BX-C genomic-fragment insulator-seq screen
Systematic screening of enhancer-blocking insulators in Drosophila identifies their DNA sequence determinantsA barcoded dual-fluorescent episomal MPRA screened approximately 339 kb spanning the Drosophila Bithorax complex (BX-C) in S2R+ cells. Reporter RNA mCherry/eGFP 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; two independently cloned reporter libraries were transfected per biological replicate for the BX-C screen. The BX-C RNA-seq reverse-transcription primer did not add a UMI, and each barcode’s insulator strength was calculated as mCherry reporter reads divided by eGFP reporter reads.
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 BX-C 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-read ratio across all retained fragment/bin overlaps.
- rep1_median_mcherry_egfp_ratio
- Median unnormalized mCherry/eGFP ratio for Rep1 overlaps.
- rep2_median_mcherry_egfp_ratio
- Median unnormalized mCherry/eGFP 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 mCherry and 3 eGFP RNA-seq reads per barcode. Package QC additionally restricted records to the expected BX-C interval chr3R:16650000-17000000, required finite ratios and mCherry/eGFP counts of at least 3, and confirmed that each source table had no duplicate barcode. This retained 186,581 of 198,998 Rep1 rows and 226,723 of 241,844 Rep2 rows; 6,756 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; those were excluded from this BX-C table, while the original rows remain in raw_data. The source table contains reporter RNA 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.