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| Status |
Public on Feb 17, 2010 |
| Title |
Small RNA expression and strain specificity in the rat |
| Organism |
Rattus norvegicus |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Background Digital gene expression (DGE) profiling has become an established tool to study RNA expression. Here, we provide an in-depth analysis of small RNA DGE profiles from two different rat strains (BN-Lx and SHR) from six different rat tissues (spleen, liver, brain, testis, heart, kidney). We describe the expression patterns of known and novel micro (mi)RNAs and piwi-interacting (pi)RNAs. We confirmed the expression of 589 known miRNAs and identified 56 miRNAs homologous to known human or mouse miRNAs, as well as 45 new rat miRNAs. Furthermore, we confirmed specific A to I editing in brain for mir-376a/b/c and identified mir-377 as a novel editing target. In accordance with earlier findings, we observed a highly tissue-specific expression pattern for all tissues analyzed. The brain was found to express the highest number of tissue-specific miRNAs, followed by testis. Notably, our experiments also revealed robust strain-specific differential miRNA expression in the liver that is caused by genetic variation between the strains. Finally, we identified two types of germline-specific piRNAs in testis, mapping either to transposons or in strand-specific clusters. Taken together, the small RNA compendium described here advances the annotation of small RNAs in the rat genome. Strain and tissue-specific expression patterns furthermore provide a strong basis for studying the role of small RNAs in regulatory networks as well as biological process like physiology and neurobiology that are extensively studied in this model system.
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| Overall design |
Small RNAs from 6 tissues were cloned and sequenced. Tissues included whole brain, liver, spleen, heart, testis, kidney. Tissues were sequenced from 2 rats: one BN-Lx rat and one SHR rat. For strain-specific miRNA expression we included 4 replicate whole livers, i.e. from 2 BN-Lx rats and 2 SHR rats.
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| Contributor(s) |
Linsen SE, de Wit E, de Bruijn E, Cuppen E |
| Citation(s) |
20403161 |
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| Submission date |
Nov 17, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Sam Linsen |
| E-mail(s) |
s.linsen@hubrecht.eu
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| Phone |
+312121828
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| Organization name |
Hubrecht Institute
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| Department |
Genome Biology
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| Lab |
Cuppen lab
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| Street address |
Uppsalalaan 8
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| City |
Utrecht |
| ZIP/Postal code |
3584CT |
| Country |
Netherlands |
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| Platforms (1) |
| GPL9690 |
AB SOLiD System (Rattus norvegicus) |
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| Samples (16)
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| Relations |
| SRA |
SRP001897 |
| BioProject |
PRJNA120555 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE19054_RAW.tar |
280.0 Kb |
(http)(custom) |
TAR (of TXT) |
| GSE19054_README.txt.gz |
552 b |
(ftp)(http) |
TXT |
| GSE19054_hairpins_rat.fa.gz |
13.0 Kb |
(ftp)(http) |
FA |
| GSE19054_mature_6tissues.fa.gz |
37.5 Kb |
(ftp)(http) |
FA |
| GSE19054_mature_liver_replicates.fa.gz |
19.9 Kb |
(ftp)(http) |
FA |
| GSE19054_piRNA_clusters.txt.gz |
3.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
| Raw data are available in SRA |
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