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SRX7666678: GSM4293616: Hs_H1_BG97_3D_d11_ctrl_Riboseq_replicate1_5; Homo sapiens; RNA-Seq
1 ILLUMINA (Illumina HiSeq 4000) run: 44.1M spots, 2.2G bases, 860.5Mb downloads

Submitted by: NCBI (GEO)
Study: The role of long noncoding RNAs during pancreas development
show Abstracthide Abstract
LncRNAs are developmentally regulated and highly cell type-specific non-coding RNAs that have emerged as important regulators of cell fate commitment and maintenance. In this study, we dissected the role of lncRNAs in human pancreas development by classifying lncRNAs based on their dynamic regulation, subcellular localization, and engagement with ribosomes during the stepwise differentiation of human embryonic stem cells (hESCs) towards pancreatic fate. We then deleted 10 candidate lncRNAs in hESCs and characterized the knockout phenotypes of pancreatic developmental intermediates, prioritizing dynamically regulated lncRNAs with validated translation potential and proximity to developmental TFs. This small-scale loss-of-function screen revealed that most lncRNAs are dispensable for pancreatic development and the regulation of nearby genes. We identify LINC00261 as the first translated lncRNA involved in human endocrine cell development, and show that it regulates gene expression in pancreatic progenitor cells in trans rather than cis. Through systematic dissection of LINC00261's coding and noncoding functions, we can exclude a role for the produced micropeptides in this process. Instead, we posit that, over the course of pancreatic differentiation, the biological activity of multiple lncRNAs is controlled by a regulatory, translation machinery dependent mechanism that employs ribosome engagement and short open reading frame translation to dose lncRNA activity in the nucleus. It is conceivable that inadequate nuclear LINC00261 dosage during human pancreas development could predispose individuals to developing diabetes. Overall design: RNA-seq and Ribo-seq analysis of H1 embryonic stem cells differentiated towards the pancreatic endocrine cell fate.
Sample: Hs_H1_BG97_3D_d11_ctrl_Riboseq_replicate1_5
SAMN13975844 • SRS6094908 • All experiments • All runs
Organism: Homo sapiens
Library:
Instrument: Illumina HiSeq 4000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: Total RNA was extracted using either Trizol or the QIAGEN RNeasy Mini Kit. For cell fractionation experiments, the Paris Kit (Thermo Fisher Scientific) was used. Libraries were prepared according to Illumina's (TruSeq Stranded Total RNA Library Prep Gold; TruSeq Stranded mRNA Library Prep; TruSeq Ribo Profile (Mammalian) or Roche's (KAPA mRNA HyperPrep Kit) instructions
Experiment attributes:
GEO Accession: GSM4293616
Links:
Runs: 1 run, 44.1M spots, 2.2G bases, 860.5Mb
Run# of Spots# of BasesSizePublished
SRR1100588444,053,3762.2G860.5Mb2020-08-04

ID:
10007444

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