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| Status |
Public on Dec 02, 2020 |
| Title |
input_H3K9me2_ChIP-Seq_S.bicolor_60d |
| Sample type |
SRA |
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| Source name |
tillering stage plant
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| Organism |
Sorghum bicolor |
| Characteristics |
tissue: aerial tissue
developmental stage: tillering stage 60d after germination
antibody: no antibody
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| Growth protocol |
green-house plant
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sixty-day fresh above-ground tissues were collected at the tillering stage for O. sativa vg. japonica, O. glaberrima, O. punctata, O. brachyantha, L. perrieri, and S. bicolor. Two-week fresh above-ground tissues at the seedling stage were also collected for O. sativa and O. brachyantha. ChIP experiments were performed as described in Gendrel et al. 2005 with minor modification. Briefly, 4g (for seedling stage) or 8g (for tillering stage) tissue were fine grounded in liquid nitrogen, followed by 3% formaldehyde fixation step. Nucleus were extracted and chromatin was sonicated into 300-500bp fragments in Bioruptor (Diagenode). Since each antibody has its own concentration and binding efficiency, we tested the optimal antibody volume for each antibodies. Typically we use 20ul antibody (1ug/ul) in a 350ul-400ul hybrid solution.
The final DNA precipitation was used for library construction with the NEB Next N6240 kit (New England BioLabs) and decoded by Hiseq 2000 (Ilumina) with pair end 90bp strategy.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
input H3K9me2 ChIP-Seq S.bicolor 60d
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| Data processing |
Typically 16-25 million read pairs for each library were obtained after removal of adaptor and low quality reads by flexbar2.5.
Clean reads were then mapped to genomes by Bowtie with default parameters (-v 0 –m 1). For repressive marks (H3K9me2 and H3K27me), we simply let Bowtie to randomly choose multi-hit positions when reads align to repeat-rich regions (-v 0 –M1 --best).
Since a single nucleosome often occupies about 147bp DNA, we linked mapped read pairs into single end reads for all ChIP libraries.
The resulting bed file was then used to call signal enrichment peaks by MACS2 and at the same time a genome wide signal density file was generated by genomeCoverageBed. The final peaks and density results were used for downstream qualitative and quantitative analysis.
We developed a pipeline to simultaneously visualize the comparative genomic features and the chromatin state.
Genome_build: We downloaded and used the rice genome version 6.1 from the MSU official ftp. Four IOMAP (International Oryza Map Alignment Project) genomes, Oryza glaberrima, Oryza punctata, Oryza brachyantha RS2, Leersia perrieri and the sorgJGI2.0 were applied for bowtie mapping.
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| Submission date |
Feb 12, 2019 |
| Last update date |
Dec 02, 2020 |
| Contact name |
Lei Li |
| E-mail(s) |
lil@ioz.ac.cn
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| Organization name |
INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES
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| Street address |
1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platform ID |
GPL20818 |
| Series (2) |
| GSE126436 |
Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary [ChIP-Seq] |
| GSE126444 |
Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary |
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| Relations |
| BioSample |
SAMN10919770 |
| SRA |
SRX5367550 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not provided for this record |
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