Resting primary human CD4+ T-cell Lenti-STARR-seq enhancer and NRE screen
Cis-regulatory atlas of primary human CD4+ T cellsAn open-chromatin library made by OMNI-ATAC of resting total human CD4+ T cells was cloned into a promoterless STARR-seq vector, packaged in an HIV-enveloped, D64V integrase-mutant lentivirus, and assayed in four independent healthy-donor CD4+ T-cell preparations. The processed table contains the genome-wide significant enhancer and negative regulatory element (NRE) calls obtained by comparing STARR RNA with the input plasmid library.
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 (resting total CD4+ T cells)
The library consists of accessible chromatin fragments from primary human CD4+ T cells cloned downstream of a chimeric intron in a promoterless pLenti-STARR reporter that uses the bacterial origin of replication as a cryptic promoter. An HIV-1 envelope was used for delivery, while the psPAX-D64V mutant integrase kept the reporter episomal to avoid positional effects. Total RNA was collected 24 hours after transduction, reverse-transcribed with a STARR transcript-specific primer, and sequenced; the input plasmid library served as the DNA/control comparator. GEO samples include the plasmid control (GSM7073572), Donors I-IV (GSM7073573-GSM7073576), and second runs for Donors III-IV (GSM7073577-GSM7073578).
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
- Generated stable identifier for the processed row; NRE_ and ENH_ prefixes distinguish the two source worksheets.
- element_type
- Final functional class reported by the study: Negative regulatory element or Enhancer.
- activity_direction
- Interpretation of the functional direction in the STARR comparison: negative for NREs and positive for enhancers.
- chrom
- Chromosome from the hg19 MACS2 narrowPeak record.
- start
- 0-based interval start from the source MACS2 narrowPeak record.
- end
- Half-open interval end from the source MACS2 narrowPeak record.
- length_bp
- Interval width calculated as end minus start.
- coordinate
- Convenience coordinate string in the form chrom:start-end using the source interval coordinates.
- macs2_peak_name
- Original MACS2 peak name retained from Supplementary Table 2.
- macs2_score
- Raw fifth field of the MACS2 narrowPeak record.
- strand
- Raw strand field from the MACS2 narrowPeak record; the source reports '.'.
- macs2_signal_value
- MACS2 signalValue, preserved from the source record.
- macs2_pvalue_neg_log10
- MACS2 -log10(P-value) significance value from the source record.
- macs2_qvalue_neg_log10
- MACS2 -log10(q-value) value from the source record.
- macs2_peak_offset
- Raw tenth MACS2 narrowPeak field, reported as the peak offset field; it is preserved without converting it to a genomic summit coordinate.
- significance_threshold_neg_log10
- Class-specific author threshold applied to the MACS2 -log10(P-value): 30 for NREs and 75 for enhancers.
- overlaps_input_atac_peak
- True because final study calls were required to overlap a strong input ATAC-seq peak.
- passes_paper_threshold
- True when the source MACS2 -log10(P-value) exceeds the class-specific author threshold.
- qc_pass
- True for rows retained after source completeness, coordinate, numeric, and paper-threshold QC.
- source_sheet
- Original Supplementary Table 2 worksheet: NRE or ENH.
Quality control
Used the authors' published QC and final-call criteria. Reads were adapter-trimmed and aligned to hg19; only uniquely mapped reads with fewer than three mismatches were used, mitochondrial reads were removed, and duplicate reads above the 75th percentile were removed by MACS2 to reduce PCR-duplication artifacts. Enhancers were called against the input plasmid with -log10(P) > 75, NREs were called with the input plasmid as treatment and STARR RNA as control with -log10(P) > 30, and both classes were retained only when overlapping a strong input ATAC-seq MACS2 narrowPeak. The processed table retains complete rows from the authors' final Supplementary Table 2 NRE and ENH worksheets and applies sanity checks for finite numeric fields, nonnegative starts, and end >= start; all 14,681 retained rows pass the paper's stated class-specific P-value threshold.
Curation notes
This is a region-focused, genome-wide accessible-chromatin STARR-seq screen rather than a variant-allele MPRA. The single processed table has 14,681 final calls: 6,267 NREs and 8,414 enhancers. It is an element-level peak-call table, not a replicate-level RNA/DNA count matrix or per-allele effect table; exact per-element read counts were not supplied as a GEO matrix. The GEO series supplies five processed bigWig tracks (plasmid plus one track for each of Donors I-IV), while the two additional GEO samples are second runs for Donors III and IV. Source MACS2 peak names are duplicated for 25 rows, so use the generated element_id for unique joins. The tenth narrowPeak field is retained verbatim because it exceeds the reported interval width in 2,004 rows, making an inferred summit coordinate unreliable.