|
| Status |
Public on Feb 21, 2014 |
| Title |
Spirodela_polyrhiza_5a |
| Sample type |
SRA |
| |
|
| Source name |
whole plants, including fronds and roots
|
| Organism |
Spirodela polyrhiza |
| Characteristics |
strain: 5a
tissue: whole plants, including fronds and roots
|
| Treatment protocol |
All the samples were immediately frozen in liquid nitrogen and stored at -80oC until further treatments.
|
| Growth protocol |
S. polyrhiza were cultured in Schenk and Hildebrandt basal salt mixture liquid medium at pH 5.8 and grown in a controlled climate chamber under a photoperiod of 16h-light (100 μmol.m-2.s-1, 23°C) and 8h-dark (15°C).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the whole plants (fronds and roots) using TRIzol reagent (Invitrogen, USA) following the manufacturer’s instructions.
Small RNAs (sRNAs) of 18-30 nt in length were first separated from the total RNA pool by size fractionation using 15% denaturing polyacrylamide gel electrophoresis. After purification, 5’ and 3’ adaptors were ligated to the sRNAs using T4 RNA ligase (Promega, Madison, WI), which were again purified and used as templates for reverse-transcription (RT) reaction. The cDNA were further purified by 15% denaturing polyacrylamide gel electrophoresis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RTA 1.12.4.2 was used for base calling.
The raw sequences were filtered as follows: 1) poor quality reads, including reads with “N” character and reads of more than 4 bases with SQ ≤ 10 or more than 6 bases with SQ value ≤ 13; 2) reads with 5’ adaptor contaminants; 3) reads without reliable 3’ adaptor; 4) reads without the inserts; 5) reads with poly A; 6) reads shorter than 18 nt.
Genome_build: Build 4.0
Supplementary_files_format_and_content: fasta file containing ID, abundance and sequences of small RNAs
|
| |
|
| Submission date |
Feb 20, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jie Tang |
| Organization name |
School of Environment and Energy, Peking University Shenzhen Graduate School
|
| Street address |
Rm. E118, PKU Campus, Shenzhen University Town
|
| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518055 |
| Country |
China |
| |
|
| Platform ID |
GPL18308 |
| Series (1) |
| GSE55208 |
Discovery of novel and conserved microRNAs in Spirodela polyrhiza by deep sequencing |
|
| Relations |
| BioSample |
SAMN02647047 |
| SRA |
SRX474218 |
