An array-synthesized CRE-seq library tested 120-bp sequences centered on CEBPB ChIP-seq summits and dinucleotide-preserving scrambled controls, with four unique 9-bp barcodes per element. The library was transfected into HepG2 cells in two independent experiments and assayed using matched plasmid DNA and reporter RNA/cDNA barcode counts.
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
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
CRE-seq used an episomal plasmid in which each 120-bp native or dinucleotide-scrambled sequence was placed upstream of a minimal promoter driving luciferase; a 9-bp barcode was read from the luciferase 3′ UTR. More than 12,000 unique 186-mer oligos were synthesized, with four barcodes per DNA element. HepG2 cells were transfected at approximately 75% confluence with FuGENE and harvested after 24 h. RNA was DNase-treated and reverse-transcribed; barcode libraries from RNA/cDNA and plasmid DNA were sequenced on an Illumina HiSeq 2000. The processed table summarizes the two HepG2 DNA samples (GSM1888227, GSM1888228) and two HepG2 RNA samples (GSM1888231, GSM1888232).
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 · 25 definitions
element_id
Original GEO site_name; dinucleotide-scrambled controls have a _scramble suffix.
genomic_locus
Coordinate from site_name with any _scramble suffix removed.
chromosome
Chromosome component of the GEO coordinate.
summit_position_hg19
Numeric coordinate from site_name, representing the CEBPB ChIP-seq summit label used for the 120-bp insert.
site_category
Original library category: HepG2-specific, K562-specific, or Shared, crossed with Pol2 or NOPol2.
binding_origin
Cell-type origin of the CEBPB binding category.
rnap2_status
Whether the source CEBPB category was associated with promoter-distal RNAP2 binding.
element_type
Native CEBPB-bound test sequence or dinucleotide-scrambled control.
has_scramble_control
Whether a scrambled element for the same genomic locus is present in the raw release.
scramble_control_passed_qc
Whether that same-locus scrambled element passed the package QC rule.
n_barcodes_total
Number of barcode sequences represented for the element in the raw matrix.
n_barcodes_retained_rep1
Number of barcodes with DNA counts greater than 200 in Rep_1.
n_barcodes_retained_rep2
Number of barcodes with DNA counts greater than 200 in Rep_2.
dna_count_sum_retained_rep1
Sum of Rep_1 DNA counts over retained barcodes.
rna_count_sum_retained_rep1
Sum of Rep_1 RNA/cDNA counts over retained barcodes.
dna_count_sum_retained_rep2
Sum of Rep_2 DNA counts over retained barcodes.
rna_count_sum_retained_rep2
Sum of Rep_2 RNA/cDNA counts over retained barcodes.
activity_ratio_median_rep1
Median Rep_1 RNA/DNA ratio across retained barcodes.
activity_ratio_median_rep2
Median Rep_2 RNA/DNA ratio across retained barcodes.
activity_ratio_mean
Final element activity: arithmetic mean of the two replicate median RNA/DNA ratios.
log2_activity
Base-2 logarithm of final element activity.
scrambled_control_95pct_activity_cutoff
Pooled 95th-percentile final activity among retained scrambled controls, in RNA/DNA units.
active_vs_scrambled_95pct
For native elements, whether final activity is above the pooled scrambled-control cutoff; blank for scrambled controls.
replicate_count
Number of independent HepG2 transfection replicates summarized.
source_sample_ids
GEO sample accessions contributing to this table: DNA Rep_1, DNA Rep_2, RNA Rep_1, and RNA Rep_2.
Quality control
The authors retained DNA barcodes with more than 200 reads and required at least two independently sequenced barcodes per element in each replicate; activity was the median RNA/DNA ratio across retained barcodes per replicate and the mean across the two replicates. The authors report R2 greater than 0.93 for replicate barcode-count concordance and defined active native sites as above the 95th percentile of scrambled controls. Package QC retained 1,948 of 3,095 HepG2 elements (1,077 native and 871 scrambled): each retained element had at least two of four DNA barcodes above the 200-read threshold in both Rep_1 and Rep_2, with finite RNA/DNA activity values. The pooled retained scrambled-control 95th-percentile cutoff was 0.91866446 RNA/DNA; 1,147 elements failing the per-replicate barcode-coverage rule were excluded.
Curation notes
The table is element-level and includes retained native and scrambled controls so the activity distribution and the package-derived activity cutoff remain inspectable. GEO site_name values are single genomic coordinates used as CEBPB summit labels, not interval endpoints; the paper states that the 120-bp insert was centered on each summit. The GEO count release does not include the underlying 120-bp oligo sequences, per-element p-values, or FDR values, so those fields are not fabricated. HepG2 was resolved to Cellosaurus CVCL:0027; the paper/GEO descriptions and current cell-line resources differ in historical disease naming, but this does not affect the reporter readout.