
%%%%%%%%%
%% TABLES %%
%%%%%%%%%

\subsection*{Supplementary Tables}

\setcounter{table}{0}
\renewcommand{\thetable}{Supplementary File 1\alph{table}}%


\begin{table}[H]
\caption {\textbf{Flow cytometry results from CMs}. Purity of the cell cultures was determined by measuring the expression of the cardiac troponin T in each CM cell line, plus one IPSC line to serve as a negative control. Columns 1-5 are: 
1) Individual;
2) Cell Type;
3) Differentiation Day;
4) Percentage of live cells;
5) Percentage of cells expressing cardiac troponin T}
% file is dropbox BittStarr/bitstarr latex/
\label{SuppTable14}
\begin{tabular}{@{}lllll@{}}
\toprule
Individual & CellType & Differentiation day & \% live & \% cTnT positive \\ \midrule 
GM18858    & CM       & 27                   & 60.3          & 95                      \\
GM18855    & CM       & 27                   & 37.6          & 74.1                    \\
GM18505    & CM       & 27                   & 58.1          & 90.7                    \\
GM18912    & CM       & 25                   & 17.2          & 84.9                    \\
GM18520    & CM       & 25                   & 11.2          & 72.3                    \\
GM19209    & CM       & 25                   & 23.8          & 44.9                    \\
GM18912    & IPSC     & 0                    & 89.9          & 0                      \\ \bottomrule
\end{tabular}
\end{table}

\begin{table}[H]
\caption {\textbf{IPSC differentiation metadata}. Columns 1-6 are: 
1) Individual;
2) Number of passages on mouse embryonic fibroblasts (MEF);
3) Number of passages without MEF;
4) Reprogramming batch;
5) Replicate;
6) Day at which cells reached confluency}
\label{SuppTable15}
\begin{tabular}{@{}llllll@{}}
\toprule
Line    & Feeder passage & FF passage & Batch & Replicate & Confluence day \\ \midrule 
GM18505 & 23              & 41          & 1     & 1         & 90              \\
GM18855 & 14              & 51          & 1     & 1         & 85              \\
GM18858 & 18              & 47          & 1     & 1         & 97              \\
GM18505 & 23              & 42          & 1     & 2         & 40              \\
GM18855 & 14              & 51          & 1     & 2         & 95              \\
GM18858 & 18              & 47          & 1     & 2         & 98              \\
GM19209 & 23              & 51          & 2     & 1         & 85              \\
GM18520 & 15              & 42          & 2     & 1         & 80              \\
GM18912 & 16              & 36          & 2     & 1         & 95              \\
GM19209 & 23              & 52          & 2     & 2         & 80              \\
GM18520 & 15              & 43          & 2     & 2         & 95              \\
GM18912 & 16              & 37          & 2     & 2         & 70             \\ \bottomrule
\end{tabular}
\end{table}

\begin{table}[H]
\caption {\textbf{CM reprogramming metadata}.Columns 1-8 are: 
1) Individual;
2) Average percent confluence on day 0;
3) Number of passages on mouse embryonic fibroblasts (MEF);
4) Number of passages without MEF;
5) Differentiation batch;
6) Day at which cells started beating;
7) Cells/ml on day 20;
8) Total number of cells from 4 plates}
\label{SuppTable16}
\begin{tabular}{@{}llllllll@{}}
\toprule
Individual & \% confluence & Feeder Passage & FF Passage & Batch & Day beating & Counts day20 & Total cells \\ \midrule 
GM18858    & 76.25                          & 18              & 41          & 1     & 7.5          & 1820000             & 54600000     \\
GM18855    & 72.5                           & 11              & 45          & 1     & 7            & 1440000             & 43200000     \\
GM18505    & 73.75                          & 23              & 35          & 1     & 8            & 1630000             & 48900000     \\
GM19209    & 83.75                          & 23              & 44          & 2     & 9.75         & 2096000             & 20960000     \\
GM18912    & 95                             & 16              & 50          & 2     & 7            & 4700000             & 70500000     \\
GM18520    & 90                             & 15              & 46          & 2     & 8            & 2630000             & 78900000    \\ \bottomrule
\end{tabular}
\end{table}

