A standard episomal STARR-seq library of FAIRE-derived genomic fragments was transfected into primary CD43-negative splenic B cells activated with LPS. Public processed data are the authors' combined 12 h/24 h (48 h/60 h transfection, RNA collected at 72 h) STARR-positive peaks overlapping FAIRE peaks, joined where possible to the supplementary enhancer-promoter resource.
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
CL:0000236
Reference genome
mm9
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
10 micrograms/ml LPS (Salmonella typhimurium) for 3 days; STARR-seq library transfected at 48 h or 60 h post-activation
Episomal mammalian STARR-seq vector with FAIRE-derived genomic fragments cloned between the GFP gene and SV40 poly(A); reporter RNA self-transcribes the tested enhancer fragment. The public processed file is a peak-call catalog rather than per-barcode DNA/RNA counts, RNA/DNA ratios, or allele-specific effects. The table includes the 11,808 unique STARR-positive peaks overlapping FAIRE-seq peaks and their available promoter/gene annotations.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (19 of 19)
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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 · 19 definitions
element_id
Stable package identifier derived from the mm9 chromosome and BED interval.
source_enhancer_id
Original enhancer identifier from the supplementary cis-regulome workbook; blank when no workbook annotation joined.
enhancer_name
Author-provided ABC enhancer name from the supplementary workbook; blank when unavailable.
chrom
mm9 chromosome from the GEO BED peak call.
start
Zero-based, half-open BED interval start coordinate.
end
Zero-based, half-open BED interval end coordinate.
length_bp
Peak interval length in base pairs, calculated as end minus start.
source_peak_set
GEO processed peak file from which the interval was taken.
starr_call_timepoints
Combined STARR-seq call spanning the 12 h and 24 h libraries.
overlaps_faire_peak
TRUE because every row is from the STARR-positive/FAIRE-overlap BED file.
in_cis_regulome_annotation
TRUE when the interval joined to at least one supplementary workbook enhancer-promoter record.
interaction_count
Number of enhancer-promoter interaction rows in the supplementary workbook for the interval.
target_gene_count
Number of unique annotated target genes for the interval.
target_genes
Semicolon-separated unique target gene symbols from the workbook.
target_transcript_ids
Semicolon-separated unique transcript identifiers from the workbook tx_id field.
target_transcript_names
Semicolon-separated unique transcript names from the workbook tx_name field.
min_promoter_distance_bp
Minimum workbook-reported enhancer-to-promoter distance in base pairs.
max_promoter_distance_bp
Maximum workbook-reported enhancer-to-promoter distance in base pairs.
qc_pass
TRUE for intervals retained after package-level coordinate validation and duplicate removal.
Quality control
Authors aligned paired-end reads with Bowtie (--very-sensitive -k 1 -m 500), generated BEDPE tags, removed random-scaffold, mitochondrial, interchromosomal, greater-than-1-kb and non-unique tags, called 300 bp peaks with HOMER findPeaks (-size 300 -minDist 300 -L 0 -center -fdr 0.05), combined replicate tags, and removed mm9 blacklisted regions. Package QC required a valid chr/start/end interval, end greater than start, and deduplicated identical intervals; 1 duplicate source row was removed, leaving 11,808 unique rows.
Curation notes
This is a region-focused STARR-seq enhancer screen, not an allele/variant MPRA; no rsIDs or alternative-allele contrasts are reported. The source overlap BED has 11,809 rows and 11,808 unique intervals. The workbook has 9,522 enhancer IDs across 9,521 unique coordinates; 9,521 overlap peaks could be joined to the workbook and 2,287 have no workbook promoter annotation. Public BED files contain no quantitative activity score, so no log2 RNA/DNA effect size was fabricated. GEO sample naming contains both 12 h and 24 h libraries plus plasmid controls; because the deposited peak call and enhancer IDs are combined, they are packaged as one experiment. The primary material is activated murine splenic B cells (CD43-negative), mapped here to the generic Cell Ontology B-cell term CL:0000236 because no more specific standardized terminal term was required by the source metadata.