A capture-enriched episomal CapSTARR-seq library of approximately 400-bp mouse genomic fragments from 28,055 DP-thymocyte DHSs plus 437 random controls was cloned with the strong ubiquitous PGK promoter and transfected into P5424 T cells in triplicate under non-stimulated conditions. The table contains the published region-level centered log2 reporter RNA/input activity scores and silencer/inactive calls after input-FPKM filtering.
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Organism
Mouse
Taxonomy ID
NCBITaxon:10090
Biosample
CVCL:WG84
Reference genome
mm9
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
DMSO / non-stimulated (NS)
Capture-enriched STARR-seq used approximately 400-bp fragments captured from C57BL/6 genomic DNA with a custom microarray covering mouse DP-thymocyte DHSs and random non-DHS controls. Inserts were cloned into an episomal STARR reporter containing the strong ubiquitous human PGK promoter, transfected into P5424 cells in triplicate, and quantified by targeted RNA sequencing 24 hours later; the reported activity is the centered log2 RNA/input signal. The paper defines silencer activity as log2 activity <= -1.
Processed data
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Visible columns (14 of 14)
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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 · 14 definitions
element_id
Unique captured-region identifier from Supplementary Table S2.
chrom
Mouse chromosome in the mm9 reference assembly.
start
0-based inclusive start coordinate of the captured DHS or random-control region.
end
0-based half-open end coordinate of the captured DHS or random-control region.
length_bp
Region length in base pairs (end minus start).
region_type
Source region class: DHS or Random control.
closest_genes
Nearby gene annotations provided in Supplementary Table S2.
activity_class
Published activity call: inactive or silencer; source exclude calls were filtered out.
log2_activity
Published centered log2 CapSTARR-seq reporter RNA/input activity score after FPKM normalization; more negative values indicate stronger repression.
is_silencer
Binary indicator equal to 1 for the published silencer call and 0 otherwise.
is_enhancer
Binary indicator for a published enhancer call; no enhancer class is reported for this pPGK condition, so all retained values are 0.
source_library
CapSTARR-seq reporter promoter library used for the table.
source_sample_id
GEO accession for the transfected/cDNA CapSTARR-seq sample.
input_sample_id
GEO accession for the non-transfected plasmid input control used for normalization.
Quality control
The authors trimmed reads with Sickle (-q 20), mapped cDNA and input reads to mm9 with Bowtie2, converted alignments to BED with SAMtools/BedTools, counted unique captured clones, normalized counts by FPKM, centered activity values, and excluded regions with input FPKM <1. The source table's exclude calls were removed; retained rows were additionally required to have valid non-negative coordinates, end > start, a finite numeric activity score, and one of the published inactive/silencer calls. No additional rows failed these checks. Biological replicates were pooled for the published region-level scores; same-library replicate Spearman correlations were reported as 0.38-0.87.
Curation notes
The table is derived from Supplementary Table S2 and contains one row per captured region, with triplicate measurements already merged by the authors. It retains input-passing random controls as useful negative controls. This is a region-focused silencer screen, not an allele-contrast or variant library. The corresponding GEO samples are cDNA GSM6124249 and input GSM6124250; the GEO raw archive contains the merged cDNA BED file GSM6124249_CapStarr_pPGK_merge.bed.gz, while the input-normalized region scores are supplied in S2. The S2 source contains 672 silencer calls for this condition. P5424 is the mouse cell line P5424 (Cellosaurus CVCL:WG84).