Experiment / E0MCH8H6TEpisomal Plasmid MPRA

HLA-G locus tiling MPRA in JEG3 cells

A distant trophoblast-specific enhancer controls HLA-G expression at the maternal–fetal interface

A 12,000-oligonucleotide library of partially overlapping 121-bp tiles spanning a 27-kb HLA-G locus was cloned into pGL4 reporter plasmids and tested in JEG3 cells with minimal TATA-box (minP) and strong SV40 (SV40P) promoters. The table contains the published Fig. 1A marker observations, recovered from the source PDF as approximate figure values.

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Organism: Human
Taxonomy ID: NCBITaxon:9606
Biosample: CVCL:0363
Reference genome: hg19
Design focus: Region-focused
Region of interest: chr6:29775000-29805000

Perturbation & assay details

Basal / Untreated

Microarray-synthesized 121-bp tiles were coupled to unique DNA tags and cloned into a pGL4 backbone with invariant firefly luciferase and either minP or SV40P. Reporter pools were cotransfected into JEG3 cells with FuGENE 6; DNA and cellular mRNA tags were sequenced in two biological replicate MPRA transfections. Enhancer activity was the tile median cDNA/DNA tag ratio divided by the library-wide median ratio.

Processed data

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

Visible columns (12 of 12)

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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 · 12 definitions

figure_point_id: Unique row identifier assigned during extraction from Fig. 1A
element_id: Approximate HLA-G tile identifier derived from the plotted hg19 coordinate; original oligo IDs were not deposited
promoter: Reporter promoter indicated by the marker shape: minP or SV40P
marker_shape: Published marker mapping: circle = minP and square = SV40P
tile_coordinate_kb: Approximate tile coordinate read from the Fig. 1A hg19 x-axis in kb
tile_coordinate_hg19_approx_bp: Approximate figure coordinate converted to base pairs
enhancer_activity_fold: Enhancer activity, defined as normalized median cDNA/DNA tag ratio; exact article-text values are used for candidate 1 and other values are approximate vector-figure readings
activity_gt_1_figure_estimate: Whether the displayed activity estimate exceeds 1
candidate_label: Top-ranked candidate label shown in the figure; blank when not labeled
qc_pass: True for points shown under the paper's P < 0.05-in-both-replicates display criterion
source_figure: Published figure source
value_source: Whether the value came from the article text or vector-figure extraction

Quality control

The Fig. 1A caption states that only tiles with P < 0.05 in both biological replicates are shown. The methods additionally define nominal candidates as activity >1 and P < 0.05 in both replicates; because replicate-level counts and P values were not deposited, the processed table retains all 95 plotted marker observations and reports the activity threshold separately rather than reconstructing it.

Curation notes

No tag-level MPRA count matrix, barcode manifest, or original tile identifiers were deposited. The table is a transparent extraction from the vector PDF of Fig. 1A. Candidate 1 uses the explicit article values of 8.4 (minP) and 12.4 (SV40P); the nearby high SV40P-only point is retained as a separate plotted tile. Approximate coordinates are read from the figure x-axis, and the figure's circle/square promoter mapping is preserved. GSE79779 is RNA-seq rather than MPRA and was not packaged as raw MPRA data.

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