ATAC-STARR-seq activity in mouse Th17 CD4+ T cells
Multi-enhancer regulatory hubs control Th17 cell identityA common pooled episomal ATAC-STARR-seq library made from mouse CD4+ T-cell open-chromatin fragments was nucleofected into in vitro polarized Th17 cells. The table reports Th17 RNA-output versus pooled input activity statistics for the 135,897 tested OCRs.
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
Th17 polarization: anti-CD3e 0.25 μg/mL plus anti-CD28 1 μg/mL, anti-IL-4 and anti-IFNγ blocking antibodies at 2 μg/mL each, IL-6 10 ng/mL, and hTGF-β1 0.3 ng/mL for 72 h; post-nucleofection recovery included Th17 cytokines and 2 h anti-CD3/CD28 restimulation.
Episomal ATAC-STARR-seq used a modified ORI-STARR-seq Thy1.1 reporter vector derived from Addgene #99296. Tagmented ATAC fragments from Th0, Th1, Th2, Th17, and Treg libraries were pooled at equal mass; the same pooled library was delivered to each subset by nucleofection. RNA output was collected after subset-cytokine recovery and restimulation, and differential activity was tested against pooled plasmid input with CSAW and edgeR.
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
- element_id
- Unique OCR/peak identifier from Supplement 1 peakID.
- assay_condition
- The assayed CD4+ T-cell subset for this child experiment.
- chromosome
- mm10 chromosome name from the source table.
- start
- 0-based, half-open mm10 interval start from the source BED-like coordinates.
- end
- Half-open mm10 interval end from the source BED-like coordinates.
- width_bp
- Element width in base pairs, calculated as end minus start.
- nearest_gene
- Nearest gene annotation supplied by the study.
- distance_to_tss_kbp
- Signed distance in kilobases from the nearest gene transcription start site, as supplied by the study.
- atac_class
- Source chromatin-accessibility class for the OCR.
- atac_subsets
- Source list of CD4+ subsets in which the OCR was accessible; blank where the source is missing.
- radial_category
- Supplement 2 radial-plot category for an exact coordinate match: Th0, Th1, Th2, Th17, Treg, or shared; blank when not listed.
- atac_peak_call
- Binary source ATAC-seq peak indicator for the assayed subset.
- atac_cpm
- Mean normalized ATAC-seq read depth in the assayed subset, in counts per million.
- pooled_input_cpm
- Normalized read depth in the pooled ATAC-STARR-seq plasmid input library, in counts per million.
- astarr_rna_cpm
- Normalized ATAC-STARR-seq RNA-output read depth for the assayed subset, in counts per million.
- p_value
- Source CSAW/edgeR raw p-value for the assayed subset versus pooled input.
- fdr
- Benjamini–Hochberg adjusted differential-activity value from the source table.
- log2_rna_dna
- Source representative log2 RNA/input fold change (rep.logFC) for the best test window in the OCR region.
- activity_call
- Derived call: active when FDR ≤0.05 and log2 RNA/input >0, repressive when FDR ≤0.05 and log2 RNA/input <0, significant_zero_effect when significant with exactly zero effect, otherwise not_significant.
- qc_pass
- TRUE for rows retained after package-level QC.
Quality control
The authors filtered paired-end output/input fragments to 150–800 bp, required mapping quality ≥20, removed PCR duplicates, counted 50-bp windows at 25-bp steps over the MACS2 union peak set (FDR <0.001), corrected composition bias with CSAW normFactors and 2,500-bp bins, combined significant windows with summit-weighted minimalTests, and controlled multiple testing with Benjamini–Hochberg (activity call FDR ≤0.05). Package QC additionally required valid mm10 chromosome coordinates, start < end, a nonempty unique peak ID, and finite nonnegative CPM/count fields with p-values and FDR in [0,1]. All 135,897 source OCR rows pass these checks and are retained; nonsignificant elements are retained because they are valid assay observations.
Curation notes
This condition corresponds to ENCODE ENCSR576KQE and the study methods’ four biological replicates for Th17. The processed table is a clean condition-specific view of Supplement 1; it preserves all source OCRs and adds the exact-coordinate radial-category join from Supplement 2. Source ATAC-STARR statistics are region-level summaries rather than replicate-level count columns.