Combined H3K27ac ChIP-lentiMPRA selection in MIA PaCa-2 cells (L1 + L2)
Efficient Selection of Enhancers and Promoters from MIA PaCa-2 Pancreatic Cancer Cells by ChIP-lentiMPRAH3K27ac-enriched chromatin fragments from MIA PaCa-2 cells were cloned next to a minimal CMV promoter in the pLVPGm.1-mP lentiviral CopGFP reporter, integrated into MIA PaCa-2 cells, and selected by puromycin followed by FACS for high GFP fluorescence. The two independently prepared output libraries (L1 and L2) were sequenced and merged by the authors into 11,264 unique mapped hg38 regions; the table provides those region-level MPRA selection outputs and genomic annotations.
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
The input library was enriched by chromatin immunoprecipitation with anti-H3K27ac antibodies, then cloned into a second-generation self-inactivating lentiviral vector carrying CopGFP under a minimal CMV promoter and a murine Pgk-1 puromycin-resistance cassette. Nodamura virus B2 protein was co-expressed during packaging to suppress RNA interference from bidirectional/antisense transcription. MIA PaCa-2 cells were transduced, puromycin-selected, and sorted for the highest GFP signal; output DNA was amplified and sequenced on an Illumina MiSeq with 2 × 150 bp paired-end reads. L1 and L2 yielded 6,244 and 5,245 mapped fragments, respectively, which were combined after merging overlapping same-orientation regions.
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 · 19 definitions
- element_id
- Unique region identifier generated from chromosome, hg38 start/end, and strand.
- source_name
- Original Table S2 region name, including coordinates and strand.
- chromosome
- Human chromosome or mitochondrial chromosome containing the mapped region.
- start_hg38
- BED-style zero-based start coordinate in GRCh38/hg38.
- end_hg38
- BED-style end coordinate in GRCh38/hg38.
- strand
- Mapped fragment orientation (+ or −).
- length_bp
- BED-style region span calculated as end_hg38 − start_hg38.
- dnase_i_hs
- Binary overlap flag for ENCODE DNase I hypersensitivity peak clusters.
- tf_binding_site
- Binary overlap flag for ENCODE transcription-factor ChIP-seq clusters.
- sea_super_enhancer
- Binary overlap flag for super-enhancers in the SEA database.
- fantom5_cage_peak
- Binary overlap flag for FANTOM5 CAGE transcription-initiation peaks.
- h3k27ac_mia_paca2
- Binary overlap flag for H3K27ac ChIP-seq peaks in MIA PaCa-2 cells.
- h3k27ac_capan2
- Binary overlap flag for H3K27ac ChIP-seq peaks in Capan-2 cells.
- mia_paca2_sedb_super_enhancer
- Binary overlap flag for MIA PaCa-2 super-enhancers from SEdb 2.0.
- associated_genes_great
- Gene symbols associated with the region by GREAT; blank when no gene was reported.
- region_class
- GREAT proximity class: proximal, distal, or unassigned.
- proximal_to_gene_5prime
- GREAT binary flag for a region within the proximal class near a gene 5′ end.
- distal_to_gene_5prime
- GREAT binary flag for a region within the distal class (2–500 kb from a gene 5′ end).
- h3k27ac_overlap_class
- Derived summary of H3K27ac overlap: both, MIA PaCa-2 only, Capan-2 only, or neither.
Quality control
The authors removed adapters and trimmed reads, mapped paired-end reads to hg38 with Bowtie2, retained properly paired primary alignments with MAPQ ≥ 10, separated orientations by alignment flags, converted reads to BEDPE/GFF, merged overlapping regions of the same orientation, calculated RPM with htseq-count, and retained regions with RPM > 10. The authors combined the two passing libraries into 11,264 unique mapped regions (Table S2); the 11,171 discarded regions summarized in Table S1 were not included. For packaging, each source row was additionally required to have a valid chromosome, start < end, a valid strand, 0/1 annotation flags, and a unique coordinate/strand identifier. All 11,264 source rows passed these checks, so no additional rows were removed.
Curation notes
This is one combined region-focused experiment because the publication treats L1 and L2 as independent selection libraries and merges their overlapping mapped fragments into a single 11,264-region map; the supplied Table S2 does not retain a per-row L1/L2 label. The study does not report barcode-level RNA/DNA ratios, allele contrasts, or variant effects in the accessible supplemental table. All table rows are authors' RPM-filtered mapped output regions, including rows without H3K27ac overlap; this preserves the complete reported output rather than restricting it to the later H3K27ac-positive subset used for gene-level analyses. The linked NGS read files were not retrievable from the cited Yandex Disk share at ingestion, so no raw FASTQ files are included.