|
| Status |
Public on Dec 18, 2016 |
| Title |
crWT-H3K27me3 |
| Sample type |
SRA |
| |
|
| Source name |
culture-regenerated WT seedling leaves
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
tissue: 12 day after germination seedling leaves
genotype/variation: culture-regenerated Dongjin
antibody: H3K27me3
|
| Growth protocol |
Rice (Oryza sativa spp. japonica) plants used in this study for ChIP-Seq and BS-Seq analysis were from the ‘DongJin’ (DJ) background, including wild type (WT), callus culture- regenerated wild type (crWT), SDG711 over-expression (line 2, 4, 5 combined) (711OX) and RNAi lines (line3, 7, 9 combined) (711RNAi) as described previously in Liu et al., 2014. Seedling leaves from all genotypes were grown in one-half-strength Murashige and Skoog medium under a 16-h-light/8-h-dark cycle at 30°C for 12 DAG (day after germination)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Leaves were harvested and fixed in formaldehyde for chromatin cross-linking, About 2g of seedling leaves were crosslinked in 1% formaldehyde under vacuum. Chromatin was extracted and fragmented to 200-750 bp by sonication, and ChIP was performed using the following antibodies: H3K27me3 (a2363, ABclonal) and Anti-SDG711. Seedling leaves were harvested and frozen in liquid nitrogen for DNA extraction using the DNeasy plant mini kit (Qiagen).
DNA from ChIP was used to construct sequencing libraries following the protocol provided by Illumina TruSeq® ChIP Sample Prep Set A. Genomic DNA (5g) was used to generate BS-Seq libraries as described in Feng et al., 2011.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
For ChIP-Seq, trimmomatic (version 0.32) was used to filter out low quality reads and crop all reads to a uniform length (45bp). Clean reads were mapped to the rice genome (RGAP version 7) by default allowing up to 2 mismatch using Bowtie2 (version 2.1.0). Peaks were called out by MACS software after removing potential duplicates of PCR by Samtools (version 0.1.17), with the default P value equal 1e-5. P value 1e-9 was used for calling out peaks of anti-SDG711, because of the largest percentage overlap of H3K27me3 marked genes and SDG711 bound genes. Gbrowse 2.0 was used to view the ChIP-Seq data. For Bisulfite-Seq, trimmomatic (version 0.32) was used to filter out low quality reads and BatMeth was used to align clean tags to the rice genome (RGAP version 7) by default parameters followed by removing PCR-amplified redundancy. Methylation levels were calculated by #C/(#C+#T).
Wig file generated by MACS software for Gbrowse view
CT.C3 files generated by BathMeth software containing all detected cytosine methylation information
Genome_build: rice genome (RGAP version 7)
|
| |
|
| Submission date |
Aug 03, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
shaoli zhou |
| E-mail(s) |
zhoushaoli@mail.hzau.edu.cn
|
| Organization name |
Huazhong Agricultural University
|
| Department |
National Key Laboratory of Crop Genetic Improvement
|
| Street address |
shizishan street
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL13834 |
| Series (1) |
| GSE71640 |
Cooperation between H3K27me3 and non-CG methylation in epigenetic regulation of genes in rice. |
|
| Relations |
| BioSample |
SAMN03955521 |
| SRA |
SRX1131812 |
