STARR-seq allelic screen in HEK293a cells
Chromatin Conformation Links Distal Target Genes to CKD LociA combined library of approximately 1,200-bp DNase-hypersensitive candidate regulatory fragments cloned from 20 donors around the rs11959928 locus was electroporated into HEK293a cells as an additional control condition. Two library-input replicates and two transcribed-RNA replicates were used to compare reference-allele prevalence.
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
Episomal STARR-seq using the pSTARR-seq_human reporter vector (Addgene plasmid 71509). Approximately 1,200-bp PCR-amplified DRE fragments containing variants with minor allele frequency >0.03 were equimolarly pooled; the library complexity was estimated at 50,000 clones. HEK293a cells were electroporated with the library, cultured for 24 hours, and polyadenylated reporter RNA was sequenced alongside library input on an Illumina NextSeq500 as 75-bp single-end reads. Supplemental Table 2 provides allele-prevalence percentages rather than raw read counts or barcode-level activity scores.
Processed data
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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 · 15 definitions
- variant_id
- Reported chr5 hg19 coordinate used as the stable variant label because the paper does not provide a separate ID for each position.
- locus_id
- The vertically merged SNP-ID label in Supplemental Table 2 identifying the assayed rs11959928 locus.
- chromosome
- Chromosome reported in Supplemental Table 2.
- position_hg19
- 1-based hg19/GRCh37 coordinate reported in Supplemental Table 2.
- input_reference_allele_pct_rep1
- Percentage of library-input molecules carrying the reference allele in input replicate 1.
- input_reference_allele_pct_rep2
- Percentage of library-input molecules carrying the reference allele in input replicate 2.
- rna_reference_allele_pct_rep1
- Percentage of transcribed reporter RNA molecules carrying the reference allele in HEK293a replicate 1.
- rna_reference_allele_pct_rep2
- Percentage of transcribed reporter RNA molecules carrying the reference allele in HEK293a replicate 2.
- delta_reference_allele_pct_rep1
- Published delta for HEK293a replicate 1, calculated as transcribed-RNA reference-allele prevalence minus input prevalence, in percentage points.
- delta_reference_allele_pct_rep2
- Published delta for HEK293a replicate 2, calculated as transcribed-RNA reference-allele prevalence minus input prevalence, in percentage points.
- input_reference_allele_pct_mean
- Arithmetic mean of the two input reference-allele prevalence percentages.
- rna_reference_allele_pct_mean
- Arithmetic mean of the two HEK293a transcribed-RNA reference-allele prevalence percentages.
- delta_reference_allele_pct_mean
- Arithmetic mean of the two published HEK293a delta values; positive values indicate relative enrichment of the reference allele in RNA versus input.
- qc_pass
- TRUE for rows retained after package completeness and numeric-range QC.
- source_table
- Source table in the publisher-supplied supplement used to create the row.
Quality control
The authors verified library complexity by dilution series but did not report count-level STARR-seq filtering thresholds. Package QC retained rows only when all six published percentage measurements (two input prevalences, two RNA prevalences, and two delta values) were present, input/RNA prevalences were in [0, 100], and delta values were in [-100, 100]. All 40 of 40 HEK293a rows pass.
Curation notes
HEK293a is the human embryonic kidney cell-line control described by the article; the package maps the name to HEK293-A (Cellosaurus CVCL:6910). The article reports a combined 20-donor library and no treatment condition. Supplemental Table 2 names the locus but not the nucleotide alleles or individual variant rsIDs, so this package preserves the source coordinates without inferring alleles or additional identifiers. The published readout is allele prevalence in input versus transcribed RNA, not an activity log2 fold-change. The same input percentages are reproduced across the three cell-type sections of the source table.