\begin{table}[H]
\caption {\textbf{Treatment concentrations}. Concentrations for all treatments used in this study. Columns 1-4 are: 
1) Treatment ID;
2) Treatment Name;
3) Final treatment concentration in the culture media;
4) Control ID}
%\url{http://genome.grid.wayne.edu/GxExC/Supp_Tables/Treat_conc.tab}
% file is dropbox BittStarr/bitstarr latex/
\label{SuppTable1}
% Please add the following required packages to your document preamble:
% \usepackage{booktabs}
%\begin{table}[]
\begin{tabular}{@{}lllll@{}}
\toprule
Treatment.ID & Common Name  & Final Conc & Control.ID & Category                                        \\ \midrule 
CO1          & Media         & --          & --         & Control                                         \\
CO2          & Ethanol       & 1uL in 10mL          & --         & Control                                         \\
T12C1        & Dexamethasone & 10-6 M      & CO2        & Steroid Hormones                                \\
T13C1        & Caffeine      & 225 ug/mL   & CO1        & Dietary components                              \\
T14C1        & Nicotine      & 100 ug/mL   & CO1        & Environmental contaminants and common chemicals \\
T15C1        & Copper        & 60 uM       & CO1        & Metal Ions                                      \\
T19C1        & Selenium      & 10 uM       & CO1        & Metal Ions                                      \\
T20C1        & Zinc          & 80 uM       & CO1        & Metal Ions                                      \\
T23C1        & Vitamin D     & 0.1uM       & CO2        & Dietary components                              \\
T24C1        & Acrylamide    & 2ng/mL      & CO1        & Environmental contaminants and common chemicals \\
T25C1        & BP-3          & 1000ng/mL   & CO2        & Environmental contaminants and common chemicals \\
T26C1        & BPA           & 20ng/mL     & CO1        & Environmental contaminants and common chemicals \\
T27C1        & Cadmium       & 2ng/mL      & CO1        & Metal Ions                                      \\
T29C1        & PFOA          & 15ng/mL     & CO1        & Environmental contaminants and common chemicals \\
T30C1        & Triclosan     & 1200ng/mL   & CO2        & Environmental contaminants and common chemicals \\
T33C1        & Insulin       & 1004.6ng/mL & CO1        & Peptide Hormones and neurotransmitters          \\
T36C1        & Vasopressin   & 0.017ng/mL  & CO1        & Peptide Hormones and neurotransmitters          \\
T37C1        & Acetylcholine & 293.9ng/mL  & CO1        & Peptide Hormones and neurotransmitters          \\
T40C1        & BHA           & 0.2ug/mL    & CO2        & Environmental contaminants and common chemicals \\
T41C1        & Ibuprofen     & 5ug/mL      & CO2        & Common drugs                                    \\
T42C1        & Acetaminophen & 50ug/mL     & CO1        & Common drugs                                    \\
T43C1        & Aspirin       & 10ug/mL     & CO2        & Common drugs                                    \\
T44C1        & Loratadine    & 50ng/mL     & CO2        & Common drugs                                    \\
T45C1        & Cetirizine    & 10ng/mL     & CO1        & Common drugs                                    \\
T47C1        & Phthalate     & 100ng/mL    & CO2        & Environmental contaminants and common chemicals \\
T4C1         & Vitamin B5    & 100 nM      & CO1        & Dietary components                              \\
T5C1         & Vitamin B6    & 10-6M       & CO1        & Dietary components                              \\
T6C1         & Vitamin A     & 10 nM       & CO2        & Dietary components                              \\
T7C1         & Vitamin E     & 50 uM       & CO2        & Dietary components                              \\
T9C1         & Aldosterone   & 10-6 M      & CO2        & Steroid Hormones                               \\ \bottomrule
\end{tabular}
\end{table}

