 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 16, 2020 |
| Title |
20140606.B-16DAF_MM17_EN |
| Sample type |
SRA |
| |
|
| Source name |
developing seeds
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
cultivar: Nipponbare
tissue: seeds
tissue subregion: Endosperm
day: 16DAF
|
| Treatment protocol |
Rice grains were collected at 04, 08 and 16 days after flowering (DAF), de-husked and immediately frozen by placing the collection tubes in liquid nitrogen. Five sub-regions of the rice grains, including CC, NE, OVT, EN and AL were dissected for further analysis (see below). The time points were selected based on the reported differentiation of the main cell types (Krishnan and Dayanandan 2003). NE is differentiated into a single layer cell at around 4 DAF, while the enlarged cells and thickenings of NE are noticed at 8 DAF (Krishnan and Dayanandan 2003). CC are visible as greenish cell layer from 4 DAF to 16 DAF. OVT locates in the ventral side of the endosperm, in conjunction with NE (Krishnan and Dayanandan 2003). EN cells are gradually developing and enlarging through 4 to 16 DAF, and the outer layer of EN cells differentiate into AL at about 16 DAF.
|
| Growth protocol |
Rice plants (Oryza sativa cv. Nipponbare) were grown in hydroponic solutions at 28°C. Solutions for the hydroponic system were prepared as previously described (Wang et al. 2013).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA extraction was done with the Qiagen RNeasy Micro Kit following manufacturer’s instruction manual. All RNA samples were adjusted to a concentration of 100 pg/µl prior to pre-amplification. Pre-amplification for the Illumina sequencing was done using the Clonetech SMARTer Ultra Low kit following the user’s manual with small modifications. In brief, the RNA samples were subjected to first strand cDNA synthesis, followed by 15 cycles of Long Distance (LD) PCR. The PCR amplified cDNA was subsequently purified by immobilizaiton on AMPure XP beads for 15 min at RT, resuspended in 15 µl nuclease-free water and stored at -20°C for further experiments and library preparation.
The TruSeq SR Cluster Kit v4-cBot-HS (Illumina, Inc, California, USA) was used for cluster generation using 8 pM of pooled normalized libraries on the cBOT. Sequencing were performed on the Illumina HiSeq 2500 single end 126 bp using the TruSeq SBS Kit v4-HS (Illumina, Inc, California, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
qc-pass
keep
|
| Data processing |
STAR for genome mapping
Threshold for data analysis were chosen to be p<0.001 and RNA-seq reads higher than 10. For a pair-wise comparison, gene expression level change higher than 2-fold and p-value<0.05 were chosen.
Differential expression was assessed with the Bioconductor packages edgeR
Genes were considered as differentially expressed if the p-value was below 0.01 and the expression fold-change was greater than 2
Genome_build: Rice: IRGSP1.0
Supplementary_files_format_and_content: raw counts
|
| |
|
| Submission date |
Jul 07, 2020 |
| Last update date |
Sep 16, 2020 |
| Contact name |
Weihong Qi |
| E-mail(s) |
weihong.qi@fgcz.ethz.ch
|
| Organization name |
ETHZ
|
| Department |
FGCZ
|
| Street address |
Winterthurerstr. 190
|
| City |
Zurich |
| ZIP/Postal code |
8075 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL18525 |
| Series (1) |
| GSE153954 |
RNA-seq analysis of different sub-regions of developing grains in rice |
|
| Relations |
| BioSample |
SAMN15464862 |
| SRA |
SRX8680715 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
