specific pairs; the article averages cCRE orientations for several downstream analyses. This is a published processed-results table, not a raw barcode-count matrix.

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