Episomal MPRA screen of lipid-associated variants in NIH 3T3 fibroblasts
Leveraging CRISPR/Cas Genome Editing Technology to Identify and Characterize Causal GWAS Variants for Blood LipidsA pooled, barcoded library of 145-bp allelic tiles representing LD-linked candidate variants at the CPNE1, ANGPTL3, and FRK loci was transfected into mouse NIH 3T3 fibroblasts. Each allele was represented by approximately 22 barcodes and measured in two independent biological transfections; the processed table retains complete rows from the published MPRA results workbook.
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 source article describes approximately 240,000 145-bp oligonucleotides representing approximately 11,000 tiles and 1,837 candidate functional variants, including 525 variants across these three loci. Major- and minor-allele tiles were centered on the variant or shifted by 40 nt, each tile was coupled to approximately 22 distinguishing 3-prime UTR barcodes, and the oligos were cloned into a pMPRA1 backbone with a minimal-promoter firefly-luciferase reporter. Relative enhancer activity was measured from reporter RNA barcode counts normalized to the corresponding transfected plasmid-pool DNA counts. Two independent biological replicate MPRA experiments were performed using FuGENE 6.
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 · 29 definitions
- element_id
- Stable package identifier for one retained allele-specific 145-bp tile.
- locus
- Source locus sheet: CPNE1, ANGPTL3, or FRK.
- variant_id
- dbSNP rs identifier parsed from the source tile label.
- chromosome
- Human chromosome number parsed from the source tile label.
- position_reported
- 1-based chromosome coordinate exactly as reported in the source tile label; the source does not state a reference assembly.
- tile_shift_code
- Source tile context code: L (left-shifted), C (centered), or R (right-shifted).
- tile_shift
- Expanded description of the tile context code.
- allele1
- Nucleotide for allele 1, parsed from the final two characters of the source tile label.
- allele2
- Nucleotide for allele 2, parsed from the final character of the source tile label.
- allele1_signal_rep1
- Source allele-1 signal in biological replicate 1: log median barcode count for the tile divided by the median barcode count for all tiles.
- allele1_signal_pvalue_rep1
- Source Mann-Whitney U-test P-value for allele-1 signal versus the median signal from all tiles in biological replicate 1; not multiple-testing corrected.
- allele2_signal_rep1
- Source allele-2 signal in biological replicate 1, calculated as for allele 1.
- allele2_signal_pvalue_rep1
- Source Mann-Whitney U-test P-value for allele-2 signal versus the median signal from all tiles in biological replicate 1; not multiple-testing corrected.
- log_ratio_rep1
- Source log-ratio of allele-1 signal to allele-2 signal in biological replicate 1.
- log_ratio_pvalue_rep1
- Source Mann-Whitney U-test P-value for equality of allele-1 and allele-2 signals in biological replicate 1; not multiple-testing corrected.
- allele1_signal_rep2
- Source allele-1 signal in biological replicate 2.
- allele1_signal_pvalue_rep2
- Source Mann-Whitney U-test P-value for allele-1 signal versus the median signal from all tiles in biological replicate 2; not multiple-testing corrected.
- allele2_signal_rep2
- Source allele-2 signal in biological replicate 2.
- allele2_signal_pvalue_rep2
- Source Mann-Whitney U-test P-value for allele-2 signal versus the median signal from all tiles in biological replicate 2; not multiple-testing corrected.
- log_ratio_rep2
- Source log-ratio of allele-1 signal to allele-2 signal in biological replicate 2.
- log_ratio_pvalue_rep2
- Source Mann-Whitney U-test P-value for equality of allele-1 and allele-2 signals in biological replicate 2; not multiple-testing corrected.
- allele1_signal_mean
- Arithmetic mean of the two source allele-1 signal values; derived by this package.
- allele2_signal_mean
- Arithmetic mean of the two source allele-2 signal values; derived by this package.
- log_ratio_mean
- Arithmetic mean of the two source log-ratio values; derived by this package.
- log_ratio_product
- Product of the two source log-ratio values; included because the source workbook ranks rows by this quantity.
- effect_direction
- Derived direction from the mean log-ratio: allele1_higher, allele2_higher, or no_difference.
- replicate_direction_consistent
- TRUE when the two replicate log-ratios have the same non-zero sign (or at least one is zero).
- source_sheet
- Original workbook sheet name for the row.
- source_row
- Original 1-based worksheet row number for the row, enabling traceability to the raw workbook.
Quality control
The published workbook states that each allele was represented by approximately 22 barcodes and marks constructs with too many barcode dropouts as NaN, indicating that they do not provide robust results. Package QC retained only rows with finite numeric values for all 12 signal, signal-P-value, log-ratio, and log-ratio-P-value fields across both biological replicates. Of 1,574 labeled tile rows in the three source sheets, 1,226 passed and 348 NaN/dropout rows were excluded (CPNE1: 602/717 retained; ANGPTL3: 449/629 retained; FRK: 175/228 retained). Source P-values are preserved as reported and were not multiple-testing corrected in the workbook.
Curation notes
The dissertation text calls the assay 3T3-L1 adipocytes, while the associated Cell Stem Cell article's methods and the MPRA workbook describe NIH 3T3 fibroblasts; this package uses NIH 3T3 (CVCL:0594) as the standardized biosample. The raw workbook is preserved as downloaded under the server-delivered filename NIHMS863825-supplement-10.xlsx; its three sheets are explicitly labeled Table S9A-C and contain the MPRA results for CPNE1, ANGPTL3, and FRK. The direct page link for Table S9 uses a different supplement filename on the current PMC server, so the workbook identity and sheet labels were used to select the source. The source does not state a reference genome assembly, so reference_genome is null and coordinates are retained as reported. The table contains published aggregate barcode statistics rather than raw sequencing reads; no genuine raw read files were included.