Pilot Sharpr-MPRA (SV40P) in HepG2
Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regionsA low-resolution episomal MPRA tested 250 H3K27ac-marked candidate regulatory regions in HepG2. Each 385-bp region was represented by nine overlapping 145-bp constructs spaced at 30-bp offsets, with 24 independent 10-nt barcodes per tile and two biological transfection 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
The pilot library used the SV40 promoter and placed barcode sequences in the reporter 3-prime UTR. Published values are normalized log2 RNA/DNA ratios after adding a pseudocount of 1, library-size normalization, and subtracting the mean activity of the two outer tile positions as an approximate background. MPRA vector backbones are Addgene plasmids #49349, #49353, and #49354.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (60 of 60)
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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 · 60 definitions
- region_id
- Original PilotDesign region identifier.
- selection_group
- Pilot selection group: high, range, or controlhigh.
- region_index
- Integer region index within the selection group.
- chromosome
- hg19 chromosome for the tiled region.
- region_start
- 0-based inclusive hg19 start of the complete 385-bp pilot span.
- region_end
- 0-based exclusive hg19 end of the complete 385-bp pilot span.
- region_center
- Midpoint of the central tile (tile 4) in hg19 coordinates.
- region_length_bp
- Span of the nine overlapping 145-bp tiles in base pairs.
- tile_count
- Number of pilot tile positions represented in the row.
- mean_activity
- Mean of the nine replicate-averaged, end-recentered tile activities.
- sd_activity
- Population standard deviation of the nine replicate-averaged tile activities.
- region_score
- Signed activity at the tile with the largest absolute replicate-averaged activity; package-derived summary.
- max_abs_activity
- Absolute value of region_score.
- max_activity_tile
- 0-based pilot tile position with the largest absolute replicate-averaged activity.
- qc_pass
- TRUE when all nine tile positions have at least one original DNA barcode count >=20 in both plasmid replicates and all published activities are finite.
- tile_0_activity_rep1
- Published end-recentered log2 RNA/DNA activity for pilot tile 0, replicate 1.
- tile_0_valid_barcodes_rep1
- Number of tile-0 barcode measurements in replicate 1 whose original plasmid DNA count is >=20.
- tile_1_activity_rep1
- Published end-recentered log2 RNA/DNA activity for pilot tile 1, replicate 1.
- tile_1_valid_barcodes_rep1
- Number of tile-1 barcode measurements in replicate 1 whose original plasmid DNA count is >=20.
- tile_2_activity_rep1
- Published end-recentered log2 RNA/DNA activity for pilot tile 2, replicate 1.
- tile_2_valid_barcodes_rep1
- Number of tile-2 barcode measurements in replicate 1 whose original plasmid DNA count is >=20.
- tile_3_activity_rep1
- Published end-recentered log2 RNA/DNA activity for pilot tile 3, replicate 1.
- tile_3_valid_barcodes_rep1
- Number of tile-3 barcode measurements in replicate 1 whose original plasmid DNA count is >=20.
- tile_4_activity_rep1
- Published end-recentered log2 RNA/DNA activity for pilot tile 4, replicate 1.
- tile_4_valid_barcodes_rep1
- Number of tile-4 barcode measurements in replicate 1 whose original plasmid DNA count is >=20.
- tile_5_activity_rep1
- Published end-recentered log2 RNA/DNA activity for pilot tile 5, replicate 1.
- tile_5_valid_barcodes_rep1
- Number of tile-5 barcode measurements in replicate 1 whose original plasmid DNA count is >=20.
- tile_6_activity_rep1
- Published end-recentered log2 RNA/DNA activity for pilot tile 6, replicate 1.
- tile_6_valid_barcodes_rep1
- Number of tile-6 barcode measurements in replicate 1 whose original plasmid DNA count is >=20.
- tile_7_activity_rep1
- Published end-recentered log2 RNA/DNA activity for pilot tile 7, replicate 1.
- tile_7_valid_barcodes_rep1
- Number of tile-7 barcode measurements in replicate 1 whose original plasmid DNA count is >=20.
- tile_8_activity_rep1
- Published end-recentered log2 RNA/DNA activity for pilot tile 8, replicate 1.
