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| Status |
Public on Jun 01, 2012 |
| Title |
sRNA_s_5 |
| Sample type |
SRA |
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| Source name |
pooled leaves from various tree species
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| Organisms |
Acer pseudoplatanus; Corylus avellana; Fagus sylvatica; Tilia platyphyllos; Ulmus glabra |
| Characteristics |
sample type: leaf extract
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| Treatment protocol |
Sampled in May 2008
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| Growth protocol |
Natural condition at Wytham Woods, Oxfordshire, UK
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from each of 30 tree leaf sample harvested in May 2008 (1 g fresh weight) using Tri-Reagent (Sigma-Aldrich), and small RNAs were isolated by polyacrylamide gel electrophoresis as previously described 1. Each small RNA sample was qualitatively and quantitatively measured by using NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific). The individual samples were mixed in equal quantities in two pools: Pool-1 contains 9 Acer pseudoplatanus, 1 Fagus sylvatica, 1 Tilia platyphyllos, 1 Betula pendula, 4 Fraxinus excelsior, 2 Quercus robur, and 1 Aesculus hippocastanum; Pool-2 contains 1 Ulmus glabra, 2 Tilia platyphyllos, 1 Acer pseudoplatanus, 1 Corylus avellana, and 6 Fagus sylvatica. Adaptor ligation and RT-PCR amplification were performed for each pool by using the Small RNA Sample Prep Kit (Illumina). Sequencing run was performed using the Genome Analyzer II for 34 cycles by commercial service (Source BioScience, Nottingham, UK). Two lanes of the flowcell were used for each of the two pools For each pooled sample, a lane with 3pM (lanes 3&5) and a lane with 6pM (lanes 4&6) of sample were used. The resulting small RNA reads were filtered by the Illumina GA pipeline software (version 1.0, Illumina software) and excised for the adaptor sequences.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
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| Data processing |
De novo assembly using SOAPdenovo program (http://soap.genomics.org.cn/soapdenovo.html)
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| Submission date |
Jun 01, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Hong zhi Cao |
| E-mail(s) |
caohongzhi@genomics.cn
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| Phone |
8675525274032
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| Organization name |
BGI-SHENZHEN
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| Department |
Bioinformatics
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| Street address |
F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District
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| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518083 |
| Country |
China |
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| Platform ID |
GPL10477 |
| Series (1) |
| GSE22079 |
De novo assembly of siRNA immunity in wild plants |
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| Relations |
| SRA |
SRX021980 |
| BioSample |
SAMN00014844 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM548934_BGISZ_s_5.clean.txt.gz |
3.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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