A pooled synthetic TF-binding-site enhancer library was delivered by lentivirus to human OVCAR-8 ovarian cancer cells (OV8), immortalized human ovarian surface epithelial cells (IOSE), and murine ID8 ovarian cancer cells. Enhancer activity was quantified from barcode-linked RNA/DNA ratios across three OV8 replicates, three IOSE replicates, and two ID8 replicates, with cancer-selective activity summarized relative to IOSE.
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
Not reported
Taxonomy ID
Not reported / not applicable
Biosample
Not reported / not applicable
Reference genome
Not reported / not applicable
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated; comparison of OV8, IOSE, and ID8 cellular contexts
The library contains synthetic tandem repeats of individual TF binding-site sequences (consensus and affinity-modulating variants) in an approximately 121-bp variable region upstream of an adenoviral minimal promoter driving EGFP. Each construct carries a 20-bp random barcode at the 3-prime end of the EGFP transcript; pooled lentiviral integration enables barcode-linked DNA and RNA quantification. Barcode-level RNA/DNA ratios were summarized by median within replicate and averaged across replicates. TREND was transduced at an estimated MOI of 5 with greater than 100-fold library representation; DNA and total RNA were collected five days after transduction and sequenced on an Illumina NovaSeq using 150-bp paired-end 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.
The single TF binding-site sequence repeated in the synthetic enhancer.
tf_name_by_ppm
TF name associated with the source position probability matrix.
tf_name_human_curated
Human-curated TF name annotation.
variable_region
Full synthetic tandem-repeat enhancer variable-region sequence.
motif_source_id
Motif matrix/source identifier used by the authors.
design_rank
Rank of the retained motif sequence within its source matrix/design.
ov8_r1_activity
Median barcode RNA/DNA activity ratio for OV8 biological replicate 1.
ov8_r2_activity
Median barcode RNA/DNA activity ratio for OV8 biological replicate 2.
ov8_r3_activity
Median barcode RNA/DNA activity ratio for OV8 biological replicate 3.
iose_r1_activity
Median barcode RNA/DNA activity ratio for IOSE biological replicate 1.
iose_r2_activity
Median barcode RNA/DNA activity ratio for IOSE biological replicate 2.
iose_r3_activity
Median barcode RNA/DNA activity ratio for IOSE biological replicate 3.
id8_r1_activity
Median barcode RNA/DNA activity ratio for ID8 biological replicate 1; blank when that sample failed coverage QC.
id8_r2_activity
Median barcode RNA/DNA activity ratio for ID8 biological replicate 2; blank when that sample failed coverage QC.
ov8_mean_activity
Authors' mean OV8 activity score across available replicate medians.
iose_mean_activity
Authors' mean IOSE activity score across available replicate medians.
id8_mean_activity
Authors' mean ID8 activity score across available replicate medians; blank when unavailable.
ov8_to_iose_activity_ratio
Authors' mean OV8 activity divided by mean IOSE activity.
id8_to_iose_activity_ratio
Authors' mean ID8 activity divided by mean IOSE activity; blank when unavailable.
log2_ov8_to_iose_activity_ratio
Base-2 logarithm of the OV8-to-IOSE activity ratio, derived for this package.
log2_id8_to_iose_activity_ratio
Base-2 logarithm of the ID8-to-IOSE activity ratio, derived when the ratio is available.
ov8_r1_n_barcode
Number of independent barcodes supporting the OV8 replicate 1 activity estimate.
ov8_r2_n_barcode
Number of independent barcodes supporting the OV8 replicate 2 activity estimate.
ov8_r3_n_barcode
Number of independent barcodes supporting the OV8 replicate 3 activity estimate.
iose_r1_n_barcode
Number of independent barcodes supporting the IOSE replicate 1 activity estimate.
iose_r2_n_barcode
Number of independent barcodes supporting the IOSE replicate 2 activity estimate.
iose_r3_n_barcode
Number of independent barcodes supporting the IOSE replicate 3 activity estimate.
id8_r1_n_barcode
Number of independent barcodes supporting the ID8 replicate 1 activity estimate; blank when unavailable.
id8_r2_n_barcode
Number of independent barcodes supporting the ID8 replicate 2 activity estimate; blank when unavailable.
id8_complete
True when both ID8 replicates have finite activity and at least 3 supporting barcodes; otherwise false.
Quality control
The authors' pipeline demultiplexed reads, collapsed UMIs, aligned reads to the reference library, removed barcodes with zero DNA or RNA counts, and applied DNA-abundance thresholds chosen to retain approximately 75% of constructs in the cancer project. The published ovarian output used sample-specific DNA thresholds of 2, 3, 5, 6, 3, 2, 30, and 35 for OV8 r1-r3, IOSE r1-r3, and ID8 r1-r2, respectively, and required at least 3 independent barcodes per enhancer. For this package, rows were retained only when all six OV8/IOSE replicate activity values were finite, all six corresponding barcode counts were at least 3, and the OV8/IOSE activity ratio was finite and positive (33,698 of 57,715 designs). ID8 activity and ratio fields are retained when the ID8-specific filters passed; incomplete ID8 fields are blank because ID8 had lower coverage and was a secondary comparison in this combined screen.
Curation notes
This is a mixed-species, multi-cell-context MPRA screen, so no single target organism or biosample CURIE is appropriate. The human OV8 line maps to Cellosaurus CVCL:1629 (NCBITaxon:9606); the paper's IOSE reagent is Applied Biological Materials T1074 and is recorded as UNMAPPED:IOSE_T1074 (NCBITaxon:9606); the murine ID8 line maps to Cellosaurus CVCL:IU14 (NCBITaxon:10090). The packaged table is based on the authors' summarized output rather than raw sequencing counts. The additional complete-case filter makes the primary OV8/IOSE comparison directly analyzable while preserving ID8 values where its lower-coverage screen passed.