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| Status |
Public on Feb 14, 2016 |
| Title |
Sample_FP2 |
| Sample type |
SRA |
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| Source name |
Young panicles
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| Organism |
Oryza sativa Indica Group |
| Characteristics |
line: WXS(F)
developmental stage: pollen mother cell formation stage
phenotype: Fertility
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| Growth protocol |
WXS rice were grown in the field in Huazhong Agricultural University, Wuhan, Hubei province (30°28′ N, 114°21′ E) from May 2014 to August 2014. When the panicle length was approximately 1 cm, then transferred sixty plants of these WXS into cooling pond to treat them with low temperature for 2 weeks. At the permissive temperature (22 °C), these rice plants was converted to a normal male-fertile line, named WXS (F). In the same time, WXS developed into no pollen male sterile rice in natural ecological rice paddy, named WXS (S). Young panicles were collected under the two different conditions at pollen mother cell formation stages and pollen meiosis stage. Rice panicles at different developmental stages, including: SP2, SP3, FP2 and FP3, were collected.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from rice young panicle at the pollen mother cell formation stages and meiosis stage using the Trizol reagent (TaKaRa, Dalian, China) according to the manufacturer’s instructions.
Small RNAs ranging 18-30nt were size fractionated from 15% polyacrylamide gel electrophoresis (PAGE), isolated from the gel and ligated with the 5’ and 3’ RNA adaptors using T4 ligase. The resulting products were reverse transcribed and amplified using 15 PCR cycles to produce sequencing libraries.
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
small RNA profiling
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| Data processing |
Automated base calling of the raw sequence and vector removal were performed with PHRED and CROSS MATCH programs
All unique sequences were aligned to the rice genome (MSU 7, ftp://ftp.plant biology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/) using SOAP for mapping.
Sequences that mapped to rice rRNA, tRNA, scRNA, snRNA or snoRNA were removed based on National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/) and Rfam RNA family databases.
Known miRNA were identified through a BLAST search against miRNA database miRBase release 20 (http://mirbase.org/)
Novel miRNAs were used to predict MIREAP (http://so urceforge.net/projects/ mireap/).
Genome_build: MSU 7
Supplementary_files_format_and_content: Tab-delimited text files include mature miRNA counts from known hairpins.
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| Submission date |
Oct 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Hongyuan zhang |
| E-mail(s) |
zhanghongyuan@whu.edu.cn
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| Phone |
+8615972104016
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| Organization name |
Wuhan Academy of Agricultural Sciences
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| Street address |
Wuhan Academy of Agricultural Sciences, Hanshi Road, Huangpi District, Wuhan,430065, Hubei Province, China
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| City |
Wuhan city |
| State/province |
Hubei Provinve, P.R. China |
| ZIP/Postal code |
430065 |
| Country |
China |
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| Platform ID |
GPL21027 |
| Series (1) |
| GSE74003 |
Small RNA profiles of the rice non-pollen male sterile line Wuxiang S reveal miRNAs involved in the fertility transition |
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| Relations |
| BioSample |
SAMN04166242 |
| SRA |
SRX1334722 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1907992_FP2.txt.gz |
9.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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