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| Status |
Public on Jul 20, 2017 |
| Title |
Smo_degradome |
| Sample type |
SRA |
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| Source name |
leaves
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| Organism |
Selaginella moellendorffii |
| Characteristics |
tissue: leaves
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| Treatment protocol |
None
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| Growth protocol |
introduced from Shenzhen, Guandong, China and cultivated in greenhouse, temperature controlled at 15~25 ˚C
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction: 1g fresh wight plant material were ground in liquid nitrogen, and the powder were resuspended in 15ml 2%CTAB(2% CTAB, 2% PVP, 100mM Tris, 25mM EDTA, 2M NaCl, 5% β-mercaptoethanol). Incubated the homogenized sample at 65˚C for 10 min. Cooled the sample to the room temperature, added 3ml chloroform,mixed thoroughly, then centrifuged the sample at 4˚C,12,000 g for 10 min. Transferred the supernantant to a new tube, added 1/4 volume of 10 M LiCl, mixed gently, then stored the sample in a 4˚C refrigerator overnight. Centrifuged the sample at 12,000 g for 30 min, discarded the aqueous. The pellet was washed with 5ml 70% EtOH twice and discarded the supernantant, air dry the pellet and dissolved the total RNA using RNase-free water.
For sample 1-25, sRNA libraries were constructed with NEBNext® Multiplex Small RNA Library kit (NEB, #E7300S). Briefly, 30ug total RNA was resolved on 15% Ura PAGE, and 15-40nt small RNAs were recovered by gel purification. 3' and 5' adaptors were ligated to the small RNAs, and reverse transcription was conducted with the RT primer complementary to the 3' adaptor. Finally, the libraries were amplified with the primers complementary to the 5' and 3' adaptor sequences. For sample 26, the dedgradome library was constructed according to Zhai et.,al (2014). Briefly, polyA-RNA was purified from 75ug total RNA with Dynabeads® mRNA Purification Kit (Thermo Fisher, #61006). 5' adaptors was ligated to polyA RNA, reverse transcription and double-stranded cDNA synthesis were performed. The product was purified with Agencourt AMPure XP (Beckman Coulter, #A63881). The double-strand DNA was digested with MmeI followed by 3' adaptor ligation. PAGE purification and recovery of ligated dsDNA products (50-75bp). Finally, the library was amplified with the primers complementary to the 5' and 3' adaptor sequences using purified dsDNA products as the template. Final PCR products with the length of 128bp was obtained and recovered from the gel.
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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 |
total RNA
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| Data processing |
Basecalls performed using Illumina CASAVA
Sequence reads were trimmed and size selected (18-42nt for sRNA data and 19-21nt for degradome data) using cutadapt v1.9.1, and then filtered to remove rRNA, tRNA, snoRNA, etc. against the annotation of Selaginella moellendorffii using bowtie with parameters -v 2 -k1.
Genome_build: None
Supplementary_files_format_and_content: filtered small reads in fasta format with read counts after understrike
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| Submission date |
May 01, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Chenjiang You |
| E-mail(s) |
chenjiang.you@ucr.edu, youchenjiang2003@hotmail.com
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| Organization name |
Fudan University
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| Street address |
2005 Songhu Rd
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| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
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| Platform ID |
GPL23399 |
| Series (1) |
| GSE98408 |
Conservation and divergence of small RNA pathways in vascular plants revealed by small RNA analyses in lycophytes and ferns |
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| Relations |
| BioSample |
SAMN06857349 |
| SRA |
SRX2773470 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2594417_Smo_degradome.fasta.gz |
96.7 Mb |
(ftp)(http) |
FASTA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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