Pooled lipid-locus MPRA in NIH 3T3 fibroblasts (two biological replicates)
Large, Diverse Population Cohorts of hiPSCs and Derived Hepatocyte-like Cells Reveal Functional Genetic Variation at Blood Lipid-Associated LociA pooled episomal reporter library tested major and minor alleles of candidate variants at the CPNE1, ANGPTL3, and FRK blood-lipid-associated loci. Each allele was placed in a 145-bp tile centered on the SNP or shifted by 40 nt (C/L/R) and linked to approximately 22 barcodes; the two independent transfection experiments are reported side by side.
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
Microarray-synthesized 145-bp oligonucleotides carried the major or minor allele in the center, or in a tile shifted by 40 nt, and each tile was coupled to approximately 22 distinguishing barcodes. Tiles were cloned into the pMPRA1 backbone upstream of a minimal promoter-firefly luciferase reporter, plasmid pools were transfected into NIH 3T3 cells with FuGENE 6, and barcode counts from cellular mRNA were compared with counts from the transfected plasmid pool. Two independent biological transfection experiments were performed. Table S9 reports source log-normalized signals and uncorrected Mann-Whitney U-test P values.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (27 of 27)
| Row | |||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | |||||||||||||||||||||||||||
| 2 | |||||||||||||||||||||||||||
| 3 | |||||||||||||||||||||||||||
| 4 | |||||||||||||||||||||||||||
| 5 | |||||||||||||||||||||||||||
| 6 | |||||||||||||||||||||||||||
| 7 | |||||||||||||||||||||||||||
| 8 | |||||||||||||||||||||||||||
| 9 | |||||||||||||||||||||||||||
| 10 | |||||||||||||||||||||||||||
| 11 | |||||||||||||||||||||||||||
| 12 | |||||||||||||||||||||||||||
| 13 | |||||||||||||||||||||||||||
| 14 | |||||||||||||||||||||||||||
| 15 | |||||||||||||||||||||||||||
| 16 | |||||||||||||||||||||||||||
| 17 | |||||||||||||||||||||||||||
| 18 | |||||||||||||||||||||||||||
| 19 | |||||||||||||||||||||||||||
| 20 | |||||||||||||||||||||||||||
| 21 | |||||||||||||||||||||||||||
| 22 | |||||||||||||||||||||||||||
| 23 | |||||||||||||||||||||||||||
| 24 | |||||||||||||||||||||||||||
| 25 | |||||||||||||||||||||||||||
| 26 | |||||||||||||||||||||||||||
| 27 | |||||||||||||||||||||||||||
| 28 | |||||||||||||||||||||||||||
| 29 | |||||||||||||||||||||||||||
| 30 | |||||||||||||||||||||||||||
| 31 | |||||||||||||||||||||||||||
| 32 | |||||||||||||||||||||||||||
| 33 | |||||||||||||||||||||||||||
| 34 | |||||||||||||||||||||||||||
| 35 | |||||||||||||||||||||||||||
| 36 | |||||||||||||||||||||||||||
| 37 | |||||||||||||||||||||||||||
| 38 | |||||||||||||||||||||||||||
| 39 | |||||||||||||||||||||||||||
| 40 | |||||||||||||||||||||||||||
| 41 | |||||||||||||||||||||||||||
| 42 | |||||||||||||||||||||||||||
| 43 | |||||||||||||||||||||||||||
| 44 | |||||||||||||||||||||||||||
| 45 | |||||||||||||||||||||||||||
| 46 | |||||||||||||||||||||||||||
| 47 | |||||||||||||||||||||||||||
| 48 | |||||||||||||||||||||||||||
| 49 | |||||||||||||||||||||||||||
| 50 |
Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 27 definitions
- element_id
- Normalized source row label identifying the rsID, chromosome, position, tile shift, and allele pair.
- locus
- Locus sheet/gene label: CPNE1, ANGPTL3, or FRK.
- variant_id
- dbSNP rs identifier of the tested variant.
