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| Status |
Public on Dec 01, 2018 |
| Title |
SR2 |
| Sample type |
SRA |
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| Source name |
Root collected 1 day after ABA-2
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| Organism |
Populus euphratica |
| Characteristics |
age: one year
treated with: ABA for 1 day
tissue: Root
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| Biomaterial provider |
Beijing Forestry university,Beijing, China
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| Treatment protocol |
For the treated groups, 1L 300 μM ABA solutions were irrigated to each pot to make sure sufficiently watered, and for the control group, pure water instead of ABA solution was applied.
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| Growth protocol |
1-year-old P. euphratica plantlets with uniformly grown were planted in individual 5 L pots containing loam soil with similar height and placed in the greenhouse at Beijing Forestry University.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 18 collections of CRs, SRs, and LRs using CTAB method (Jaakola et al., 2001; Zhou et al., 2009).
Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) according to manufacturer’s specifications.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500/2000 platform and 50bp single-end reads were generated.
Low quality reads were removed, and 10 - 30 nt sRNAs were purified without more than 10 nt single nucleotide repeats, or more than 10% poly N, or these with 5’ adapter contaminants, or with 3’ adapter or the insert tag. And then bowtie software were used to mapped the remaining sequences to the genome of P. euphratica
Mapped small RNA tags were used to looking for known miRNA. The characteristics of hairpin structure of miRNA precursor can be used to predict novel miRNA.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010):
Small RNA annotation and Target gene prediction
Genome_build: NCBI Populus euphratica unplaced genomic scaffold, PopEup_1.0 scaffold1.1, whole genome shotgun sequence; https://www.ncbi.nlm.nih.gov/assembly/GCF_000495115.1/
Supplementary_files_format_and_content: abundance measurements of novel miRNAs found in the current study and known ptc-miRNAs in the miRBase at http://www.mirbase.org/
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| Submission date |
Dec 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Conglong Lian |
| E-mail(s) |
770379183@qq.com
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| Phone |
13366602812
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| Organization name |
Beijing Forestry University
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| Street address |
35 Tsinghua Eastern Road
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| City |
Beijing |
| ZIP/Postal code |
100083 |
| Country |
China |
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| Platform ID |
GPL24346 |
| Series (2) |
| GSE107802 |
Genome-Wide Identification of ABA Responsive microRNAs in the Root of Populus euphratica |
| GSE107823 |
Genome-Wide Identification of ABA Responsive microRNAs in the root and stem of Populus euphratica |
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| Relations |
| BioSample |
SAMN08142936 |
| SRA |
SRX3453217 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2879451_SR2.txt.gz |
1.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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