DEPARTMENT OF HUMAN GENETICS / UNIVERSITY OF CHICAGOhttp://genes.uchicago.eduhttp://www.uchicago.edushapeimage_1_link_0shapeimage_1_link_1
Gilad Labhttp://giladlab.uchicago.edushapeimage_2_link_0



Blischak-et-al-Supplement

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.


Kagan-Banovich-el-al-Supplement

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


Battle-Kahn-Wang-et-al-Supplement

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. 2014 Dec 18.


Gallego Romero-Pavlovic-et-al-Supplement

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.


Banovich-et-al-Supplement

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.


LCL-Reprogramming-Protocol

This protocol outlines the procedure used in the lab to generate iPSCs from LCLs.


Tung-et-al-Code

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.


Perry-et-al-Supplement

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.


Perry-et-al-Supplement

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.


Çalişkan-et-al-Supplement

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.


Perry-et-al-Supplement

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. 


Bullaughey-et-al-cis-eQTL.zip

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.


arraySuppInfo.zip

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.


RNAseq_data.zip

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.

(RNA-seq protocol is available here: RNASeq_v2 2.doc)


Genetics_2007_supp_material.zip

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.


OR_expression.zip

Data from Zhang X, De la Cruz O, Pinto JM, Nicolae D, Firestein S and Gilad Y. Characterizing the expression of human olfactory receptor genes. Genome Biology 2007 May 17;8(5):R86. These are the RMA value from all microarray hybridizations, as well as the P-values for the null hypothesis of no expression difference between tissues.


Bioinfo_2007_Supplementary_figures.doc

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


PLoS_data.zip

This is the OR sequence data used in Gilad Y, Przeworski M, and Lancet D. Loss of olfactory receptor genes coincides with the acquisition of full trichromatic vision in primates. PLoS Biology. 2004, 2(1): 120-125


Epipedobates tricolor maintenance protocol: written | visual

This protocol outlines maintenance procedures used in the lab for long term care of Epipedobates tricolor.

Copyright © Yoav Gilad

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