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| Status |
Public on Aug 31, 2016 |
| Title |
Systematic characterization of novel lncRNAs responding to phosphate starvation in Arabidopsis thaliana |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
We sequenced the poly(A)+ and poly(A)- samples of the roots and shoots from 10-day-old WT seedlings grown under P+ and P- condition. The WT plant refers to Columbia ecotype Arabidopsis seedlings. Each condition has two replicates. After total RNA extraction, ribosomal RNAs were removed using RiboMinus™ Plant Kit repeated two times. The poly(A)+ and poly(A)- constituent were separated with oligo(dT) magnetic beads (Oligotex mRNA Mini Kit, QIAGEN). Using a 2-fold change and a P-value <0.05 as the cut-off for selecting the differentially expressed transcripts, we globally identified novel noncoding lncRNAs.
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| Overall design |
We performed a RNA-seq analysis on Columbia WT plants. Total RNAs were extracted from the shoots and roots of 10-day-old P+ and P- WT seedlings (i.e., seedling grown on P-sufficient and P-deficient media). The extracted RNAs were subjected to polyA(+) and polyA(-) RNA purification, library construction and RNA deep sequencing. We used Tophat to map reads to TAIR10 genome and used Cufflinks to assemble transcripts based on 16 datasets of RNA-seq samples.
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| Contributor(s) |
Yuan JP, Lu ZJ |
| Citation(s) |
27538394 |
| Submission date |
Jan 06, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jiapei Yuan |
| E-mail(s) |
xiaoranzizhu@163.com
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| Organization name |
Tsinghua University
|
| Street address |
Tsinghua Yuan
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platforms (2) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
| GPL17639 |
Illumina HiSeq 2500 (Arabidopsis thaliana) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA308080 |
| SRA |
SRP068145 |
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