\begin{table}[H]
\caption {\textbf{Shallow DEG results}. Results from DESeq2 using shallow sequencing data (eq. 1). Columns 1-8 are: 
1) Transcript ID;
2) FDR;
3) P-value;
4) Log2 fold change;
5) Ensembl gene ID;
6) Gene ID;
7) Cell type;
8) Treatment ID}
\url{http://genome.grid.wayne.edu/GxExC/Supp_Tables/DESeq_Shallow.tab.gz}
% file is dropbox BittStarr/bitstarr latex/
\label{SuppTable7}
\end{table}

\begin{table}[H]
\caption {\textbf{Sample information and sequencing depth for deep-sequenced libraries}. Each row represents a sequencing library. Columns 1-12 are: 
1) Library ID;
2) Plate;
3) Sequencing barcode;
4) Treatment ID;
5) Cell type;
6) Individual;
7) Plate well,
8) Control ID,
9) Treatment Name,
10) Number of sequencing reads after quality control and removal of PCR duplicates,
11) Total number of raw sequencing reads,
12) Percentage of raw sequencing reads remaining after quality control and deduplication}
\url{http://genome.grid.wayne.edu/GxExC/Supp_Tables/cv_reads.tab}
% file is dropbox BittStarr/bitstarr latex/
\label{SuppTable13}
\end{table}

\begin{table}[H]
\caption {\textbf{Deep DEG results}. Results from DESeq2 using deep sequencing data (eq. 1). Columns 1-8 are: 
1) Transcript ID;
2) FDR;
3) P-value;
4) Log2 fold change;
5) Ensembl gene ID;
6) Gene ID;
7) Cell type;
8) Treatment ID}
\url{http://genome.grid.wayne.edu/GxExC/Supp_Tables/DESeq_Deep.tab.gz}
% file is dropbox BittStarr/bitstarr latex/
\label{SuppTable8}
\end{table}

\begin{table}[H]
\caption {\textbf{DEG GO terms}. Significant gene ontology enrichments for DEGs. Tables are organized in subfolders based on cell type, and files are named according to treatment and which group of genes were used for the enrichment (upregulated, downregulated, or all DEGs). The naming convention is: \textit{Treatment ID}\texttt{\_enrichment\_summary\_}\textit{Gene group}\texttt{.txt}, where \textit{Gene group} is either \textit{upDEGs}, \textit{downDEGs}, or \textit{allDEGs} for upregulated, downregulated, and all DEGs, respectively. Columns 1-9 are: 
1) GO term ID;
2) GO description;
3) Gene ratio;
4) Background ratio;
5) P-value;
6) FDR;
7) Q-value;
8) Gene IDs for DEGs in GO term;
9) Number of DEGs in GO term}
\url{http://genome.grid.wayne.edu/GxExC/Supp_Tables/DEG_GO_terms/}
% file is dropbox BittStarr/bitstarr latex/
\label{SuppTable2}
\end{table}

\begin{table}[H]
\caption {\textbf{Cell type $\times$ treatment interaction gene expression results }. Results from DESeq2 using deep sequencing data to identify genes with Cell type $\times$ treatment interactions (Eq. 2). Columns 1-6 are: 
1) Transcript ID;
2) FDR;
3) P-value;
4) Log2 fold change;
5) Ensembl gene ID;
6) Gene ID}
\url{http://genome.grid.wayne.edu/GxExC/Supp_Tables/DESeq_CellSpecific.tab.gz}
% file is dropbox BittStarr/bitstarr latex/
\label{SuppTable17}
\end{table}

\begin{table}[H]
\caption {\textbf{QuASAR output}. Results from QuASAR for all SNPs tested for ASE. SNPs must be covered by at least 5 reads. Each row represents a SNP measured in a particular library. Columns 1-17 are: 
1) Chromosome;
2) 0-based coordinate;
3) 1-based coordinate;
4) Reference allele;
5) Alternate allele;
6) rsID;
7) Allele frequency;
8) Number of RNA-seq reads mapping to reference allele;
9) Number of RNA-seq reads mapping to alternate allele;
10) Beta: measure of ASE from QuASAR, where positive indicates increased expression of reference allele;
11) Standard error of ASE measurement from QuASAR;
12) P-value for ASE;
13) Q-value for ASE;
Columns 14-17 describe the library from where the ASE measurement comes from:
14) Plate ID;
15) Cell type;
16) Individual;
17) Name of treatment;
18) Treatment ID}
\url{http://genome.grid.wayne.edu/GxExC/Supp_Tables/Quasar_output.tab.gz}
% file is dropbox BittStarr/bitstarr latex/
\label{SuppTable3}
\end{table}

