Low-complexity HARPE DPR-tag library in HeLa cells
Identification of the human DPR core promoter element using machine learningA low-complexity HARPE library tested a 13-nucleotide DPR sequence variant together with randomized 3-nucleotide tags after transient transfection into HeLa cells. Reporter RNA/cDNA and recovered plasmid DNA were sequenced, and tag-level observations were averaged to obtain one transcription-strength measurement per DPR sequence.
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.
Perturbation & assay details
Transient low-complexity HARPE library transfection into HeLa cells (Lipofectamine 3000); no additional treatment
The library restricts the DPR randomization to a two-base-per-position 13-nucleotide design and adds a randomized 3-nucleotide downstream tag, producing multiple tag measurements per DPR sequence. activity_score is the mean of the RNA RPM/DNA RPM scores across tags within each replicate, followed by averaging the two biological replicates.
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 · 18 definitions
- element_id
- Package-assigned stable identifier for the DPR sequence.
- tested_sequence
- 13-nucleotide low-complexity DPR sequence variant.
- sequence_length
- Length of tested_sequence in nucleotides.
- dna_count_rep1
- Sum of published plasmid DNA read counts across tags for biological replicate 1.
- rna_count_rep1
- Sum of published reporter RNA/cDNA read counts across tags for biological replicate 1.
- dna_rpm_rep1
- Sum of published DNA RPM values across tags for biological replicate 1.
- rna_rpm_rep1
- Sum of published RNA RPM values across tags for biological replicate 1.
- activity_score_rep1
- Mean of the published tag-level RNA RPM/DNA RPM transcription-strength scores for replicate 1.
- dna_count_rep2
- Sum of published plasmid DNA read counts across tags for biological replicate 2.
- rna_count_rep2
- Sum of published reporter RNA/cDNA read counts across tags for biological replicate 2.
- dna_rpm_rep2
- Sum of published DNA RPM values across tags for biological replicate 2.
- rna_rpm_rep2
- Sum of published RNA RPM values across tags for biological replicate 2.
- activity_score_rep2
- Mean of the published tag-level RNA RPM/DNA RPM transcription-strength scores for replicate 2.
- n_tags_rep1
- Number of randomized 3-nucleotide tag observations aggregated for the DPR sequence in replicate 1.
- n_tags_rep2
- Number of randomized 3-nucleotide tag observations aggregated for the DPR sequence in replicate 2.
- 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, required at least three tag observations per DPR sequence in each replicate, matched the two biological replicates by exact tested_sequence, and retained only sequence elements detected in both replicates; zero-RNA tag observations were retained in the sequence-level mean.
Curation notes
The low-complexity library is the paper's high-confidence DPR dataset; raw GEO files are GSM4145004 and GSM4145005. This table intentionally collapses the raw DPR-tag pairs to one row per DPR sequence using the paper's mean tag-level score rule. Scores are relative RNA/DNA ratios, not log2 fold changes or allele-specific effects. HeLa is represented by Cellosaurus CVCL:0030.