|
| Status |
Public on Mar 27, 2012 |
| Title |
RxT line,Col-0 13-day seedlings |
| Sample type |
SRA |
| |
|
| Source name |
13-day seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
strain: Columbia-0 wild type
line: RxT
tissue: seedlings
developmental stage: 13-day old
rna: small RNA
|
| Treatment protocol |
Columbia-0 plants were treated with 100 Gy γ-irradiation and placed in a growth chamber at 22℃ for 1.5 h. Seedlings without γ-irradiation treatment were used as controls.
|
| Growth protocol |
All plants were grown in Murashige and Skoog (MS) medium at 16-h-light/8-h-dark photoperiod. Human DR-GFP/U2OS cells [U2OS derivative cell line harboring an integrated HR reporter construct (DR-GFP)] were grown in Dulbecco's modified Eagle's medium with 10% fetal bovine serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Small RNAs were extracted from whole plants or the purified AGO2 complex by Trizol reagent (Invitrogen), resolved on a 15% denaturing PAGE gel, and visualized by SYBR-Gold (Invitrogen) staining. Gel slices within the range of 18-28 nt were excised, and the RNAs were eluted and purified for small RNA library construction. Cloning of small RNAs from Arabidopsis and human cells was carried out essentially as described in Mi et al., Cell, 2008. The Illumina GA IIx was used for sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
All reads obtained from Illumina GA IIx were sorted into respective libraries by parsing their barcodes. Then the adaptor sequences were removed using ‘vectorstrip’ in the EMBOSS package. Small RNA reads with length of 18-28nt were retained.
|
| |
|
| Submission date |
Mar 07, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Yijun Qi |
| E-mail(s) |
qiyijun@biomed.tsinghua.edu.cn
|
| Organization name |
National Institute of Biological Sciences
|
| Lab |
Yijun Qi's lab
|
| Street address |
#7 Science Park Road, Zhongguancun Life Science Park
|
| City |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
| |
|
| Platform ID |
GPL11221 |
| Series (1) |
| GSE36338 |
A Role for Small RNAs in DNA Double-Strand Break Repair |
|
| Relations |
| SRA |
SRX127928 |
| BioSample |
SAMN00809259 |
