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Series GSE45741 Query DataSets for GSE45741
Status Public on Aug 10, 2013
Title Primate genome architecture linked with formation mechanisms and functional consequences of structural variation
Platform organisms Macaca mulatta; Pan troglodytes; Pongo pygmaeus
Sample organisms Macaca mulatta; Pan troglodytes; Pongo abelii
Experiment type Genome variation profiling by genome tiling array
Summary While nucleotide-resolution maps of genomic structural variants (SVs) have provided insights into the origin and impact on phenotypic diversity in humans, comparable maps in nonhuman primates have thus far been lacking. Using massively parallel DNA sequencing we constructed fine-resolution, species-specific structural variation and segmental duplication maps for five chimpanzees, five orang-utans, and five rhesus macaques. The SV maps, comprising thousands of deletions, duplications, and mobile element insertions, revealed a high activity of retrotransposition in macaques. Non-allelic homologous recombination, linked with genomic architecture, primarily shaped the genomes of great apes resulting in different SV formation mechanism landscapes across species, with distinct functional consequences. Transcriptome analyses across nonhuman primates and humans revealed significant effects of species-specific gene duplications on gene expression, with these effects displaying remarkable diversity in direction and magnitude. Thirteen inter-species gene duplications coincided with the species-specific gain of expression in a new tissue, implicating these duplications in function acquisition.
 
Overall design Agilent arrays were custom designed for probes to be relatively evenly spaced across the reference genomes of chimpanzee, orang-utan, and rhesus macaque. For each species 9 one million probe arrays were used to cover the autosomes and a single 400k probe array was used for the sex chromosomes.
 
Contributor(s) Gokcumen O, Tischler V, Tica J, Zhu Q, Iskow R, Lee E, Fritz MH, Langdon A, Stütz AM, Pavlidis P, Benes V, Mills R, Park P, Lee C, Korbel JO
Citation(s) 24014587
Submission date Apr 03, 2013
Last update date Oct 18, 2013
Contact name Charles Lee
E-mail(s) clee@rics.bwh.harvard.edu
Organization name Brigham and Women's Hospital/Harvard Medical School
Department Pathology
Lab Lee Lab--Molecular Genetic Research Unit
Street address 221 Longwood Ave., EBRC-422
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platforms (30)
GPL16900 Agilent-034029 PanTro_HD_1M_1
GPL16901 Agilent-034030 PanTro2_HD_1M_2
GPL16902 Agilent-034031 PanTro_HD_1M_3
Samples (30)
GSM1113470 PanTro2 (1 of 9)
GSM1113471 PanTro2 (2 of 9)
GSM1113472 PanTro2 (3 of 9)
Relations
BioProject PRJNA196636

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE45741_RAW.tar 2.7 Gb (http)(custom) TAR (of TXT)
Processed data included within Sample table
Processed data provided as supplementary file

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