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Sample GSM889259 Query DataSets for GSM889259
Status Public on Mar 27, 2012
Title RxT line in dcl2-1 mutant background, 13-day seedlings
Sample type SRA
 
Source name 13-day seedlings
Organism Arabidopsis thaliana
Characteristics strain: Columbia-0 dcl2-1 mutant
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 SRX127931
BioSample SAMN00809262

Supplementary file Size Download File type/resource
GSM889259_dcl2_mutant.unique_counts.txt.gz 19.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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