Experiment / E3ZQ33X8WPromoter / Core Promoter MPRA

HARPE full DPR library in vitro

Identification of the human DPR core promoter element using machine learning

A HARPE plasmid library with the 19-nucleotide DPR segment randomized from +17 to +35 relative to the initiator +1 TSS was transcribed in vitro with HeLa nuclear extract in a TATA-less SCP1m core-promoter background. Reporter RNA/cDNA and plasmid DNA were sequenced to quantify sequence-specific transcription strength.

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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:0030
Reference genome: Not reported / not applicable
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

In vitro transcription with HeLa nuclear extract; no additional treatment

Custom HARPE assay based on a modified SuRE episomal plasmid with an invariant promoter cassette and randomized DPR. Twelve standard in vitro transcription reactions were pooled per sample; activity_score is RNA RPM divided by DNA RPM, and the extract source is HeLa nuclear extract.

Processed data

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

Visible columns (16 of 16)

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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 · 16 definitions

element_id: Package-assigned stable identifier for the tested sequence.
tested_sequence: 19-nucleotide randomized DPR sequence corresponding to positions +17 through +35.
sequence_length: Length of tested_sequence in nucleotides.
dna_count_rep1: Published plasmid DNA read count for biological replicate 1.
rna_count_rep1: Published reporter RNA/cDNA read count for biological replicate 1.
dna_rpm_rep1: Published plasmid DNA read count normalized to reads per million for replicate 1.
rna_rpm_rep1: Published reporter RNA/cDNA read count normalized to reads per million for replicate 1.
activity_score_rep1: Transcription strength for replicate 1, calculated as RNA RPM divided by DNA RPM.
dna_count_rep2: Published plasmid DNA read count for biological replicate 2.
rna_count_rep2: Published reporter RNA/cDNA read count for biological replicate 2.
dna_rpm_rep2: Published plasmid DNA read count normalized to reads per million for replicate 2.
rna_rpm_rep2: Published reporter RNA/cDNA read count normalized to reads per million for replicate 2.
activity_score_rep2: Transcription strength for replicate 2, calculated as RNA RPM divided by DNA RPM.
n_replicates: Number of biological replicates represented in the row (2).
activity_score_mean: Arithmetic mean of the two replicate activity scores.
activity_score_sd: Sample standard deviation of the two replicate activity scores.

Quality control

The GEO inputs had already been filtered by exact flanking-sequence and expected-length read matching, removal of likely index-contamination/invariant reads, and DNA count >=10 with DNA RPM >=0.75. This package re-applied those thresholds, retained finite A/C/G/T sequences, matched the two biological replicates by exact tested_sequence, and retained only sequence elements detected in both replicates; zero-RNA elements were retained as informative inactive measurements.

Curation notes

HARPE is a custom high-throughput randomized promoter assay rather than a conventional barcode-per-oligo MPRA; the sequence itself identifies the downstream variant. Source files are GSM4144998 and GSM4144999 from GEO GSE139635. Scores are relative RNA/DNA ratios, not log2 fold changes or allele-specific effects; the library is synthetic and has no genomic rsIDs or coordinates. HeLa nuclear extract is the biological source; the assay is cell-free.

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