CapStarr-seq enhancer activity in NIH-3T3 mouse fibroblasts
High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seqThe same targeted CapStarr-seq library of approximately 7,542 mouse candidate CRMs was transfected into NIH-3T3 fibroblasts as a non-lymphoid control condition. The table contains the 7,152 candidate CRMs passing the source input-library capture filter, with NIH-3T3 fold-change activity and the authors' activity class.
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 NIH-3T3 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. NIH-3T3 is the ATCC CRL-1658 fibroblast line and serves as the non-lymphoid comparison condition; the GEO series supplies one NIH-3T3 output sample.
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 · 11 definitions
- element_id
- Stable derived identifier from candidate CRM 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.
- 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; these are regulatory-domain associations rather than experimentally demonstrated enhancer targets.
- nih3t3_fold_change
- NIH-3T3 CapStarr-seq signal over input-library signal, reported as a fold change.
- nih3t3_log2_activity
- Derived log2 of the NIH-3T3 fold change; blank when the source fold change is zero or unavailable.
- activity_class
- Authors' NIH-3T3 activity group: Inactive, Weak, or Strong.
- qc_pass
- true for every retained row; all candidate CRMs passed the authors' input-FPKM capture filter.
- source_supplementary_data
- Publisher Supplementary Data 1, the CRM activity workbook.
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. CRMs with input FPKM <1 were excluded (390 of 7,542), leaving the 7,152 candidate CRMs in this table; NIH-3T3 fold change was classified 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 CTCF-control workbook reports only merged P5424 scores, so those controls are retained in the P5424 child table and not duplicated here as rows without NIH-3T3 measurements.
Curation notes
NIH-3T3 is represented by Cellosaurus CVCL:0594 and was used as a non-lymphoid fibroblast control for the P5424 T-cell condition. The 7,152 candidate CRM rows contain 4,407 Inactive, 2,559 Weak, and 186 Strong NIH-3T3 calls. The source workbook does not report a separate NIH-3T3 replicate-level table for these scores; the GEO series lists one NIH-3T3 CapStarr-seq sample. CTCF controls are not duplicated because Supplementary Data 2 reports only their merged P5424 score.