Experiment / E5OAY1JHSStandard STARR-seq

SCC25 endogenous p63-bound element STARR-seq

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

The five-variant p63-bound regulatory-element library was assayed in SCC25 head-and-neck squamous cell carcinoma cells to examine epithelial-context dependence of p63RE activity. This processed table uses the author-filtered WT/mut matched subset and retains one row per enhancer family.

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:1682
Reference genome: GRCh38
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated; endogenous p63

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. For this cross-cell-line analysis, WT and GC-preserving p63RE-mutant constructs were paired; approximately 50 million cells per biological replicate were transfected by lipofection, harvested after 24 h, and poly(A)+ reporter RNA was 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, with the WT-versus-mutant log2 effect derived here.

Processed data

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

Visible columns (25 of 25)

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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 · 25 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.
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.
log2_wt_over_mut: Derived log2(rna_dna_wt / rna_dna_mut), the p63RE-dependent WT-versus-mutant effect.
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 cross-cell-line view, only elements with matched WT and mut records in both DNA and RNA libraries were retained (9,697 element families; 19,394 rows for SCC25 in Supplementary Table S3). The package additionally required a complete WT/mut family and non-missing RNA/DNA values; no further biological-activity filter was applied.

Curation notes

SCC25 is the human tongue squamous carcinoma line Cellosaurus CVCL:1682. The processed table is the authors’ 9,697-element WT/mut-only subset used for Figure 5 comparisons. The package retains the current GEO SCC25 replicate-4 raw-count file in raw_data; the processed values remain the authors’ normalized Supplementary Table S3 values.

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