 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 04, 2018 |
| Title |
CP_ZnF8_control_r3 |
| Sample type |
SRA |
| |
|
| Source name |
Tiller bases
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
experiment objectives: analysis of differentially expressed genes
tissue: Tiller bases
development stage: Tillering stage
genotype: control plants of ZnF8 transgenic lines
phenotype: erect growth
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol according to the instructions.
P-aired-end libraries were constructed using a TruSeq RNA Sample Preparation Kit v2.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw reads were mapped to the reference genome by TopHat using default parameters.
Cuffdiff was used to calculate the FPKM (fragments per kilobase of exon per million mapped reads) of each gene and to identify the differentially-expressed genes (fold change ≥ 2, P < 0.001) between the CP-PROG1, CP-ZnF5, CP-ZnF7, CP-ZnF8 and control plants.
The functional category analysis of the differentially-expressed genes was performed by the AgriGO and KEGG databases.
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0, MSU7
|
| |
|
| Submission date |
Jun 28, 2018 |
| Last update date |
Jul 04, 2018 |
| Contact name |
Ma Xin |
| Organization name |
China Agricultural University
|
| Street address |
2 Yuanmingyuan West Road, Haidian District, Beijing, China, 2 Yuanmingyuan West Road, Haidian District, Beijing, China
|
| City |
Beijing |
| State/province |
--- Select a state --- |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
|
| Platform ID |
GPL18525 |
| Series (1) |
| GSE116423 |
Chromosomal deletions drove parallel domestication of plant architecture in Asian and African rice |
|
| Relations |
| BioSample |
SAMN09516007 |
| SRA |
SRX4321427 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3231398_CP_ZnF8_r3.fpkm.txt.gz |
267.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
