K562 eSTARR-seq candidate regulatory element screen with SCP1 promoter
Transcription imparts architecture, function and logic to enhancer unitsK562 cells were electroporated with an episomal eSTARR-seq library of human genomic candidate elements and controls downstream of the synthetic core promoter SCP1. Both forward and reverse cloning orientations were assayed, and enhancer activity was quantified from RNA/DNA UMI ratios across three biological replicates.
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
This is the SCP1-promoter version of the eSTARR-seq assay: an episomal, self-transcribing reporter adaptation with a 12-nt UMI, UMI deduplication, tagmentation, and orientation-specific alignment. The reporter is nearly identical to the MYC-promoter construct except that the mammalian synthetic core promoter SCP1 is used; candidate elements were selected from K562 regulatory annotations and assayed with controls.
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 · 35 definitions
- element_id
- Unique released eSTARR sequence identifier.
- sequence_length_bp
- Length of the tested element in base pairs from the ENCODE quantification file.
- chromosome
- hg19 chromosome from the released element BED annotation; blank for elements without a genomic BED interval.
- start_hg19
- 0-based inclusive hg19 start coordinate from the released element BED annotation.
- end_hg19
- 0-based exclusive hg19 end coordinate from the released element BED annotation.
- dna_forward_rep1_umi
- Unique UMI count in post-transfection DNA, forward orientation, biological replicate 1.
- dna_forward_rep2_umi
- Unique UMI count in post-transfection DNA, forward orientation, biological replicate 2.
- dna_forward_rep3_umi
- Unique UMI count in post-transfection DNA, forward orientation, biological replicate 3.
- rna_forward_rep1_umi
- Unique UMI count in reporter RNA, forward orientation, biological replicate 1.
- rna_forward_rep2_umi
- Unique UMI count in reporter RNA, forward orientation, biological replicate 2.
- rna_forward_rep3_umi
- Unique UMI count in reporter RNA, forward orientation, biological replicate 3.
- dna_reverse_rep1_umi
- Unique UMI count in post-transfection DNA, reverse orientation, biological replicate 1.
- dna_reverse_rep2_umi
- Unique UMI count in post-transfection DNA, reverse orientation, biological replicate 2.
- dna_reverse_rep3_umi
- Unique UMI count in post-transfection DNA, reverse orientation, biological replicate 3.
- rna_reverse_rep1_umi
- Unique UMI count in reporter RNA, reverse orientation, biological replicate 1.
- rna_reverse_rep2_umi
- Unique UMI count in reporter RNA, reverse orientation, biological replicate 2.
- rna_reverse_rep3_umi
- Unique UMI count in reporter RNA, reverse orientation, biological replicate 3.
- dna_forward_rep1_cpm
- Forward DNA UMI count normalized to counts per million within the replicate's forward signal file.
- dna_forward_rep2_cpm
- Forward DNA UMI count normalized to counts per million within the replicate's forward signal file.
- dna_forward_rep3_cpm
- Forward DNA UMI count normalized to counts per million within the replicate's forward signal file.
- rna_forward_rep1_cpm
- Forward RNA UMI count normalized to counts per million within the replicate's forward signal file.
- rna_forward_rep2_cpm
- Forward RNA UMI count normalized to counts per million within the replicate's forward signal file.
- rna_forward_rep3_cpm
- Forward RNA UMI count normalized to counts per million within the replicate's forward signal file.
- dna_reverse_rep1_cpm
- Reverse DNA UMI count normalized to counts per million within the replicate's reverse signal file.
- dna_reverse_rep2_cpm
- Reverse DNA UMI count normalized to counts per million within the replicate's reverse signal file.
- dna_reverse_rep3_cpm
- Reverse DNA UMI count normalized to counts per million within the replicate's reverse signal file.
- rna_reverse_rep1_cpm
- Reverse RNA UMI count normalized to counts per million within the replicate's reverse signal file.
- rna_reverse_rep2_cpm
- Reverse RNA UMI count normalized to counts per million within the replicate's reverse signal file.
- rna_reverse_rep3_cpm
- Reverse RNA UMI count normalized to counts per million within the replicate's reverse signal file.
- forward_log2_activity
- Released forward-orientation voom log2 RNA/DNA activity effect.
- forward_q_value
- Released FDR-adjusted q-value for the forward-orientation activity test.
- reverse_log2_activity
- Released reverse-orientation voom log2 RNA/DNA activity effect.
- reverse_q_value
- Released FDR-adjusted q-value for the reverse-orientation activity test.
- combined_log2_activity
- Released combined log2 activity score from the forward and reverse measurements.
- activity_call
- Released activity classification, either Enhancer or Inactive.
Quality control
ENCODE-released voom quantifications were used; rows with call=NA or undefined forward/reverse/logFC statistics were removed. The processed table additionally requires non-missing RNA and post-transfection DNA UMI signals in both forward and reverse orientations for all three biological replicates. The paper's active-enhancer criterion is FDR-adjusted P < 0.1 and log2 fold change >= 1 in both orientations; raw sequencing reads were not packaged.
Curation notes
This processed table uses ENCODE eSTARR1 SCP quantification together with the released three-replicate DNA/RNA signal files. It is a promoter-context comparison to the MYC experiment, not an allele-contrast MPRA; tested sequences are natural genomic fragments and controls.