B73 leaf accessible-chromatin STARR-seq enhancer activity in maize mesophyll protoplasts
Widespread long-range cis-regulatory elements in the maize genomeA leaf ATAC-seq library from B73 second leaves was cloned into an episomal STARR-seq reporter and transiently transfected into maize mesophyll protoplasts. The processed table summarizes the deposited RNA/input activity track for all fully covered leaf accessible chromatin regions (ACRs), including distal, proximal, and genic ACRs.
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 episomal reporter used a cauliflower mosaic virus 35S core promoter, GFP open reading frame, CcdB cloning site, and an Arabidopsis RBCS1A-derived polyadenylation signal. The main library was made from 400–700-bp fragments of a B73 second-leaf ATAC-seq library, transfected into approximately 15 million etiolated-leaf mesophyll protoplasts by PEG and incubated for 14 hours at 22°C; poly(A)+ reporter RNA and matched plasmid input were sequenced as paired-end 35-bp reads on an Illumina NextSeq 500. The GEO series contains STARR B73 DNA high (GSM4284452), STARR B73 DNA scaled (GSM4284453), and STARR B73 RNA (GSM4284454); the deposited activity file is a base-pair-resolution RNA/input fragments-per-million ratio track. An approximately 150-kb B73 BAC containing the tb1 control region was assayed as a positive-control library, but no separate BAC activity table was deposited and it is not represented as a second processed experiment here.
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 · 16 definitions
- acr_id
- Synthetic stable identifier derived from the ACR chromosome and interval coordinates.
- chromosome
- Chromosome label normalized to chr1 through chr10.
- start
- 0-based inclusive ACR start coordinate on AGPv4.
- end
- 0-based exclusive ACR end coordinate on AGPv4.
- summit
- Leaf ATAC-seq ACR summit coordinate from Supplementary Data Table S1a.
- length_bp
- ACR width in base pairs.
- acr_type
- Source ACR proximity class: distal, proximal, or genic.
- chromatin_group
- Source leaf ACR chromatin-group label: Unmodified, K27me3, Kac, Transcribed, Ungrouped, or NA.
- dacr_non_transcribed
- TRUE for distal ACRs whose source chromatin group is not Transcribed; FALSE otherwise.
- max_activity_ratio
- Maximum deposited STARR RNA/input fragments-per-million ratio across the ACR interval.
- log2_max_activity_ratio
- Base-2 logarithm of max_activity_ratio; blank when the maximum ratio is zero.
- mean_activity_ratio
- Base-pair-length-weighted mean of the deposited RNA/input ratio across the ACR interval.
- activity_interval_count
- Number of run-length activity intervals from the GEO track overlapping the ACR.
- activity_bases_covered
- Number of ACR base pairs covered by the deposited activity track.
- activity_coverage_fraction
- activity_bases_covered divided by length_bp.
- qc_pass
- TRUE for every row retained after coordinate, coverage, and finite-value QC.
Quality control
The authors trimmed adapter, quality, and minimum-length sequence with Trimmomatic, mapped STARR-RNA and STARR-input reads uniquely to AGPv4 with Bowtie, removed reads overlapping BAC-contaminated regions, called STARR peaks with MACS2, and controlled peak FDR below 0.05 by Benjamini–Hochberg. The source ACR catalog was Supplementary Data Table S1a, containing 32,481 leaf ACR rows; package QC required nonnegative BED-style coordinates, a summit inside the interval, chromosome 1–10 coordinates, complete coverage by the GEO RNA/input track, and finite nonnegative activity values. The GEO activity track contained 5,949,004 valid run-length intervals and fully covered chromosomes 1–10. The 370 ACR rows on B73V4 contigs were excluded because the quantitative track has no contig data, leaving 32,111 QC-passing rows. Zero maximum activity values were retained as valid low/no reporter-output measurements; the public ratio file does not provide a per-ACR p-value or FDR column.
Curation notes
This is one processed experiment representing the leaf ATAC-seq-derived ACR screen; the BAC/tb1 assay is treated as a positive-control sub-assay because the public release provides no separate machine-readable BAC activity table. Supplementary Data Table S1a has 32,481 rows, including 370 B73V4 contig intervals absent from the GEO STARR track; all 32,111 chromosome-1-to-10 rows were fully covered and retained. The processed values are derived from the deposited run-length RNA/input ratio track by interval overlap, with max_activity_ratio matching the paper's maximum-within-ACR activity concept. No oligo sequences, barcode-level counts, strand-specific counts, or row-level significance values were available in the deposited quantitative file, and no raw FASTQ files are included per package scope. The source paper describes this STARR-seq experiment as a single biological replicate.