IRF3-targeted TF-ChIP-STARR-seq in HeLa cells during Sendai virus response
An evolutionarily conserved constellation of functional cis-elements programs the virus-responsive fate of the human (epi)genomeAn episomal 1xSp1-STARR-seq library was built from IRF3-ChIP DNA fragments isolated from HeLa cells 6 h after Sendai virus exposure, transfected into HeLa cells, and assayed after mock treatment or 6 h Sendai virus infection. The processed table contains the 1,949 paper-defined IRF3-STARR-highly-activated elements (IRF3-SHAe) and their signal summaries from two technical replicates per condition.
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
Mock infection (0 h) versus Sendai virus Cantell strain infection (6 h; approximately 180–200 HAU/ml; MOI 2 for HeLa)
TF-ChIP-STARR-seq, a targeted episomal STARR-seq adaptation. IRF3-bound genomic fragments were recombined into a 1xSp1-STARR-seq vector downstream of a GFP reporter; the inserted fragment is self-transcribed in the reporter RNA. The public GEO tracks are RPKM-normalized STARR-transcript signal tracks for HeLa mock and Sendai-virus-infected cells, with two technical replicates per time point; target enrichment was by IRF3 ChIP rather than capture hybridization.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (19 of 19)
| Row | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | |||||||||||||||||||
| 2 | |||||||||||||||||||
| 3 | |||||||||||||||||||
| 4 | |||||||||||||||||||
| 5 | |||||||||||||||||||
| 6 | |||||||||||||||||||
| 7 | |||||||||||||||||||
| 8 | |||||||||||||||||||
| 9 | |||||||||||||||||||
| 10 | |||||||||||||||||||
| 11 | |||||||||||||||||||
| 12 | |||||||||||||||||||
| 13 | |||||||||||||||||||
| 14 | |||||||||||||||||||
| 15 | |||||||||||||||||||
| 16 | |||||||||||||||||||
| 17 | |||||||||||||||||||
| 18 | |||||||||||||||||||
| 19 | |||||||||||||||||||
| 20 | |||||||||||||||||||
| 21 | |||||||||||||||||||
| 22 | |||||||||||||||||||
| 23 | |||||||||||||||||||
| 24 | |||||||||||||||||||
| 25 | |||||||||||||||||||
| 26 | |||||||||||||||||||
| 27 | |||||||||||||||||||
| 28 | |||||||||||||||||||
| 29 | |||||||||||||||||||
| 30 | |||||||||||||||||||
| 31 | |||||||||||||||||||
| 32 | |||||||||||||||||||
| 33 | |||||||||||||||||||
| 34 | |||||||||||||||||||
| 35 | |||||||||||||||||||
| 36 | |||||||||||||||||||
| 37 | |||||||||||||||||||
| 38 | |||||||||||||||||||
| 39 | |||||||||||||||||||
| 40 | |||||||||||||||||||
| 41 | |||||||||||||||||||
| 42 | |||||||||||||||||||
| 43 | |||||||||||||||||||
| 44 | |||||||||||||||||||
| 45 | |||||||||||||||||||
| 46 | |||||||||||||||||||
| 47 | |||||||||||||||||||
| 48 | |||||||||||||||||||
| 49 | |||||||||||||||||||
| 50 |
Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 19 definitions
- element_id
- Stable element identifier assigned from the IRF3-SHAe source workbook row.
- chromosome
- hg19 chromosome name.
- start
- 0-based inclusive genomic start coordinate from the source workbook/BED representation.
- end
- 0-based exclusive genomic end coordinate from the source workbook/BED representation.
- length_bp
- Element length in base pairs (end - start).
- tf_target
- ChIP target used to define the library; IRF3.
- element_class
- Reported functional element class, IRF3-SHAe.
- rna_0h_exp1_mean_rpkm
- Mean RPKM signal across the element in the mock-infection STARR-transcript track, technical replicate 1; bigWigAverageOverBed mean0 statistic.
- rna_0h_exp2_mean_rpkm
- Mean RPKM signal across the element in the mock-infection STARR-transcript track, technical replicate 2; bigWigAverageOverBed mean0 statistic.
- rna_6h_exp1_mean_rpkm
- Mean RPKM signal across the element in the 6 h Sendai-virus STARR-transcript track, technical replicate 1; bigWigAverageOverBed mean0 statistic.
- rna_6h_exp2_mean_rpkm
- Mean RPKM signal across the element in the 6 h Sendai-virus STARR-transcript track, technical replicate 2; bigWigAverageOverBed mean0 statistic.
- rna_0h_mean_rpkm
- Arithmetic mean of the two 0 h technical-replicate element signals.
- rna_6h_mean_rpkm
- Arithmetic mean of the two 6 h technical-replicate element signals.
- log2_rna_fc_exp1_6h_vs_0h_pc1
- Technical replicate 1 log2 response, log2((6 h mean RPKM + 1)/(0 h mean RPKM + 1)); the 1 is a 1-RPKM pseudocount.
- log2_rna_fc_exp2_6h_vs_0h_pc1
- Technical replicate 2 log2 response, log2((6 h mean RPKM + 1)/(0 h mean RPKM + 1)); the 1 is a 1-RPKM pseudocount.
- log2_rna_fc_6h_vs_0h_pc1
- Log2 Sendai-virus response from the condition means, log2((rna_6h_mean_rpkm + 1)/(rna_0h_mean_rpkm + 1)); this is derived from RPKM tracks and is not the paper's original unnormalized-count statistic.
- technical_replicate_log2_fc_difference
- Replicate 1 log2 response minus replicate 2 log2 response.
- min_rna_track_coverage_fraction
- Minimum fraction of the element covered by a non-missing value across the four packaged RNA tracks.
- qc_status
- PASS_PAPER_SHAe indicates the element was present in the paper's final SHAe list and passed package-level coordinate and track-coverage checks.
Quality control
The study reports FastQC 0.73, adapter/low-quality trimming with Trim Galore 0.6.7, Bowtie2 alignment to hg19, depth normalization with Picard Downsample SAM/BAM, MAPQ filtering at 10, technical-replicate merging, and MACS2 peak calling with --bw 300, --qvalue 0.01, and --keep-dup all. Final statistically and biologically significant elements required FDR ≤ 0.01, enrichment over input ≥ 3, and average ≥ 25 counts; chrY, chrM, chrUn, and ENCODE hg19 blacklist regions were excluded. The source SHAe list additionally required unnormalized STARR-transcript fold change for 6 h/0 h ≥ 1.44 and P < 0.05. For this package, only the 1,949 coordinate records in the paper's final IRF3-SHAe workbook were retained; positive-length coordinates and complete coverage in all four packaged RNA tracks were required, and all 1,949 passed.
Curation notes
The paper's public TFs-ChIP-STARR-seq workbook supplies coordinates and final SHAe membership but not per-element counts or P values. Therefore the table's per-element signal and response columns are derived from the deposited GEO RPKM bigWigs; use the raw tracks to reproduce or replace the pseudocount-based summaries. This is a region/enhancer screen rather than a variant-contrast library, and no alleles or variant IDs were supplied. HeLa is Cellosaurus CVCL_0030, represented as CVCL:0030 to follow the requested CURIE syntax; the assay was performed in HeLa ATCC CCL-2 cells.