|
Status |
Public on Sep 06, 2023 |
Title |
PANDA anti-Flag |
Sample type |
SRA |
|
|
Source name |
seedling
|
Organism |
Oryza sativa |
Characteristics |
tissue: seedling strain: Taibei 309 genotype: WT antibody: anti-Flag (Cell Signaling, #14793)
|
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 |
SAMN21368581 |
SRA |
SRX12122723 |