|
| Status |
Public on Jun 13, 2024 |
| Title |
DJ_DS_IP_rep1_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
4-leaf seedling
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
treatment: Drought
antibody: anti-ONAC023 polyclonal antibody
|
| Treatment protocol |
Drought treatment was carried out by stopping water supply for 7 days until the relative soild water content was below 10%. Heat treatment was performed by placing the seedlings in a growth chamber with the air temperature of 45˚C and relative humidity of 70% for 6 hours.
|
| Growth protocol |
The onac023 mutant and DJ seeds were sprouted on half-strength MS medium in the dark for 2-3 days at 28°C, and then 4-5 days in the greenhouse. The seedlings were then moved to pots with sand/paddy (1:3) soil under natural conditions at Wuhan, China.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The total RNAs were extracted from the seedlings using TRIzol reagent (Invitrogen™) according to the manufacturer’s instructions. The ChIP assay was performed according to Chris Bowler (Bowler et al., 2004) with some modifications. Briefly, 3 g seedling tissue were cross-linked in 1% formaldehyde by vacuum for 30 minutes. The chromatin was extracted on ice as described by Bowler method and sheared to 200-500 bp fragments by sonication. Subsequently, the DNA fragments were immunoprecipitated by homemade anti-ONAC023 polyclonal antibody. The ChIP DNA was eluted, purified, and dissolved in ddH2O.
RNA-seq and ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
mutCK_D.pooled.IP_vs_input.bw
|
| Data processing |
Sequencing reads were mapped to rice reference genome (MSU7) using Hisat2 (for RNA-seq) and Bowtie2 (for ChIP-seq)
RNA-seq transcripts were assembled and count by StringTie and the differential expression was determined by R package DESeq2
ChIP-seq peaks and the signal tracks were generated by MACS2.
Genome_build: MSU7
Supplementary_files_format_and_content: The tab-delimited text file (count.txt) includes read counts for each RNA-seq sample. The bigWig files (.bw) record ChIP-Seq tag densities.
|
| |
|
| Submission date |
Sep 02, 2021 |
| Last update date |
Jun 13, 2024 |
| Contact name |
Yu Chang |
| E-mail(s) |
yuchang@mail.hzau.edu.cn
|
| Organization name |
Huazhong Agricultural University
|
| Department |
National Key Laboratory of Crop Genetic Improvement
|
| Street address |
No.1, Shizishan Street, Hongshan District
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL23876 |
| Series (1) |
| GSE183241 |
Stress-induced nuclear translocation of transcription factor ONAC023 improves drought and heat tolerance through integrated regulation of multiple processes in rice |
|
| Relations |
| BioSample |
SAMN21195198 |
| SRA |
SRX11993661 |
