Experiment / E3YJ2FY55Silencer / Repressor MPRA

HepG2 ReSE silencer screen

Systematic identification of silencers in human cells

The K562 FAIRE-enriched approximately 200-bp ReSE library was assayed in HepG2 cells. AP20187-selected survivors were compared with untreated controls in two biological replicates, and the table contains the published significantly enriched silencer fragments.

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Organism: Human
Taxonomy ID: NCBITaxon:9606
Biosample: CVCL:0027
Reference genome: hg19
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

1 nM AP20187 for 18 h; apoptotic cells removed by removing the medium, surviving cells expanded for 5 days (versus untreated control)

The same K562 FAIRE-enriched integrated ReSE lentiviral library was tested in adherent HepG2 cells at MOI 0.5. AP20187-induced apoptosis depleted cells lacking a repressive insert; surviving inserts were sequenced and analyzed with Bowtie against hg19, HTSeq quality-filtered counts, median normalization, and MAGeCK negative-binomial modeling.

Processed data

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

Visible columns (7 of 7)

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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 · 7 definitions

element_id: ReSE fragment identifier from the published ID field.
chrom: Chromosome for the tested fragment in hg19.
start: 0-based inclusive fragment start coordinate, matching the GEO BED file.
end: 0-based exclusive fragment end coordinate, matching the GEO BED file.
length_bp: Fragment length in base pairs, calculated as end minus start.
fdr: MAGeCK/BH false-discovery rate for enrichment after AP20187 selection in HepG2 cells versus untreated control.
fold_enrichment: Published semi-quantitative fold change/enrichment for the post-selection fragment abundance.

Quality control

The authors used two biological replicates, Bowtie alignment to hg19, a quality ≥30 read-count filter, median normalization for library size and count distributions, and MAGeCK negative-binomial testing with Benjamini–Hochberg FDR. Fragments with FDR < 0.01 were retained as significant hits. Package QC additionally required a valid hg19 chromosome, nonnegative start, end > start, unique element ID, finite FDR in [0, 0.01), and finite positive fold enrichment; the Supplementary Table and matching GEO BED file agreed for all 1,662 retained rows, so no source rows were removed.

Curation notes

This is a pooled integrated lentiviral ReSE survival screen rather than a conventional barcode RNA/DNA MPRA; it is categorized as Silencer / Repressor MPRA because pooled reporter constructs are selected for transcriptional repression and quantified by sequencing. The library was made from K562 FAIRE regions, so it is an accessible-chromatin subset rather than an unbiased whole-genome library. The processed table is the authors' FDR < 0.01 hit list and does not contain raw per-replicate counts or oligo sequences. Hep-G2 was resolved to Cellosaurus CVCL:0027.

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