PU.1 MPRA-ChIP assay at chr21q22 candidate SNPs
A disease-associated gene desert directs macrophage inflammation through ETS2The MPRA vector library was transfected into TPP macrophages from six healthy donors, followed by minimal-sonication PU.1 immunoprecipitation and barcode sequencing. The processed table contains the source six-donor allele-specific PU.1-binding readout for three SNPs in the chr21q22 enhancer.
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 TPP macrophages; PU.1 immunoprecipitation after MPRA library transfection
Six healthy-donor TPP macrophage samples were sequenced on an Illumina MiSeq with 50-bp single-end reads. The processed values are taken from Source Data Extended Data Fig. 4, sheet 4f, whose label defines them as log2-fold change of the ratio of PU.1-bound alleles (risk:non-risk).
Episomal MPRA library coupled to a PU.1 chromatin immunoprecipitation readout. The transfected library was minimally sonicated to remove contaminants without chromatin shearing, PU.1-bound barcodes were sequenced, and allele-specific binding was summarized as the normalized risk:non-risk PU.1-bound ratio.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (4 of 4)
| Row | ||||
|---|---|---|---|---|
| 1 | ||||
| 2 | ||||
| 3 | ||||
| 4 | ||||
| 5 | ||||
| 6 | ||||
| 7 | ||||
| 8 | ||||
| 9 | ||||
| 10 | ||||
| 11 | ||||
| 12 | ||||
| 13 | ||||
| 14 | ||||
| 15 | ||||
| 16 | ||||
| 17 | ||||
| 18 |
Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 4 definitions
- sample_id
- Source sample label for one of six MPRA-ChIP donor measurements.
- variant_id
- Variant identifier for the tested chr21q22 SNP.
- log2_fold_change_risk_vs_nonrisk
- Source-provided log2 fold change of the ratio of PU.1-bound risk to non-risk alleles; positive values indicate greater risk-allele binding.
- source_sheet
- Source workbook worksheet containing the measurement, here sheet 4f.
Quality control
The paper describes MPRA library preparation, minimal sonication, PU.1 immunoprecipitation, MiSeq sequencing, and QuASAR-MPRA analysis. The supplied source workbook provides complete values for all six samples and three reported variants; no separate row-level QC threshold or raw barcode counts were supplied for this ChIP-coupled readout, so all complete source measurements were retained.
Curation notes
This is a distinct MPRA-ChIP experiment rather than the eight-donor transcriptional MPRA. The source sheet reports risk/non-risk labels but does not provide nucleotide identities or raw barcode counts, so those labels and the six-donor summary values are preserved without remapping to the standard MPRA ref/alt labels.