FAIRE-coupled STARR-seq enhancer screen in LPS-activated murine splenic B cells
Organizational properties of a functional mammalian cis-regulomeFAIRE-derived genomic fragments from LPS-activated murine splenic B cells were cloned into a self-transcribing active regulatory region (STARR-seq) plasmid and electroporated into activated B cells. Libraries transfected at 48 hours (24-hour readout) or 60 hours (12-hour readout) after LPS activation were harvested at 72 hours; combined peak calls identify functional accessible enhancers.
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
10 µg/ml Salmonella typhimurium LPS for 72 hours; STARR-seq plasmid library transfected at 48 or 60 hours after activation
Episomal STARR-seq reporter containing native FAIRE-derived fragments downstream of the promoter and upstream of the polyadenylation site; the inserted enhancer sequence served as its own RNA-seq tag. Fragments were approximately 100–400 bp and the reported peak calls were 300 bp; 12-hour and 24-hour post-transfection conditions were represented by biological and library replicates. The GEO release provides enhancer-level peak calls rather than continuous per-element RNA/DNA ratios or barcode-level effect estimates.
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 · 28 definitions
- element_id
- Stable element identifier; published ABC enhancer name where available, otherwise a deterministic STARR-seq coordinate identifier
- published_abc_ids
- Semicolon-separated published ABC enhancer name(s) linked to this enhancer coordinate
- chromosome
- mm9 chromosome
- start_mm9
- 0-based start coordinate of the STARR-seq peak in mm9
- end_mm9
- 0-based exclusive end coordinate of the STARR-seq peak in mm9
- width_bp
- Peak width in base pairs
- strand
- Strand reported/used for the STARR-seq enhancer call; * indicates strand-independent testing
- starrseq_peak_set
- STARR-seq peak-call timing set represented in this row
- starr_positive
- TRUE for a released STARR-seq peak passing the authors' peak-calling workflow
- faire_overlap
- TRUE because the source set is the released STARR-seq peak set overlapping FAIRE-seq peaks
- faire_peak_overlap_count
- Number of released activated-B-cell FAIRE-seq peak intervals overlapping this enhancer
- enhancer_promoter_link_count
- Number of enhancer-promoter links for this enhancer coordinate in the supplementary cis-regulome workbook
- target_gene_count
- Number of distinct target genes in the supplementary enhancer-promoter links
- target_genes
- Semicolon-separated target gene symbols from the supplementary workbook
- target_transcript_count
- Number of distinct target transcript identifiers in the supplementary links
- target_transcript_ids
- Semicolon-separated target transcript identifiers from the supplementary workbook
- target_transcripts
- Semicolon-separated target transcript names from the supplementary workbook
- min_enhancer_promoter_distance_bp
- Minimum reported enhancer-to-promoter distance across linked promoters
- median_enhancer_promoter_distance_bp
- Median reported enhancer-to-promoter distance across linked promoters
- max_enhancer_promoter_distance_bp
- Maximum reported enhancer-to-promoter distance across linked promoters
- hic_interaction_count
- Number of distinct released Hi-C interaction rows whose anchors overlap a linked enhancer-promoter pair
- hic_interaction_read_count_max
- Maximum interaction read count among matched released Hi-C rows
- hic_z_score_max
- Maximum Hi-C interaction z-score among matched released rows
- hic_logp_min
- Minimum (most significant) Hi-C logP value among matched released rows
- h3k27ac_peak_overlap_count
- Number of released activated-B-cell H3K27ac peak intervals overlapping this enhancer
- h3k4me3_peak_overlap_count
- Number of released activated-B-cell H3K4me3 peak intervals overlapping this enhancer
- super_enhancer_overlap_count
- Number of released activated-B-cell H3K27ac super-enhancer intervals overlapping this enhancer
- qc_pass
- TRUE for rows retained after source-call and package interval/duplicate QC
Quality control
The authors retained unique paired-end tags, discarded tags longer than 1 kb, removed random-scaffold, mitochondrial, cross-chromosome and mm9-blacklisted mappings, and called 300-bp peaks with HOMER findPeaks (-size 300 -minDist 300 -L 0 -center -fdr 0.05); replicate STARR-seq tags were combined for peak calling. For this package, exact duplicate enhancer coordinates and invalid intervals were removed. The table contains the 11,808 unique rows in the released STARR-seq/FAIRE-seq overlap BED, and every retained row is an author-reported positive functional call.
Curation notes
The study contains STARR-seq libraries transfected at two time points (48 and 60 hours after LPS activation) with replicate and library runs; the authors combined replicate tags for the reported calls. No continuous MPRA activity/effect-size table was included in the compact GEO supplementary release, so this package uses one row per unique released STARR-seq/FAIRE-overlap peak and adds genomic context. The source overlap BED contains 11,809 rows but one exact duplicate; after de-duplication the table contains 11,808 rows. The published cis-regulome workbook contains 32,422 enhancer-promoter links, 9,521 unique enhancer coordinates and 9,522 enhancer IDs; one coordinate is associated with two IDs. Of the 11,808 functional peaks, 9,521 have published ABC links and 2,287 remain unlinked in that workbook and therefore have blank target fields. Hi-C fields were computed by half-open interval overlap of released Hi-C anchors against the released workbook enhancer/promoter intervals; histone fields are counts of overlaps with released BED peaks. Coordinates retain the source mm9 convention.