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| Status |
Public on Jul 27, 2012 |
| Title |
454_stage1 |
| Sample type |
SRA |
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| Source name |
coleoptiles, radicals, shoot, and tillering leaves
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| Organism |
Oryza sativa |
| Characteristics |
tissue: coleoptiles, radicals, shoot, and tillering leaves
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| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNAs were extracted and fractionated according to the user manual of Qiagen RNA/DNA kit. The RNA fractions between 50-500 nt in length were collected and checked by the polyacylamide gel before the cDNA library was constructed. 5’ end structure specific adaptors and 3’ end adaptors were sequentially ligated to the isolated ncRNAs according to previously established methods (Deng et al., 2006). cDNAs were obtained by reverse transcription without amplification. The cDNAs with both end adaptors served as the single stranded DNA (ssDNA) library for the deep 454 sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
454 GS FLX Titanium |
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| Data processing |
The validated reads were mapped to rice genome MSU 6.1
discarding the tRNA- and rRNA-related loci
The consensus sequences of these multiple reads loci met each of the following criteria before being considered as a putative ncRNA:a) at least one perfectly matched read with the annotated rice genome was observed; b) the novel non-coding transcript had at least one trim and defined terminus; c) at least two non-redundant reads or reads from different sequencing libraries were found.
Genome_build: MSU 6.1
Supplementary_files_format_and_content: bed files were generated against ref genome MSU6.1; Scores represent mapped reads;
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| Submission date |
Jul 27, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei Chen |
| E-mail(s) |
cnchw@163.com
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| Organization name |
Peking University
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| Street address |
No.5 Yiheyuan Road
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL15856 |
| Series (1) |
| GSE39695 |
Global identification and characterization of intermediate-size non-coding RNAs in Oryza sativa |
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| Relations |
| SRA |
SRX171209 |
| BioSample |
SAMN01095772 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM977851_454_stage1.bed.gz |
10.1 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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