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| Status |
Public on Sep 08, 2017 |
| Title |
Small RNAs in Hibiscus syriacus (Ovary) |
| Sample type |
SRA |
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| Source name |
ovary
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| Organism |
Hibiscus syriacus |
| Characteristics |
tissue: ovary
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from Hibiscus syriacus tissue samples (leaf, root, flower, and ovary) using TRI Reagent solution (MRC), according to the manufacturer’s protocol. Both the flower and ovary were pretreated with CTAB buffer [2% CTAB, 2% polyvinylpyrrolidone K 30, 100 mM Tris (pH 8.0), 25 mM EDTA, 2 M NaCl, and 2% β-mercaptoethanol] followed by TRI Reagent extraction, as previously described (Peng et al., 2014).
A small RNA sequencing library was constructed using the Small RNA Sample Prep Kit (Illumina), according to the manufacturer’s instructions. As previously described (Hwang et al., 2013), 10 μg of total RNAs was resolved using 15% urea-PAGE, and size fractions of small RNAs between 18 and 30 nt were prepared. The prepared small RNAs were ligated to the 3′ and 5′ adapter, and cDNA was synthesized using RT-PCR. cDNAs were amplified using PCR and submitted for Illumina/Solexa sequencing.
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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
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| Data processing |
Poor-quality small RNA reads and adapter sequences were eliminated using the FASTX toolkit, and the reads whose length was between 18 and 26 nt were selected for further analysis.
High-quality small RNAs (reads of ≥50) were mapped to the reference genome of Hibiscus syriacus and the perfectly mapped sequences were selected (≤42 times).
The filtered reads were analyzed to identify the putative miRNAs in the modified algorithm (Hwang et al., 2013; Meyers et al., 2008).
After identification, the miRNA candidates were classified to either the conserved miRNAs or novel miRNAs through a BLASTN search with miRBase.
The reads of miRNAs from each library were normalized to read per 10 million (RP10M).
Genome_build: MGA.V09 (https://hibiscus.kobic.re.kr/hibiscus.en/)
Supplementary_files_format_and_content: *fa: Fasta format; each data file contains sequence and raw reads. Header line definition: >X-Y, where X=rank in descending order (for example, 4 means that the read is the fourth largest read), and Y=abundance of raw read.
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| Submission date |
May 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Chanseok Shin |
| E-mail(s) |
[email protected]
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| Organization name |
Seoul National University
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| Department |
Agricultural Biotechnology
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| Lab |
Biochemistry
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| Street address |
1, Gwanak-ro, Gwanak-gu
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| City |
Seoul |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
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| Platform ID |
GPL23518 |
| Series (1) |
| GSE99329 |
Small RNA transcriptome of Hibiscus syriacus provides insights into the potential influence of microRNAs in flower development and terpene synthesis |
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| Relations |
| BioSample |
SAMN07169351 |
| SRA |
SRX2858580 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2641684_len_O.fa.gz |
37.3 Mb |
(ftp)(http) |
FA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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