|
| Status |
Public on Sep 28, 2016 |
| Title |
LM2 [miRNA] |
| Sample type |
SRA |
| |
|
| Source name |
potato leaf
|
| Organism |
Solanum tuberosum |
| Characteristics |
cultivar: Solanum tuberosum L. cv.Zhuangshu No.3
age: Eight-week-old
tissue: leaf
growth condition: Plantlets were shifted to the dark for 3 days and exposed to red light for 12,24,and 48 h
|
| Treatment protocol |
Eight-week-old plantlets were shifted to the dark 3 day and subsequently re-exposed to red light (～19.7μmol m−2s−1, 630 nm). Then, the leaves of plantlets were harvested after 12, 24, and 48 h, respectively. Dark-grown plantlets were collected as the control. The leaves were collected and immediately frozen in liquid nitrogen.In vitro generated microtubers were treated under the same conditions as described previously.
|
| Growth protocol |
Plantlets were cultured in MS medium at 22℃ under long-day photoperiod (16 h light/8h dark) condition.To induce microtubers, eight-week-old plantlets were added to 20 ml liquid MS medium containing 8% sucrose. These plantlets grew in growth cabinet at 19℃ under darkness condition. After eight weeks, in vitro generated microtubers were harvested.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from leaves and tuber’s peel with TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s procedure. Equal amounts of each RNA samples were pooled at 12, 24 and 48 h time points and the quality were checked by Agilent 2100 bioanalyzer.
Small RNAs (18-30 nt) were isolated from total RNA by polyacrylamide gel electrophoresis, and ligated to 3‘illumina adapter. The adapter-ligated sRNA were transcribed into cDNA by Super-script II Reverse Transcriptase (Invitrogen) to generate sRNA libraries. Small RNA libraries were subjected to deep sequencing with Illumina HiSeq 2000 at LC Sciences (Hangzhou, China).
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: leaf_miRNAs.txt
|
| Data processing |
Using the UEA sRNA workbench Filter Tool (Stocks et al. 2012), sRNA reads were mapped onto plant t/rRNAs sequences obtained from RFAM version 10, the Genomic tRNA Database and EMBL release 95, then the matched sequences were discarded.
To identify the isoforms of known miRNA, the miRProf tool was run with clean sRNA reads. The reads were mapped with at most 1 nt mismatch to known Viridiplantae mature miRNA annotated in miRBase 21.
To identify novel miRNAs and their precursors, the unique reads were submitted to the miRCat pipeline and default plant parameters were defined. miRCat maps sRNA sequence to the potato reference genome (PGSC DM v4.03 pseudomolecules) using PatMaN(Prufer et al. 2008).
Supplementary_files_format_and_content: tab-delimited text file include read count and RPM values for each sample.
|
| |
|
| Submission date |
Apr 06, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yan Qiao |
| Organization name |
Gansu Agricultural University
|
| Department |
College of Agronomy
|
| Street address |
No. 1 Yingmen village, Anning District
|
| City |
Lanzhou |
| State/province |
Gansu Province |
| ZIP/Postal code |
730070 |
| Country |
China |
| |
|
| Platform ID |
GPL16436 |
| Series (2) |
| GSE79984 |
Integrated RNA-seq and sRNA-seq analysis reveals miRNA effects on secondary metabolism in Solanum tuberosum L [miRNA-seq] |
| GSE79986 |
Integrated RNA-seq and sRNA-seq analysis reveals miRNA effects on secondary metabolism in Solanum tuberosum L |
|
| Relations |
| BioSample |
SAMN04621328 |
| SRA |
SRX1683993 |