\begin{table}[H]
\caption {\textbf{ANOVA results with all cell types analyzed together}. Results from ANOVA model with all cell types to identify SNPs with ASE (eq. 3 and 4). Columns 1-8 are:
1) SNP by individual identifier;
2) Residual degrees of freedom;
3) Residual sum of squares;
4) Degrees of freedom;
5) Sum of squares;
6) F-value;
7) P-value;
8) FDR.}
\url{http://genome.grid.wayne.edu/GxExC/Supp_Tables/ANOVA_allCell.tab}
% file is dropbox BittStarr/bitstarr latex/
\label{SuppTable9}
\end{table}

\begin{table}[H]
\caption {\textbf{ANOVA results with cell types analyzed separately}. Results from ANOVA model with each cell type analyzed separately to identify SNPs with ASE (eq. 6 and 7). Columns 1-9 are:
1) SNP by individual identifier;
2) Residual degrees of freedom;
3) Residual sum of squares;
4) Degrees of freedom;
5) Sum of squares;
6) F-value;
7) P-value;
8) FDR;
9) Cell type.}
\url{http://genome.grid.wayne.edu/GxExC/Supp_Tables/ANOVA_cellSep.tab}
% file is dropbox BittStarr/bitstarr latex/
\label{SuppTable_ANOVAsep}
\end{table}

\begin{table}[H]
\caption {\textbf{Fixed effects model output with all cell types analyzed together}. Results from the linear model with all cell types analyzed together to identify cASE. Columns 1-8 are: 
1) Variable in the linear model being tested (in Eq. 5; e.g. cell type, treatment, etc.);
2) Estimate;
3) Standard error;
4) Test statistic;
5) P-value;
6) Degrees of freedom;
7) Rank;
8) SNP by individual identifier.}
\url{http://genome.grid.wayne.edu/GxExC/Supp_Tables/FixedEffect_allCell.tab}
% file is dropbox BittStarr/bitstarr latex/
\label{SuppTable10}
\end{table}

\begin{table}[H]
\caption {\textbf{Number of significant tests from fixed effect model for all cell types analyzed together}. Summary of results from \ref{SuppTable10}, including the number of significant tests (FDR $<$ 10\%) per variable. Columns 1-3 are:
1) Variable in the linear model being tested (in Eq. 5; e.g. treatment, plate,etc);
2) Number of tests performed;
3) Number of tests with FDR $<$ 10\%.}
\label{SuppTable_SigTestAll}
\begin{tabular}{@{}lll@{}}
\toprule
Term                      & \# tests & \# Sig. \\ \midrule 
IPSC                      & 13009      & 4084     \\
CM                        & 13009      & 3782     \\
Acetaminophen             & 12903      & 106      \\
Aldosterone               & 12941      & 93       \\
Cadmium                   & 12941      & 135      \\
Caffeine                  & 12912      & 111      \\
Copper                    & 12932      & 159      \\
Dexamethasone             & 12926      & 114      \\
Insulin                   & 12950      & 107      \\
Nicotine                  & 12928      & 108      \\
Selenium                  & 12891      & 140      \\
Triclosan                 & 12927      & 101      \\
VitaminA                  & 12929      & 119      \\
Zinc                      & 12841      & 116      \\
Acetaminophen x Cell Type & 12189      & 70       \\
Aldosterone x Cell Type   & 12370      & 59       \\
Cadmium x Cell Type       & 12454      & 73       \\
Caffeine x Cell Type      & 12308      & 57       \\
Copper x Cell Type        & 12301      & 109      \\
Dexamethasone x Cell Type & 12345      & 71       \\
Insulin x Cell Type       & 12369      & 60       \\
Nicotine x Cell Type      & 12277      & 57       \\
Selenium x Cell Type      & 12089      & 53       \\
Triclosan x Cell Type     & 12371      & 55       \\
VitaminA x Cell Type      & 12372      & 59       \\
Zinc x Cell Type          & 12040      & 60     \\ \bottomrule
\end{tabular}
\end{table}

