sintHiChIP: Benchmark Chromatin Interaction Data for GM12878 and K562 Cells

Processed HiChIP chromatin interaction data identifies loops at FDR < 0.01 using multiple methods. The dataset contains results for GM12878 lymphoblastoid cells (H3K27ac and cohesin targets) and K562 erythroleukemia cells (H3K27ac target). Authored by Weiyue Ding and last updated in May 2026, it provides 158.1 MB of processed analysis results derived from raw sequencing data.

Use Cases

• Benchmark chromatin loop callers based on the inclusion of eight distinct analysis methods.
• Compare chromatin interaction landscapes based on the two different protein targets (H3K27ac and cohesin).
• Analyze cell-type-specific chromatin architecture based on data from GM12878 and K562 cell lines.
• Validate new HiChIP analysis pipelines against established benchmark results.

Strengths

• Includes results from eight distinct analysis methods (sintHiChIP, MAPS, MMCT-Loop, FitHiChIP, HiC-DC+, hichipper, cLoops, cLoops2).
• Covers two human cell lines (GM12878 and K562) and two chromatin targets (H3K27ac and cohesin).
• Data is processed and filtered to a consistent statistical threshold (FDR < 0.01).
• Files are provided in a standard, compressed bioinformatics format (gzipped BEDPE).

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Data may reflect bias inherent to the specific cell lines and experimental conditions used.

Provenance

Source

figshare

Collection Method

Derived from raw HiChIP sequencing data available in NCBI GEO, processed with sintHiChIP and benchmark methods.

Freshness

Last updated 2026-05-14 14:11:23; freshness should be verified.