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Series GSE55504 Query DataSets for GSE55504
Status Public on Apr 08, 2014
Title Domains of genomewide gene expression dysregulation in Down syndrome [RNA-seq]
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Trisomy 21 (T21) is the most frequent genetic cause of cognitive impairment. To assess the perturbations of gene expression in T21, and to eliminate the noise of the genomic variability, we studied the transcriptome of fetal fibroblasts from a pair of monozygotic twins discordant for T21. Here we show that the differential expression between the twins is organized in domains along all chromosomes that are either up- or downregulated. These gene expression dysregulation domains (GEDDs) can be defined by the expression level of their gene content, and are well conserved in induced pluripotent stem cells derived from the twins’ fibroblasts. Comparison of the transcriptome of the Ts65Dn mouse model of DS and wild-type, also showed GEDDs along the mouse chromosomes that were syntenic in human. The GEDDs correlate with the lamina-associated (LADs) and replication domains of mammalian cells. The overall LADs position was not altered in trisomic cells. However, the H3K4me3 profile of the trisomic fibroblasts was modified and accurately followed the GEDD pattern. These results suggest that the nuclear compartments of trisomic cells undergo modifications of the chromatin environment influencing the overall transcriptome and that GEDDs may therefore contribute to some T21 phenotypes.
Overall design mRNA-Seq profiling in Down syndrome: fibroblasts derived from a pair of monozygotic twins discordant for trisomy 21 (4 replicates), iPS cells from the same pair of discordant twins, fibroblasts from a pair of normal monozygotic twins, fibroblasts from 16 unrelated individuals (8 trisomic and 8 euploid controls), fibroblasts from the Ts65Dn mouse model of Down syndrome (1 trisomic mouse and 1 control wt).
Contributor(s) Letourneau A, Santoni FA, Bonilla X, Sailani M, Gonzalez D, Kind J, Chevalier C, Thurman R, Sandstrom RS, Hibaoui Y, Popadin K, Falconnet E, Gagnebin M, Gehrig C, Vannier A, Guipponi M, Farinelli L, Robyr D, Garieri M, Migliavacca E, Borel C, Deutsch S, Feki A, Stamatoyannopoulos JA, Herault Y, van Steensel B, Guigo R, Antonarakis SE
Citation(s) 24740065
Submission date Mar 03, 2014
Last update date Apr 27, 2020
Contact name Audrey Letourneau
Organization name University of Geneva Medical School
Department Genetic Medicine and Development
Street address Rue Michel-Servet 1
City Geneva
ZIP/Postal code 1211
Country Switzerland
Platforms (3)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (30)
GSM1338311 T1DS Rep0
GSM1338312 T2N Rep0
GSM1338313 T1DS Rep1
This SubSeries is part of SuperSeries:
GSE55426 Domains of genomewide gene expression dysregulation in Down syndrome
BioProject PRJNA239814
SRA SRP039348

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Supplementary file Size Download File type/resource
GSE55504_Expression_iPS_cells.txt.gz 841.4 Kb (ftp)(http) TXT
GSE55504_final_QN_4rep_file.sorted.txt.gz 5.6 Mb (ftp)(http) TXT
GSE55504_final_mouse_QN_file.txt.gz 789.5 Kb (ftp)(http) TXT
GSE55504_final_unr_QN_file.txt.gz 3.3 Mb (ftp)(http) TXT
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