|
| Status |
Public on Feb 09, 2017 |
| Title |
Heukgyeong_seedling |
| Sample type |
SRA |
| |
|
| Source name |
O.sativa_Japonica_seedling_Heukgyeong
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
age: 1 week
tissue: seedling
subspecies: Heukgyeong
|
| Growth protocol |
The uniformly germinated seeds were transferred into Yoshida nutrient solution and grown under a 16-hour light (28°C) /8-hour dark (25°C) photoperiod for 1 week
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted by using TRIzol Reagent (Invitrogen). For grains, the husks of the seeds were removed before RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
small RNAs
|
| Data processing |
For all small rna libraries, after (1) trim three prime adaptor and (2) filter out low quality or adaptor contaminated reads, we retain only short trimmed reads of sizes from 19 to 30 nt.
The retained reads were search against the Rfam database using the SOAP software, the reads mapped to structural RNAs [rRNA, tRNA, small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA)] with more than 2 mismatches were removed, reads corresponding to repeats/transposons were also discarded by performing searches against the repeat database (http://www.girinst.org/server/RepBase/).
The remaining reads that corresponded to the precursor of all known rice miRNAs from miRBase ( Release 14, http://www.mirbase.org/index.shtml) were used to estimate the expression level of each rice miRNA
Reads counts were calculated by the the read number of each gene or region by total mapped read number in each library.
For transcriptome libraries, all the reads were mapped to the reference genome of rice (Oryza sativa L. ssp. japonica cv. Nipponbare) using Bowtie software package. Reads which could be mapped equally well to multiple locations without mismatch or with up to 2 mismatches were assigned to one position at random and were retained for further analyses as described previously[29]. The reads count for each gene or genomic region ,which according to the tige6.0 gff3 file, were recovered
Genome_build: Oryza sativa
Supplementary_files_format_and_content: tab-delimited text files include read counts values for each miRNAs or mRNAs
|
| |
|
| Submission date |
Aug 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Munan Xie |
| E-mail(s) |
meximus@126.com
|
| Phone |
+86-13570393727
|
| Organization name |
Sun Yat-sen University
|
| Department |
School of life sciences
|
| Lab |
State Key Laboratory of Biocontrol
|
| Street address |
No.135 Xin Gangxi Road, Haizhu District,
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510275 |
| Country |
China |
| |
|
| Platform ID |
GPL13834 |
| Series (1) |
| GSE71925 |
Variation in the expression of miRNAs and mRNAs in rice (Oryza sativa) |
|
| Relations |
| SRA |
SRX1141130 |
| BioSample |
SAMN03980161 |
