CapStarr-seq enhancer activity in the P5424 mouse T-cell line
High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seqA targeted CapStarr-seq library captured approximately 400-bp fragments spanning 7,542 candidate mouse cis-regulatory modules (CRMs) and was transfected into the P5424 immature T-cell line. The table retains the authors' 7,152 input-qualified candidate CRMs plus the 69 published CTCF-bound control regions, with two P5424 biological replicate scores and the merged enhancer score where available.
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
Basal / Untreated
Genomic DNA from C57BL/6 mouse thymus was sheared, size-selected at approximately 330-430 bp, captured with a custom SureSelect microarray, and cloned by homologous recombination into a mammalian STARR-seq vector. The episomal reporter library was electroporated into P5424 cells; after 24 h, reporter RNA and plasmid DNA were sequenced on an Ion PGM, and enhancer activity was quantified as captured-sample FPKM divided by input-library FPKM. P5424 was tested in two biological replicates; the source table reports the pooled replicate score for downstream classification.
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 · 15 definitions
- element_id
- Stable derived identifier from element type and the reported genomic coordinates; the source workbook does not provide a separate element ID.
- element_type
- candidate_CRM for a captured candidate cis-regulatory module or CTCF_control for a published CTCF-bound control region.
- chromosome
- Mouse chromosome reported by the source workbook.
- start_mm9
- Reported genomic start coordinate on the mm9/NCBI37 assembly.
- end_mm9
- Reported genomic end coordinate on the mm9/NCBI37 assembly.
- associated_genes
- Comma-separated genes assigned to the candidate CRM by GREAT; blank for the CTCF controls because no gene association is reported in Supplementary Data 2.
- p5424_rep1_fold_change
- P5424 replicate 1 CapStarr-seq signal over input-library signal, reported as a fold change; blank for CTCF controls.
- p5424_rep1_log2_activity
- Derived log2 of the P5424 replicate 1 fold change; blank when the source fold change is zero or unavailable.
- p5424_rep2_fold_change
- P5424 replicate 2 CapStarr-seq signal over input-library signal, reported as a fold change; blank for CTCF controls.
- p5424_rep2_log2_activity
- Derived log2 of the P5424 replicate 2 fold change; blank when the source fold change is zero or unavailable.
- p5424_merged_fold_change
- Pooled P5424 CapStarr-seq signal over input-library signal, reported as a fold change; for CTCF controls this is the merged score supplied in Supplementary Data 2.
- p5424_merged_log2_activity
- Derived log2 of the pooled P5424 fold change; blank when the source fold change is zero or unavailable.
- activity_class
- Authors' activity group for the P5424 merged score: Inactive, Weak, or Strong.
- qc_pass
- true for every retained row; candidate CRMs passed the authors' input-FPKM capture filter and CTCF controls have a published quantified score.
- source_supplementary_data
- Publisher supplementary workbook supplying the row: Supplementary Data 1 for candidate CRMs or Supplementary Data 2 for CTCF controls.
Quality control
The authors mapped CapStarr-seq reads to mouse NCBI37/mm9, retained uniquely aligned reads and unique fragments to reduce PCR-amplification redundancy, and quantified elongated fragment overlaps with each CRM as FPKM. The two P5424 biological replicates were assessed separately and were highly reproducible (R²=0.90) before pooling. CRMs with input FPKM <1 were excluded (390 of 7,542), leaving 7,152 candidate CRMs; the authors classified merged P5424 fold change as Inactive (<1.5), Weak (1.5 to <3), or Strong (≥3). This package applies no additional exclusion to the published rows and derives finite log2 activity as log2(fold change); zero fold-change values have a blank log2 field. The 69 CTCF controls are retained exactly as published in Supplementary Data 2 because their merged P5424 scores are available.
Curation notes
P5424 is an immortalized mouse T-cell line derived from early developing T cells and is represented by Cellosaurus CVCL:WG84. The candidate CRM rows are the 7,152 regions retained after the paper's input-FPKM filter, with 4,440 Inactive, 2,279 Weak, and 433 Strong merged P5424 calls. The CTCF control sheet contains 69 regions and only merged P5424 fold changes, so replicate-level fields and associated genes are intentionally blank for those rows. Associated genes are GREAT regulatory-domain assignments, not experimentally demonstrated enhancer targets. The source calls the library CRMs rather than allelic variants; this is therefore a region-focused experiment.