MCF10A endogenous p63-bound element STARR-seq

A five-variant STARR-seq MPRA library of 17,310 human p63-bound regulatory elements was transiently assayed in TP53+/+ MCF10A cells. Each retained row is an enhancer family containing WT, p63RE mutant, p63RE shuffle, flanking-region shuffle, and full-sequence shuffle measurements.

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:0598
Reference genome: GRCh38
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

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

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.

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 is the TP53+/+ parental context (Cellosaurus CVCL:0598). The processed table uses the 10,129-element five-variant subset from Supplementary Table S3 rather than the smaller WT/mut-only subset used for cross-cell-line comparisons. Coordinates and all five insert sequences are joined from Supplementary Table S1; this is a motif/context assay, not a natural-allele variant study.

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MCF10A endogenous p63-bound element STARR-seq

Processed data

Quality control

Curation notes

Cite OpenMPRA

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