K562 eSTARR-seq enhancer-unit and synthetic pair library with MYC promoter
Transcription imparts architecture, function and logic to enhancer unitsIndividual human enhancer units and pooled synthetic pairs of those units were tested in K562 cells using an episomal eSTARR-seq reporter with the MYC promoter. Randomly paired units were joined with a constant 25-bp linker to evaluate whether adjacent enhancer activities combine or are dominated by the stronger unit.
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
Pooled strand-overlap-extension PCR generated random pairs of active eSTARR-seq enhancer units joined by a constant 25-bp sequence, and individual units were retested in the same pool. The released ENCODE signal tables report the forward orientation for this fusion library; normFC is the released normalized eSTARR activity value and was not recomputed.
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 · 20 definitions
- element_id
- Unique individual-unit or concatenated-pair sequence identifier.
- element_type
- Whether the record is an individual enhancer unit or a synthetic concatenation.
- unit_1_id
- Identifier of the first natural enhancer unit in the tested record.
- unit_2_id
- Identifier of the second natural enhancer unit for a concatenated pair; blank for individual units.
- linker_length_bp
- Length of the constant linker between paired units; 25 bp for concatenations and blank for individual units.
- sequence_length_bp
- Length of the tested sequence in base pairs from the authors' fusion FASTA.
- 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_forward_rep1_cpm
- Forward DNA UMI count normalized to counts per million within the replicate's signal file.
- dna_forward_rep2_cpm
- Forward DNA UMI count normalized to counts per million within the replicate's signal file.
- dna_forward_rep3_cpm
- Forward DNA UMI count normalized to counts per million within the replicate's signal file.
- rna_forward_rep1_cpm
- Forward RNA UMI count normalized to counts per million within the replicate's signal file.
- rna_forward_rep2_cpm
- Forward RNA UMI count normalized to counts per million within the replicate's signal file.
- rna_forward_rep3_cpm
- Forward RNA UMI count normalized to counts per million within the replicate's signal file.
- normFC
- Released normalized eSTARR activity score for the individual or concatenated sequence.
- p_value
- Released source P.Value for the eSTARR activity measurement; no adjusted value was supplied in this file.
Quality control
All 234 released ENCODE element quantifications (46 individual units and 188 concatenated pairs) had complete forward-orientation DNA and RNA UMI signals in all three biological replicates and were retained. The released synthetic-pair quantification is the post-filtered set from the eSTARR pipeline; raw sequencing reads were not packaged.
Curation notes
The table is based on ENCODE ENCSR585AGE/ENCFF194CFN and the corresponding three post-transfection DNA signal files from ENCSR036YOP. Individual units and fusions are intentionally kept in one table because they were tested in the same library; sequence IDs can be joined to eSTARR_EnhFusions.fa in raw_data. The source P.Value is nominal/unadjusted as released.