GM18507 human LCL BiT-STARR-seq allele-specific reporter assay
High-throughput characterization of genetic effects on DNA–protein binding and gene transcriptionA biallelic targeted STARR-seq library containing 75,501 published direction-specific result records representing 43,500 SNPs was tested in the GM18507 human lymphoblastoid cell line. Nine biological transfections and seven DNA-library replicates were analyzed with UMI-aware QuASAR-MPRA to measure allele-specific reporter expression relative to the input plasmid allele proportion.
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
BiT-STARR-seq is a targeted, biallelic STARR-seq adaptation. Synthetic 230 bp inserts containing 200 bp of regulatory sequence centered on the SNP were cloned downstream of the minimal promoter in episomal pGL4.23. Each regulatory region was represented by reference and alternate oligos where available; the RNA library received random UMIs during cDNA synthesis to identify and remove PCR duplicates. The library was nucleofected into GM18507 LCLs, with nine biological transfection replicates from seven independent cell-growth cultures; cells were harvested after 24 h. Polyadenylated RNA/cDNA and plasmid DNA libraries were sequenced on an Illumina NextSeq 500. The processed source table reports direction-specific forward (fw) and reverse (rv) QuASAR-MPRA summaries.
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 · 16 definitions
- rsid
- dbSNP rs identifier for the tested SNP.
- chromosome
- Chromosome label reported in the source table.
- position_grch37_0based
- 0-based SNP coordinate on the GRCh37/hg19 reference used by the study.
- position_grch37_1based
- 1-based SNP coordinate on the GRCh37/hg19 reference; source pos1 field.
- oligo_identifier
- Direction-specific source identifier formed as rsID_fw or rsID_rv.
- reported_beta
- Combined QuASAR-MPRA allele-specific effect estimate from source field betas_T; sign follows the source convention.
- reported_beta_se_comb
- Combined standard error for the reported QuASAR-MPRA effect estimate.
- reported_beta_low
- Lower reported value associated with the combined effect estimate; source field betas_T_low.
- reported_beta_high
- Upper reported value associated with the combined effect estimate; source field betas_T_high.
- reported_z_score
- Combined QuASAR-MPRA z statistic reported by the authors.
- dna_reference_proportion
- Estimated reference-allele proportion in the input plasmid DNA library (source DNA_prop).
- p_value
- Combined QuASAR-MPRA two-sided p-value (source p_comb).
- fdr
- Benjamini–Hochberg adjusted p-value for the combined QuASAR-MPRA test (source padj_comb).
- direction
- Reporter insert orientation reported by the authors: fw = forward, rv = reverse.
- significant_fdr_0_10
- Boolean flag indicating fdr < 0.10, matching the paper's primary ASE threshold.
- nominal_p_0_05
- Boolean flag indicating p_value < 0.05; this is a nominal threshold and is not the primary FDR call.
Quality control
The authors aligned reads with HISAT2 using a GRCh37 1000 Genomes SNP index, removed PCR duplicates with UMItools and applied a Q20 filter, then used mpileup for allele counts. Their published filters required more than 7 summed DNA counts per SNP with at least one reference and alternate count in either direction, followed by more than 1 RNA count per SNP and at least one count for both alleles; 50,609 SNPs passed the DNA stage and the final RNA-filtered set contained 43,500 SNPs. QuASAR-MPRA combined replicate estimates by fixed effects and used Benjamini–Hochberg correction. Package QC additionally required valid rsID/coordinate/orientation relationships, pos1 = pos + 1, positive combined standard error, DNA proportion and p/FDR values in [0,1], and unique direction-specific identifiers. All 75,501 records from the published Supplemental Table S1 passed these checks and were retained; no rows were removed by package QC.
Curation notes
This package contains one MPRA experiment: the cellular BiT-STARR-seq assay. BiT-BUNDLE-seq, the paper's orthogonal in-vitro NFKB1 binding assay using the same input DNA library, is not represented as a second MPRA experiment; its published source tables are retained in raw_data for context. The processed table is intentionally one row per source direction-specific record rather than collapsing fw/rv rows into one SNP, because the paper analyzes reporter orientation separately. GM18507 is an EBV-transformed Yoruba male lymphoblastoid cell line and is resolved to Cellosaurus CVCL:9632. The public SRA accession is SRP154945; raw FASTQ files were omitted per the requested scope, while SRA experiment metadata are retained.