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| Status |
Public on Apr 24, 2015 |
| Title |
Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Circular RNAs (circRNAs) are an endogenous class of animal RNAs. Despite their abundance, their function and expression in the nervous system are unknown. Therefore, we sequenced RNA from different brain regions, primary neurons, isolated synapses, as well as during neuronal differentiation. Using these and other available data, we discovered and analyzed thousands of neuronal human and mouse circRNAs. circRNAs were extraordinarily enriched in the mammalian brain, well conserved in sequence, often expressed as circRNAs in both human and mouse, and sometimes even detected in Drosophila brains. circRNAs were overall upregulated during neuronal differentiation, highly enriched in synapses, and often differentially expressed compared to their mRNA isoforms. circRNA expression correlated negatively with expression of the RNA-editing enzyme ADAR1. Knockdown of ADAR1 induced elevated circRNA expression. Together, we provide a circRNA brain expression atlas and evidence for important circRNA functions and values as biomarkers.
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| Overall design |
To assess circRNA expression in mammalian brain, we sequenced and analyzed mouse brain regions (hippocampus, cerebellum, prefrontal cortex and olfactory bulb), various neuronal differentiation (mouse P19 and human SH-SY5Y cells) and maturation (mouse cortical neurons) stages, and subcellular compartments in mouse (synaptoneurosomal fraction, cytoplasmic fraction, whole brain lysate).
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| Contributor(s) |
Rybak-Wolf A, Stottmeister C, Glazar P, Pino N, Giusti S, Hanan M, Behm M, Bartok O, Ashwal-Fluss R, Jens M, Herzog M, Schreyer L, Papavasileiou P, Ivanov A, Öhman M, Refojo D, Kadener S, Rajewsky N |
| Citation(s) |
25921068 |
| Submission date |
Feb 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Petar Glazar |
| Organization name |
Max Delbrück Center for Molecular Medicine
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| Department |
Systems Biology of Gene Regulatory Elements
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| Lab |
Rajewsky lab
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| Street address |
Robert Rössle Str. 10 (H. 87)
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| City |
Berlin |
| ZIP/Postal code |
13092 |
| Country |
Germany |
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| Platforms (4)
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| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (25)
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| GSM1611266 |
P19_Day_12 |
| GSM1665895 |
P19 exp2 day 0 |
| GSM1665896 |
P19 exp2 day 4 |
| GSM1665897 |
P19 exp2 day 12 |
| GSM1665898 |
fractionation, brain_lysate |
| GSM1665899 |
fractionation, synaptoneurosomes |
| GSM1665900 |
fractionation, cytoplasm |
| GSM1665901 |
primary neurons, day 1 |
| GSM1665902 |
primary neurons, day 7 |
| GSM1665903 |
primary neurons, day 14 |
| GSM1665904 |
primary neurons, day 21 |
| GSM1665905 |
primary neurons, day 28 |
| GSM1665906 |
brain regions, hippocampus |
| GSM1665907 |
brain regions, cerebellum |
| GSM1665908 |
brain regions, prefrontal cortex |
| GSM1665909 |
brain regions, olfactory bulb |
| GSM1665910 |
SH-SY5Y exp1 day 0 |
| GSM1665911 |
SH-SY5Y exp1 day 2 |
| GSM1665912 |
SH-SY5Y exp1 day 4 |
| GSM1665913 |
SH-SY5Y exp2 day 0 |
| GSM1665914 |
SH-SY5Y exp2 day 4 |
| GSM1665915 |
SH-SY5Y exp2 day 8 |
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| Relations |
| BioProject |
PRJNA275421 |
| SRA |
SRP055027 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE65926_RAW.tar |
450.0 Kb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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