|
| Status |
Public on Jan 21, 2018 |
| Title |
oxJ5 ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
rice shoot apex
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
tissue: 2-3 mm shoot apex from 5-day-old shoot
genotype: JMJ705 overexpression in the wildtype background
chip antibody: anti-FLAG (Sigma, F1804)
|
| Growth protocol |
Seeds with indicated genotypes were surface-sterilized and germinated in media containing 0.3% phytagel supplemented with 2% (w/v) sucrose at 28 °C (in light) and 24 °C (in dark) with a 14 h light/10 h dark cycle for 5 days, then the shoot apex were taken with a scalpel under a dissecting microscope.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Shoot apex were cross-linked in 1% formaldehyde under vacuum. Chromatin was extracted and fragmented to 200 to 500 bp by sonication, and ChIP was performed using the anti-FLAG antibody.
Libraries were constructed following the Illumina TruSeq ChIP Sample Prep Set A protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Sequence reads from all libraries were filtered by Trimmomatic (version 0.32)
Clean reads were mapped to the MSU 7.0 rice genome using Bowtie 2 (version 2.1.0)
Samtools (version 0.1.17) was used to remove potential PCR duplicates
MACS software (39) was used to call peaks with the default parameters
Genome_build: MSU 7.0
Supplementary_files_format_and_content: wig files and text file with called peaks.
|
| |
|
| Submission date |
Dec 19, 2017 |
| Last update date |
Jan 24, 2018 |
| Contact name |
Saifeng Cheng |
| E-mail(s) |
chengsaifeng@yeah.net
|
| Phone |
+02787281800
|
| Organization name |
Huazhong Agricultural University
|
| Department |
National Key Laboratory of Crop Genetic Improvement
|
| Street address |
No.1,Shizishan Street
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL23876 |
| Series (1) |
| GSE104306 |
WOX11 recruits a histone H3K27me3 demethylase to promote gene expression during shoot development in rice |
|
| Relations |
| BioSample |
SAMN08203777 |
| SRA |
SRX3483228 |
