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| Status |
Public on Feb 14, 2018 |
| Title |
Cell-type specific sequencing of microRNAs from complex animal tissues II |
| Organisms |
Drosophila melanogaster; Mus musculus |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| 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.
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| Overall design |
two replicates with 12 libraries each: 12 libraries of 10-fold decreasing dilution series of RNA from S2-S cells (DmHen1-KO) expressing AthHEN1 into RNA from Mmu ES cells: 2 libraries with RNA from S2-S cells (DmHen1-KO) expressing AthHEN1 mixed in 1:1 ratio with RNA from Mmu ES cells, one subjected to periodate treatment (ox+) and one left untreated. 2 libraries with RNA from S2-S cells (DmHen1-KO) expressing AthHEN1 mixed in 1:10 ratio with RNA from Mmu ES cells, one subjected to periodate treatment (ox+) and one left untreated. 2 libraries with RNA from S2-S cells (DmHen1-KO) expressing AthHEN1 mixed in 1:100 ratio with RNA from Mmu ES cells, one subjected to periodate treatment (ox+) and one left untreated. 2 libraries with RNA from S2-S cells (DmHen1-KO) expressing AthHEN1 mixed in 1:1000 ratio with RNA from Mmu ES cells, one subjected to periodate treatment (ox+) and one left untreated. 2 libraries with RNA from S2-S cells (DmHen1-KO) expressing AthHEN1 mixed in 1:10,000 ratio with RNA from Mmu ES cells, one subjected to periodate treatment (ox+) and one left untreated. 2 libraries with RNA from S2-S cells (DmHen1-KO) expressing AthHEN1 mixed in 1:100,000 ratio with RNA from Mmu ES cells, one subjected to periodate treatment (ox+) and one left untreated.
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| Contributor(s) |
Alberti C, Manzenreither R, Sowemimo I, Burkard TR, Wang J, Cochella L, Ameres SL |
| Citation(s) |
29481550 |
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| Submission date |
Oct 01, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Chiara Alberti |
| E-mail(s) |
chiara.alberti@imp.ac.at
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| Organization name |
IMP
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| Street address |
Campus-Vienna-Biocenter 1
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| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platforms (1) |
| GPL21227 |
Illumina HiSeq 2500 (Drosophila melanogaster; Mus musculus) |
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| Samples (36)
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| GSM2800834 |
ox+ 1:10 AthHEN1_S2-S+mES |
| GSM2800835 |
ox- 1:100 AthHEN1_S2-S+mES |
| GSM2800836 |
ox+ 1:100 AthHEN1_S2-S+mES |
| GSM2800837 |
ox- 1:1,000 AthHEN1_S2-S+mES |
| GSM2800838 |
ox+ 1:1,000 AthHEN1_S2-S+mES |
| GSM2800839 |
ox- 1:10,000 AthHEN1_S2-S+mES |
| GSM2800840 |
ox+ 1:10,000 AthHEN1_S2-S+mES |
| GSM2800841 |
ox- 1:100,000 AthHEN1_S2-S+mES |
| GSM2800842 |
ox+ 1:100,000 AthHEN1_S2-S+mES |
| GSM2865750 |
ox+ 1:1 AthHEN1_S2-S+mES (replica 2) |
| GSM2865751 |
ox- 1:1 AthHEN1_S2-S+mES (replica 2) |
| GSM2865752 |
ox- 1:10 AthHEN1_S2-S+mES (replica 2) |
| GSM2865753 |
ox+ 1:10 AthHEN1_S2-S+mES (replica 2) |
| GSM2865754 |
ox- 1:100 AthHEN1_S2-S+mES (replica 2) |
| GSM2865755 |
ox+ 1:100 AthHEN1_S2-S+mES (replica 2) |
| GSM2865756 |
ox- 1:1,000 AthHEN1_S2-S+mES (replica 2) |
| GSM2865757 |
ox+ 1:1,000 AthHEN1_S2-S+mES (replica 2) |
| GSM2865758 |
ox- 1:10,000 AthHEN1_S2-S+mES (replica 2) |
| GSM2865759 |
ox+ 1:10,000 AthHEN1_S2-S+mES (replica 2) |
| GSM2865760 |
ox- 1:100,000 AthHEN1_S2-S+mES (replica 2) |
| GSM2865761 |
ox+ 1:100,000 AthHEN1_S2-S+mES (replica 2) |
| GSM2865762 |
ox+ 1:1 AthHEN1_S2-S+mES (replica 3) |
| GSM2865763 |
ox- 1:1 AthHEN1_S2-S+mES (replica 3) |
| GSM2865764 |
ox- 1:10 AthHEN1_S2-S+mES (replica 3) |
| GSM2865765 |
ox+ 1:10 AthHEN1_S2-S+mES (replica 3) |
| GSM2865766 |
ox- 1:100 AthHEN1_S2-S+mES (replica 3) |
| GSM2865767 |
ox+ 1:100 AthHEN1_S2-S+mES (replica 3) |
| GSM2865768 |
ox- 1:1,000 AthHEN1_S2-S+mES (replica 3) |
| GSM2865769 |
ox+ 1:1,000 AthHEN1_S2-S+mES (replica 3) |
| GSM2865770 |
ox- 1:10,000 AthHEN1_S2-S+mES (replica 3) |
| GSM2865771 |
ox+ 1:10,000 AthHEN1_S2-S+mES (replica 3) |
| GSM2865772 |
ox- 1:100,000 AthHEN1_S2-S+mES (replica 3) |
| GSM2865773 |
ox+ 1:100,000 AthHEN1_S2-S+mES (replica 3) |
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| This SubSeries is part of SuperSeries: |
| GSE104470 |
Cell-type specific sequencing of microRNAs from complex animal tissues |
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| Relations |
| BioProject |
PRJNA412779 |
| SRA |
SRP119210 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE104466_RAW.tar |
300.0 Kb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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