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Series GSE44875 Query DataSets for GSE44875
Status Public on Jun 01, 2014
Title LncRNA DEANR1 facilitates human endoderm differentiation by activating FOXA2 expression
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Long non-coding RNAs (lncRNAs) regulate diverse biological processes including cell lineage specification. Here we report transcriptome profiling of human endoderm and pancreatic cell lineages using purified cell populations. Analysis of the data sets allowed the identification of hundreds of lncRNAs exhibiting differentiation stage-specific expression patterns. As a first step in characterizing these lncRNAs, we focus on an endoderm-specific lncRNA DEANR1 (Definitive Endoderm Associated long Non-coding RNA1) and demonstrate that it plays an important role in human endoderm differentiation. DEANR1 contributes to endoderm differentiation by positively regulating endoderm factor FOXA2 expression. Importantly, overexpression of FOXA2 is able to rescue endoderm differentiation defects caused by DEANR1 depletion. Mechanistically, DEANR1 facilitates FOXA2 activation by helping SMAD2/3 recruitment to the FOXA2 promoter. Thus, our study not only reveals a large set of differentiation stage-specific lncRNAs, but also characterizes a novel lncRNA important for endoderm differentiation.
Overall design Here we perform RNA-seq based transcriptome profiling using undifferentiated human ESCs (one sample), definitive endoderm (two replicates), pancreatic progenitors(three replicates) as well as sorted human primary alpha cells (two replicates), beta cells (two replicates) and exocrine cells (one sample). Moreover, we perform RNA-seq based transcriptome profiling for WT, FOXA2 knockdown, and DEANR1 knockdown of differentiated definitive endoderm samples (two replicates for each).
Contributor(s) Jiang W, Liu Y, Zhang Y
Citation(s) 25843708
Submission date Mar 05, 2013
Last update date May 15, 2019
Contact name Yuting Liu
Organization name Harvard Medical School
Department Department of Genetics
Lab Yi Zhang lab
Street address 82 Walnut St. Unit 3
City Brookline
State/province MA
ZIP/Postal code 02445
Country USA
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (17)
GSM1093229 ES2
GSM1093230 DE1
GSM1093231 DE2
BioProject PRJNA192215
SRA SRP019241

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Supplementary file Size Download File type/resource
GSE44875_Gene_expression_FPKM_FOXA2KD_DEANR1KD_150220.txt.gz 485.3 Kb (ftp)(http) TXT
GSE44875_processed_FPKM_genes_human_pancreatic_lineage_140112.txt.gz 784.0 Kb (ftp)(http) TXT
GSE44875_processed_FPKM_lncRNAs_human_pancreatic_lineage_140112.txt.gz 894.6 Kb (ftp)(http) TXT
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