|
| Status |
Public on Sep 06, 2023 |
| Title |
WT_Input |
| Sample type |
SRA |
| |
|
| Source name |
seedling
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: seedling
strain: Taibei 309
genotype: WT
antibody: none
|
| Treatment protocol |
2 replicates for RNA-seq and 1 replicate for ChIP-seq
|
| Growth protocol |
13 hours daytime with the temperature of 23 oC, and 11 hours dark with the temperate of 20 oC
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The H3K27me3 ChIP-seq assay was performed using the panda mutant and its wild type cultivar ‘Taibei 309’. The PANDA ChIP-seq assay were performed using the plants expressing pUBI::PANDA-Flag in the japonica rice cultivar ‘Taibei 309’
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the rice7 genome assembly using bowtie2 with default parameter
peaks were called using macs2 with follow settings : --extsize 200 -q 0.001 --nomodel
Genome_build: rice7
Supplementary_files_format_and_content: wig files were generated using deeptools; Scores represent enrichment
|
| |
|
| Submission date |
Sep 09, 2021 |
| Last update date |
Sep 06, 2023 |
| Contact name |
Pengyue Zhang |
| E-mail(s) |
zhangpy195@163.com
|
| Organization name |
NanJing Argriculture University
|
| Street address |
No.1, Weigang Street, Xuanwu District, Nanjing
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210095 |
| Country |
China |
| |
|
| Platform ID |
GPL23013 |
| Series (2) |
| GSE183789 |
PANDA epigenetically regulates the trade-off between panicle number and grain size in rice [ChIP-Seq] |
| GSE183796 |
PANDA epigenetically regulates the trade-off between panicle number and grain size in rice |
|
| Relations |
| BioSample |
SAMN21368589 |
| SRA |
SRX12122721 |
