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Series GSE37111 Query DataSets for GSE37111
Status Public on Oct 25, 2012
Title Transcriptome-wide identification of LIN28A targets in mouse embryonic stem cell (A3-1) [Illumina Seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Other
Summary LIN28A is a highly-conserved RNA-binding protein which is known to be involved in embryonic development, stem cell maintenance and proliferation. LIN28A is expressed in various types of cancer, and they are associated with advanced tumor malignancy. In embryonic stem cell, LIN28A specifically binds to let-7 precursors to suppress biogenesis of the let-7 microRNA family. In addition, Lin28 was reported to bind several mRNAs such as Oct4, cyclin A/B and histone H2A to activate their translation. For comprehensive understanding of the interaction between LIN28A and their target RNAs, we exploited UV-crosslinking and immunoprecipitation (CLIP) to capture their in vivo binding to target RNAs. LIN28A-binding RNAs were identified in a mouse embryonic stem cell line using multiple monoclonal and polyclonal antibodies. The result shows that LIN28A preferentially binds to let-7 precursors through GGAG binding motif, which is consistent with our previous results. We also identified that LIN28A binding is enriched in a certain subset of mRNAs. To understand the function of the novel LIN28A-mRNA binding, we carried out ribosome profiling from LIN28A-depleted mouse embryonic stem cells.
 
Overall design Examination of RNA binding of LIN28A and translation in mouse embryonic stem cell.
 
Contributor(s) Cho J, Chang H, Kim VN
Citation(s) 23102813
Submission date Apr 09, 2012
Last update date May 15, 2019
Contact name Hyeshik Chang
E-mail(s) hyeshik@snu.ac.kr
Phone +82-2-887-1343
Organization name Institute for Basic Science
Department Center for RNA Research
Lab Narry Kim Lab
Street address Building 504 Room 531, School of Biological Sciences, Seoul National University, 599 Gwanangno, Gwanak-gu
City Seoul
State/province South Korea
ZIP/Postal code 08826
Country South Korea
 
Platforms (2)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (8)
GSM910950 A3-1 PolyA+ RNA-seq - untreated
GSM910951 A3-1 PolyA+ RNA-seq - siLuc
GSM910952 A3-1 PolyA+ RNA-seq - siLin28a
This SubSeries is part of SuperSeries:
GSE37114 LIN28A targets, regulation of microRNA biogenesis, and effect on transcriptome in A3-1 cells
Relations
SRA SRP012118
BioProject PRJNA158351

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

Supplementary file Size Download File type/resource
GSE37111_clip.txt.gz 763.6 Kb (ftp)(http) TXT
GSE37111_polya.txt.gz 794.7 Kb (ftp)(http) TXT
GSE37111_rpf.txt.gz 305.3 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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