Hybrid-selection STARR-seq of K562 promoter fragments
Compatibility rules of human enhancer and promoter sequencesTagmented K562 genomic DNA was hybrid-selected against probes targeting gene promoters, producing 300–700-bp fragments with 10-bp UMIs for a targeted STARR-seq library. Four K562 biological replicates were sequenced to quantify RNA/DNA activity for millions of promoter-region fragments.
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.
Perturbation & assay details
Basal / Untreated
Capture/hybrid-selection STARR-seq of genomic DNA fragments targeting K562 gene promoters. Fragments were amplified with a 10-bp UMI, cloned into the hSTARR-seq_ori reporter (using the bacterial ORI as the reporter promoter), transiently transfected into K562 cells, and measured across four biological RNA replicates with one DNA-input column in the deposited count table.
Processed data
50 rows per page. Click a cell to inspect its full value.
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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 · 8 definitions
- chrom
- Chromosome name from the deposited GEO fragment table.
- start
- Fragment start coordinate as reported by GEO; source orientation is preserved, so minus-strand rows can have start greater than end.
- end
- Fragment end coordinate as reported by GEO; source orientation is preserved.
- strand
- Fragment strand reported by GEO.
- umi
- 10-bp unique molecular identifier assigned to the hybrid-selected fragment.
- dna_input_count
- Deposited K562 plasmid-DNA input count; rows with fewer than 25 were excluded by QC.
- rna_total_count
- Sum of the four deposited biological-replicate RNA counts (Pb, Pc, PD, and PA).
- activity_log2_rna_dna
- log2(rna_total_count / dna_input_count); blank when the summed RNA count is zero.
Quality control
Author QC: fragments were aligned to hg19 with Bowtie2, fragments with fewer than 25 aligned DNA reads were discarded, and biological replicate reproducibility was assessed (reported R² = 0.91). The processed table applies the published DNA-input threshold and retains zero-RNA fragments that passed it; their activity field is blank because log2(RNA/DNA) is undefined at RNA = 0. Retained fragments: 4,167,292 of 5,730,500.
Curation notes
The source table is a targeted promoter pool rather than an unbiased whole-genome STARR-seq library. Coordinates are preserved exactly as deposited, including reversed start/end order on minus-strand fragments; use the strand field when canonicalizing intervals. The full per-replicate source counts remain in raw_data.