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| Status |
Public on Dec 12, 2018 |
| Title |
SAM2 |
| Sample type |
SRA |
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| Source name |
SAM
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| Organism |
Populus tomentosa |
| Characteristics |
tissue: shoot tips
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| Growth protocol |
Healthy shoot tips and surrounding leaves of P. tomentosa, were collected from 20-year-old plants growing under natural conditions at Yangzhou University, Yangzhou, China (32.39°N, 119.42°E).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from the shoot tips (SAM) and surrounding leaves via the Trizol method with a slight modification to the manufacturer’s instructions for the TaKaRa MiniBEST plant RNA extraction kit (TaKaRa Bio Inc., Japan).
RNA libraries were prepared for sequencing using standard Illumina protocols.
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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 |
SAM_vs_leaf.final.diff.txt
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| Data processing |
Raw sequence data were obtained via the RNA high-throughput sequencing process, and then filtered to remove contaminating reads, adapter sequences, poly-A tails, and other artifacts. All high-quality sequences, including those with only a single unique read, were used for further analysis.
Sequences reads were mapped to the Populus trichocarpa genome database downloaded from ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/002/775/GCA_000002775.2_Poptr2_0/ by SOAP according to the default settings. The GenBank and Rfam databases were employed to annotate the rRNAs, snRNAs, snoRNAs, and tRNAs in the sRNA library. Repeat overlapping sequences were annotated as repeat-associated sRNAs. Matching sRNAs without annotation were stored in an unannotated file.
To identify known miRNAs from the SAM and leaves of P. tomentosa, the bioinformatics pipeline was used to annotate known miRNAs, both conserved and lineage-specific. In the present study, all miRNAs belonging to families already annotated in the miRBase Registry (http://www.mirbase.org) in the P. trichocarpa database were defined as known. Potentially novel miRNAs and their hairpin precursors were predicted using the MIREAP (http://sourceforge.net/projects/mireap/) software from the remaining unannotated reads. The essential criteria of plant miRNAs were used to screen the novel miRNA candidates.
The expression frequency of miRNAs was normalized to one million by total clean reads of miRNAs in each library (TPM = miRNA count/total count of clean reads×1,000,000). The differential expression change of miRNA reads between the SAM and leaf libraries was calculated as follows: The fold change = log2 (SAM/Leaf). Both fold change > 1 and FDR < 0.05 were used to define the differentially expressed miRNAs.
Genome_build: Populus trichocarpa genome (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/002/775/GCA_000002775.2_Poptr2_0/)
Supplementary_files_format_and_content: The tab-delimited text file includes miRNA_name; SAM; leaf; log2FC; FDR; Regulated; Target Geneid and Swissprot_annotation(.txt)
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| Submission date |
Dec 11, 2018 |
| Last update date |
Dec 14, 2018 |
| Contact name |
Biao Jin |
| E-mail(s) |
bjin@yzu.edu.cn
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| Phone |
13056359569
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| Organization name |
Yangzhou University
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| Department |
College of Horticulture and Plant Protection
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| Lab |
Jin Lab
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| Street address |
Wenhui east road no. 48
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| City |
Yangzhou |
| State/province |
Jiangsu |
| ZIP/Postal code |
225009 |
| Country |
China |
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| Platform ID |
GPL25314 |
| Series (1) |
| GSE100282 |
Identification and analysis of microRNAs in the SAM and leaves of Populus tomentosa |
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| Relations |
| BioSample |
SAMN10580834 |
| SRA |
SRX5125644 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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