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| Status |
Public on Nov 28, 2015 |
| Title |
Genome-wide profiling of long non-coding RNAs in Arabidopsis |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Other
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We developed a stringent selection pipeline for lncRNA identification, combining high-throughput RNA sequencing and computational approaches. Using this pipeline, we annotated 1,353 lncRNAs in Arabidopsis thaliana. We further found that one fifth of the lncRNAs were associated with Polycomb repressive complex 2 (PRC2). Some PRC2-associated lncRNAs could repress the transcription of their neighboring genes through mediating histone H3 lysine 27 trimethylation.
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| Overall design |
Identification of Arabidopsis lncRNA through high throughput sequencing.
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| Contributor(s) |
Li J, Wu Y, Hu Y, Guo W, Zhang MQ, Qi Y |
| Citation(s) |
30498193 |
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| Submission date |
Dec 03, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Yijun Qi |
| E-mail(s) |
qiyijun@biomed.tsinghua.edu.cn
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| Organization name |
National Institute of Biological Sciences
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| Lab |
Yijun Qi's lab
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| Street address |
#7 Science Park Road, Zhongguancun Life Science Park
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| City |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
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| Platforms (1) |
| GPL11221 |
Illumina Genome Analyzer IIx (Arabidopsis thaliana) |
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| Samples (12)
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| GSM1048068 |
polyA+ RNAs from whole cell extract, seedling |
| GSM1048069 |
total RNAs from whole cell extract, seedling |
| GSM1048070 |
non-polyA RNAs from whole cell extract, seedling |
| GSM1048071 |
total RNAs from cytoplasmic extract, seedling |
| GSM1048072 |
non-polyA RNAs from cytoplasmic extract, seedling |
| GSM1048073 |
total RNAs from nuclear extract, seedling |
| GSM1048074 |
non-polyA RNAs from nuclear extract, seedling |
| GSM1048075 |
polyA+ RNAs from whole cell extract, inflorescence |
| GSM1048076 |
total RNAs from nuclear extract, inflorescence |
| GSM1048077 |
mock RIP-seq, seedling |
| GSM1048078 |
CLF RIP-seq, seedling |
| GSM1048079 |
H3K27me3 ChIP-seq, seedling |
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| Relations |
| BioProject |
PRJNA182746 |
| SRA |
SRP017399 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE42695_RAW.tar |
313.9 Mb |
(http)(custom) |
TAR (of TXT, WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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