Synthetic CTCF-insulator mutagenesis insulator-seq screen
Systematic screening of enhancer-blocking insulators in Drosophila identifies their DNA sequence determinantsAn episomal insulator-seq MPRA tested 32 synthetic 190-bp CTCF-centered wild-type regions and their motif-point-mutation, sequence-shuffle, and context-replacement derivatives in Drosophila S2R+ cells. Two biological replicates and independent barcoded copies were collapsed to construct-level median mCherry/eGFP activity ratios.
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
The library comprised 32 selected 190-bp wild-type regions centered on CTCF motifs plus 102 designed variants per wild type: motif point mutations (MPM), 10-bp overlapping context shuffles (SF), and progressively larger symmetric context replacements (RC). A 6-bp construct barcode distinguished synthesized fragments, and the eve/synthetic RNA-seq reverse-transcription primer added an 8N UMI. One synthetic reporter library was transfected into each of two biological replicates; construct strength was summarized as the median mCherry/eGFP unique-UMI ratio across independently barcoded copies. The normalized_insulator_strength column applies the paper’s per-parent mean WT/SF/MPM baseline.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (23 of 23)
| Row | |||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | |||||||||||||||||||||||
| 2 | |||||||||||||||||||||||
| 3 | |||||||||||||||||||||||
| 4 | |||||||||||||||||||||||
| 5 | |||||||||||||||||||||||
| 6 | |||||||||||||||||||||||
| 7 | |||||||||||||||||||||||
| 8 | |||||||||||||||||||||||
| 9 | |||||||||||||||||||||||
| 10 | |||||||||||||||||||||||
| 11 | |||||||||||||||||||||||
| 12 | |||||||||||||||||||||||
| 13 | |||||||||||||||||||||||
| 14 | |||||||||||||||||||||||
| 15 | |||||||||||||||||||||||
| 16 | |||||||||||||||||||||||
| 17 | |||||||||||||||||||||||
| 18 | |||||||||||||||||||||||
| 19 | |||||||||||||||||||||||
| 20 | |||||||||||||||||||||||
| 21 | |||||||||||||||||||||||
| 22 | |||||||||||||||||||||||
| 23 | |||||||||||||||||||||||
| 24 | |||||||||||||||||||||||
| 25 | |||||||||||||||||||||||
| 26 | |||||||||||||||||||||||
| 27 | |||||||||||||||||||||||
| 28 | |||||||||||||||||||||||
| 29 | |||||||||||||||||||||||
| 30 | |||||||||||||||||||||||
| 31 | |||||||||||||||||||||||
| 32 | |||||||||||||||||||||||
| 33 | |||||||||||||||||||||||
| 34 | |||||||||||||||||||||||
| 35 | |||||||||||||||||||||||
| 36 | |||||||||||||||||||||||
| 37 | |||||||||||||||||||||||
| 38 | |||||||||||||||||||||||
| 39 | |||||||||||||||||||||||
| 40 | |||||||||||||||||||||||
| 41 | |||||||||||||||||||||||
| 42 | |||||||||||||||||||||||
| 43 | |||||||||||||||||||||||
| 44 | |||||||||||||||||||||||
| 45 | |||||||||||||||||||||||
| 46 | |||||||||||||||||||||||
| 47 | |||||||||||||||||||||||
| 48 | |||||||||||||||||||||||
| 49 | |||||||||||||||||||||||
| 50 |
Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 23 definitions
- variant_id
- Author-provided synthetic construct Name from the GEO count table.
- parent_fragment
- Canonical parent label parsed from the construct Name; wild-type and all derivative variants share this label.
- mutation_position
- Numeric mutation position encoded in the construct Name; blank for WT constructs.
- mutation_strategy
- Construct strategy encoded in the Name: WT wild type, MPM motif point mutation, SF sequence shuffle, or RC replace-context mutation.
- variant_index
- Author-provided construct/variant index encoded in the Name.
- fragment_position_in_reporter
- Whether the construct was assigned to the left (L) or right (R) reporter position.
- rep1_barcode_count
- Number of QC-passing independently barcoded observations for the construct in Rep1.
- rep2_barcode_count
- Number of QC-passing independently barcoded observations for the construct in Rep2.
- total_barcode_count
- Total QC-passing barcode observations across both biological replicates.
- replicate_presence_count
- Number of biological replicates with at least one QC-passing barcode observation.
- rep1_median_mcherry_count
- Median mCherry unique-UMI count across Rep1 barcodes for the construct.
- rep1_median_egfp_count
- Median eGFP unique-UMI count across Rep1 barcodes for the construct.
- rep1_median_ratio
- Median Rep1 mCherry/eGFP unique-UMI ratio across barcodes.
- rep2_median_mcherry_count
- Median mCherry unique-UMI count across Rep2 barcodes for the construct.
- rep2_median_egfp_count
- Median eGFP unique-UMI count across Rep2 barcodes for the construct.
- rep2_median_ratio
- Median Rep2 mCherry/eGFP unique-UMI ratio across barcodes.
- merged_median_ratio
- Median mCherry/eGFP unique-UMI ratio across all QC-passing barcodes and both replicates; construct-level activity score.
- merged_log2_median_ratio
- Base-2 logarithm of the construct-level merged_median_ratio.
- parent_wt_median_ratio
- Merged median ratio for the parent’s WT construct, when present.
- normalized_to_parent_wt
- Construct merged_median_ratio divided by the parent WT median ratio, when a WT ratio is available.
- parent_wt_sf_mpm_mean_ratio
- Mean merged ratio of the parent’s WT, SF, and MPM constructs; the paper’s baseline for synthetic normalization.
- normalized_insulator_strength
- Construct merged_median_ratio divided by parent_wt_sf_mpm_mean_ratio.
- source_replicates
- Biological replicate labels represented in the construct-level summary.
Quality control
The authors identified synthetic constructs from the DNA-seq fragment database, used unique UMIs for RNA quantification, and retained barcodes with at least 3 unique-UMI mCherry and 3 unique-UMI eGFP observations. Package QC additionally required finite mCherry/eGFP ratios, non-empty parseable construct names, and unique barcodes within each source table. All 83,541 Rep1 rows and all 91,236 Rep2 rows passed these read-level checks and were collapsed to 3,544 named construct rows; 3,528 constructs were observed in both biological replicates and 16 in one. The table retains non-insulator and mutated constructs as useful assay controls; the paper’s downstream 23-of-32 wild-type insulator selection is not used as a sequencing QC filter.
Curation notes
The source construct names were kept as the authoritative identifiers. The processed table includes 32 WT rows, 2,006 MPM rows, 1,236 SF rows, and 270 RC rows across 34 parent labels; two parent labels have derivative observations but no WT row in the released count tables, so WT-based fields are blank for those parents. The authors’ repository sequence map does not cover every released construct family, and no sequence was inferred or substituted. S2R+ was resolved to Cellosaurus CVCL:Z831.