A 300-construct library of human 200-bp cis-regulatory elements, each linked to a unique six-base pegRNA barcode, was integrated into PE2(+) K562 cells with piggyBac in triplicate. Transcribed pegRNA barcodes provide the direct RNA reporter (MPRA-style) readout, while synthetic and endogenous HEK3 barcode insertions provide paired DNA-recording measurements.
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:0004
Reference genome
Not reported / not applicable
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
The 5′ ENGRAM construct uses a CRE-minP promoter to drive a Csy4-processed pegRNA carrying a CRE-specific six-base insertion barcode. The library and a synthetic HEK3 DNA tape were introduced into PE2(+) K562 cells by piggyBac; at day 5, barcode counts were obtained separately from pegRNA transcripts, synthetic HEK3 DNA, and endogenous HEK3 DNA. The packaged count tables are the authors' processed files and do not include raw FASTQ reads.
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 · 30 definitions
element_id
Stable package identifier for the construct, based on its source design row.
source_design_row
One-based row number in Enhancer_designs.txt, excluding its header.
element_name
Enhancer or control name from the authors' design file.
element_class
Package classification: positive_control, negative_control, gene_linked_CRE, or sequence_only_CRE.
sequence
The designed 200-bp CRE/control sequence.
sequence_length_bp
Length of sequence in base pairs.
barcode
Six-base insertion/pegRNA barcode in the design orientation.
reference_mpra_rna_dna_ratio
Source design annotation labeled 'replicate 1, RNA/DNA ratio'; not recomputed from the packaged count tables.
rna_count_rep1
Author-provided count for the matched transcribed pegRNA barcode in RNA replicate 1.
rna_count_rep2
Author-provided count for the matched transcribed pegRNA barcode in RNA replicate 2.
rna_count_rep3
Author-provided count for the matched transcribed pegRNA barcode in RNA replicate 3.
rna_count_total
Sum of the three matched RNA barcode counts.
rna_log2_fraction_rep1
Log2((RNA barcode count + 1)/(sum of counts for all 300 design barcodes + 1)) in RNA replicate 1.
rna_log2_fraction_rep2
Log2((RNA barcode count + 1)/(sum of counts for all 300 design barcodes + 1)) in RNA replicate 2.
rna_log2_fraction_rep3
Log2((RNA barcode count + 1)/(sum of counts for all 300 design barcodes + 1)) in RNA replicate 3.
rna_log2_fraction_all
Pooled RNA log2 barcode fraction using the three replicate counts and their pooled design-barcode denominator.
synthetic_tape_dna_count_rep1
Author-provided count for the matched synthetic-HEK3 DNA-tape barcode in replicate 1.
synthetic_tape_dna_count_rep2
Author-provided count for the matched synthetic-HEK3 DNA-tape barcode in replicate 2.
synthetic_tape_dna_count_rep3
Author-provided count for the matched synthetic-HEK3 DNA-tape barcode in replicate 3.
synthetic_tape_dna_count_total
Sum of the three matched synthetic-HEK3 DNA-tape barcode counts.
synthetic_tape_dna_log2_fraction_rep1
Log2((synthetic-tape DNA barcode count + 1)/(sum of counts for all 300 design barcodes + 1)) in replicate 1.
synthetic_tape_dna_log2_fraction_rep2
Log2((synthetic-tape DNA barcode count + 1)/(sum of counts for all 300 design barcodes + 1)) in replicate 2.
synthetic_tape_dna_log2_fraction_rep3
Log2((synthetic-tape DNA barcode count + 1)/(sum of counts for all 300 design barcodes + 1)) in replicate 3.
synthetic_tape_dna_log2_fraction_all
Pooled synthetic-tape DNA log2 barcode fraction using the three replicate counts and their pooled design-barcode denominator.
endogenous_hek3_dna_count_rep1
Matched endogenous HEK3 DNA barcode count in replicate 1; no reverse-complement transformation was applied to the observed count key.
endogenous_hek3_dna_count_rep2
Matched endogenous HEK3 DNA barcode count in replicate 2; no reverse-complement transformation was applied to the observed count key.
endogenous_hek3_dna_count_rep3
Matched endogenous HEK3 DNA barcode count in replicate 3; no reverse-complement transformation was applied to the observed count key.
endogenous_hek3_dna_count_total
Sum of the three matched endogenous HEK3 DNA barcode counts.
rna_minus_synthetic_tape_log2_fraction_all
Pooled RNA log2 fraction minus pooled synthetic-tape DNA log2 fraction; a comparative recording-versus-reporting score, not a conventional plasmid RNA/DNA activity ratio.
qc_status
All rows in this table passed the package-level five-read threshold in all RNA and synthetic-tape DNA replicates.
Quality control
The published analysis excludes barcodes with fewer than five reads. For this package, design barcodes were matched after reverse-complementing observed RNA and synthetic-tape barcode strings as in the authors' notebook; only constructs with at least five counts in each of the three RNA replicates and each of the three synthetic-tape DNA replicates were retained (292 of 300 constructs). Endogenous HEK3 counts were retained as an auxiliary measurement but were not used for row retention because this target is lower-copy and substantially sparser.
Curation notes
This is the 300-CRE benchmark in the supplied preprint, published under the title Symbolic recording of signalling and cis-regulatory element activity to DNA. The source design file contains one row per construct/barcode and has repeated enhancer names, so source_design_row and element_id preserve row identity. The direct RNA values are normalized barcode fractions because the packaged author files do not provide plasmid-input DNA counts; reference_mpra_rna_dna_ratio is retained only as the authors' source annotation for comparison. The endogenous HEK3 counts are sparse relative to synthetic-tape counts and are therefore supplementary rather than the primary activity measure.