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Series GSE135577 Query DataSets for GSE135577
Status Public on Aug 08, 2022
Title Ribosome profiling of WT E14, Dgcr8_KO, Dorsha_KO, Dicer_KO and Ago1&2_Double_KO mouse embryonic stem cells
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary miRNAs are short regulatory single stranded RNA sequences that upon complementary binding to mRNAs lead to the inhibition or degradation of their targets. This regulatory mechanisms has been shown to play crucial roles throughout the whole life cycle of animals and plants as well as in disease. While a plethora of methods exist to predict targets of miRNA, which suggest that up to 80% of the genome is miRNA regulated, it has recently been reported that many of these predictions are false positives, cell type specific or represent non-functional binding. In order to identify the subset of real functional miRNAs and their targets, we established miRNA pathway mutants in mouse embryonic stem cells (mESC), allowing the dissection of canonical and non-canonical functions of pathway members. Additional data integration of downstream regulatory layers (CLIP-seq, ribosome profiling and MS) enabled us to follow and track down real functional miRNA-gene interactions, which reduced the miRNA genome regulation to approximately 1%.
Overall design Purpose: The goals of this study was to obtain the ribosome binding profile of WT and RNAi mutant mESCs.
Ribosome profiling of different RNAi mutant mouse embryonic stem cells (E14) were generated by deep sequencing, in duplicate, using Illumina HiSeq2500.
Contributor(s) Ciaudo C
Citation(s) 35899551
Submission date Aug 08, 2019
Last update date Oct 17, 2022
Contact name Constance Ciaudo
Organization name ETH Zurich
Department D-BIOL
Lab Ciaudo
Street address Otto-Stern-Weg 7, HPL G.31
City Zurich
State/province Zurich
ZIP/Postal code 8093
Country Switzerland
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (10)
GSM4018772 ESCs, WT_1
GSM4018773 ESCs, WT_2
GSM4018774 ESCs, Dgcr8_KO1
BioProject PRJNA559348
SRA SRP217845

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Supplementary file Size Download File type/resource
GSE135577_ribo.txt.gz 275.6 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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