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Series GSE54966 Query DataSets for GSE54966
Status Public on May 15, 2015
Title Transcriptomic analysis reveals novel long non-coding RNAs critical for vertebrate development [Illumina]
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Long non-coding RNAs (lncRNAs) have emerged as critical regulators of gene expression and chromatin modifications, with important functions in development and disease. Here we sought to identify and functionally characterize lncRNAs critical for vascular vertebrate development with significant conservation across species. Genome-wide transcriptomic analyses during human vascular lineage specification enabled the identification of three conserved novel lncRNAs: TERMINATOR, ALIEN and PUNISHER that are specifically expressed in pluripotent stem cells, mesoderm and endothelial cells, respectively. Gene expression profiling, alongside RNA immunoprecipitation coupled to mass spectrometry, revealed a wide range of new molecular networks and protein interactors related to post-transcriptional modifications for all three lncRNAs. Functional experiments in zebrafish and murine embryos, as well as differentiating human cells, confirmed a developmental-stage specific role for each lncRNA during vertebrate development. The identification and functional characterization of these three novel non-coding provide a comprehensive transcriptomic roadmap and shed new light on the molecular mechanisms underlying human vascular development.
Overall design shRNA knock down of lncRNAs followed by DNA methylation profiling
Contributor(s) Kurian L, Aguirre A, Benner C, Izpisua-Belmonte JC
Citation(s) 25739401
Submission date Feb 13, 2014
Last update date Mar 22, 2019
Contact name Christopher Benner
Organization name University of California, San Diego (UCSD)
Department Medicine
Street address 9500 Gilman Dr. MC 0640
City La Jolla
State/province California
ZIP/Postal code 92093-0640
Country USA
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (8)
GSM1327321 H1 shCtrl
GSM1327322 H1 shTerminator
GSM1327323 H1 shCtrl r2
This SubSeries is part of SuperSeries:
GSE54969 Transcriptomic analysis reveals novel long non-coding RNAs critical for vertebrate development
BioProject PRJNA238181

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

Supplementary file Size Download File type/resource
GSE54966_RAW.tar 183.1 Mb (http)(custom) TAR
GSE54966_non-normalized.txt.gz 18.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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