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Series GSE104378 Query DataSets for GSE104378
Status Public on Feb 14, 2018
Title Cell-type specific sequencing of microRNAs from complex animal tissues I
Organism Caenorhabditis elegans
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary MicroRNAs (miRNAs) play an essential role in the post-transcriptional regulation of animal development and physiology. However, in vivo studies linking miRNA-function to the biology of distinct cell types within complex tissues remain challenging, partly due to the difficulties in achieving cellular resolution using available miRNA-profiling methods. Here, we report an in vivo small RNA-tagging approach that enables high-throughput sequencing of tissue- and cell type-specific miRNAs in animals, which we call microRNome by methylation-dependent sequencing, or mime-seq. The method combines orthogonal, cell-type-specific 3´ terminal 2’-O-methylation of animal miRNAs by the plant-specific methyltransferase HEN1, with oxidation-sensitive small RNA cloning and high-throughput sequencing. We show that mime-seq uncovers the miRNomes of rare cells within C. elegans and Drosophila at unprecedented specificity and sensitivity, enabling miRNA profiling with single-cell resolution in whole animals. Mime-seq overcomes the current challenges in tissue- and cell-type-specific small RNA profiling and provides novel entry points for understanding the function of miRNAs in spatially restricted physiological settings.
 
Overall design 46 small RNA libraries from L1-staged C. elegans. For most of the samples (40/46 libraries) there are two conditions (untreated and treated with sodium periodate) and two biological replicates: 4 libraries for wild-type, non-transgenic worms; 4 libraries for rab-3:Ath-HEN1, henn-1(0) worms; 4 libraries for unc-31:Ath-HEN1, henn-1(0) worms; 4 libraries for rgef-1:Ath-HEN1, henn-1(0) worms; 4 libraries for elt-2:Ath-HEN1, henn-1(0) worms; 4 libraries for myo-2:Ath-HEN1, henn-1(0) worms; 4 libraries for ASE:Ath-HEN1, henn-1(0) worms; 4 libraries for ASE:Ath-HEN1 worms; 4 libraries for myo-3:Ath-HEN1, henn-1(0) worms; 4 libraries for myo-3:Ath-HEN1 worms. For the remaining samples (6/46 libraries) there are two conditions (untreated and treated with sodium periodate) and three biological replicates: 6 libraries for rps-5-3:Ath-HEN1, henn-1(0) worms.
 
Contributor(s) Alberti C, Manzenreither R, Sowemimo I, Burkard TR, Wang J, Cochella L, Ameres SL
Citation(s) 29481550
Submission date Sep 28, 2017
Last update date Jul 25, 2021
Contact name Chiara Alberti
E-mail(s) chiara.alberti@imp.ac.at
Organization name IMP
Street address Campus-Vienna-Biocenter 1
City Vienna
ZIP/Postal code 1030
Country Austria
 
Platforms (1)
GPL18245 Illumina HiSeq 2500 (Caenorhabditis elegans)
Samples (46)
GSM2796300 WT No Treatment (N2) 32793
GSM2796301 WT Treatment (N2) 32794
GSM2796302 WT No Treatment (N2) 34092
This SubSeries is part of SuperSeries:
GSE104470 Cell-type specific sequencing of microRNAs from complex animal tissues
Relations
BioProject PRJNA412474
SRA SRP119052

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE104378_RAW.tar 200.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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