 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 01, 2015 |
| Title |
LYP9_mixture of E, M, L (targets) |
| Sample type |
SRA |
| |
|
| Source name |
LYP9 rice
|
| Organism |
Oryza sativa |
| Characteristics |
hybrid: Liang-You-Pei 9 (LYP9, age-sensitive rice)
tissue: leaf
developmental stage: mixture of early,middle and late stage of grain-filling of leaves
|
| Treatment protocol |
The flag leaves at early, middle and late stages of grain-filling of two hybrid rice, N2Y6 and LYP9 (named as N2Y6-E, N2Y6-M, N2Y6-L, LYP9-E, LYP9-M and LYP9-L, respectively), were collected, respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with the Total RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada) according to the manufacturer’s instructions. Small RNA libraries were generated from the two samples using the Illumina Truseq Small RNA Preparation kit according to Illumina’s TruSeq Small RNA Sample Preparation Guide. The purified cDNA library was used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina GAIIx following vendor’s instruction for running the instrument. Raw sequencing reads were obtained using Illumina’s Sequencing Control Studio software version 2.8 (SCS v2.8) following real-time sequencing image analysis and base-calling by Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70). A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis. Degradome library was constructed following with methods previously described by Ma et al.(2010).CleaveLand3.0 and LC Science’s ACGT301-DGEv1.0 program were used to detect potentially sliced targets of known and novel miRNA.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Sample 14
Sample name: BS02
processed data file: Table S4.xls
|
| Data processing |
A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for miRNA sequencing data analysis (Li et al. 2010; Wei et al. 2011). ACGT101_DGE was used for DGE sequencing data analysis. A Public software package, CleaveLand3.0 was used for analyzing Degradome sequencing data.
Genome_build: MSU Release 7.0 (http://www.phytozome.net/rice.php), miRbase20.0
Supplementary_files_format_and_content: xls format and miRNAs and targets prediction results
|
| |
|
| Submission date |
Oct 09, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
bo shen |
| E-mail(s) |
bshen65@163.com
|
| Organization name |
Hangzhou normal university
|
| Street address |
Cangqian road
|
| City |
Hangzhou |
| ZIP/Postal code |
311121 |
| Country |
China |
| |
|
| Platform ID |
GPL15432 |
| Series (1) |
| GSE62200 |
Genome-wide analysis of microRNAs and their targets involving in leaf senescence of rice |
|
| Relations |
| BioSample |
SAMN03102590 |
| SRA |
SRX729978 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
