A 676-member library of 133-bp core promoters plus four synthetic controls was transfected into HEK293 and K562 cells, mixed 1:1, and read out by 10x single-cell RNA sequencing with cBC/rBC reporter barcodes. The table contains author mean activities for both cell types across two biological replicates and joined DESeq2 statistics where the promoter gene name was unambiguous.
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_mixed_cell_population
Reference genome
Not reported / not applicable
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
Episomal plasmid transfection with a two-level barcode design: a promoter/cis-regulatory-sequence barcode (cBC) identifies each library member and a 25-bp random barcode (rBC) serves as a single-cell plasmid-copy proxy. Reporter RNA barcodes and endogenous transcriptomes share the 10x cell barcode; activity is normalized to rBC abundance and summarized by cell type.
Processed data
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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 · 35 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.
hek293_sc_activity_rep1
Author Supplementary Table 1 mean scMPRA activity for HEK293 cells, biological replicate 1.
hek293_sc_activity_rep2
Author Supplementary Table 1 mean scMPRA activity for HEK293 cells, biological replicate 2.
hek293_sc_activity_mean
Arithmetic mean of the two HEK293 scMPRA replicate activities.
k562_sc_activity_rep1
Author Supplementary Table 1 mean scMPRA activity for K562 cells, biological replicate 1.
k562_sc_activity_rep2
Author Supplementary Table 1 mean scMPRA activity for K562 cells, biological replicate 2.
k562_sc_activity_mean
Arithmetic mean of the two K562 scMPRA replicate activities.
k562_vs_hek293_sc_log2_ratio
Log2 of K562 mean scMPRA activity divided by HEK293 mean scMPRA activity.
deseq2_base_mean
DESeq2 baseMean from Supplementary Table 2 for the K562-versus-HEK293 comparison.
deseq2_log2_fold_change_k562_vs_hek293
DESeq2 log2 fold change for K562 relative to HEK293.
deseq2_lfc_se
Standard error of the DESeq2 log2 fold change.
deseq2_stat
DESeq2 Wald statistic.
deseq2_pvalue
DESeq2 Wald-test p-value.
deseq2_padj
DESeq2 multiple-testing-adjusted p-value.
differential_call
Derived call matching the paper’s reported set: K562_up or K562_down when the exported DESeq2 Wald p-value is < 0.01 and absolute log2 fold change is > 0.3; otherwise not_significant.
Quality control
Author QC removed cells with fewer than 1000 genes or high mitochondrial counts in the scRNA-seq processing, required correct-length cBC/rBC barcodes and corrected 10x barcodes by Hamming distance ≤1, retained high-confidence quads using the 1-read elbow threshold with Hamming rescue, and removed mixed-cell scMPRA cells with fewer than 100 associated UMIs. Supplementary Table 1 reports 676 HEK293 and 674 K562 promoter measurements; the package retains the 674 elements with finite measurements in both cell types and both replicates. DESeq2 values are retained when the Supplementary Table 2 gene name maps uniquely to the library annotation. The differential_call reproduces the paper’s reported 11-up/59-down set using the exported Wald p-value < 0.01 and absolute log2 fold change > 0.3; the paper text calls this an adjusted-p-value threshold, whereas the exported padj column yields a different count.
Curation notes
HEK293 and K562 are distinct immortalized human cell lines in one mixed-cell droplet experiment (Cellosaurus CVCL:0045 and CVCL:0004, respectively); the single biosample field is therefore represented as UNMAPPED. The four SCP1 controls have synthetic sequences and blank genomic annotation fields. The author paper does not state a reference genome assembly for the coordinate labels, so reference_genome is null. The scMPRA activities and DESeq2 results are author-provided summaries; the K562/HEK293 log2 ratio is derived here from the two cell-type means. The paper reports 11 K562-up and 59 K562-down promoters at its stated significance/effect-size cutoffs, but the supplementary DESeq2 columns numerically reproduce that set with pvalue < 0.01 rather than padj < 0.01; both columns are retained for transparent reuse.