Genome-wide STARR-seq enhancer screen in barley cultivar Morex protoplasts
Identification of Highly Repetitive Enhancers with Long-range Regulation Potential in Barley via STARR-seqRandomly ultrasonicated 500–800 bp genomic DNA fragments from barley cultivar Morex were cloned into a modified pBI221 self-transcribing reporter and transfected into barley leaf protoplasts. Two biological replicates were merged for genome-wide enhancer calling, yielding 7,323 reported peaks with cDNA/input enrichment and corrected P values.
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
Episomal plant STARR-seq using a modified pBI221 vector containing randomly sheared Morex genomic fragments. Input plasmid DNA and reporter cDNA were sequenced on NovaSeq PE150; the paper reports two biological replicates, duplicate removal, and merged peak calling with BasicSTARRseq and Bonferroni correction. The reported Table S1 coverage fields are merged enhancer-level sample (cDNA) and control (input plasmid) coverage, not barcode-level or replicate-level 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 · 20 definitions
- enhancer_id
- Stable package identifier formed from the source enhancer number.
- source_enhancer_number
- Enhancer number reported in Supplementary Table S1.
- chromosome
- MorexV2.44 chromosome or unplaced sequence label reported by the study, including chrUn.
- start
- 1-based inclusive start coordinate of the reported enhancer peak.
- end
- 1-based inclusive end coordinate of the reported enhancer peak.
- width_bp
- Reported enhancer width in base pairs; it equals end minus start plus one for all retained rows.
- strand
- Source strand field; '*' indicates the orientation-agnostic peak representation used by the study.
- cdna_sample_coverage
- Merged STARR-seq reporter cDNA sample coverage reported in Table S1.
- plasmid_input_coverage
- Merged input plasmid control coverage reported in Table S1.
- p_value_reported
- P value reported for the STARR-seq peak; zero is retained as supplied where the source reported numerical underflow or rounding to zero.
- enrichment_reported
- Reported cDNA sample over input plasmid enrichment, interpreted by the paper as predicted enhancer strength.
- atac_seq_overlap
- TRUE when the Table S1 enhancer overlaps a barley ATAC-seq peak; otherwise FALSE.
- repeat_annotated
- TRUE when at least one RepeatMasker alignment in Table S2 matches the enhancer coordinates.
- repeat_match_count
- Number of RepeatMasker alignment rows joined to the enhancer.
- repeat_classes_families
- Semicolon-separated unique RepeatMasker class/family labels from Table S2.
- repeat_names
- Semicolon-separated unique RepeatMasker matching-repeat names from Table S2.
- repeat_strands
- Semicolon-separated RepeatMasker query orientations: C for complement and + for same orientation.
- repeat_max_score
- Maximum Smith–Waterman alignment score among joined RepeatMasker matches; blank when no match exists.
- repeat_query_covered_bp
- Union length in base pairs of joined RepeatMasker query intervals clipped to the 500-bp enhancer span.
- qc_pass
- TRUE for every row retained after the package QC checks described above.
Quality control
Table S1 is the authors' reported enhancer-call table after two-replicate merging, read mapping, PCR duplicate removal, BasicSTARRseq analysis, and Bonferroni correction. For this package, rows were retained only when chromosome, start, end, and width were numeric and consistent, reported enrichment was >1.3, and reported P value was <0.001; all 7,323 source rows passed. RepeatMasker annotations from Table S2 were joined by exact chromosome/start/end coordinates and aggregated; no source rows required removal.
Curation notes
This is a genome-wide barley STARR-seq enhancer screen rather than an allele-contrast MPRA. The primary source table contains 7,323 called peaks with merged coverage and no per-barcode or per-replicate count matrix. RepeatMasker annotations cover 3,917 unique enhancers from 4,785 alignments, and 63 rows are marked as overlapping barley ATAC-seq peaks. The 45-element tobacco dual-luciferase assay is validation rather than a separate MPRA experiment and is not represented as a child experiment.