Nipponbare stem-protoplast whole-genome STARR-seq
Global Quantitative Mapping of Enhancers in Rice by STARR-seqRandomly fragmented genomic DNA from rice cultivar Nipponbare was cloned into an episomal STARR-seq reporter and transfected into protoplasts isolated from green stem tissue of two-week-old seedlings. RNA output and input plasmid DNA were sequenced 16 hours after transfection in two independent biological replicates, yielding the shared enhancer set represented here.
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 pBI221 reporter containing a 35S mini promoter and GFP/intron reporter architecture with NOS polyadenylation elements. Approximately 700-bp genomic fragments were tested in rice stem protoplasts; plasmid input and self-transcribed RNA were recovered after 16 hours and sequenced as 150-bp paired-end libraries on Illumina HiSeq X Ten.
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 · 25 definitions
- element_id
- Stable identifier assigned to each shared merged rice STARR-seq enhancer.
- chromosome
- Rice chromosome name exactly as supplied by the GEO merged peak file.
- start_bp
- Start coordinate of the shared merged enhancer, preserved from GEO and Supplementary Table S3.
- end_bp
- End coordinate of the shared merged enhancer, preserved from GEO and Supplementary Table S3.
- dhs_sensitivity
- Supplementary Table S3 annotation indicating whether the enhancer overlaps a DNase I hypersensitive site (With DHS or Without DHS).
- epigenetic_cluster
- Author-defined epigenetic cluster assignment from Supplementary Table S3 (clusters 1-8).
- rep1_peak_count
- Number of replicate-1 author-filtered peak calls overlapping the shared merged enhancer.
- rep1_peak_start_bp
- Start coordinate of the representative replicate-1 peak call, selected by highest enrichment.
- rep1_peak_end_bp
- End coordinate of the representative replicate-1 peak call, selected by highest enrichment.
- rep1_sample_cov
- STARR-seq cDNA/sample coverage for the representative replicate-1 peak (GEO sampleCov).
- rep1_control_cov
- Input plasmid/control coverage for the representative replicate-1 peak (GEO controlCov).
- rep1_pvalue
- Unadjusted peak-enrichment P value for the representative replicate-1 call (GEO pVal).
- rep1_bonferroni_pvalue
- Bonferroni-corrected peak-enrichment P value for the representative replicate-1 call (GEO CpVal).
- rep1_enrichment
- STARR-seq cDNA-to-input enrichment for the representative replicate-1 call.
- rep2_peak_count
- Number of replicate-2 author-filtered peak calls overlapping the shared merged enhancer.
- rep2_peak_start_bp
- Start coordinate of the representative replicate-2 peak call, selected by highest enrichment.
- rep2_peak_end_bp
- End coordinate of the representative replicate-2 peak call, selected by highest enrichment.
- rep2_sample_cov
- STARR-seq cDNA/sample coverage for the representative replicate-2 peak (GEO sampleCov).
- rep2_control_cov
- Input plasmid/control coverage for the representative replicate-2 peak (GEO controlCov).
- rep2_pvalue
- Unadjusted peak-enrichment P value for the representative replicate-2 call (GEO pVal).
- rep2_bonferroni_pvalue
- Bonferroni-corrected peak-enrichment P value for the representative replicate-2 call (GEO CpVal).
- rep2_enrichment
- STARR-seq cDNA-to-input enrichment for the representative replicate-2 call.
- mean_replicate_enrichment
- Arithmetic mean of the representative replicate-1 and replicate-2 enrichment values.
- rep2_to_rep1_enrichment_ratio
- Representative replicate-2 enrichment divided by representative replicate-1 enrichment.
- passes_shared_replicate_qc
- Boolean flag indicating that both representative replicate calls satisfy enrichment >=1.3 and corrected P <0.001 and belong to the shared merged set.
Quality control
The processed GEO peak files already apply the authors' QC: uniquely mapped paired-end reads were retained, PCR duplicates were removed, BasicSTARRseq peaks were Bonferroni-corrected, and calls were required to have enrichment >=1.3 and corrected P <0.001. The paper retained only enhancer peaks detected in both biological replicates; the packaged table therefore contains the 9,642 author-provided shared merged intervals. When multiple filtered peak calls overlapped one merged interval in a replicate, the highest-enrichment call was used for that replicate's representative metrics and the number of overlapping calls was retained in *_peak_count.
Curation notes
This is a region-focused whole-genome enhancer screen, not an allele- or variant-focused MPRA. The table preserves the 9,642 shared intervals and author annotations one-for-one; it does not include raw sequencing reads. GEO and Supplementary Table S3 use matching start/end values, so coordinates were not re-based or normalized. The source GEO merged file contains a small number of overlapping adjacent records, which were retained as supplied. The biosample is represented as rice stem-derived primary protoplasts; no unambiguous requested UBERON or terminal Cell Ontology identifier was determined for this plant preparation, so UNMAPPED:rice_stem_protoplasts is used.