Experiment / E4TO59SL8Silencer / Repressor MPRA

K562 ReSE silencer screen

Systematic identification of silencers in human cells

A pooled library of approximately 200-bp K562 FAIRE-enriched genomic fragments was integrated into K562 cells upstream of an EF-1α-FKBP-Casp9 reporter. 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:0004
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, surviving cells expanded for 5 days (versus untreated control)

The ReSE library contained more than 177,000 FAIRE-enriched fragments from K562 cells, cloned approximately 15 bp upstream of the EF-1α promoter in pLenti-FKBP-delCasp9-Puro. Lentivirus was delivered at MOI 0.5. Silencer-mediated repression of FKBP-Casp9 allowed cells to survive AP20187-induced apoptosis; surviving inserts were quantified by Illumina sequencing. Reads were aligned to hg19 with Bowtie, quality ≥30 reads were counted with HTSeq, and median-normalized counts were analyzed with a MAGeCK negative-binomial model.

Processed data

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

Visible columns (7 of 7)

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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 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 2,664 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 processed table is the authors' FDR < 0.01 hit list and does not contain raw per-replicate counts or oligo sequences. K-562 was resolved to Cellosaurus CVCL:0004.

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