SuRE34 focused BAC library in K562: basal, hemin, and solvent-control conditions
Genome-wide mapping of autonomous promoter activity in human cellsA focused SuRE library made from nine human BACs spanning approximately 1.3 Mb was cloned as random 0.1-1 kb genomic fragments and transiently transfected into K562 cells. Duplicate released coordinate/strand records were merged, then plasmid-input PCR replicates were combined with basal K562, solvent-control, and 50 uM hemin RNA barcode counts to report normalized fragment activity and the hemin response.
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 K562; 50 uM hemin or solvent control added 1 h after nucleofection and harvested 24 h later
SuRE34 is an episomal plasmid barcode reporter assay using a promoter-less GFP transcription unit and random 20-bp barcodes. The focused library was derived from nine BAC intervals; RNA barcode counts were measured for basal K562 cells and for hemin-treated and solvent-control conditions. Aggregate RNA and plasmid counts were library-size normalized to counts per billion before calculating log2 RNA/DNA activity with a +1 normalized-unit pseudocount.
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 · 21 definitions
- fragment_id
- Deterministic fragment identifier in the form chromosome:start-end:strand
- chromosome
- hg19 chromosome containing the focused-library fragment
- start
- Zero-based genomic start coordinate as released by GEO
- end
- Genomic end coordinate as released by GEO
- strand
- Orientation of the genomic fragment in the SuRE reporter
- fragment_length_bp
- Fragment length in base pairs, calculated as end - start
- ipcr_barcode_observations
- Sum of iPCR observations supporting the fragment association across merged coordinate rows
- source_coordinate_rows
- Number of released rows merged for this chromosome/start/end/strand coordinate
- plasmid_input_count
- Sum of four released plasmid-input PCR replicate counts
- basal_rna_count
- Sum of the two released basal K562 RNA PCR replicate counts
- solvent_rna_count
- Sum of the two released solvent-control RNA PCR replicate counts
- hemin_rna_count
- Sum of the two released hemin-treated RNA PCR replicate counts
- plasmid_input_norm_per_billion
- Plasmid input count normalized to all-source-row plasmid reads per billion
- basal_rna_norm_per_billion
- Basal K562 RNA count normalized to all-source-row basal RNA reads per billion
- solvent_rna_norm_per_billion
- Solvent-control RNA count normalized to all-source-row solvent RNA reads per billion
- hemin_rna_norm_per_billion
- Hemin-treated RNA count normalized to all-source-row hemin RNA reads per billion
- basal_activity_log2_rna_dna
- Basal log2 reporter activity, log2((basal RNA norm + 1)/(plasmid DNA norm + 1))
- solvent_activity_log2_rna_dna
- Solvent-control log2 reporter activity, log2((solvent RNA norm + 1)/(plasmid DNA norm + 1))
- hemin_activity_log2_rna_dna
- Hemin-treated log2 reporter activity, log2((hemin RNA norm + 1)/(plasmid DNA norm + 1))
- hemin_vs_solvent_log2fc
- Hemin response as hemin_activity_log2_rna_dna - solvent_activity_log2_rna_dna
- activity_detected_in_any_condition
- 1 if any basal, solvent-control, or hemin RNA count is nonzero, otherwise 0
Quality control
The GEO release contains fragments retained by the authors' barcode-length, alignment, mapping-quality, and multi-position barcode filtering. Duplicate rows with the same chromosome, start, end, and strand were merged by summing their iPCR and count values, collapsing 781,022 source rows to 736,574 coordinate/strand keys. For packaging, valid keys were required to have non-negative numeric counts and at least 2 aggregate iPCR barcode observations; 500,448 processed fragments passed and 236,126 keys were excluded. All RNA observations, including zero counts, were retained after mapping QC because zero reporter RNA is an informative no-detection result. Aggregate condition counts were normalized using totals over all valid source rows, then activity was calculated as log2((RNA_norm + 1)/(DNA_norm + 1)); no raw sequencing reads were used.
Curation notes
The GEO series design describes the focused BAC work as one library experiment with hemin and control conditions. Sample labels are internally uneven: basal samples include Brep1/Brep2, while hemin and solvent-control samples are labeled Brep2; the released labels and PCR replicate structure are preserved through aggregate columns. Multiple released rows share identical coordinate/strand keys, so they were summed before QC in accordance with the paper's description of aggregating identical-position barcode observations. This is not a variant-focused assay and has no rsID/allele columns. Table 1 of the supplementary PDF supplies the nine broad BAC intervals used for region_of_interest.