Elorbany and Popp et al 2021 (data upload pending)
Supplementary data for Elorbany R, Popp JM, Rhodes K, Strober BJ, Barr KA, Qi G, Gilad Y and Battle A. Single-cell sequencing reveals lineage-specific dynamic genetic regulation of gene expression during human cardiomyocyte differentiation.
Supplementary data for Hsiao CJ, Tung P, Blischak JD, Burnett J, Barr K, Dey KK, Stephens M, and Y Gilad. Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis.
Supplementary data for Blake LE, Thomas SJ, Blischak JD, Hsiao CJ, Chavarria C, Myrthil M, Gilad Y, and Pavlovic BJ. A comparative study of endoderm differentiation in humans and chimpanzees.
These are the supplementary data for Cusanovich DA, Caliskan M, Billstrand C, Michelini K, Chavarria C, De Leon S, Mitrano A, Lewellyn N, Elias JA, Chupp GL, Lang RM, Shah SJ, DeCara JM, Gilad Y, and Ober C. Integrated Analyses of Gene Expression and Genetic Association Studies in a Founder Population. Hum Mol Genet. 2016 Feb 29. doi: 10.1093/hmg/ddw061.
These are the supplementary data for Blischak JD, Tailleux L, Mitrano A, Barreiro L, and Gilad Y. Mycobacterial infection induces a specific human innate immune response. Sci Rep. 2015 Nov 20;5:16882. doi: 10.1038/srep16882.
These are the supplementary data for Kagan CL, Banovich NE, Pavlovic BJ, Patterson K, Gallego Romero I, Pritchard JK, and Gilad, Yoav. Genetic Variation, Not Cell Type of Origin, Underlies Regulatory Differences in iPSCs bioRxiv. 2015 Jan: http://dx.doi.org/10.1101/013888
These are the supplementary data for Battle A, Kahn Z, Wang SH, Mitrano A, Ford MJ, Pritchard JK, and Gilad Y. Impact of regulatory variation from RNA to protein. Science. 2015, 347(6222):664-7. doi: 10.1126/science.1260793.
Genotype data and RNA sequencing data from the 72 YRI LCL lines used in this study are available on GEO (GSE19480) and GEUVADIS (E-GEUV-3; ArrayExpress), as is the ribosome profiling data generated in this study (GSE61742). The YRI LCLs have also been used to measure a variety of genomic phenotypes, including H3K27ac (GSE58852), DNA methylation (GSE57483), chromatin accessibility (DNAse-seq; GSE31388), transcriptional elongation rates and initiation frequencies (4sU-seq; GSE75220), RNA decay (GSE37451), and protein levels (PXD001406).
These are the supplementary data for Gallego Romero I, Pavlovic BJ, Hernando-Herraez I, Zhou X, Ward MC, Banovich NE, Kagan CL, Burnett JE, Huang CH, Mitrano A, Chavarria CI, Friedrich Ben-Nun I, Li Y, Sabatini K, Leonardo TR, Parast M, Marques-Bonet T, Laurent LC, Loring JF, Gilad Y. A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics. Elife. 2015 Jun 23;4. doi: 10.7554/eLife.07103.
These are the supplementary data for Banovich NE, Lan X, McVicker G, van de Geijn B, Degner JF, Blischak JD, Roux J, Pritchard JK, and Gilad Y. Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels. PLoS Genetics 2014 Sep 18;10(9):e1004663.
This protocol outlines the procedure used in the lab to generate iPSCs from LCLs.
This is the supplemental R code for Tung J, Barreiro LB, Johnson ZP, Hansen KD, Michopolous V, Toufexis D, Wilson ME, and Gilad Y. Social environment is associated with gene regulatory variation in the rhesus macaque immune system. PNAS. 2012 Apr 24;109(17):6490-5.
These are the supplementary data for Perry GH, Reeves D, Melsted P, Ratan A, Miller W, Michelini K, Louis EE, Pritchard JK, Mason CE, & Gilad Y. A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar. Genome Biology and Evolution. Genome Biology and Evolution. 2012 Jan;4(2):126-135.
These are the supplementary data for Perry GH, Melsted P, Marioni JC, Wang Y, Bainer R, Pickrell JK, Michelini K, Zehr S, Yoder AD, Stephens M, Pritchard JK, and Gilad Y. Comparative RNA sequencing reveals substantial genetic variation in endangered primates. Genome Research. 2012 Jan 31;22:602-610.
These are the supplementary data (including the corrected supplementary figure S13) for Çalişkan M, Cusanovich DA, Ober C, Gilad Y. The effects of EBV transformation on gene expression levels and methylation profiles. Human Molecular Genetics. 2011 Apr 15;20(8):1643-52.
These are the supplementary data and code for Perry G, Marioni JC, Melsted P, Gilad Y. Genomic-scale capture and sequencing of endogenous DNA from feces. Molecular Ecology. 2010 Dec; 19(24):5332-44.
These are the real time PCR data for Bullaughey K, Chavarria CI, Coop G, Gilad Y. Expression quantitative trait loci detected in cell-lines are often present in primary tissues. Hum Mol Genet. 2009 18(22): 4296-303.
These are the supplementary methods, figures, and tables S1 and S7 for Blekhman R, Oshlack A, Chabot AE, Smyth GK and Gilad Y. Gene regulation in primates evolves under tissue-specific selection pressures. PLoS Genetics 2008 Nov 21; 4(11): e1000271.
This is the processed array and Solexa data for Marioni JC, Mason CE, Mane SM, Stephens M and Gilad Y. RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Research 2008 Sep;18(9):1509-17.
These are the supplementary tables and figures (including raw luminescence levels from the reporter gene assays) for Chabot AE, Shrit RA, Blekhman R and Gilad Y. Using reporter gene assays to identify cis regulatory differences between humans and chimpanzees. Genetics 2007, 176(4):2069-76.
These are the supplementary figures for Oshlack A, Chabot AE, Smyth GK and Gilad Y. Using DNA microarrays to study gene expression in closely related species. Bioinformatics 2007, Advance Access published on March 23, 2007
This protocol outlines maintenance procedures used in the lab for long term care of Epipedobates tricolor.