Experiment / E6P5IL6ZQTargeted / Cap-STARR-seq

Targeted STARR-seq enhancer reporter assay in MCF7

Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic

The targeted genomic fragments used for CHEQ-seq were inserted downstream of the transcription start site in a self-transcribing STARR-seq reporter and assayed in MCF7 cells under p53-high (wild-type TP53 plus Nutlin-3a) and p53-low (stable TP53 knockdown) conditions. The table contains fixed-length genomic fragments with matched plasmid and reporter cDNA counts and re-derived activity effects.

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Organism: Human
Taxonomy ID: NCBITaxon:9606
Biosample: CVCL:0031
Reference genome: hg19
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

p53-high: 5 uM Nutlin-3a for 24 h in MCF7 TP53-wild-type cells; p53-low: stable TP53 knockdown MCF7 cells, untreated

The same targeted/captured TP53 ChIP-seq and control regions were cloned 3' of the reporter transcription start site, allowing active fragments to self-transcribe rather than use a barcode. Illumina reads were mapped with STAR, genomic intervals were extended to 400 bp and identical locations collapsed, and plasmid-region counts were used for library-coverage normalization before DESeq2 differential analysis. Two biological replicates were available for each p53-high and p53-low condition; untreated wild-type plasmid libraries are retained as DNA controls.

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 · 35 definitions

fragment_id: Unique packaged STARR fragment identifier.
coordinate: Genomic interval in chr:start-end form after the paper's 400-bp extension.
chrom: Chromosome or contig from the supplied mapped region.
start: Zero-based genomic start coordinate.
end: Genomic end coordinate; retained intervals are exactly 400 bp long.
fragment_length: Length of the retained genomic interval in base pairs.
plasmid_N1_count: Raw/supplied plasmid DNA count in p53-high replicate 1 (WT TP53 plus Nutlin-3a).
plasmid_N2_count: Raw/supplied plasmid DNA count in p53-high replicate 2 (WT TP53 plus Nutlin-3a).
plasmid_WT1_count: Raw/supplied plasmid DNA count in untreated MCF7 WT replicate 1.
plasmid_WT2_count: Raw/supplied plasmid DNA count in untreated MCF7 WT replicate 2.
plasmid_KD1_count: Raw/supplied plasmid DNA count in p53-low stable TP53-knockdown replicate 1.
plasmid_KD2_count: Raw/supplied plasmid DNA count in p53-low stable TP53-knockdown replicate 2.
cDNA_N1_count: Raw/supplied reporter cDNA count in p53-high replicate 1.
cDNA_N2_count: Raw/supplied reporter cDNA count in p53-high replicate 2.
cDNA_KD1_count: Raw/supplied reporter cDNA count in p53-low replicate 1.
cDNA_KD2_count: Raw/supplied reporter cDNA count in p53-low replicate 2.
plasmid_N1_cpm: Library-size-scaled plasmid count per million for p53-high replicate 1.
plasmid_N2_cpm: Library-size-scaled plasmid count per million for p53-high replicate 2.
plasmid_KD1_cpm: Library-size-scaled plasmid count per million for p53-low replicate 1.
plasmid_KD2_cpm: Library-size-scaled plasmid count per million for p53-low replicate 2.
cDNA_N1_cpm: Library-size-scaled reporter cDNA count per million for p53-high replicate 1.
cDNA_N2_cpm: Library-size-scaled reporter cDNA count per million for p53-high replicate 2.
cDNA_KD1_cpm: Library-size-scaled reporter cDNA count per million for p53-low replicate 1.
cDNA_KD2_cpm: Library-size-scaled reporter cDNA count per million for p53-low replicate 2.
log2_activity_p53_high_rep1: Re-derived log2 STARR activity for p53-high replicate 1, reporter cDNA CPM relative to matched plasmid CPM.
log2_activity_p53_high_rep2: Re-derived log2 STARR activity for p53-high replicate 2, reporter cDNA CPM relative to matched plasmid CPM.
log2_activity_p53_low_rep1: Re-derived log2 STARR activity for p53-low replicate 1, reporter cDNA CPM relative to matched plasmid CPM.
log2_activity_p53_low_rep2: Re-derived log2 STARR activity for p53-low replicate 2, reporter cDNA CPM relative to matched plasmid CPM.
log2fc_nutlin_vs_p53_low_rep1: Re-derived log2 fold change of p53-high versus p53-low STARR activity for replicate 1.
log2fc_nutlin_vs_p53_low_rep2: Re-derived log2 fold change of p53-high versus p53-low STARR activity for replicate 2.
log2fc_nutlin_vs_p53_low_mean: Mean of the two replicate-level p53-high versus p53-low log2 fold changes.
cDNA_high_nonzero_replicates: Number of p53-high cDNA replicates with a nonzero supplied count.
cDNA_low_nonzero_replicates: Number of p53-low cDNA replicates with a nonzero supplied count.
replicate_direction_consistent: Whether both replicate log2 fold changes have the same activation/repression direction.
effect_size_call_1_5_log2: Effect-size-only call using the paper's absolute 1.5 log2 fold-change threshold and replicate-direction concordance; not a significance call.

Quality control

The paper cleaned reads, mapped them with STAR, extended mapped regions to 400 bp, collapsed identical genomic locations, normalized cDNA by library size and plasmid-region coverage, and used DESeq2 differential analysis. Package QC retained valid coordinate records exactly 400 bp long with at least 10 combined p53-high plasmid counts and at least 10 combined p53-low plasmid counts: 48,832 of 468,305 supplied regions. cDNA-zero regions were not removed because inactive STARR elements are biologically informative; all retained rows have valid genomic coordinates and the stated DNA coverage minimum.

Curation notes

The supplied GEO STARR files are count summaries described by GEO as normalized HTSeq outputs; CPM columns apply a further common library-size scaling for the packaged table. The archives do not include the authors' DESeq2 p-values/adjusted p-values or sequence FASTA, so the log2fc and threshold calls are re-derived effect summaries rather than significance results. cDNA-zero rows remain when they pass DNA coverage QC because lack of reporter output is informative for a region-focused assay.

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