HepG2 GRAMc genome-scale cis-regulatory activity
Unbiased genome-scale identification of cis-regulatory modules in the human genome by GRAMcTwo independent batches of an episomal, DNA-barcoded reporter library containing randomly fragmented approximately 800-bp human genomic inserts were assayed in HepG2 cells. The processed table contains the publicly reported repeat-element enrichment summary across GRAMc activity bins.
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
Random genomic fragments were cloned upstream of an SCP-GFP reporter and tagged with random N25 DNA barcodes. Input plasmid DNA barcode counts and expressed RNA barcode counts were used to estimate insert activity relative to background in two independent HepG2 batches. The study also describes separate transcription-factor perturbation validation libraries, but the packaged table is the genome-scale basal assay summary.
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 · 8 definitions
- repeat_class
- Published repeat-element or genomic repeat annotation category.
- total_annotated_elements
- Number of annotated elements in the corresponding reference repeat category.
- log2_enrichment_g5
- Published log2 enrichment of the repeat category in the strongest GRAMc activity bin (G5; >5x background).
- log2_enrichment_g4l5
- Published log2 enrichment in the G4L5 activity bin (>=4x and <5x background).
- log2_enrichment_g3l4
- Published log2 enrichment in the G3L4 activity bin (>=3x and <4x background).
- log2_enrichment_g2l3
- Published log2 enrichment in the G2L3 activity bin (>=2x and <3x background).
- log2_enrichment_g1l2
- Published log2 enrichment in the G1L2 activity bin (>=1x and <2x background).
- log2_enrichment_l1
- Published log2 enrichment in the inactive L1 activity bin (<1x background).
Quality control
The study combined barcode counts for each insert, retained inserts meeting the reported input and expressed-barcode count thresholds in both batches, normalized activity to the middle 30% background distribution, and called a CRM when one batch reached at least 5x background and the other reached at least 4.5x background. The two batches had Pearson correlation 0.95. For the packaged summary, rows were retained only when the published repeat label was non-empty, Total was a positive integer, and all non-Null scores were finite; all 57 published rows passed, with Null values represented as blank cells.
Curation notes
This is a genuine MPRA study, but the public sources accessible during ingestion did not provide a barcode-by-insert coordinate/count matrix or a downloadable GEO/SRA-style processed library table. The one-table-per-experiment constraint is therefore represented by the study's disclosed Table 2 repeat-element enrichment summary, which is useful for regulatory-element class analysis but is not a variant-level effect table. The requested bioRxiv full-text PDF was rate-limited; full_text.txt is a clearly labeled text extraction of the open GRAMc patent disclosure that reproduces the relevant methods and summary results.