|
| Status |
Public on Aug 11, 2023 |
| Title |
GA-H3K27me3-2 |
| Sample type |
SRA |
| |
|
| Source name |
seedling
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
tissue: seedling
genotype: WT
chip antibody: H3K27me3(Diagenode, C15410195)
treatment: GA
|
| Treatment protocol |
In chemical treatment experiments, 100 uM GA (Sigma, G1025) was supplied to seedlings through the roots for various durations.
|
| Growth protocol |
Seedlings were grown in one-half-strength Murashige and Skoog medium under 14-h light/10-h dark cycles at 28/24 °C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin fragments were incubated with antibody-coated beads overnight, after extensive washing, immunoprecipitated chromatin was de-cross-linked and retrieved for sequencing.
ChIP DNA libraries were prepared using a TruSeq DNA Sample Preparation Kit v2 (Illumina, San Diego, CA, USA)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
TrimGalore (version 0.6.6) was used to trim the adaptors and remove low quality reads from the raw reads.
Clean reads were mapped to the rice genome (MSU7.0) by Bowtie2 (version 2.4.4).
The bigwig files were generated using bamCoverage with the parameters “-bam -binSize 10 –normalize Using RPKM” in deepTools (version 3.5.0).
MACS2 (version 2.2.7.1) was used to call histone modification peaks with the parameters (-g 4.01e8 --broad --broad-cutoff 0.1 -B), and input sample was used as control.
Assembly: MSU version 7.0 rice genome
Supplementary files format and content:bigWig, broadPeak(except for Input sample)
|
| |
|
| Submission date |
Mar 07, 2023 |
| Last update date |
Aug 11, 2023 |
| Contact name |
Qi Li |
| E-mail(s) |
[email protected]
|
| Organization name |
Huazhong Agricultural University
|
| Department |
Hongshan District
|
| Street address |
Lion Rock Street
|
| City |
Wuhan |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL27860 |
| Series (1) |
| GSE226812 |
Chromatin mechanism of DELLA-mediated gene repression and Gibberellin-induced gene activation in rice |
|
| Relations |
| BioSample |
SAMN33611634 |
| SRA |
SRX19582580 |