- chromosome
- Human chromosome from the source tile label.
- position_grch37
- 1-based genomic coordinate on GRCh37/hg19 from the source tile label.
- tile_shift
- Source tile placement relative to the variant: C=centered, L=left-shifted, or R=right-shifted.
- allele_1
- Allele 1 represented by the first allele in the source label.
- allele_2
- Allele 2 represented by the second allele in the source label.
- source_rank
- Original 1-based row rank within the Table S9 locus sheet before QC filtering; the source sheets were ranked by the product of the two replicate log-ratios.
- allele_1_signal_rep1
- Replicate 1 allele 1 signal: log of median barcode counts for the tile divided by median counts for all tiles.
- allele_1_pvalue_rep1
- Replicate 1 uncorrected Mann-Whitney U-test P value for allele 1 signal versus the median signal from all tiles.
- allele_2_signal_rep1
- Replicate 1 allele 2 signal: log of median barcode counts for the tile divided by median counts for all tiles.
- allele_2_pvalue_rep1
- Replicate 1 uncorrected Mann-Whitney U-test P value for allele 2 signal versus the median signal from all tiles.
- log_ratio_rep1
- Replicate 1 source log-ratio comparing allele 1 signal with allele 2 signal.
- log_ratio_pvalue_rep1
- Replicate 1 uncorrected Mann-Whitney U-test P value for equal allele-specific signals.
- allele_1_signal_rep2
- Replicate 2 allele 1 signal: log of median barcode counts for the tile divided by median counts for all tiles.
- allele_1_pvalue_rep2
- Replicate 2 uncorrected Mann-Whitney U-test P value for allele 1 signal versus the median signal from all tiles.
- allele_2_signal_rep2
- Replicate 2 allele 2 signal: log of median barcode counts for the tile divided by median counts for all tiles.
- allele_2_pvalue_rep2
- Replicate 2 uncorrected Mann-Whitney U-test P value for allele 2 signal versus the median signal from all tiles.
- log_ratio_rep2
- Replicate 2 source log-ratio comparing allele 1 signal with allele 2 signal.
- log_ratio_pvalue_rep2
- Replicate 2 uncorrected Mann-Whitney U-test P value for equal allele-specific signals.
- mean_allele_1_signal
- Arithmetic mean of the two replicate allele 1 signal values (derived field).
- mean_allele_2_signal
- Arithmetic mean of the two replicate allele 2 signal values (derived field).
- mean_log_ratio
- Arithmetic mean of the two replicate log-ratio values; the source log base is not specified (derived field).
- absolute_mean_log_ratio
- Absolute value of mean_log_ratio (derived field).
- log_ratio_product_rep1_rep2
- Product of the two replicate log-ratio values; this is the ranking metric stated in Table S9 (derived field).
- replicate_direction_concordant
- TRUE when the two replicate log-ratio values have the same nonzero sign; otherwise FALSE (derived field).
Quality control
Applied the authors' source QC: Table S9 marks tiles with too many barcode dropouts as NaN, so any tile with NaN in one or more of the 12 replicate signal/P-value fields was excluded. We additionally required numeric finite measurements and P values in the interval [0,1]. A total of 1,226 of 1,574 source tile rows were retained: 602 CPNE1, 449 ANGPTL3, and 175 FRK rows. No new significance cutoff or multiple-testing correction was imposed; the source P values are uncorrected as described in Table S9.
Curation notes
The manuscript describes approximately 525 candidate variants across these three loci (239 at CPNE1, 210 at ANGPTL3, and 76 at FRK), while the downloaded Table S9 workbook contains 242, 213, and 76 unique rsID labels and 717, 629, and 228 tile rows, respectively. The published workbook was preserved and only explicitly marked/invalid rows were filtered. The assay host is mouse NIH 3T3, whereas the library sequences represent human GRCh37/hg19 alleles. The included Table S10 workbook contains ancillary validation oligonucleotides and was not used to create table.csv.