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Series GSE60308 Query DataSets for GSE60308
Status Public on Dec 07, 2016
Title Selective reactivation of human X-linked genes in female fibroblasts reprogrammed by cell fusion
Organisms Homo sapiens; Homo sapiens x Mus musculus hybrid cell line
Experiment type Expression profiling by high throughput sequencing
Summary In female mammals, one of the two X chromosomes is silenced as pluripotent cells differentiate. This process, termed X-inactivation, is random and results in mosaic expression of many X-linked genes in female tissues. Although X-inactivation can be reversed in vitro by reprogramming, the extent varies according to species, operator and conditions. Here, we have reprogrammed cloned female human fibroblasts by fusing them with mouse ESCs and examined the kinetics of X-linked gene re-expression. Allele-specific RNA sequencing analysis was used to determine the expression from the inactive X chromosome. This study revealed that a subset of loci within domains prone to escape X-inactivation, or that showed variable expression between somatic clones, were consistently reactivated upon pluripotent reprogramming. This suggests that stochastic events may be stabilised by reprogramming, and conversely, that variable expression is predictive for Xi genes susceptible to re-activation.
Overall design We performed RNA-sequencing of two human fibroblast clones derived from TERT-immortalised NHDF17914 (Lonza) and expressing reciprocal X chromosomes (i.e. clone 12 and 34) before and at 0, 4 and 6 days after fusion with mouse ESC (E14Tg2a:puroR). Two biological replicates were sequenced for each clone.
Contributor(s) Cantone I, Dharmalingam G
Citation(s) 28118853
Submission date Aug 11, 2014
Last update date Jul 12, 2019
Contact name Gopuraja Dharmalingam
Organization name MRC London Institute of Medical Sciences
Department Epigenetics section
Street address Faculty of Medicine, Imperial College, Hammersmith Hospital Campus
City London
ZIP/Postal code W12 0NN
Country United Kingdom
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL19068 Illumina HiSeq 2500 (Homo sapiens x Mus musculus hybrid cell line)
Samples (15)
GSM1470716 Clone 12 hF Replicate 1
GSM1470717 Clone 12 hF Replicate 2
GSM1470718 Clone 12 day0 Replicate 1
BioProject PRJNA258003
SRA SRP045425

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Supplementary file Size Download File type/resource
GSE60308_FPKM_hg19.xlsx 8.3 Mb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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