Whole-genome STARR-seq enhancer screen in ST cells
Genome-wide identification of functional enhancers and their potential roles in pig breedingA sheared pig genomic DNA STARR-seq library was transfected into the porcine testicular ST cell line in two biological replicates. cDNA/output and input-plasmid libraries were sequenced, and significant 600-bp enhancer windows were called with BasicSTARRseq.
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
BX-795 0.5 µM + C16 0.5 µM during plasmid transfection
Episomal self-transcribing reporter assay using a modified pGL3-basic vector: the SCP1 promoter was placed upstream of a GFP reporter with a synthetic intron, and randomly sheared 500–800-bp pig genomic fragments were cloned into the reporter. The library was transfected with TurboFect, and poly(A)+ RNA-derived cDNA and input plasmid DNA were sequenced on Illumina HiSeq X Ten. Two biological replicates were generated for this cell line; the supplied calls are 600-bp windows.
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 · 17 definitions
- call_id
- Unique packaged call identifier formed from the enhancer locus and biological replicate.
- enhancer_id
- Coordinate-based locus identifier; the same locus can occur in both biological replicates.
- cell_line
- Porcine cell line used for the STARR-seq assay.
- chromosome
- Chromosome or scaffold name from the Sscrofa11.1 supplementary table.
- start
- Start coordinate of the reported STARR-seq window, preserved from Supplementary Table S4.
- end
- End coordinate of the reported STARR-seq window, preserved from Supplementary Table S4.
- strand
- Reported strand field; * indicates unstranded.
- length_bp
- Window length in base pairs (end - start + 1; reported source value is 600 for these calls).
- replicate
- Biological replicate number (1 or 2).
- cdna_coverage
- BasicSTARRseq SampleCov value, treated as STARR-seq cDNA/output coverage.
- input_plasmid_coverage
- BasicSTARRseq ControlCov value, treated as input-plasmid/control coverage.
- enrichment
- BasicSTARRseq enrichment statistic reported for the cDNA/output relative to input/control.
- p_value
- BasicSTARRseq binomial-test p-value reported by the authors.
- fdr
- Benjamini-Hochberg false-discovery rate reported by the authors.
- source_sheet
- Worksheet name in the packaged Supplementary Table S4 workbook.
- source_row
- 1-based Excel row number in the source worksheet.
- qc_pass
- TRUE because the row passed the package QC thresholds and interval validation.
Quality control
The authors trimmed reads with Trimmomatic v0.39 (TruSeq2-PE.fa:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, MINLEN:36), aligned reads with Bowtie2 v2.3.5.1 (--no-discordant -X 2000), retained paired uniquely mapped reads with SAMtools v1.3.1 (view -bS -f 2 -q 5), removed PCR duplicates with Picard, and assessed replicate reproducibility using Pearson correlation in deepTools. BasicSTARRseq calls supplied in the source worksheet were required to have enrichment >1.0, p-value <0.001, and FDR <0.1. Package QC additionally required valid numeric coordinates, a positive interval length matching the reported length, and all three call thresholds; rows failing these checks were excluded. Exact duplicate coordinates within a replicate were collapsed to the most statistically significant source record. ST cells were treated with 0.5 µM each of BX-795 and C16 during transfection. The source workbook contains 3,798 calls for replicate 1 and 3,494 unique-coordinate calls for replicate 2 after the stated call thresholds; the source worksheet had one exact duplicate coordinate, retained once using the lowest source p-value.
Curation notes
This experiment uses a common whole-genome library made from 500–800-bp genomic DNA fragments from one Diannan small-ear pig, cloned into a modified pGL3-basic backbone with the SCP1 promoter and a GFP reporter containing a synthetic intron. The processed table preserves replicate-level BasicSTARRseq 600-bp window calls from Supplementary Table S4 rather than replacing them with the paper’s merged 2,576-locus summary. Coordinates are preserved as reported by the supplement; the paper does not state a coordinate-system convention in the table. `cdna_coverage` and `input_plasmid_coverage` follow the source SampleCov/ControlCov labels and are interpreted as cDNA/output and input-plasmid/control coverage. No allelic or variant contrast is present in this library. Package QC retained 7292 rows across the two replicates. Per-sheet retained counts: {'ST cells replicate 1': 3798, 'ST cells replicate 2': 3494}. Rows excluded for malformed values or threshold failure: {'ST cells replicate 1': 0, 'ST cells replicate 2': 0}. Exact-coordinate duplicate collapses: [{'sheet': 'ST cells replicate 2', 'replicate': 2, 'coordinate': 'chr12:59522334-59522933', 'kept_source_row': '1722', 'dropped_source_row': '1723'}].