A single library of 15,753 fully designed 200-mer oligos representing native promoter/PIC regions and synthetic core-promoter and transcription-factor configurations was integrated into the AAVS1 safe-harbor locus of K562 cells. Single-copy integrants were sorted into 16 eGFP/mCherry expression bins, and oligo barcode sequencing was used to estimate promoter activity and cell-to-cell noise.
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
hg19
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
The assay used a dual-fluorophore pZDonor reporter with the tested sequence driving eGFP and a constitutive EF1alpha-mCherry cassette for normalization. A ZFN-mediated double-strand break and homologous recombination targeted the library to the AAVS1 locus in a modified K562 line with two AAVS1 copies; an mCherry gate selected single-copy integrants. After growth to clear nonintegrated plasmid, cells were FACS-sorted into 16 eGFP/mCherry bins, and an 11-mer oligo barcode plus Illumina sequencing identified the distribution of each oligo across bins.
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 · 59 definitions
element_id
Stable package identifier formed as oligo_<oligo_index>.
oligo_index
Unique oligo index from the GEO processed library matrix.
source_table
Supplemental expression/design table(s) in which this oligo index appears; blank means no matching available annotation table.
annotation_row_count
Number of raw supplemental annotation rows mapped to this oligo index before distinct values were combined.
design_category
Normalized design class derived from the supplemental table; unannotated entries are explicitly labeled.
sequence_set
Original supplemental Set label.
promoter_name
Name of a characterized full-length promoter for Supplemental Table S2 entries.
transcript_id
Ensembl transcript identifier(s) for a native core-promoter entry.
organism
Original organism label for characterized promoter blocks.
chromosome
Chromosome from the original hg19 annotation, when supplied.
tss_position
Reported transcription-start position for characterized promoter blocks.
oligo_start_in_promoter
Start position of the tiled oligo within the characterized promoter sequence.
midpoint_start_hg19
Start coordinate of the PIC-binding midpoint interval on hg19.
midpoint_end_hg19
End coordinate of the PIC-binding midpoint interval on hg19.
cp_start_hg19
Start coordinate of the tested core-promoter interval on hg19; coordinate orientation follows the source table.
cp_end_hg19
End coordinate of the tested core-promoter interval on hg19; coordinate orientation follows the source table.
reference_order
Original REF_order identifier for the PIC-binding sequence.
pic_binding_id
Original TFIIB ChIP-exo binding identifier.
chip_exo_reads_sum
TFIIB ChIP-exo read-count score used in PIC-site selection.
encode_region_name
ENCODE chromatin-region class for the PIC-binding sequence.
orientation
Tested orientation of a PIC or TF binding sequence, as supplied (Fw/Rv).
background
Synthetic promoter background sequence name.
tested_elements
Description of the core-element perturbation tested in the oligo.
core_element_source
Source label for the synthetic core-element design.
core_configuration
Six-character core-element presence/configuration code from Supplemental Table S7.
breu
Whether the upstream BRE element is present in the synthetic design.
breu_sequence
BREu sequence used in the design.
breu_position
BREu position relative to the TSS in the design.
tata
Whether the TATA element is present in the synthetic design.
tata_sequence
TATA sequence used in the design.
tata_position
TATA position relative to the TSS in the design.
bred
Whether the downstream BRE element is present in the synthetic design.
bred_sequence
BREd sequence used in the design.
bred_position
BREd position relative to the TSS in the design.
initiator
Whether the initiator (Inr) element is present in the synthetic design.
initiator_sequence
Initiator sequence used in the design.
initiator_position
Initiator position relative to the TSS in the design.
mte
Whether the motif ten element is present in the synthetic design.
mte_sequence
MTE sequence used in the design.
mte_position
MTE position relative to the TSS in the design.
dpe
Whether the downstream core promoter element is present in the synthetic design.
dpe_sequence
DPE sequence used in the design.
dpe_position
DPE position relative to the TSS in the design.
motif_info
Original motif identifier and transcription-factor/domain annotation from the TF activity screen.
transcription_factor
TF tested in the homotypic-site multiplicity screen.
motif_length
Length of the tested TF motif in nucleotides.
motif_sequence
Sequence of the tested TF motif.
motif_count
Number of homotypic TF sites in the oligo.
motif_positions
Positions of the planted TF motifs in the activity-screen design.
predefined_positions
Indices of the predefined motif positions selected for the multiplicity design.
actual_positions
Actual motif positions in the oligo sequence.
native_k562_rpm_mean
Mean endogenous K562 CAGE expression in RPM used to select native core promoters.
total_reads_bins
Total barcode reads summed across the 16 FACS expression bins.
mean_expression_gfp_mcherry
GEO Weighted_Avg; weighted mean eGFP/mCherry expression score across bins.
noise_cv_published
GEO CV value; published noise score from the expression-bin distribution (the paper describes noise as CV^2).
mean_log10_expression
Mean expression on the log10 scale from the GEO processed matrix.
std_log10_expression
Standard deviation of expression on the log10 scale from the GEO processed matrix.
activity_call_1_58_threshold
Activity call using the supplemental-methods empty-vector threshold of 1.58 for mean eGFP/mCherry.
oligo_sequence
164-nt variable sequence for the designed oligo, excluding constant library priming regions.
Quality control
The authors normalized reads from each FACS bin to the bin fraction, zeroed bins below 1/(16 x 10) = 0.625%, smoothed bin values with MATLAB smooth() using a three-bin span, detected the dominant peak spanning at least three adjacent bins, and treated smaller peaks as technical noise. Oligos with fewer than 100 reads were assigned NaN and excluded from the published measurements. Package QC retained 14,332 of 15,753 GEO oligo rows: Total_reads_bins had to be at least 100, all four published score fields (Weighted_Avg, CV, Std_log10, and Mean_log10) had to be finite, and the oligo sequence had to be a valid 164-nt A/C/G/T/N sequence. This excluded 1,373 low-read rows and 48 rows with invalid or unavailable scores. The 326 finite negative values in the published CV column were retained unchanged as source values; they are flagged in agent_comments because the paper describes the noise metric as CV^2.
Curation notes
This is one targeted-integration/FACS-binning MPRA experiment with a mixed library: native characterized promoter tiles, PIC ChIP-exo sequences, native human core promoters, synthetic core-element configurations and distance shifts, TF binding-site activity, and TF site multiplicity. The package therefore uses one table with standardized columns and semicolon-joins distinct supplemental annotations when the source repeats an oligo index for identical sequences or shared controls (40 oligo indices have multiple source annotation rows). The GEO processed matrix contains 15,753 unique oligo indices; 14,332 pass the package QC. The source reports 326 finite negative values in its CV column even though the methods describe a squared coefficient of variation; these values were preserved rather than reinterpreted. The GEO platform labels the library as synthetic construct (taxid 32630), but the biological assay was performed in human K562 cells, resolved to Cellosaurus CVCL:0004. The reference build for the native/PIC genomic annotations is hg19; the synthetic designs have no single genomic region, so region_of_interest is null. Raw sequencing reads were intentionally not included.