CD36 eQTL episomal MPRA in K562
Functionalization of CD36 cardiovascular disease and expression associated variants by interdisciplinary high throughput analysisAn episomal plasmid MPRA assayed 81 platelet CD36 eQTL SNPs and 10 known regulatory positive-control constructs in human K562 cells, with 40 unique 10-bp barcodes per allele or construct. The library was transfected and RNA harvested 48 hours later; this table reports the published allele/construct transcription shifts and t-test, Mann–Whitney U-test, and Bayesian model statistics.
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
Each allele of each CD36 SNP and control was represented by 40 unique 10-bp barcodes. Inserts used 150 bp of genomic context, a minimal promoter–luciferase cassette derived from pNL3.2, and barcodes downstream of luciferase in the pMPRA1 backbone. The pooled library was transfected into K562 cells and RNA was harvested after 48 hours; barcode sequences were required to have Q>30 at every base, and three cDNA RNA libraries plus two plasmid-DNA libraries were sequenced on an Illumina MiSeq. The traditional analysis used depth-normalized RNA/DNA ratios with t-tests and Mann–Whitney U-tests plus FDR correction; a coupled negative-binomial Bayesian model also estimated posterior transcription shifts. The processed table combines the complete positive-control and CD36-variant summary tables.
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 · 19 definitions
- element_id
- Identifier exactly as printed in the complete MPRA result table; controls and CD36 SNP labels are both retained.
- element_class
- positive_control for known regulatory constructs or CD36_eQTL for the 81 tested CD36 variants.
- target_gene
- Target gene represented by the construct label; CD36 for eQTL rows and the corresponding control gene for positive controls.
- variant_id
- Normalized dbSNP rs identifier for CD36 rows; blank for positive controls.
- comparison
- Contrast represented by transcription_shift: mutant minus reference for positive controls or alternate minus reference for CD36 SNPs.
- transcription_shift
- Published activity difference between the mutant/alternate and reference construct, as reported by the paper.
- t_test_p_value
- Unadjusted p-value from the paper's t-test comparison of construct activities.
- t_test_q_value
- FDR-adjusted q-value for the paper's t-test.
- u_test_p_value
- Unadjusted p-value from the paper's Mann–Whitney U-test comparison.
- u_test_q_value
- FDR-adjusted q-value for the paper's Mann–Whitney U-test.
- bayesian_posterior_mean
- Posterior mean transcription shift from the paper's coupled negative-binomial Bayesian model.
- bayesian_95_ci_low
- Lower bound of the printed 95% Bayesian credible interval for transcription shift.
- bayesian_95_ci_high
- Upper bound of the printed 95% Bayesian credible interval for transcription shift.
- t_test_significant_q_lt_0_05
- Derived TRUE when t_test_q_value is less than 0.05.
- u_test_significant_q_lt_0_05
- Derived TRUE when u_test_q_value is less than 0.05.
- bayesian_ci_excludes_zero
- Derived TRUE when the printed 95% credible interval lies entirely above or below zero.
- paper_reported_functional
- TRUE for the 19 controls/SNPs explicitly enumerated by the paper as MPRA-functional across its reported methods.
- source_table
- Complete MPRA supplement source: S1 positive controls or S2 CD36 variants.
- qc_pass
- TRUE when the row is present in the released complete result table and has finite summary statistics; all retained rows pass.
Quality control
The paper required Q>30 at every barcode base, discarded low-representation plasmid barcodes for the traditional ratio analysis, and evaluated three cDNA and two plasmid-DNA libraries. The released QC table reports cDNA usable-read fractions of 0.69, 0.72, and 0.70 with zero-count barcode fractions of 0.09, 0.09, and 0.12, and plasmid usable-read fractions of 0.71 and 0.70 with zero-count fractions of 0.07 and 0.06. All 91 released result rows had finite reported statistics and were retained; non-significance was not treated as a QC failure.
Curation notes
This package represents one MPRA experiment; luciferase, EMSA, and CRISPR follow-ups are not separate MPRA experiments. The downloaded supplement files are named by their printed table contents. The paper explicitly enumerates 19 functional entries (9 controls and 10 CD36 SNPs), which is followed by paper_reported_functional. The complete S1/S2 tables contain printed Bayesian intervals excluding zero for 28 rows; bayesian_ci_excludes_zero is therefore a mechanical flag from the source intervals and is retained separately so the discrepancy with the paper's enumerated hit set is visible. The source label rs17154155_ALT is preserved in element_id and normalized to rs17154155 in variant_id.