\begin{table}[H]
\caption {\textbf{Fixed effects model output with cell types analyzed separately}. Results from the fixed effects model with cell types analyzed separately to identify cASE. Columns 1-9 are: 
1) Variable in the linear model being tested (in Eq. 6; e.g. treatment, plate, etc.);
2) Estimate;
3) Standard error;
4) Test statistic;
5) P-value;
6) Degrees of freedom;
7) Rank;
8) SNP by individual identifier;
9) Cell type.}
\url{http://genome.grid.wayne.edu/GxExC/Supp_Tables/FixedEffect_cellSep.tab}
% file is dropbox BittStarr/bitstarr latex/
\label{SuppTable_FixedSep}
\end{table}

\begin{table}[H]
\caption {\textbf{Number of significant tests from fixed effect model for cell types analyzed separately}. Summary of results from \ref{SuppTable_FixedSep}, including the number of significant tests (FDR $<$ 10\%) per variable. Columns 1-4 are:
1) Cell type;
2) Variable in the linear model being tested (in Eq. 6; e.g. treatment, plate,etc);
3) Number of tests performed;
4) Number of tests with FDR $<$ 10\%.}
\label{SuppTable_SigTestSep}
\begin{tabular}{@{}llll@{}}
\toprule
Cell & Term          & Num tests & Num sig \\ \midrule 
CM   & Acetaminophen & 6524       & 35       \\
CM   & Aldosterone   & 6590       & 38       \\
CM   & Cadmium       & 6573       & 53       \\
CM   & Caffeine      & 6556       & 45       \\
CM   & Copper        & 6598       & 46       \\
CM   & Dexamethasone & 6524       & 39       \\
CM   & Insulin       & 6561       & 37       \\
CM   & Nicotine      & 6372       & 56       \\
CM   & Selenium      & 6517       & 31       \\
CM   & Triclosan     & 6551       & 39       \\
CM   & VitaminA      & 6549       & 37       \\
CM   & Zinc          & 6566       & 36       \\
IPSC & Acetaminophen & 6573       & 38       \\
IPSC & Aldosterone   & 6589       & 40       \\
IPSC & Cadmium       & 6577       & 44       \\
IPSC & Caffeine      & 6535       & 35       \\
IPSC & Copper        & 6544       & 47       \\
IPSC & Dexamethasone & 6578       & 42       \\
IPSC & Insulin       & 6580       & 39       \\
IPSC & Nicotine      & 6587       & 46       \\
IPSC & Selenium      & 6442       & 49       \\
IPSC & Triclosan     & 6601       & 41       \\
IPSC & VitaminA      & 6578       & 40       \\
IPSC & Zinc          & 6040       & 50       \\
LCL  & Acetaminophen & 6682       & 16       \\
LCL  & Aldosterone   & 6820       & 13       \\
LCL  & Cadmium       & 6897       & 21       \\
LCL  & Caffeine      & 6863       & 22       \\
LCL  & Copper        & 6546       & 31       \\
LCL  & Dexamethasone & 6770       & 22       \\
LCL  & Insulin       & 6861       & 14       \\
LCL  & Nicotine      & 6760       & 16       \\
LCL  & Selenium      & 6741       & 24       \\
LCL  & Triclosan     & 6903       & 13       \\
LCL  & VitaminA      & 6877       & 13       \\
LCL  & Zinc          & 6776       & 25      \\ \bottomrule
\end{tabular}
\end{table}

