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Series GSE45157 Query DataSets for GSE45157
Status Public on Jun 01, 2013
Title Trans-chromosomal regulation by a novel lincRNA required for adipogenesis that escapes X-chromosome inactivation
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Long noncoding RNAs (lncRNAs) have emerged as an important layer of genome regulation with common mechanistic themes including the formation of ribonucleoprotein complexes. Here, we present a novel X-linked lncRNA termed linc-Firre that escapes X-chromosome inactivation and forms trans-chromosomal interactions required for adipogenesis. Linc-Firre is exclusively nuclear and forms punctate expression foci on chromatin near its site of transcription on both X-chromosomes in human and mouse. Both the localization of linc-Firre and the association with the nuclear matrix protein hnRNPU require a conserved repeating RNA domain, R2D2. Collectively, these results reveal a lincRNA that escapes X-chromosome inactivation with a critical role in driving cell fate decisions by trans-chromosomal interactions.
Overall design Replicate RNA-Seq analyses of oligo-mediated knockdowns of linc-FIRRE and hnRNPU in two different cellular contexts; HeLa cells and mouse embryonic stem cells. Also included are Firre knockout and wild-type mouse embryonic stem cells.
Contributor(s) Hacisuleyman E, Goff LA, Trapnell C, Sauvageau M, McClanahan P, Kelley D, Cabili M, Hendrickson D, Engreitz J, Guttman M, Lennox K, Rigo F, Beal M, Johansson H, Orjalo A, Lander E, Lodish H, Sun L, Raj A, Rinn JL
Citation(s) 24463464
Submission date Mar 14, 2013
Last update date May 15, 2019
Contact name Loyal A Goff
Organization name Johns Hopkins University
Department Institute of Genetic Medicine
Lab Goff
Street address 733 N. Broadway Avenue
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
Platforms (3)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (21)
GSM1098174 mESC_Scr_Gapmer_1
GSM1098175 mESC_Scr_Gapmer_2
GSM1098176 mESC_Scr_Gapmer_3
BioProject PRJNA193156
SRA SRP019270

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Supplementary file Size Download File type/resource 3.8 Mb (ftp)(http) TAB
GSE45157_mESC_KO_vs_WT_diff.txt.gz 1.3 Mb (ftp)(http) TXT
GSE45157_mESC_KO_vs_WT_fpkm.txt.gz 340.2 Kb (ftp)(http) TXT 2.4 Mb (ftp)(http) TAB
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