Targeted BAC-derived STARR-seq of the MYC locus in K-562 under JQ1
Transcriptional plasticity promotes primary and acquired resistance to BET inhibitionA BAC-fragment library covering approximately 91% of the surrounding 3.1 Mb MYC region, together with 25 genic control BACs, was cloned into an episomal STARR-seq vector with a minimal MYC promoter. The library was electroporated into K-562 cells and assayed after 24 h in DMSO vehicle or 250 nM JQ1.
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
DMSO vehicle or 250 nM JQ1 for 24 h
Twenty-one BACs span the MYC locus and 25 additional BACs are genic controls. BAC DNA was fragmented and cloned into a human STARR-seq vector containing a minimal MYC promoter; 500 µg of library was electroporated into 1×10^8 K-562 cells per condition. Poly(A)+ reporter RNA and input plasmid DNA were sequenced in 50-cycle paired-end runs on an Illumina HiSeq 2000, and the public GEO products are normalized bigWig tracks.
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
- peak_id
- Deterministic identifier for a QC-passing re-called STARR-seq peak
- chrom
- Chromosome in the hg19 reference assembly
- start
- 0-based half-open genomic start coordinate
- end
- 0-based half-open genomic end coordinate
- summit
- Midpoint of the 500-bp window with the highest QC enrichment
- width_bp
- Width of the merged peak interval in base pairs
- source_bac_ids
- Semicolon-separated BAC clone IDs overlapping the peak
- source_bac_numbers
- Semicolon-separated row numbers from the supplementary BAC table
- n_source_bacs
- Number of overlapping source BAC clones
- library_part
- Whether the peak lies in the MYC-locus BACs or a genic control BAC
- input_mean_rpm
- Mean normalized input-library coverage across the peak interval
- dmso_mean_rpm
- Mean normalized STARR-seq RNA coverage after 24 h DMSO
- jq1_mean_rpm
- Mean normalized STARR-seq RNA coverage after 24 h 250 nM JQ1
- dmso_input_enrichment
- Mean DMSO STARR-seq coverage divided by mean input coverage
- jq1_input_enrichment
- Mean JQ1 STARR-seq coverage divided by mean input coverage
- log2_jq1_vs_dmso
- Log2 ratio of mean JQ1 STARR-seq coverage to mean DMSO coverage
- active_condition
- Condition(s) containing a QC-passing input-enriched window within the peak
- max_qc_enrichment
- Maximum stabilized 500-bp output/input enrichment used for QC
- max_output_reads_per_kb_equiv
- Approximate maximum output read density per kb inferred from the normalized 50-bp coverage track
- qc_status
- QC outcome; all rows in this filtered table are PASS
Quality control
The study pipeline removed adapters with cutadapt v1.4.25, discarded reads shorter than 18 bp, aligned to hg19 with Bowtie v1.0.0, removed duplicate alignments with identical start/end/strand, normalized mapped reads, subsampled the two STARR-seq conditions to 10^5 reads, called peaks against the input library with MACS2, required at least 3-fold enrichment and 5 reads/kb, and merged calls across DMSO and JQ1. Because GEO provides normalized bigWig tracks rather than the original peak matrix, table.csv was re-derived over the published BAC union using 500-bp windows at 50-bp steps; a stabilized input-normalized enrichment of at least 3 in either condition, at least 5 reads/kb equivalent output support, and overlap with a published BAC were required. Only the 162 passing regions are included.
Curation notes
This is one STARR-seq screen represented by two treatment conditions, not two independent experiments. The paper reports 156 identified STARR-seq peaks; the public normalized bigWig tracks were re-called here with a transparent 500-bp/50-bp operationalization of the published input-enrichment criteria, yielding 162 QC-passing regions. GEO did not expose a replicate-level STARR-seq count matrix or peak-level FDR values, so no replicate p-values are asserted. Coordinates and coverage values are hg19 and BEDGraph/bigWig-style; input, DMSO, and JQ1 tracks plus the BAC source table are retained in raw_data.