HARPE long-TATA library in HeLa cells
Identification of the human DPR core promoter element using machine learningA modified HARPE plasmid library randomized the long TATA region from -32 to -21 relative to the initiator +1 TSS and linked each TATA variant to a downstream barcode. The library was transiently transfected into HeLa cells; reporter RNA/cDNA and recovered plasmid DNA were sequenced to quantify TATA-dependent transcription strength.
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 long-TATA HARPE library transfection into HeLa cells (Lipofectamine 3000); no additional treatment
The upstream randomized TATA sequence was linked to a downstream 15-nucleotide barcode by paired-end sequencing of the starting library. Barcode-to-TATA conversion tables were used to assign RNA and DNA observations; TATA variants with multiple linked barcodes were collapsed by the mean barcode-level activity score. activity_score is RNA RPM divided by DNA RPM.
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 · 20 definitions
- element_id
- Package-assigned stable identifier for the tested TATA sequence.
- tested_sequence
- 12-nucleotide randomized long-TATA sequence corresponding to positions -32 through -21.
- sequence_length
- Length of tested_sequence in nucleotides.
- dna_count_rep1
- Sum of published plasmid DNA read counts across linked barcodes for biological replicate 1.
- rna_count_rep1
- Sum of published reporter RNA/cDNA read counts across linked barcodes for biological replicate 1.
- dna_rpm_rep1
- Sum of published DNA RPM values across linked barcodes for biological replicate 1.
- rna_rpm_rep1
- Sum of published RNA RPM values across linked barcodes for biological replicate 1.
- activity_score_rep1
- Mean of linked-barcode RNA RPM/DNA RPM transcription-strength scores for replicate 1.
- dna_count_rep2
- Sum of published plasmid DNA read counts across linked barcodes for biological replicate 2.
- rna_count_rep2
- Sum of published reporter RNA/cDNA read counts across linked barcodes for biological replicate 2.
- dna_rpm_rep2
- Sum of published DNA RPM values across linked barcodes for biological replicate 2.
- rna_rpm_rep2
- Sum of published RNA RPM values across linked barcodes for biological replicate 2.
- activity_score_rep2
- Mean of linked-barcode RNA RPM/DNA RPM transcription-strength scores for replicate 2.
- n_barcodes_rep1
- Number of linked barcode observations aggregated for the TATA sequence in replicate 1.
- n_barcodes_rep2
- Number of linked barcode observations aggregated for the TATA sequence in replicate 2.
- mean_barcode_freq_rep1
- Mean source Freq value across linked barcode mappings for replicate 1.
- mean_barcode_freq_rep2
- Mean source Freq value across linked barcode mappings for 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, barcode-to-TATA conversion filtering, and DNA count >=10 with DNA RPM >=0.75. This package re-applied those thresholds, retained finite A/C/G/T TATA 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
Raw GEO files are GSM4145012 and GSM4145013; the barcode conversion table is included in raw_data. This table collapses linked barcodes to one row per TATA sequence using the paper's mean activity rule. 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 is represented by Cellosaurus CVCL:0030.