Experiment / E41RCJVEQStandard STARR-seq

MCF10A TP53-knockout p63-bound element STARR-seq

Crosstalk between paralogs and isoforms influences p63-dependent regulatory element activity

The same five-variant p63-bound regulatory-element STARR-seq MPRA library was assayed in MCF10A TP53−/− cells to isolate p63-dependent activity from p53 activity. Each retained row is an enhancer family containing WT, p63RE mutant, p63RE shuffle, flanking-region shuffle, and full-sequence shuffle measurements.

Download processed table (CSV)Raw source data API documentation

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: Human
Taxonomy ID: NCBITaxon:9606
Biosample: CVCL:JM25
Reference genome: GRCh38
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated; endogenous ΔNp63α in MCF10A TP53−/−

The episomal pGB118 STARR-seq library used 119–120 bp inserts centered on a p63 response element (p63RE) from 17,310 genomic p63 ChIP-seq regions. Each insert was represented by WT, GC-preserving p63RE mutant, p63RE shuffle, GC-preserving flanking-region shuffle, and GC-preserving full-sequence shuffle constructs. Approximately 50 million cells per biological replicate were transfected by lipofection; cells were harvested after 24 h, poly(A)+ reporter RNA was converted to cDNA, and plasmid DNA and RNA libraries were sequenced as single-end 100-bp reads on an Illumina NextSeq 2000. Values in table.csv are the authors’ total-read-normalized RNA/DNA ratios from Supplementary Table S3, paired by enhancer family, with log2 WT/control effects derived here.

Processed data

50 rows per page. Click a cell to inspect its full value.

Visible columns (34 of 34)

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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 · 34 definitions

element_id: Genomic p63RE interval identifier in chr_start_stop form.
source_unique_id: Supplementary Table S1 identifier containing the p63RE motif sequence.
chrom: Chromosome containing the p63RE.
p63re_start: Source p63RE start coordinate on GRCh38.
p63re_stop: Source p63RE stop coordinate on GRCh38.
element_length_bp: Length of the synthesized genomic-context insert, 119 or 120 bp, excluding adapters.
strand: p63RE strand reported by the source design table.
obs_score: p63 ChIP-seq observation score from the source meta-analysis.
p63re_class: Source p63RE motif class, such as primary or secondary.
p63re_type: Source class of the central motif: Unique p63RE or p53RE+p63RE.
p53_binding: Source YES/NO flag for p53-compatible binding at the p63RE.
obs_p53_score: p53 observation score from the source meta-analysis; blank where unavailable.
gc_percent: GC content of the synthesized element in percent.
cell_line: Cell-line label used in Supplementary Table S3.
variants_in_table: Pipe-delimited list of construct variants represented by the row.
qc_pass: TRUE for enhancer families passing the author and package completeness filters.
activity_call: Authors’ p63RE-dependent activity class: Activating, Repressing, or Unchanged.
wt_sequence: WT 119–120 bp synthesized insert sequence from Supplementary Table S1.
mut_sequence: p63RE-mutant synthesized insert sequence from Supplementary Table S1.
shuffle_sequence: p63RE-shuffled synthesized insert sequence from Supplementary Table S1.
flank_shuffle_sequence: Synthesized insert with the flanking region shuffled from Supplementary Table S1.
full_shuffle_sequence: Fully shuffled synthesized insert sequence from Supplementary Table S1.
rna_dna_wt: Authors’ total-read-normalized RNA/DNA reporter activity for WT.
rna_dna_mut: Authors’ total-read-normalized RNA/DNA reporter activity for the p63RE mutant.
rna_dna_shuffle: Authors’ total-read-normalized RNA/DNA reporter activity for the p63RE shuffle.
rna_dna_flank_shuffle: Authors’ total-read-normalized RNA/DNA reporter activity for the flanking-region shuffle.
rna_dna_full_shuffle: Authors’ total-read-normalized RNA/DNA reporter activity for the full shuffle.
log2_wt_over_mut: Derived log2(rna_dna_wt / rna_dna_mut), the p63RE-dependent WT-versus-mutant effect.
log2_wt_over_shuffle: Derived log2(rna_dna_wt / rna_dna_shuffle).
log2_wt_over_flank_shuffle: Derived log2(rna_dna_wt / rna_dna_flank_shuffle).
log2_wt_over_full_shuffle: Derived log2(rna_dna_wt / rna_dna_full_shuffle).
rna_replicates: Number of biological RNA replicates contributing to the source value.
dna_replicates: Number of plasmid DNA library replicate columns supporting the source assay.
source_table: Supplementary workbook and sheet from which the normalized values were read.

Quality control

The authors mapped reads by exact pattern matching, removed regulatory elements with <2 CPM in the plasmid DNA library or <0.1 CPM in the cDNA library, and normalized reads to the total reads per sample before averaging replicate expression values. For this primary five-variant view, only elements with WT, mut, shuffle, flankShuffle, and fullShuffle matches in both DNA and RNA libraries were retained (10,129 element families; 50,645 rows per cell line in Supplementary Table S3). The package additionally required a complete five-variant family and non-missing RNA/DNA values; no further biological-activity filter was applied.

Curation notes

MCF10A TP53−/− is the Cellosaurus CVCL:JM25 derivative of MCF10A. Supplementary Table S3 also contains a 9,697-element WT/mut-only p53KO view for cross-cell-line analyses; this package uses the 10,129-element five-variant view shared with MCF10A WT so the complete motif-context design is retained.

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