eve-locus genomic-fragment insulator-seq screen
Systematic screening of enhancer-blocking insulators in Drosophila identifies their DNA sequence determinantsA barcoded dual-fluorescent episomal MPRA screened an approximately 345-kb region around the Drosophila even-skipped (eve) locus in S2R+ cells. Reporter RNA mCherry/eGFP unique-UMI ratios from two biological replicates were assigned to mapped genomic fragments and summarized as 50-bp genomic-bin insulation scores.
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
Insulator-seq used a plasmid containing the OpIE2 enhancer, minimal hsp70 promoters, and eGFP and mCherry reporter genes. Genomic fragments linked to reporter barcodes were cloned between the enhancer and the eGFP promoter, transiently transfected into Drosophila S2R+ cells, and harvested 72 h later; one reporter library was transfected into each of two biological replicates for the eve screen. The eve RNA-seq reverse-transcription primer added an 8N UMI, and each barcode’s insulator strength was calculated as mCherry unique-UMI counts divided by eGFP unique-UMI counts.
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 · 19 definitions
- screen
- Screen label for the eve locus assay.
- genomic_bin_50bp
- dm6 chromosome and 50-bp bin interval; every retained fragment contributes to each bin it overlaps by at least 1 bp.
- chromosome
- dm6 chromosome of the genomic bin.
- bin_start
- Start coordinate of the 50-bp genomic bin.
- bin_end
- End coordinate of the 50-bp genomic bin.
- fragment_observation_count
- Number of retained mapped fragment/barcode observations overlapping the bin; a fragment can contribute to multiple bins.
- unique_fragment_count
- Number of distinct retained mapped fragment observations contributing to the bin.
- unique_barcode_count
- Number of distinct reporter barcodes contributing to the bin.
- replicate_count
- Number of biological replicates represented in the bin.
- rep1_fragment_observation_count
- Number of Rep1 fragment/bin overlap observations.
- rep2_fragment_observation_count
- Number of Rep2 fragment/bin overlap observations.
- median_mcherry_egfp_ratio
- Median unnormalized mCherry/eGFP reporter unique-UMI ratio across all retained fragment/bin overlaps.
- rep1_median_mcherry_egfp_ratio
- Median unnormalized mCherry/eGFP unique-UMI ratio for Rep1 overlaps.
- rep2_median_mcherry_egfp_ratio
- Median unnormalized mCherry/eGFP unique-UMI ratio for Rep2 overlaps.
- median_normalized_insulator_strength
- Final pooled median insulation strength for the bin after replicate-median normalization and scaling to the mean of the two replicate medians.
- rep1_median_normalized_insulator_strength
- Rep1 median normalized insulation strength among fragment/bin overlaps.
- rep2_median_normalized_insulator_strength
- Rep2 median normalized insulation strength among fragment/bin overlaps.
- median_log2_normalized_insulator_strength
- Median log2 of the normalized fragment insulation strengths contributing to the bin.
- source_replicates
- Biological replicate labels represented in the bin.
Quality control
The authors mapped DNA-seq barcode/fragment associations to dm6 with Bowtie2, discarded barcodes associated with multiple genomic fragments, and required at least 3 unique-UMI mCherry and 3 unique-UMI eGFP RNA observations per barcode. Package QC additionally restricted records to the expected eve interval chr2R:9780000-10135000, required finite ratios and mCherry/eGFP counts of at least 3, and confirmed that each source table had no duplicate barcode. This retained 190,080 of 383,107 Rep1 rows and 208,344 of 396,751 Rep2 rows; 7,004 50-bp bins were generated from the retained fragments. Non-significant but QC-passing bins were retained.
Curation notes
The processed table follows the paper’s final bin-level presentation: raw mapped barcode observations were normalized within replicate and pooled, then each 50-bp bin was summarized by the median strength of all overlapping fragments. The GEO raw-count tables contain a minority of off-locus mappings and many low-count eve observations; those were excluded from this processed table, while the original rows remain in raw_data. The source table contains reporter RNA unique-UMI counts and mapped fragment coordinates rather than per-barcode DNA counts; DNA sequencing was used to establish the barcode-to-fragment mapping. S2R+ was resolved to Cellosaurus CVCL:Z831.