Broad episomal library containing the CRE spacing/distance, CRE number/affinity, single-CRE designs, and expression controls, measured in two biological replicates at baseline and 25 µM forskolin.
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:0063
Reference genome
GRCh38
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
0 or 25 µM forskolin for 3 h
Synthetic 150-bp cis-regulatory elements were placed upstream of a minimal promoter/luciferase reporter and associated with random 20-nt barcodes; element activity is summarized from barcode RNA/DNA ratios after forskolin treatment.
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 · 46 definitions
element_id
Stable identifier assigned to the unique tested element in this packaged library.
library_subpool
Source library subpool or follow-up design family.
design_library
Design family encoded by the paper/GEO element name.
element_name
Original construct name from the GEO barcode-variant mapping table.
element_sequence
5-prime-to-3-prime variant sequence after reverse-complementing the sequencing-oriented mapping sequence.
sequence_length_bp
Length of the reported variant sequence in base pairs.
background_id
Paper background identifier used for background normalization when available.
site_configuration
Compact interpretation of the CRE-site or background design.
cre_site_1
State of CRE site 1 (consensus, weak, or no_site) when encoded by the construct name.
cre_site_2
State of CRE site 2 (consensus, weak, or no_site) when encoded by the construct name.
cre_site_3
State of CRE site 3 (consensus, weak, or no_site) when encoded by the construct name.
cre_site_4
State of CRE site 4 (consensus, weak, or no_site) when encoded by the construct name.
cre_site_5
State of CRE site 5 (consensus, weak, or no_site) when encoded by the construct name.
cre_site_6
State of CRE site 6 (consensus, weak, or no_site) when encoded by the construct name.
cre_spacing_bp
CRE-to-CRE spacing in base pairs when encoded by the design.
cre_distance_bp
CRE-to-promoter distance in base pairs when encoded by the design.
scramble_distance_bp
Distance of a 10-bp background scramble from the promoter in base pairs.
scramble_similarity
Per-position similarity score of a background scramble to its original background.
dna_barcode_count
Number of mapped barcodes passing the DNA read threshold for the element.
dna_read_sum
Sum of raw DNA barcode reads for barcodes passing the DNA read threshold.
activity_0uM_repA
Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
activity_0uM_repB
Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
activity_0uM_mean
Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
mad_0uM_repA
Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
mad_0uM_repB
Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
rna_barcodes_0uM_repA
Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
rna_barcodes_0uM_repB
Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
activity_25uM_repA
Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
activity_25uM_repB
Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
activity_25uM_mean
Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
mad_25uM_repA
Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
mad_25uM_repB
Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
rna_barcodes_25uM_repA
Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
rna_barcodes_25uM_repB
Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
log2_activity_0uM_mean
Base-2 logarithm of the element-level mean RNA/DNA activity ratio for the named condition.
log2_induction_0uM_vs_0uM
Base-2 log induction relative to the baseline condition, using the element-level mean activity ratios.
log2_activity_25uM_mean
Base-2 logarithm of the element-level mean RNA/DNA activity ratio for the named condition.
log2_induction_25uM_vs_0uM
Base-2 log induction relative to the baseline condition, using the element-level mean activity ratios.
background_normalized_activity_0uM_repA
Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_activity_0uM_repB
Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_activity_0uM_mean
Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_log2_activity_0uM_mean
Base-2 logarithm of mean activity normalized within replicate to the matching no-CRE background.
background_normalized_activity_25uM_repA
Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_activity_25uM_repB
Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_activity_25uM_mean
Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_log2_activity_25uM_mean
Base-2 logarithm of mean activity normalized within replicate to the matching no-CRE background.
Quality control
Barcode DNA read count >5, more than 7 DNA-qualified barcodes per element, and positive element median activity in both replicates and both forskolin conditions; RNA/DNA counts were normalized per sample to one million reads.
Curation notes
The first run's published R script uses a >5 DNA-read cutoff (later runs use >6). Packaged 9117 retained elements from 1964850 mapped barcodes; activity is an element-level median over barcode ratios.