Enhancer L scanning-mutagenesis MPRA in JEG3 cells
A distant trophoblast-specific enhancer controls HLA-G expression at the maternal–fetal interfaceA second MPRA tested approximately 12,000 Enhancer L variants, including all single substitutions plus series of consecutive substitutions and small insertions/deletions, with an average of 16 tags per variant and approximately 200,000 variant–tag combinations. The table is a 121-position summary of the SV40P mutual-information bars and significance colors published in Fig. 4A.
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
The scanning-mutagenesis library used the same episomal pGL4/barcoded firefly-luciferase workflow in JEG3 cells. Fig. 4A shows the SV40P result; red bars indicate a significant change from original Enhancer L activity by Mann–Whitney U test at 5% FDR and blue bars are not significant. The figure also displays a nucleotide-level additive-contribution matrix, preserved in raw_data.
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 · 11 definitions
- element_id
- Unique position-level identifier for the 121-bp Enhancer L reference sequence
- variant_position_1based
- 1-based position within the 121-bp Enhancer L sequence represented on the Fig. 4A x-axis
- promoter
- Reporter promoter represented in Fig. 4A, SV40P
- mutual_information_bits_figure_estimate
- Approximate height of the Fig. 4A mutual-information bar in bits
- significance_5pct_fdr
- Whether the bar is red/significant by the paper's Mann–Whitney U test at 5% FDR
- effect_class
- Figure significance class: significant_change or not_significant
- motif_id
- Approximate left-to-right motif interval label M1–M5 read from the shaded regions in Fig. 4A; blank outside those intervals
- predicted_tf_family
- Approximate CEBP or GATA family label shown over the corresponding shaded motif interval
- qc_pass
- True because the position was plotted in Fig. 4A and retained; this is not a raw-read coverage flag
- source_figure
- Published figure source
- data_provenance
- Figure-vector extraction and precision note
Quality control
The paper reports an average of 16 tags per variant and classifies Fig. 4A bars using a Mann–Whitney U test with 5% FDR. Red/blue significance is an outcome flag, not a sequencing-QC exclusion. Since raw tag counts and per-variant coverage filters were not deposited, all 121 plotted position bars are retained and marked qc_pass=true; figure-derived mutual-information values are approximate.
Curation notes
No allele-level variant table, barcode manifest, tag counts, or reference/alternate base identities were deposited. This is therefore a position-level summary of the published Fig. 4A scan, not a reconstruction of all 12,000 variants. Bar heights were extracted from the vector PDF; sub-pixel bars are recorded as 0.000. Motif IDs and CEBP/GATA family labels are approximate assignments from the five shaded intervals and labels in Fig. 4A. The original raster additive-contribution matrix is preserved in raw_data/figure_4A_additive_matrix.jpg.