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| Status |
Public on Nov 28, 2018 |
| Title |
La2 [miRNA-Seq] |
| Sample type |
SRA |
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| Source name |
juvenile lanceolate leaf
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| Organism |
Populus euphratica |
| Characteristics |
leaf shape: lanceolate
tree age: 4-6 years
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| Growth protocol |
The juvenile linear,lanceolate,ovate and broad-ovate leaf groups were respectively sampled from 0-3, 4-6, 8-12 and over 20 years old P. euphratica in Alar (81°17′56.52″ E, 40°32′36.90″ N), Xinjiang province, China at April 2017
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the mirVanamiRNA Isolation Kit (Ambion) following the manufacturer’s protocol
The small RNA libraries were constructed using RNA extracted from juvenile linear,lanceolate,ovate and broad-ovate leaves.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
small RNA sequencing
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| Data processing |
The known miRNAs were identified by aligning against miRBase v.21 database (http://www.mirbase.org/,mismatch=0)
Unannotated small RNAs were analyzed by mirdeep2 (-c -j -l 18 -m ) to predict novel miRNAs
miRNAs were quantified and normalized to TPM (transcript per million).
Supplementary_files_format_and_content: tab-delimited text files include TPM values and precursor coordinate of novel miRNAs
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| Submission date |
Oct 04, 2018 |
| Last update date |
Nov 28, 2018 |
| Contact name |
Shaowei Qin |
| E-mail(s) |
qinshaowei2005@126.com
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| Organization name |
Tarim University
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| Department |
College of Life Sciences
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| Street address |
Hongqiao Road 705
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| City |
Alar |
| State/province |
Xinjiang |
| ZIP/Postal code |
843300 |
| Country |
China |
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| Platform ID |
GPL25640 |
| Series (2) |
| GSE120821 |
Genome-wide analysis of RNAs associated with Populus euphratica Oliv. heterophyll morphogenesis [miRNA-Seq] |
| GSE120822 |
Genome-wide analysis of RNAs associated with Populus euphratica Oliv. heterophyll morphogenesis |
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| Relations |
| BioSample |
SAMN10147586 |
| SRA |
SRX4779238 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3416403_La2miRNA.txt.gz |
2.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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