\begin{table}[H]
\caption {\textbf{cASE gene overlap in other G$\times$E studies}. Information from significant cASE genes which replicate (p $<$ 0.05) in another G$\times$E study. 
Columns 1-2 describe the gene:
1) Ensembl gene ID;
2) Gene ID;
Columns 3-10 describe the cASE SNP:
3) cASE treatment;
4) SNP identifier;
5) Measurement of cASE effect from linear model;
6) Standard error of cASE measurement;
7) Test statistic;
8) P-value;
9) FDR;
10) Degrees of freedom;
Columns 11-20 describe the G$\times$E SNP in the replication datasets:
11) rsID;
12) Treatment condition;
13) Cell type;
14) Effect size;
15) P-value;
16) FDR;
17) Significance as reported by study (TRUE or FALSE);
18) Author and year;
19) DOI;
20) Supplemental table from which the results for the  replication analysis were obtained.}
\url{http://genome.grid.wayne.edu/GxExC/Supp_Tables/cASE_GxE_rep.tab}
% file is dropbox BittStarr/bitstarr latex/
\label{SuppTable4}
\end{table}

\begin{table}[H]
\caption {\textbf{cASE overlap with doxorubicin reQTLs}. Information on treatment cASE genes in CMs which overlap with doxorubicin reQTLs from~\cite{Knowles2018}. Columns 1-10 describe the cASE gene: 
1) SNP identifier;
2) Treatment;
3) Treatment ID;
4) Measurement of cASE effect from linear model;
5) Standard error of cASE measurement;
6) Test statistic;
7) P-value;
8) FDR;
9) Ensembl gene ID;
10) Gene ID.}
% file is dropbox BittStarr/bitstarr latex/
\label{SuppTable5}
{\scriptsize
\begin{tabular}{@{}llllllllll@{}}
\toprule
SNP\_Individual     & term          & Treatment.ID & Estimate & S.E. & Statistic & $p$-value & FDR  & ENSG            & Gene ID     \\ \midrule 
rs72873318\_GM18858 & Acetaminophen & T42C1        & 0.57     & 0.094     & 6         & 0.00019 & 0.088 & ENSG00000138759 & FRAS1    \\
rs3751862\_GM18520  & Caffeine      & T13C1        & 0.98     & 0.14      & 7.2       & 0.00037 & 0.093 & ENSG00000135698 & MPHOSPH6 \\
rs1425486\_GM18858  & Caffeine      & T13C1        & 0.58     & 0.11      & 5.5       & 0.00019 & 0.088 & ENSG00000145431 & PDGFC    \\
rs55815425\_GM18520 & Caffeine      & T13C1        & 0.9      & 0.18      & 5.1       & 0.00021 & 0.09  & ENSG00000198130 & HIBCH    \\
rs7670138\_GM18912  & Copper        & T15C1        & -1.5     & 0.3       & -5.2      & 0.00039 & 0.094 & ENSG00000153012 & LGI2     \\
rs57348345\_GM19209 & Copper        & T15C1        & 2.3      & 0.43      & 5.2       & 0.00053 & 0.098 & ENSG00000136267 & DGKB     \\
rs10070440\_GM18912 & Dexamethasone & T12C1        & 1.1      & 0.24      & 4.8       & 0.00056 & 0.099 & ENSG00000122012 & SV2C     \\
rs3760\_GM18912     & Dexamethasone & T12C1        & 0.68     & 0.11      & 6.2       & 0.00015 & 0.086 & ENSG00000078674 & PCM1     \\
rs1425486\_GM18858  & Dexamethasone & T12C1        & 0.58     & 0.1       & 5.5       & 0.00019 & 0.088 & ENSG00000145431 & PDGFC    \\
rs77438708\_GM18912 & Insulin       & T33C1        & -1.2     & 0.21      & -5.6      & 0.00011 & 0.085 & ENSG00000125124 & BBS2     \\
rs72873318\_GM18858 & Nicotine      & T14C1        & 0.67     & 0.12      & 5.6       & 0.00034 & 0.093 & ENSG00000138759 & FRAS1    \\
rs2303650\_GM18855  & Nicotine      & T14C1        & 0.59     & 0.11      & 5.4       & 0.00061 & 0.1   & ENSG00000198677 & TTC37    \\
rs1331260\_GM18855  & Selenium      & T19C1        & -1.1     & 0.23      & -4.8      & 0.00041 & 0.096 & ENSG00000107249 & GLIS3    \\
rs3760\_GM18912     & Triclosan     & T30C1        & 0.7      & 0.088     & 8         & 2.2e-05 & 0.064 & ENSG00000078674 & PCM1     \\
rs9644500\_GM19209  & Triclosan     & T30C1        & 2.2      & 0.44      & 5         & 0.00038 & 0.093 & ENSG00000169436 & COL22A1  \\
rs1425486\_GM18858  & VitaminA      & T6C1         & 0.69     & 0.1       & 6.6       & 4.1e-05 & 0.069 & ENSG00000145431 & PDGFC     \\ \bottomrule
\end{tabular}
}
\end{table}

