|
| Status |
Public on Sep 14, 2016 |
| Title |
Sample_Os_0h_RNA_Seq |
| Sample type |
SRA |
| |
|
| Source name |
base region（2 mm) of 7 mm rice leaf explants at time 0 DAC on Callus Induced Medium
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
tissue: base region of young leaf
|
| Treatment protocol |
The rice leaf was grown at 0, 2 and 5 days on Callus Induced Medium.
|
| Growth protocol |
Rice was grown at 29ºC with a 12-h light (~ 80000 Lux) and 12-h dark photoperiod in the greenhouse or plant chamber.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction using Trizol protocols.
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China) using Illumina HiSeq 3000 following the manufacturer’s instructions (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
sample 1
|
| Data processing |
The sequencing reads were cleaned, including removing bases with low quality score (<20) and irregular GC content based on FastQC, cutting sequencing adaptor followed by filtering short reads.
The cleaned reads were mapped to Oryza Sativa genome (msu7) using BOWTIE2.2.9 for DNA sequencing and TOPHATv2.0.8 for RNA sequencing, both with default settings.
The duplicated reads were removed, and only alignments with MAPQ score > 20 were kept for further analysis.
HTSeq-count was used to preprocess the RNA-seq alignments and deseq was used to detect the differentially expressed genes.
Genome_build: MSU7
Supplementary_files_format_and_content: read counts for genes(msu7) was provided. The format is tab delimited file format. Each row contains two columns: the first is the feature, and the second is the count of reads which are mapped to the feature.
|
| |
|
| Submission date |
Sep 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Lin XU |
| E-mail(s) |
xulin01@sibs.ac.cn
|
| Phone |
86-21-54924101
|
| Organization name |
Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences
|
| Department |
Chinese Academy of Sciences
|
| Street address |
300 Fenglin Road
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL13834 |
| Series (1) |
| GSE86869 |
RNA-seq analysis of gene transcripts during callus formation from the basal part of young rice leaf explants |
|
| Relations |
| BioSample |
SAMN05768338 |
| SRA |
SRX2162090 |
