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Series GSE54968 Query DataSets for GSE54968
Status Public on May 15, 2015
Title Transcriptomic analysis reveals novel long non-coding RNAs critical for vertebrate development [RNA-Seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
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 Time course RNA-Seq analysis H1 ESCs differentiated into endothelial cells
Contributor(s) Kurian L, Aguirre A, Benner C, Izpisua-Belmonte JC
Citation(s) 25739401
Submission date Feb 13, 2014
Last update date May 15, 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)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (6)
GSM1327339 H1 Day 0
GSM1327340 H1 Day 2
GSM1327341 H1 Day 4
This SubSeries is part of SuperSeries:
GSE54969 Transcriptomic analysis reveals novel long non-coding RNAs critical for vertebrate development
BioProject PRJNA238180
SRA SRP037762

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Supplementary file Size Download File type/resource
GSE54968_gencode.expression.txt.gz 2.2 Mb (ftp)(http) TXT
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