|
| Status |
Public on Nov 25, 2015 |
| Title |
F1 single-end |
| Sample type |
SRA |
| |
|
| Source name |
flower buds
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
tissue: flower buds
|
| Growth protocol |
Seeds from the cultivated rice subspecies Oryza sativa L. ssp. Japonica were grown in a greenhouse in Singapore . Flower buds were collected before flowering and flowers were collected at the flowering day. Flag leaves and roots were collected at the before- and after-flowering stage. The before-flowering sample was defined as a mixture of different stages in a period from panicle initiation to 1 day before flowering. The after-flowering sample was defined as a mixture of different stages after the flowering day. Milk grains and mature seeds were also collected.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using the Qiagen RNeasy Plant Mini kit. Total RNA was treated with Turbo DNase I (Life Technologies AM2238) according to product specification. DNase I treated RNA was then applied again to an RNeasy spin column with 0.5 volumes of ethanol, washed and eluted according to the manufacturer’s instructions.
Sequencing libraries were prepared using the Illumina Stranded mRNA sample Prep kit, set A (RS-122-2101, Illumina Inc.) according to the manufacturer's instructions. The quality and size of cDNA libraries for sequencing were checked using the Agilent 2200 TapeStation system (Agilent Inc.). The libraries were sequenced for 100 cycles on HiseqTM 2500 (Illumina Inc.)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
directional single-end RNA-seq
|
| Data processing |
After quality control analysis of raw sequencing datasets, RNA-seq sequences were aligned to the rice genome using TopHat. Then the mapped sequences of each sample were assembled by Cufflinks. Fragments per kilobase of exon per million fragments mapped of assembled transcripts (FPKM) were calculated and normalized using Cuffcompare and Cuffdiff with global normalization parameters.
Genome_build: Oryza sativa L. ssp. Japonica, MSU Rice Genome Annotation Project Release 7
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for all Samples
|
| |
|
| Submission date |
Apr 02, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Huan Wang |
| E-mail(s) |
hwang01@rockefeller.edu
|
| Organization name |
The Rockefeller University
|
| Lab |
Chua Nam-Hai
|
| Street address |
1230 York Avenue
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL18525 |
| Series (1) |
| GSE56463 |
Transcriptome profiling of various organs at different developmental stages in rice (single-end) |
|
| Relations |
| BioSample |
SAMN02716064 |
| SRA |
SRX507920 |
