The same 676-member core-promoter library was transfected separately into K562 and HEK293 cells for bulk MPRA validation. The table contains author GEO counts for reporter RNA and input plasmid DNA plus the author-provided log2 RNA/DNA activity score for each cell line.
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
UNMAPPED:HEK293_K562_bulk_validation
Reference genome
Not reported / not applicable
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
Separate episomal plasmid transfections in K562 and HEK293 cells; reporter barcodes were amplified from bulk RNA and input DNA, and activities were computed as log2(RNA counts/DNA counts), with barcode activities averaged per promoter. The GEO supplementary table provides the promoter-level normalized scores used here.
Processed data
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Visible columns (27 of 27)
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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 · 27 definitions
element_id
Unique core-promoter library identifier (genomic coordinate string or synthetic control name).
sequence
DNA sequence of the tested core-promoter insert from the author library.
sequence_length
Length of sequence in nucleotides.
chromosome
Chromosome field supplied by the author library annotation; blank for synthetic controls.
start
Start coordinate supplied by the author library annotation.
end
End coordinate supplied by the author library annotation.
strand
Strand supplied by the author library annotation.
supporting_dataset
Supporting dataset label supplied by the author library annotation.
gene_id
Host gene identifier supplied by the author library annotation.
gene_name
Host gene name supplied by the author library annotation.
housekeeping_vs_developmental
Author classification of the host promoter as housekeeping (hk) or developmental (dev).
initiation_type
Author annotation of transcription-initiation type.
library_class
Author composite promoter class based on motif and housekeeping/developmental annotations.
tata_box_motif_score
TATA-box motif score from the author library annotation.
tata_box_core_promoter
Author indicator/annotation for a TATA-box core promoter.
cpg_island_core_promoter
Author indicator/annotation for a CpG-island core promoter.
tct_motif_score
TCT motif score from the author library annotation.
tct_ribosomal_core_promoter
Author indicator/annotation for a TCT/ribosomal core promoter.
initiator_motif_score
Initiator motif score from the author library annotation.
dpe_motif_score
Downstream promoter element motif score from the author library annotation.
dpe_core_promoter
Author indicator/annotation for a DPE core promoter.
k562_bulk_rna_count
Author GEO count for the K562 bulk reporter-RNA barcode pool.
hek293_bulk_rna_count
Author GEO count for the HEK293 bulk reporter-RNA barcode pool.
bulk_input_dna_count
Author GEO count for the input plasmid DNA barcode pool.
k562_bulk_log2_rna_dna_activity
Author-provided K562 log2 RNA/DNA activity score (GEO field k562_norm).
hek293_bulk_log2_rna_dna_activity
Author-provided HEK293 log2 RNA/DNA activity score (GEO field hek_norm).
k562_minus_hek293_bulk_log2_activity
K562 author activity score minus HEK293 author activity score.
Quality control
The paper’s bulk-MPRA method averaged barcode activities after calculating log2 RNA/DNA ratios. The package retained all 676 library elements with a library annotation, finite RNA/DNA counts and finite author activity scores; every retained input-DNA count is greater than zero. No additional read-level QC was possible from the compact GEO summary table.
Curation notes
This is a validation assay distinct from the single-cell experiments but uses the same library; K562 and HEK293 are represented together because the GEO summary table reports both conditions per promoter. The author paper does not state a reference genome assembly for the coordinate labels, so reference_genome is null. The *_bulk_log2_rna_dna_activity columns preserve GEO’s k562_norm and hek_norm values rather than recomputing them from the rounded counts.