FOXA1 knockout HEK293T UDI-UMI-STARR-seq
Quantifying the impact of genetic mutations on enhancer dynamicsA targeted library of candidate enhancer regions was assayed in HEK293T cells carrying a stable CRISPR/Cas9-mediated FOXA1 deletion, with three biological replicates and a matched CRISPR control (CC). The table reports fragment-level reporter activity, peak status, DESeq2 differential activity versus CC, and linked target-gene expression statistics where supplied.
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
CRISPR/Cas9-mediated deletion of FOXA1
Episomal UDI-UMI-STARR-seq adapted from CapSTARR-seq and UMI-STARR-seq. Sheared human genomic DNA fragments were enriched with custom hybridization/capture probes for 46,142 candidate enhancer regions, cloned into a STARR-seq plasmid, and subdivided into 500-bp windows with a 50-bp step. Output reporter RNA and input plasmid libraries carried UMI pairs and unique dual indexes; three biological replicates were performed per control/perturbation line, and 24 output plus 3 input libraries were sequenced as 150-bp paired-end reads. Activity is normalized output/input read depth; differential activity is the authors' DESeq2 log2 fold change for FOXA1 versus CC; target genes are from the authors' nearest-gene/ABC-linked Supplementary Data 3.
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 · 17 definitions
- fragment_id
- Unique source fragment identifier in chrom_start_end form; coordinates follow BED-like 0-based, half-open conventions.
- chromosome
- Chromosome parsed from fragment_id.
- start
- 0-based inclusive genomic start parsed from fragment_id.
- end
- 0-based exclusive genomic end parsed from fragment_id.
- fragment_length
- End minus start in bp; source rows range from 451 to 500 bp.
- control_activity_log2_output_input
- Source CC 'rpm' value: log2 of output reporter-read depth divided by input plasmid-read depth after library-size normalization.
- control_peak
- Binary STARRPeaker active-peak call for the CRISPR control (CC); 1 means active.
- control_category
- Source CC category; populated for always_active/always_inactive annotations and blank otherwise.
- condition_activity_log2_output_input
- Source FOXA1 'rpm' value: log2 normalized output/input reporter activity.
- condition_peak
- Binary STARRPeaker peak call in the FOXA1 perturbation library.
- differential_log2fc_condition_vs_control
- DESeq2 log2 fold change of fragment read depth in the FOXA1 library versus CC; positive values indicate increased activity.
- differential_padj_condition_vs_control
- DESeq2 multiple-testing-adjusted p-value for FOXA1 versus CC.
- differential_activity_category
- Source category derived from peak state and differential activity; induced/repressed use adjusted p <0.01, while gained/lost additionally reflect peak state.
- target_gene_id
- Ensembl gene identifier, with version when supplied, linked to the fragment by the authors' nearest-gene/ABC analysis; blank when no link was supplied.
- target_gene_name
- Gene symbol for target_gene_id.
- target_gene_log2fc_condition_vs_control
- DESeq2 log2 fold change for the linked target gene in FOXA1 versus CC.
- target_gene_neglog10_padj_condition_vs_control
- Negative log10 of the adjusted p-value for the linked target-gene expression comparison, as supplied in Supplementary Data 3.
Quality control
The authors' STARRDUST pipeline removed reads with base quality <30, unresolved Ns in UMI regions, duplicate UMI pairs, and swapped UDI pairs; BWA/Samtools processing then removed low-quality, multimapped, and off-target reads using -F 2828 -f 2 -q 30. They report RNA RIN >9.5/10 for all samples, approximately 45 million reads per library, and inter-replicate correlations of 0.80–0.99. The supplied Supplementary Data 1 is treated as downstream of the source input-coverage filter; the public processing code retains regions with >150 input reads in every replicate. Package QC additionally required unique valid coordinates, 451–500 bp positive fragment lengths, binary peak flags, finite activity/log2FC/padj values with 0 ≤ padj ≤ 1, and allowed source categories. All 67,080 source rows passed and were retained.
Curation notes
The paper is a version-1 preprint and uses a targeted episomal UDI-UMI-STARR-seq assay; it is represented under Targeted / Cap-STARR-seq because the library was generated by hybridization/capture. The parent paper describes 253,632 overlapping fragments, while Supplementary Data 1 supplies 67,080 downstream rows after source coverage filtering. This table retains source statistics rather than recomputing them, is sorted by genomic coordinate, and has target-gene fields for 1,273 fragments where Supplementary Data 3 provided a FOXA1-linked gene. The source condition label is FOXA1; the matched control is the non-KO CRISPR control line (CC).