\begin{table}[H]
\caption {\textbf{Treatment cASE gene overlap in atrial fibrillation GWAS}. Significant treatment cASE genes which were associated with atrial fibrillation risk in GWAS~\cite{Nielsen2018}. 
Columns 1-2 describe the gene:
1) Ensembl gene ID;
2) Gene ID;
Columns 3-10 describe the cASE SNP:
3) SNP by individual  identifier;
4) cASE treatment name;
5) Treatment ID;
6) Measurement of cASE effect from linear model;
7) Standard error of cASE measurement;
8) Test statistic;
9) P-value;
10) FDR;
11) Degrees of freedom.}
\url{http://genome.grid.wayne.edu/GxExC/Supp_Tables/cASE_AFib.tab}
% file is dropbox BittStarr/bitstarr latex/
\label{SuppTable12}
\end{table}

\begin{table}[H]
\caption {\textbf{Mixed effects model output with all cell types analyzed together}. Results from the mixed effects model with all cell types analyzed together to quantify ASE variance. Columns 1-6 are: 
1) SNP by individual identifier;
2) Variance due to treatment;
3) Variance due to cell type;
4) Variance due to treatment $\times$ cell type interaction;
5) Variance due to control;
6) Variance due to residual.}
\url{http://genome.grid.wayne.edu/GxExC/Supp_Tables/MixedEffect_allCell.tab}
% file is dropbox BittStarr/bitstarr latex/
\label{SuppTableMixed_All}
\end{table}

\begin{table}[H]
\caption {\textbf{Mixed effects model output with cell types analyzed separately}. Results from the mixed effects model with cell types analyzed separately to quantify ASE variance. Columns 1-9 are: 
1) SNP by individual identifier;
2) Ensembl gene ID;
3) Gene ID;
4) Variance due to treatment;
5) Variance due to plate;
6) Variance due to control;
7) Variance due to residual;
8) Cell type.}
\url{http://genome.grid.wayne.edu/GxExC/Supp_Tables/MixedEffect_cellSep.tab}
% file is dropbox BittStarr/bitstarr latex/
\label{SuppTableMixed_Sep}
\end{table}

\begin{table}[H]
\caption {\textbf{ASE GO terms}. Gene ontology enrichments for genes with high or low ASE variance. Files are named according to cell type, variance type (treatment, residual, or plate), and high/low variance using the following naming convention: \textit{cell type}\_\textit{variance type}\_\textit{high/low variance}\_\texttt{GO.txt} Columns 1-9 are: 
1) GO term ID;
2) GO description;
3) Gene ratio;
4) Background ratio;
5) P-value;
6) FDR;
7) Q-value;
8) Gene IDs for high or low variance genes in GO term;
9) Number of high or low variance genes in GO term.}
\url{http://genome.grid.wayne.edu/GxExC/Supp_Tables/ASE_GO/}
% file is dropbox BittStarr/bitstarr latex/
\label{SuppTable6}
\end{table}

\begin{table}[H]
\caption {\textbf{TWAS abbreviations}. Abbreviations for TWAS found in ~\cite{Zhang2020}. Additional details on TWAS studies can be found in ~\cite{Zhang2020}. Columns 1-2 are: 
1) TWAS name as seen in Zhang et al;
2) TWAS abbreviation used in Figure ~\ref{figure4}A,B.}
\url{http://genome.grid.wayne.edu/GxExC/Supp_Tables/TWAS_abbrev.tab}
% file is dropbox BittStarr/bitstarr latex/
\label{SuppTable11}
\end{table}
