An evolutionary sequence library tested 11 present-day primate orthologs and nine FastML ancestral reconstructions for active enhancer tiles in the same episomal STARR-seq vector. Each sequence carried degenerate barcodes and was measured in three biological HepG2 transfections; the table reports author enrichment scores plus a derived within-tile difference from the human sequence when the deposited human reference is present.
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:0027
Reference genome
hg19
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated; 1 ng/mL puromycin selection for 24 h after transfection
Episomal STARR-seq in HepG2 tested the evolutionary alternatives of the selected tiles: human, chimpanzee, gorilla, orangutan, gibbon, rhesus macaque, crab-eating macaque, baboon, vervet, marmoset, squirrel monkey, and nine reconstructed ancestral nodes. Five-base degenerate barcodes distinguished independent measurements. Error-free sequence matches were retained; for each barcode-tile pair the normalized RNA/DNA ratio was log2-transformed and averaged over barcode pairs and three biological replicates.
Processed data
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Visible columns (18 of 18)
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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
Stable package row identifier assigned in source-row order.
tile_id
Stable package grouping identifier for all sequence labels sharing the same deposited coordinate.
source_element_id
Original composite identifier from the GEO/Supplementary Table S4 score table, including coordinate and sequence label.
coordinate_hg19
Coordinate component of source_element_id, with the sequence label removed; stored as reported under the source hg19 header.
chromosome
Chromosome or contig parsed from coordinate_hg19.
start
Start boundary parsed from coordinate_hg19.
end
End boundary parsed from coordinate_hg19.
reported_length_bp
end minus start in the source boundary convention; this is the deposited mapped interval length and varies among ortholog labels.
sequence_label
Source suffix identifying the present-day assembly/species label or ancestral node label N2-N10.
sequence_type
Present-day primate or Ancestral reconstruction, parsed from sequence_label.
species_or_ancestor
Readable species name for present-day labels or 'ancestral reconstruction N#' for reconstructed nodes.
tile_n_deposited_sequences
Number of deposited score rows sharing the same coordinate group.
human_reference_present
TRUE when the coordinate group contains a deposited human row labeled hg38.
activity_score_log2_rna_dna
Author-deposited enrichment score, described in the paper as log2 normalized RNA/DNA activity.
activity_delta_vs_human_log2
Derived activity_score_log2_rna_dna minus the hg38 score for the same tile; blank when no human score is deposited.
qc_pass
TRUE for rows retained after package-level identifier, score, and coordinate integrity QC.
source_row
1-based row number in the decompressed GEO file, including its header as row 1.
source_file
Relative path to the compressed source table in raw_data.
Quality control
Author QC was retained: barcode-tile pairs required >10 DNA reads, zero-RNA ratios were excluded before log transformation, and elements with fewer than six independent measurements were filtered after averaging measurements across three biological replicates. Package integrity QC additionally required a nonempty composite identifier, a finite score, and a valid coordinate plus sequence label; all 5,218 deposited rows passed. The paper text states 5,426 scored sequences across 344 tiles, but the deposited GEO table and Supplementary Table S4 contain 5,218 rows across 340 coordinate groups; the deposited values are retained verbatim rather than supplemented or imputed.
Curation notes
Source: GSE113978_Ortholog_scores.tsv.gz and Supplementary Table S4. The source contains 5,218 rows and 340 coordinate groups, with 262 groups containing the human hg38-labeled reference; the main text reports 5,426 rows and 344 tiles, a discrepancy preserved here as provenance. The human-relative delta is a transparent subtraction of already log2-scaled source scores and is not an imputed effect size. Source coordinates are retained exactly, including the header's hg19 designation and the human sequence label hg38.