|
| Status |
Public on Dec 01, 2015 |
| Title |
RICE-H3K23ac |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar: Nipponbare
tissue: leaf
|
| Growth protocol |
Arabidopsis plants were grown on soil at 21 degree under continuous light for 2 weeks. Oryza sativa was grown on MS medium at 28 degree under short day condition (8hrs light and 16hrs dark)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP genomic DNA protocols are followed by Zhong et al., Nat Struct Mol Biol, 2012, 19:870-850
ChIP library was constructed by using the Ovation Ultralow Library Kit (NuGen, Part No. 0330)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Genomic DNA isolated from immnuoprecipitated chromatin using H3K23ac antibody (07-355 Millipore)
|
| Data processing |
ChIPseq reads were filtered for average QC score>30. Reads were mapped with Bowtie2 to the TAIR10/MSU7.0 genome, with default parameters. Reads mapping to identical positions in the genome were collapsed into one read.
Genome_build: TAIR10 for Arabidopsis; MSU7.0 for Rice
Supplementary_files_format_and_content: bigwig file generated by UCSC "bedGraphToBigWig" scipts
|
| |
|
| Submission date |
Jun 01, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Xuehua Zhong |
| Organization name |
Wisconsin Institute for Discovery
|
| Department |
Epigenetics
|
| Street address |
330 N. Orchard St.
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53705 |
| Country |
USA |
| |
|
| Platform ID |
GPL13160 |
| Series (1) |
| GSE69426 |
High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns and functions in Arabidopsis and rice |
|
| Relations |
| BioSample |
SAMN03754115 |
| SRA |
SRX1044779 |
