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| Status |
Public on Dec 18, 2016 |
| Title |
osdrm2-H3K27me3 |
| Sample type |
SRA |
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| Source name |
DongJin-seedling
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| Organism |
Oryza sativa Japonica Group |
| Characteristics |
tissue: 12 day seedling
genotype/variation: DongJin
antibody: H3K27me3
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| 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 callus culture-regenerated wild type (WT), SDG711 over-expression (line 2, 4, 5 combined) (711OX) and osdmr2 mutant plants as described previously (Liu et al., 2014). Seedling leaves of callus culture-regenerated wild type (WT), SDG711 over-expression lines or osdrm2 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) were harvested and frozen in liquid nitrogen for DNA, RNA or chromatin extraction.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
About 2 g 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 (Liu et al., 2014). The precipitated samples were analyzed by high throughput sequencing. For genomic bisulfite sequencing, the total genomic DNA of callus culture- regenerated wild type (WT), SDG711 over-expression lines were prepared using the DNeasy plant mini kit (Qiagen). Genomic DNA (5 g) was used to generate BS-Seq libraries as previously described (Feng et al., 2011). Sequencing was performed at the Novogene Bioinformatics Technology Co. Ltd, China.
DNA from ChIP was used to construct sequencing libraries following the protocol provided by Illumina TruSeq® ChIP Sample Prep Set A described in http://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseqchip/truseq-chip-sample-prep-guide-15023092-b.pdf.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
Chromatin IP against H3K27me3
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| Data processing |
Raw reads was generated by HiSeq 3000. Trimmomatic (version 0.32) was used to filter out low quality reads and crop all reads to a uniform length (45bp) (Bolger et al., 2014). Clean reads were mapped to the rice genome (RGAP version 7) by default allowing up to 2 mismatch using Bowtie2 (version 2.1.0) (Trapnell et al., 2012). Samtools (version 0.1.17) is used to remove potential PCR duplication. Peaks of H3K27me3 were called out by MACS software with the default P value (1e-5), and peaks of anti-SDG711 using P value=1e-9 because of the largest percentage overlap of H3K27me3 marked genes and SDG711 bound genes, and the output wig files were used for viewing the data by Gbrowse 2.0. For BS-seq anaylais, Trimmomatic (version 0.32) was used to filter out low quality reads and BatMeth (Lim et al., 2012) 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).
Genome_build: RGAP version 7.0
Supplementary_files_format_and_content: tag numbers in each gene body
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| Submission date |
Aug 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
shaoli zhou |
| E-mail(s) |
zhoushaoli@mail.hzau.edu.cn
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| Organization name |
Huazhong Agricultural University
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| Department |
National Key Laboratory of Crop Genetic Improvement
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| Street address |
shizishan street
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| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
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| Platform ID |
GPL22250 |
| Series (1) |
| GSE71640 |
Cooperation between H3K27me3 and non-CG methylation in epigenetic regulation of genes in rice. |
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| Relations |
| BioSample |
SAMN05513990 |
| SRA |
SRX2004186 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2262915_osdrm2_K27_gene_tags.txt.gz |
369.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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