H3K27ac enhancer tiling library B
Analysis of long and short enhancers in melanoma cell statesA 190 bp tiling CHEQ-seq MPRA densely sampled H3K27ac-selected melanoma regions with tiles shifted 10 bp downstream relative to library A. Library B includes wild-type tiles, motif-focused mutant tiles, and shuffled negative controls assayed across multiple melanoma cell-line 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
CHEQ-seq 190 bp tile library with the library-B 10 bp offset; library B included wild-type, motif-mutated, and shuffled sequences. Reporter activity was quantified by CPM-normalized cDNA/plasmid fold change across the replicate/cell-line columns supplied by GEO.
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 · 21 definitions
- element_id
- Unique 190 bp tile identifier from the author processed table.
- parent_region_id
- Parent H3K27ac region inferred from the tile identifier before the tile suffix.
- genomic_coordinates
- hg19 tile coordinates parsed from the tile identifier.
- tile_length_bp
- Designed tile length in base pairs, generally 190 bp.
- sequence_class
- Author class for the tile: wt, mut, or shuffled.
- variant_design
- Mutation or design suffix supplied after the author’s tile delimiter; blank for unmodified tiles.
- phenotype
- Authors’ phenotype relationship annotation for the parent region.
- mm001_rep1_activity_fc
- CPM-normalized reporter cDNA/plasmid fold-change for MM001 replicate 1.
- mm029_rep1_activity_fc
- CPM-normalized reporter cDNA/plasmid fold-change for MM029 replicate 1.
- mm029_rep2_activity_fc
- CPM-normalized reporter cDNA/plasmid fold-change for MM029 replicate 2.
- mm057_rep1_activity_fc
- CPM-normalized reporter cDNA/plasmid fold-change for MM057 replicate 1.
- mm057_rep2_activity_fc
- CPM-normalized reporter cDNA/plasmid fold-change for MM057 replicate 2.
- mm087_rep1_activity_fc
- CPM-normalized reporter cDNA/plasmid fold-change for MM087 replicate 1.
- mm087_rep3_activity_fc
- CPM-normalized reporter cDNA/plasmid fold-change for MM087 replicate 3.
- mm087_rep4_activity_fc
- CPM-normalized reporter cDNA/plasmid fold-change for MM087 replicate 4.
- mm099_rep1_activity_fc
- CPM-normalized reporter cDNA/plasmid fold-change for MM099 replicate 1.
- mm099_rep2_activity_fc
- CPM-normalized reporter cDNA/plasmid fold-change for MM099 replicate 2.
- n_measured_replicates
- Number of finite activity measurements among the library-B replicate columns.
- mean_activity_fc
- Arithmetic mean of available tile activity fold changes; derived during packaging.
- log2_mean_activity_fc
- Base-2 logarithm of mean_activity_fc; derived during packaging.
- qc_pass
- TRUE for rows retained after removing all-missing tiles and applying source/agent QC.
Quality control
Author processing used Q>30 barcode reads, at least 5 barcodes per enhancer, plasmid-input normalization, shuffled controls/null modeling, and sample-level OutlierD/coverage filtering described in the paper. Rows with no finite activity in any replicate were removed (497 rows); valid partial measurements and wild-type, mutant, and shuffled controls were retained.
Curation notes
The source table contains 7,393 designed rows; 6,896 tiles with at least one finite activity value were retained. Library B is kept separate from library A because its tile offset and replicate design differ.