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 synthetic SCP1 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 activity calls after input-FPKM filtering.
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.
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 synthetic SCP1 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 and SCP1 enhancer activity as log2 activity > 1.
Processed data
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Visible columns (14 of 14)
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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, silencer, or SCP1 enhancer; 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 equal to 1 for the published SCP1 enhancer call and 0 otherwise.
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/enhancer 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 (the final duplicated SCP1 header was interpreted as SCP1_signal from its paired status/signal values) 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/enhancer screen, not an allele-contrast or variant library. The corresponding GEO samples are cDNA GSM6124247 and input GSM6124248; the GEO raw archive contains the merged cDNA BED file GSM6124247_CapStarr_SCP1_merge.bed.gz, while the input-normalized region scores are supplied in S2. The S2 source contains 1,249 silencer calls and 943 enhancer calls for this condition. P5424 is the mouse cell line P5424 (Cellosaurus CVCL:WG84).