WT enhancer-pair library, developmental core promoter in ecdysone-treated S2 cells
Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in DrosophilaThe 1000-oligo wild-type/control pair library was assayed toward DSCP in S2 cells treated with 20-hydroxyecdysone after electroporation. The deposited table contains 716,152 oriented pair measurements and includes ecdysone-inducible candidate sequences.
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
~42 μM 20-hydroxyecdysone for 24 h after electroporation
Custom UMI-STARR-seq/peSTARR-seq assay: 249-bp candidate oligos were fused in defined 5′ and 3′ positions around an inert spacer, cloned downstream of a Drosophila core promoter, and quantified by internally normalized reporter RNA/input DNA sequencing. The processed source table reports DESeq2-normalized inferred individual activities and paired RNA/input log2 fold changes. Cells received approximately 42 μM 20-hydroxyecdysone after the one-hour recovery period and were collected at 24 h.
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 · 28 definitions
- left_element_id
- Identifier of the sequence in the 5′/left position of the tested oriented pair.
- right_element_id
- Identifier of the sequence in the 3′/right position of the tested oriented pair.
- left_sequence_group
- Sequence class/group from the corresponding oligo design sheet for the left element.
- left_sequence_detail
- More specific design category from the corresponding oligo design sheet for the left element.
- left_chromosome
- Chromosome/contig label for the left oligo design; may be blank for synthetic or unavailable coordinates.
- left_start
- Start coordinate of the left oligo in the stated reference assembly.
- left_end
- End coordinate of the left oligo in the stated reference assembly.
- left_strand
- Strand of the left oligo design.
- right_sequence_group
- Sequence class/group from the corresponding oligo design sheet for the right element.
- right_sequence_detail
- More specific design category from the corresponding oligo design sheet for the right element.
- right_chromosome
- Chromosome/contig label for the right oligo design; may be blank for synthetic or unavailable coordinates.
- right_start
- Start coordinate of the right oligo in the stated reference assembly.
- right_end
- End coordinate of the right oligo in the stated reference assembly.
- right_strand
- Strand of the right oligo design.
- left_robust_control
- TRUE when the left sequence passed the authors’ robust negative-control z-score filter.
- right_robust_control
- TRUE when the right sequence passed the authors’ robust negative-control z-score filter.
- left_activity_log2
- DESeq2-normalized inferred individual activity of the left sequence, expressed as log2 activity relative to the core-promoter negative-control baseline.
- left_activity_fdr
- FDR-adjusted one-sided test for left individual activity versus robust control pairs.
- right_activity_log2
- DESeq2-normalized inferred individual activity of the right sequence, expressed as log2 activity relative to the core-promoter negative-control baseline.
- right_activity_fdr
- FDR-adjusted one-sided test for right individual activity versus robust control pairs.
- pair_activity_log2
- DESeq2 log2 fold change for reporter RNA versus input DNA for the tested pair.
- pair_activity_fdr
- DESeq2 FDR-adjusted significance value for the paired reporter activity; blank means the pair FDR was not estimable in the deposited table.
- pair_fdr_estimable
- TRUE when pair_activity_fdr is numeric and FALSE when it is blank/not estimable.
- left_activity_class
- Inactive/Low/Medium/Strong class using authors’ activity rule: log2 activity >1 and FDR <0.05, with cut points at 2 and 4.
- right_activity_class
- Inactive/Low/Medium/Strong class using authors’ activity rule: log2 activity >1 and FDR <0.05, with cut points at 2 and 4.
- left_active
- TRUE when left_activity_log2 >1 and left_activity_fdr <0.05.
- right_active
- TRUE when right_activity_log2 >1 and right_activity_fdr <0.05.
- pair_fdr_significant
- TRUE when pair_activity_fdr <0.05, FALSE when it is numeric and ≥0.05, and blank when pair FDR is not estimable.
Quality control
Author QC was retained: heterotypic pairs required at least 5 UMI-collapsed reads in each input replicate; pair activity was computed with a pseudocount using DESeq2 with at least two replicates; normalization used robust negative-control pair counts; control sequences were retained when their mean control-pair activity z-score was between −1 and 1; individual activity required at least 10 robust controls; and homotypic pairs and pairs lacking either individual activity were removed. Active individual sequences were defined as log2 activity >1 with FDR <0.05. Package QC additionally retained only rows with finite left/right individual activity and finite pair log2 activity. No rows were removed by this final check in these deposited FC tables. Missing pair FDRs are retained as not estimable rather than treated as a failed activity measurement.
Curation notes
Source: GEO GSE245033_WT_oligo_pool_dCP_S2_ecdysone_FC_table.txt.gz. The package retained 716,152 of 716,152 deposited rows after the finite-activity check (filtered: 0; unmapped sequence IDs: 0). 55,029 retained rows have no estimable pair FDR in the deposited table; their pair_activity_log2 values remain usable. Sequence classes and coordinates are joined from the compact exported design sheet in raw_data.