 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 21, 2017 |
| Title |
Wild type Rice |
| Sample type |
SRA |
| |
|
| Source name |
total RNAs, seedling
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
strain/ecotype: Nipponbare
tissue: seedlings
developmental stage: two-weeks-old
|
| Treatment protocol |
N/A
|
| Growth protocol |
For growing Arabidopsis thaliana and rice, seeds were grown on the half MS media. And maize seeds were planted on soil in the growth room.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using Trizol (Sigma), and then were treated with TURBO DNA-free kit (ambion) for removing DNA contamination.
Libraries were constructed through applying TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) in accordance with the manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
strand-specific RNA-seq
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Adaptor and low quality sequences were trimmed with trim-galore (v0.3.3, --stringency 6); Clean reads were aligned to reference genomes (TAIR10 for Arabidopsis, TIGR release 7 for rice and AGPv2 for maize) using Tophat2 with following parameters: -N 5 --read-edit-dist 5 (v2.0.14).
Mapped reads from three biological replicates for Arabidopsis and rice were merged and then assembled with Cufflinks respectively (v2.2.1) (15). For maize, mapped reads were assembled with Cufflinks firstly and then merged with Cuffmerge.
Genome_build: Arabidopsis TAIR10; Rice TIGR release 7; Maize AGPv2
Supplementary_files_format_and_content: GTF files including assembled transcripts, FPKM
|
| |
|
| Submission date |
Jan 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Dong Wang |
| E-mail(s) |
dongwang@ncu.edu.cn
|
| Phone |
(86) 15921240757
|
| Organization name |
Nanchang University
|
| Street address |
Hong Gu Tan New Road, No. 999
|
| City |
Nanchang |
| State/province |
JiangXi |
| ZIP/Postal code |
330031 |
| Country |
China |
| |
|
| Platform ID |
GPL18525 |
| Series (2) |
| GSE76798 |
Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in Plants (I) |
| GSE92444 |
Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in Plants |
|
| Relations |
| BioSample |
SAMN04403348 |
| SRA |
SRX1528702 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2038042_Rice_transcripts.gtf.gz |
4.2 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
