Experiment / E5VV1KP8VEpisomal Plasmid MPRA

Allele-specific plasmid MPRA across 10 acute lymphoblastic leukemia cell lines

Investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment

A plasmid library containing 175-bp sequences centered on 1,696 reference/alternative regulatory SNVs was tested in seven B-ALL cell lines (697, BALL1, Nalm6, REH, RS411, SEM, SUPB15) and three T-ALL cell lines (CEM, Jurkat, P12-Ichikawa). Each allele was represented by 28 unique 3′-UTR barcodes and each cell line had four transfections; table.csv retains one row per variant–phenotype–cell-line result with the authors’ differential statistics and count-derived allele activities.

Download processed table (CSV)Raw source data API documentation

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.

Organism: Human
Taxonomy ID: NCBITaxon:9606
Biosample: CVCL:0079;CVCL:1075;CVCL:0207;CVCL:0065;CVCL:0092;CVCL:1630;CVCL:1650;CVCL:0093;CVCL:0095;CVCL:0103
Reference genome: hg19
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

The pMPRA1 plasmid carries the 175-bp reference or alternative sequence, restriction sites, a unique 10-bp barcode in the reporter 3′ UTR, and a minimal promoter driving truncated eGFP. Oligos were cloned by Gibson assembly after emulsion PCR, libraries were electroporated with the Neon system, and reporter RNA and plasmid DNA were sequenced on an Illumina NovaSeq 6000. The authors analyzed RNA and DNA barcode counts after merging all barcodes for each allele with mpralm.

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 · 25 definitions

variant_id: rsID of the regulatory variant tested.
sentinel_variant_id: Sentinel GWAS variant associated with the tested variant; blank for positive controls or missing GEO annotations.
phenotype: Pharmacogenomic or ALL phenotype associated with the variant in the source table.
cell_line: ALL cell line used for the four-replicate MPRA measurement.
chromosome: HG19 chromosome label from the author/GEO result table; positive controls retain the source label.
position_hg19: HG19 1-based variant position; blank for positive controls without a genomic coordinate.
is_positive_control: yes for the source ALL susceptibility positive-control rows, otherwise no.
ref_dna_count_sum: Sum of the four reference-allele plasmid DNA barcode counts from the GEO DNA-input file.
alt_dna_count_sum: Sum of the four alternative-allele plasmid DNA barcode counts from the GEO DNA-input file.
ref_rna_count_sum: Sum of the four reference-allele reporter RNA barcode counts for this cell line.
alt_rna_count_sum: Sum of the four alternative-allele reporter RNA barcode counts for this cell line.
ref_activity_log2_rna_dna: Derived mean reference-allele log2 RNA/DNA activity across four replicates after per-library CPM normalization and a +1 CPM pseudocount.
alt_activity_log2_rna_dna: Derived mean alternative-allele log2 RNA/DNA activity across four replicates after per-library CPM normalization and a +1 CPM pseudocount.
derived_allelic_log2_effect_alt_minus_ref: Derived alternative-minus-reference difference between the two mean log2 RNA/DNA activities.
author_log2_fold_change_alt_vs_ref: Author-provided source-table logFC from the mpralm analysis; the REF/ALT count labels support the alternative-versus-reference interpretation.
author_average_expression: Author-provided AveExpr value from the mpralm result.
author_t_statistic: Author-provided t statistic for the allele-specific comparison.
author_p_value: Author-provided two-sided p value for the allele-specific comparison.
author_adjusted_p_value: Author-provided Benjamini–Hochberg adjusted p value.
author_b_statistic: Author-provided moderated B statistic from the mpralm result.
author_significant_fdr_0_05: yes when the author adjusted p value is below 0.05, otherwise no.
reproducible_concordant_in_at_least_3_cell_lines: yes when the variant–phenotype pair appears in Supplementary Data 4 as reproducible and concordant in at least three ALL cell lines, otherwise no.
regulatory_context: Supplementary Data 4 annotation such as promoter, distal intergenic, or TSS-distal without CHiC; blank when not in that list.
promoter_or_promoter_chic_gene: Gene at a nearby promoter or connected by promoter CHiC in Supplementary Data 4; blank when unavailable.
great_gene_associations: GREAT gene associations supplied in Supplementary Data 4, including signed distances when supplied.

Quality control

The authors trimmed MPRA reads to exact barcode sequences without mismatches, counted all matching barcodes, and used mpralm on RNA and DNA counts after merging counts across barcodes for each allele. Plasmid construction included insert-size and gel checks, and the library-transfection design used four independent transfections per cell line. Package QC required a recognized cell line, finite author logFC/AveExpr/t/P.Value/adj.P.Val/B values, and positive reference/alternative DNA and RNA aggregate counts in the matching GEO count files; all 26,300 author rows passed and were retained. Count-derived activity values are the mean of four replicate log2((allele RNA CPM + 1)/(allele DNA CPM + 1)) values, and author significance is adj.P.Val < 0.05.

Curation notes

The processed table follows the current GEO release GSE225263_MPRA_ALL_CELL_LINES.txt.gz and includes 26,300 rows spanning 1,696 unique variants, 1,749 variant–phenotype associations, and 10 cell lines. The source spreadsheet and GEO release differ only in formatting/precision and positive-control placeholder conventions; source spreadsheets and count files are preserved in raw_data. The count-derived activity is an independently transparent CPM summary, not a refit of mpralm. The 47 variants tested in both orientations are not separately represented because the public result is already collapsed to the variant-level allele comparison. Cellosaurus identifiers correspond to the named DSMZ cell lines: 697, BALL-1, CCRF-CEM, Jurkat, NALM-6, P12-Ichikawa, Reh, RS4;11, SEM, and SUP-B15.

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