MOLP-8 plasma-cell-line MPRA screen
Functional dissection of inherited non-coding variation influencing multiple myeloma riskTransient episomal plasmid MPRA of multiple-myeloma risk-linked alleles in the human MOLP-8 plasma-cell myeloma line. The library tested reference and alternative alleles for 1,039 designed variants across six sequence contexts, with three biological replicates; the packaged table contains the 820 variant summaries supplied in Supplementary Data 1.
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
The pGL4.23-derived library used a minimal promoter, GFP reporter, partial 3' UTR, and random 20-nt 3' barcodes. Each variant was represented by reference and alternative 120-bp oligos in both strands and three windows with the variant at -20, 0, or +20 bp from the center, flanked by 15-bp adapters. The library was electroporated into MOLP-8 cells; reporter RNA was collected 48 h later and sequenced on an Illumina NextSeq 1 x 75 bp platform. Barcode activity was bi = log2((1 + normalized RNA counts)/(1 + normalized DNA counts)); the reported log2 allele score is the weighted alternative-versus-reference average across six contexts and three biological replicates.
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 · 9 definitions
- variant_id
- Reported rs identifier; one source row contains a pipe-delimited group of rsIDs.
- reference_allele
- Reference allele or sequence reported in Supplementary Data 1; indel sequences are retained as supplied.
- alternative_allele
- Alternative allele or sequence reported in Supplementary Data 1; indel sequences are retained as supplied.
- log2_allelic_activity
- Author MPRA-score log2 effect of the alternative relative to the reference allele, integrated across six genomic contexts and three biological replicates in MOLP-8 cells.
- p_value
- Author MPRA-score P value for the integrated allele effect.
- q_value
- Author MPRA-score FDR-adjusted Q value for the integrated allele effect.
- fdr_5pct_significant
- Derived boolean flag; true when q_value is less than 0.05.
- strong_effect_abs_log2_gt_0.2
- Derived boolean flag; true when the absolute log2_allelic_activity is greater than 0.2.
- effect_direction
- Derived qualitative direction: alternative_higher, alternative_lower, or no_difference.
Quality control
Author QC excluded oligo alignments with more than four mismatches or a mismatch within 10 bp of the variant, required at least two supporting reads for an oligo-barcode mapping, and resolved multi-oligo barcode mappings only when more than 50 reads supported one oligo at at least 95% of reads. The authors report 1.73 million oligo-barcode pairs mapping to 12,378 of 12,468 designed oligos. For the processed table, rows additionally required a unique reported variant ID, nonempty DNA allele strings, finite log2/P/Q values, and P/Q values in [0,1]. All 820 rows in the supplied final variant-summary spreadsheet passed these checks; nonsignificant biological results were retained.
Curation notes
The article describes 1,039 synthesized variants, while its supplied Supplementary Data 1 contains 820 final variant-summary rows; this table follows the supplied MPRA result layer. The MOLP-8 table reproduces the paper's reported 28 variants with q < 0.05. Applying the paper's stated absolute log2 score > 0.2 threshold to the supplied values marks 22 of those rows as strong, whereas the narrative reports 21; no row was removed for this discrepancy. MOLP-8 is listed by the paper as DSMZ ACC-569 and is represented here by Cellosaurus CVCL:2124 (MOLP-8/MOLP8).