- tile_8_valid_barcodes_rep1
- Number of tile-8 barcode measurements in replicate 1 whose original plasmid DNA count is >=20.
- tile_0_activity_rep2
- Published end-recentered log2 RNA/DNA activity for pilot tile 0, replicate 2.
- tile_0_valid_barcodes_rep2
- Number of tile-0 barcode measurements in replicate 2 whose original plasmid DNA count is >=20.
- tile_1_activity_rep2
- Published end-recentered log2 RNA/DNA activity for pilot tile 1, replicate 2.
- tile_1_valid_barcodes_rep2
- Number of tile-1 barcode measurements in replicate 2 whose original plasmid DNA count is >=20.
- tile_2_activity_rep2
- Published end-recentered log2 RNA/DNA activity for pilot tile 2, replicate 2.
- tile_2_valid_barcodes_rep2
- Number of tile-2 barcode measurements in replicate 2 whose original plasmid DNA count is >=20.
- tile_3_activity_rep2
- Published end-recentered log2 RNA/DNA activity for pilot tile 3, replicate 2.
- tile_3_valid_barcodes_rep2
- Number of tile-3 barcode measurements in replicate 2 whose original plasmid DNA count is >=20.
- tile_4_activity_rep2
- Published end-recentered log2 RNA/DNA activity for pilot tile 4, replicate 2.
- tile_4_valid_barcodes_rep2
- Number of tile-4 barcode measurements in replicate 2 whose original plasmid DNA count is >=20.
- tile_5_activity_rep2
- Published end-recentered log2 RNA/DNA activity for pilot tile 5, replicate 2.
- tile_5_valid_barcodes_rep2
- Number of tile-5 barcode measurements in replicate 2 whose original plasmid DNA count is >=20.
- tile_6_activity_rep2
- Published end-recentered log2 RNA/DNA activity for pilot tile 6, replicate 2.
- tile_6_valid_barcodes_rep2
- Number of tile-6 barcode measurements in replicate 2 whose original plasmid DNA count is >=20.
- tile_7_activity_rep2
- Published end-recentered log2 RNA/DNA activity for pilot tile 7, replicate 2.
- tile_7_valid_barcodes_rep2
- Number of tile-7 barcode measurements in replicate 2 whose original plasmid DNA count is >=20.
- tile_8_activity_rep2
- Published end-recentered log2 RNA/DNA activity for pilot tile 8, replicate 2.
- tile_8_valid_barcodes_rep2
- Number of tile-8 barcode measurements in replicate 2 whose original plasmid DNA count is >=20.
- tile_0_activity_mean
- Mean of the published replicate-1 and replicate-2 activities for pilot tile 0.
- tile_1_activity_mean
- Mean of the published replicate-1 and replicate-2 activities for pilot tile 1.
- tile_2_activity_mean
- Mean of the published replicate-1 and replicate-2 activities for pilot tile 2.
- tile_3_activity_mean
- Mean of the published replicate-1 and replicate-2 activities for pilot tile 3.
- tile_4_activity_mean
- Mean of the published replicate-1 and replicate-2 activities for pilot tile 4.
- tile_5_activity_mean
- Mean of the published replicate-1 and replicate-2 activities for pilot tile 5.
- tile_6_activity_mean
- Mean of the published replicate-1 and replicate-2 activities for pilot tile 6.
- tile_7_activity_mean
- Mean of the published replicate-1 and replicate-2 activities for pilot tile 7.
- tile_8_activity_mean
- Mean of the published replicate-1 and replicate-2 activities for pilot tile 8.
Quality control
The authors' SHARPR Normalize pipeline retained barcode measurements with original plasmid DNA counts >=20, added a pseudocount of 1, normalized RNA and DNA by library totals, and summarized barcodes per tile. This package additionally required all nine tile positions to have at least one DNA-qualified barcode in each plasmid replicate and required all published normalized values to be finite. 250 of 250 region rows passed this package QC; 0 were excluded.
Curation notes
The selection groups are high, range, and controlhigh; they reflect how pilot regions were selected from H3K27ac dip scores and are not allelic variant classes. Coordinates and sequences are retained in Pilot_counts_sequences.zip. region_score and max_abs_activity are package-derived summaries of the published tile-level table.