A locus-wide episomal STARR-seq library was built from 11 murine BACs spanning the Tbx3/Tbx5 regulatory domain and transfected into COS-7 cells. The processed table contains deposited murine intervals responsive to SG4 or Wnt co-transfection relative to pcDNA control, with replicate support and BAC provenance annotations.
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:0224
Reference genome
mm9
Design focus
Region-focused
Region of interest
chr5:118828656-120745441
Perturbation & assay details
pcDNA control; SG4 (Smad1, Smad4, Alk3, and Gata4); Wnt (Tcf4 plus LiCl)
BAC DNA was sonicated to approximately 500–1000 bp fragments and cloned into a pSTARR self-transcribing reporter. Murine library transfections used COS-7 cells; SG4 and Wnt response libraries were compared with pcDNA control. The processed table is an interval-call table rather than an oligo-level RNA/DNA count matrix because GEO deposited thresholded BED calls and normalized BigWig tracks, not the underlying per-fragment score table.
Processed data
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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 · 26 definitions
element_id
Stable identifier composed from assay, condition, replicate, and original BED line number.
library_species
Species of the genomic BAC library tested.
reference_genome
Genome assembly used for the deposited coordinates.
chromosome
Chromosome name from the BED call.
start_0based
0-based inclusive interval start from BED.
end_0based
0-based exclusive interval end from BED.
length_bp
Interval length in base pairs.
coordinate
Human-readable chromosome:start-end representation of the BED interval.
condition
Response condition that exceeded the source threshold: SG4 or Wnt.
replicate
Deposited replicate number for the response condition.
Whether this call overlaps a call from another replicate of the same condition by at least 50 bp.
replicate_support_count
Number of condition replicates with a call overlapping this interval by at least 50 bp, including its own replicate.
call_reproducibility
Replicate overlap classification for the source call.
bac_id
One or more source BAC identifiers overlapping the interval.
bac_coordinates
mm9 coordinates of the overlapping source BAC(s) from Supplementary Table 7.
response_bigwig_file
Deposited response-condition BigWig filename when available; blank for Wnt because GEO supplied no matching Wnt BigWig.
control_bigwig_file
Matched deposited pcDNA control BigWig filename when available; blank when no matching response BigWig is available.
mean_response_track_signal
Mean value of the deposited response BigWig over the interval; a normalized track signal, not an imputed log2 effect size.
mean_control_track_signal
Mean value of the matched deposited pcDNA BigWig over the interval; a normalized track signal.
active_call
All retained rows are active source BED calls.
qc_pass
True for rows retained after source-call and package QC filters.
Quality control
The authors mapped reads to mm9, compared 50-bp bins with bamCompare, excluded bins with read count <75, merged adjacent bins, and called responsive regions at log2(response/control) >0.585 (fold change >1.5). Package QC additionally required valid nonnegative BED coordinates, intervals at least 50 bp long, and overlap with at least one murine source BAC from Supplementary Table 7; exact duplicates were absent. One off-library chr19 call was excluded. Retained rows are source-positive calls: 180 SG4 replicate 1, 216 SG4 replicate 2, and 253 Wnt replicate 1 (649 total). Calls overlapping the other SG4 replicate by at least 50 bp are annotated but not required, because Wnt has one deposited replicate.
Curation notes
The paper’s allele-specific variant tests were follow-up luciferase assays, so this STARR-seq table intentionally reports region-level regulatory calls rather than fabricating rsID/allele effects. The deposited BED line counts (181/216 SG4 and 253 Wnt before package QC) differ slightly from the counts stated in the article Results (216 SG4 and 257 Wnt); the table follows the public GSE145257 files and records source lines for traceability. The eLife data-availability metadata names GSE125257, but that accession is currently unrelated; GSE145257 is the matching TBX3 STARR-seq series. COS-7 is represented by Cellosaurus CVCL:0224; the target organism denotes the mouse library sequence source.