Genome-wide Ss-STARR-seq silencer screen in HEK293T cells
Uncovering the whole genome silencers of human cells via Ss-STARR-seqApproximately 300 bp randomly sheared human genomic fragments were cloned downstream of the hPGK promoter in the GFP-containing Ss-STARR-seq episomal reporter and transfected into HEK293T (293T) cells. CRADLE was used to call silencer intervals from input-library DNA versus cellular reporter RNA; the table contains the deposited interval-level activity calls.
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
Episomal self-transcribing reporter adapted for silencer detection: genomic fragments were placed downstream of a strong hPGK promoter, and reduced reporter RNA relative to input DNA indicates repression. Cells were collected 24 hours after nucleofection; the study included additional 293T output libraries to assess reproducibility.
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 · 9 definitions
- element_id
- Stable package identifier for the silencer interval within this experiment.
- chromosome
- hg38 chromosome name.
- start_0based
- 0-based inclusive interval start from the deposited BED file.
- end_0based_exclusive
- 0-based exclusive interval end from the deposited BED file.
- length_bp
- Interval length in base pairs, calculated as end minus start.
- midpoint_0based
- Interval midpoint in 0-based coordinates, calculated from start and end.
- activity_input_over_output
- Published Ss-STARR-seq silencer activity score, defined as normalized input DNA RPM divided by output RNA RPM; values >=2 meet the reported silencer cutoff.
- log2_activity_input_over_output
- Base-2 logarithm of the published input-over-output activity score.
- source_bed_row
- 1-based line number in the deposited BED file, including its header, retained for provenance.
Quality control
The study trimmed adapters, low-quality bases, and short reads with Trim Galore (-q20, length 25), aligned clean reads to hg38 with Bowtie2, removed PCR duplicates with Sambamba, retained reasonable paired-end alignments, tested bins with more than 20 reads, and applied CRADLE bias correction for shearing, PCR, mappability, and G-quadruplex effects. CRADLE peak calling used rbin=300, wbin=100, d=20, and FDR=0.05; final silencer calls required activity fold change >=2 in the three biological-replicate screen. For this package, rows were additionally required to have four valid fields, canonical hg38 chromosome names, in-bounds coordinates with length <=10,000 bp, finite numeric activity >=2, and unique coordinates. 125,247 of 125,307 deposited rows passed.
Curation notes
The GEO sample metadata incorrectly labels 293T as Mus musculus; the paper describes human cell lines, uses hg38, and HEK293T is a human Cellosaurus entry, so this experiment is standardized to Homo sapiens and CVCL:0063. The deposited BED reports 125,307 intervals; package QC excluded 60 malformed, noncanonical, out-of-bounds, implausibly long (>10 kb), or non-finite-activity rows, leaving 125,247 table rows. The table is an interval-level processed call set and does not contain raw sequencing reads.