Experiment / E7YNIGVCNTransposon-integrated MPRA

Tornado circular versus linear Pol III barcode bulk MPRA

Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters

Circular U6-Tornado barcodes and truncated linear barcodes were integrated into K562 cells with piggyBac and compared by bulk RNA/DNA barcode counting. The table provides per-barcode normalized activity for the two barcode architectures in duplicate biological replicates.

Download processed table (CSV)Raw source data API documentation

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: Other
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

The p053 U6-Tornado library produces circular oBC RNA and p054 produces a matched truncated linear barcode RNA. Both libraries were piggyBac-integrated into K562 cells; barcode UMI counts from genomic DNA and RNA were used for steady-state expression/activity.

Processed data

50 rows per page. Click a cell to inspect its full value.

Visible columns (14 of 14)

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Page 1 · 50 rows · More results available

Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.

Column dictionary · 14 definitions

barcode_id: Unique Pol III barcode identifier.
barcode_sequence: Barcode nucleotide sequence.
barcode_type: Circular Tornado oBC or linear barcode class.
plasmid_origin: Originating plasmid/library annotation joined from the barcode list.
biological_replicate: K562 biological replicate identifier.
dna_umi: Genomic-DNA UMI count for the barcode.
rna_umi: RNA UMI count for the barcode.
dna_reads: Genomic-DNA sequencing read count.
rna_reads: RNA sequencing read count.
dna_umi_normalized: DNA UMI count divided by total DNA UMI count for the replicate and barcode type.
rna_umi_normalized: RNA UMI count divided by total RNA UMI count for the replicate and barcode type.
activity_rna_over_dna: Normalized RNA/DNA barcode activity.
qc_pass: TRUE for barcodes passing the paper-derived >50 DNA UMI filter.
source_table: GEO source table used to create the row.

Quality control

The paper defined valid plasmid-library barcodes using high-count modes (>9 UMIs for p053 and >5 UMIs for p054), removed 34 barcode sequences shared between the two libraries, and retained expression barcodes represented by more than 50 DNA UMIs. The processed table applies the >50 DNA UMI filter and requires finite sample normalization denominators.

Curation notes

The GEO count table does not carry a cell-line column; K562 is taken from the paper's Pol III methods section. The barcode list, count matrix and plasmid maps are retained in raw_data.

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