|
| Status |
Public on Mar 19, 2019 |
| Title |
ZH11-D2-Input |
| Sample type |
SRA |
| |
|
| Source name |
4-leaf-stage seedling
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
tissue: 4-leaf-stage seedling
genotype/variation: ZH11-WT
treatment: Drought
chip antibody: None
sample type: ChIP-seq Input
|
| Treatment protocol |
After germination, the 1-week-old seedlings that were of uniform growth status were moved to pots filled with sandy soil. The transgenic and WT plants were grown in a half-and-half manner (10 plants each) in the pots. At the 4-leaf stage, the seedlings were subjected to drought stress treatment by stopping water for 10-15 days until the leaves were curled and turned yellow.
|
| Growth protocol |
The transgenic and ZH11-WT 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 leaves of SNAC1-OE lines and ZH11-WT plants using TRIzol reagent (InvitrogenTM) according to the manufacturer’s instructions. The ChIP assay was performed according to Chris Bowler (Bowler et al., 2004) with some modifications. Briefly, 3g shoot tissues from 4-leaf-stage seedlings 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 custom-made anti-SNAC1 polyclonal antibody generated using full-length SNAC1 protein. The combined DNAs were 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 |
processed data file: Peaks_ZH11_D_VS_SNAC1OE_N.txt
processed data file: Peaks_ZH11_N_VS_ZH11_D.txt
|
| Data processing |
Sequencing reads were mapped to rice reference genome using Hisat2 (for RNA-seq) and Bowtie2 (for ChIP-seq).
RNA-seq transcripts were assembled and counted by StringTie and the differential expression was determined by DESeq2.
ChIP-seq peaks were called by MACS2 and peak annotation and differential binding identification were done by ChIPseeker and DiffBind, respectively.
Genome_build: Rice Genome Annotation Project (RGAP) Release 7
Supplementary_files_format_and_content: All_gene_FPKM.txt: Tab-delimited text file includes FPKM values for each RNA-seq sample.
Supplementary_files_format_and_content: Peaks_*.txt: Tab-delimited text files include normalized peak counts and fold changes for ChIP-seq samples.
|
| |
|
| Submission date |
Mar 18, 2019 |
| Last update date |
Mar 20, 2019 |
| 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) |
| GSE128495 |
Genome-wide identification of SNAC1-targeted genes involved in drought response in rice |
|
| Relations |
| BioSample |
SAMN11162441 |
| SRA |
SRX5538673 |
