The shared 145-nt enhancer library was transfected into human 786-O cells to measure cell-type-specific reporter activity. Reporter mRNA counts from two released replicates were compared with plasmid-DNA library counts and summarized as DESeq2 log2(RNA/DNA) activity estimates.
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:1051
Reference genome
GRCh38
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
The library consists of Fast SeqProp and DEN AI-designed enhancers, motif-embedding and multi-target/tunable designs, genome-derived DHS controls, shuffled negatives, and labeled comparator controls. Reporter activity is represented by two mRNA read-count replicates and the supplied DESeq2 baseMean, log2FC, standard error, p-value, and adjusted p-value columns; plasmid DNA is represented by eight released DNA read-count columns.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (34 of 34)
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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 · 34 definitions
element_id
Unique identifier for the tested 145-nt library element.
sequence
5-prime-to-3-prime nucleotide sequence tested in the reporter library.
sequence_length
Sequence length in nucleotides; all retained elements are 145 nt.
category
Authors' design/control category, including single-, double-, triple-target, tunable, motif-embedding, and control categories.
source
Sequence source or design method: fsp (Fast SeqProp), den (Deep Exploration Network), genome_dhs (genomic DHS), motif_embedding, shuffled, or labeled comparator MPRA sources.
intended_target
Intended target human DHS biosample name(s), comma-separated; blank for negative controls.
assay_cell_is_intended_target
True when the current human assay cell line is one of the element's intended target names; false for off-targets and controls; blank for the mouse-retina experiment.
tunable_setpoint
DHS64 target accessibility setpoint for tunable elements; blank when not applicable.
background_id
Identifier of the background sequence used for motif embedding, when applicable.
motif_id
Motif identifier for motif-embedding constructs, when applicable.
motif_name
Motif name for motif-embedding constructs, when applicable.
motif_consensus
Consensus sequence for the embedded motif, when applicable.
motif_rc
Reverse-complement/orientation annotation for the embedded motif, when applicable.
n_motifs_embedded
Number of motifs embedded in the construct, when applicable.
motif_spacing
Motif spacing annotation for motif-embedding constructs, when applicable.
dna_count_mean
Arithmetic mean of the eight available plasmid-DNA read counts (two reads per library/date field).
dna_count_min
Minimum plasmid-DNA read count among the eight available DNA replicate columns.
dna_count_total
Sum of the eight available plasmid-DNA read counts.
dna_replicate_count
Number of plasmid-DNA read-count columns used for the aggregate; eight.
dna_qc_pass_min10
Package QC flag; true means every plasmid-DNA replicate had at least 10 reads. Only true rows are present.
mrna_count_r1
Reporter mRNA read count for replicate 1 in this condition.
mrna_count_r2
Reporter mRNA read count for replicate 2 in this condition; blank for mouse retina, for which only one column was released.
mrna_count_total
Sum of the released reporter mRNA read counts for this condition.
mrna_detected_replicates
Number of released mRNA replicates with a count greater than zero.
activity_replicate_count
Number of mRNA read-count replicates available for this condition.
activity_base_mean
DESeq2 baseMean for the condition-specific reporter activity comparison.
activity_log2fc
DESeq2 log2 fold-change estimate for reporter RNA relative to plasmid DNA (log2FC).
activity_lfcse
DESeq2 standard error of the log2FC estimate.
activity_pval
DESeq2 p-value for the reporter RNA-versus-DNA activity estimate.
activity_padj
DESeq2 multiple-testing-adjusted p-value for the activity estimate.
activity_fdr_below_0_05
Derived flag indicating activity_padj < 0.05.
activity_direction
Derived direction of activity_log2fc: increases, decreases, or no_change.
dhs_signal_in_assayed_cell
Released measured DHS accessibility signal for the assayed human cell, when the element is genome-sourced; blank otherwise and always blank for mouse retina.
dhs_pred_in_assayed_cell
Released DHS64-predicted accessibility for the assayed human cell; blank for mouse retina.
Quality control
Author-processed counts and DESeq2 outputs were used. Package QC required a nonempty unique element ID, an exact 145-nt A/C/G/T sequence, finite numeric published activity statistics for this condition, and at least 10 reads in each of the eight available plasmid-DNA read columns; 9,060 of 9,061 released elements passed and 1 element was excluded for a DNA replicate below 10 reads. pairwise log1p DNA-count Pearson r ranged from 0.927 to 0.999; Across retained elements, log1p mRNA read-count replicate Pearson r = 0.982. Zero mRNA counts in one or both replicates were retained because they represent potentially inactive elements; no mRNA-count threshold was imposed.
Curation notes
Cellosaurus resolution: 786-O (CVCL:1051). The focal target is a human immortalized cell line; Cellosaurus IDs are resolved to the parental line named by the paper/repository. The paper describes ten focal human cell lines; the released table also has HEK293 and HMC3 extra human-line outputs, which remain in raw_data but are not materialized as additional child experiments. The released processed table includes 75 negative/control elements and 40 labeled comparator-MPRA elements; they are retained and identified by source/category rather than silently discarded. 786_O table contains the shared library and the condition-specific activity columns only. Zero mRNA counts in one or both replicates were retained because they represent potentially inactive elements; no mRNA-count threshold was imposed.