Accessible chromatin fragments isolated from Atlantic salmon liver were cloned into a pSTARR-seq reporter carrying the Atlantic salmon EF1α core promoter and transfected into primary salmon hepatocytes. Poly(A)+ cDNA RNA abundance 24 hours after transfection was contrasted with input plasmid DNA by DESeq2 after splitting fragments into length bins.
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.
Organism
NCBITaxon:8030
Taxonomy ID
NCBITaxon:8030
Biosample
CL:0000182
Reference genome
ICSASG_v2 (GCF_000233375.1)
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated (no experimental treatment; reporter transfection)
Episomal pSTARR-seq construct with the Atlantic salmon EF1α core promoter (NC_027326.1:7785458-7785702); Omni-ATAC fragments were size-selected at approximately 30-280 bp and inserted upstream of the reporter transcript. Five input plasmid library and five plasmid-cDNA sequencing runs are listed under ENA project PRJEB81135. The paper reports 4,267,201 mapped unique fragments before package QC and uses the RNA/cDNA-versus-DNA input log2 fold change as regulatory activity.
Processed data
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Visible columns (13 of 13)
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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 · 13 definitions
fragment_id
Original mapped fragment identifier from the authors' RDS, formatted as chromosome number:start-end.
chrom
RefSeq chromosome contig corresponding to the source chromosome number (NC_027300.1 through NC_027328.1).
start
Fragment start coordinate from the mapped source identifier; 0-based BED-style coordinate.
end
Fragment end coordinate from the mapped source identifier; half-open BED-style end coordinate.
fragment_length
Fragment length calculated as end minus start.
length_bin
DESeq2 fragment-length interval used as the analysis stratum.
base_mean
DESeq2 mean of normalized counts across the DNA-input and RNA/cDNA assay samples.
log2_rna_dna
DESeq2 log2 fold change for RNA/cDNA abundance relative to DNA input plasmid abundance.
lfc_se
DESeq2 standard error of log2_rna_dna.
wald_stat
DESeq2 Wald statistic for the RNA/cDNA-versus-DNA contrast.
p_value
DESeq2 Wald-test p-value for the RNA/cDNA-versus-DNA contrast.
padj
Benjamini-Hochberg adjusted p-value from DESeq2.
regulatory_class
Paper-style activity class: up when padj ≤ 0.1 and log2_rna_dna > 0, down when padj ≤ 0.1 and log2_rna_dna < 0, otherwise noeffect.
Quality control
The authors checked reporter-library complexity and the fraction of cloned fragments mapping within open chromatin, counted mapped unique fragment locations, and applied DESeq2 with independent filtering separately within fragment-length bins. For this package, rows were retained only when baseMean met the per-bin DESeq2 independent-filter threshold and baseMean, log2FoldChange, lfcSE, stat, pvalue, and padj were finite. This retained 3,590,323 of 4,267,201 source fragments; 676,878 rows with missing padj were removed. Regulatory significance was not used as a QC filter, so up-, down-, and no-effect fragments are all retained.
Curation notes
This is one ATAC-STARR-seq MPRA experiment, not an allele-contrast MPRA: the assayed library consists of native accessible liver DNA fragments. The packaged table is the authors' fragment-level DESeq2 result, not barcode-level counts or raw reads. The original RDS and liver narrowPeak source are retained in raw_data; the large Zenodo archive's unrelated TE/evolutionary inputs and all ENA FASTQ files are omitted. Atlantic salmon is Salmo salar (NCBI Taxonomy 8030); primary hepatocyte is mapped to Cell Ontology CL:0000182.