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| Status |
Public on May 08, 2023 |
| Title |
ChIP-seq of holocentric Chionographis japonica to determine the centromere distribution and genome organization |
| Organisms |
Secale cereale; Chionographis japonica |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
To determine the distribution of centromere units in the genome of holocentric Chionographis japonica, we performed CENH3-ChIPseq using the customized species-specific CENH3 antibody. We mixed the chromatins of C. japonica and Secale cereal (inbred line Lo7) to dilute the highly abundant centromeric Chio satellite repeats (16%) in the C. japonica genome before immunoprecipitation. In addition, to determine the large-scale genome organization, we performed ChIPseq by targeting the evolutionarily conserved eu- and heterochromatin-specific histone marks H3K4me2 and H33K9me2
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| Overall design |
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for chromatin repeat CENH3 as well as conserved eu- and heterochromatin-specific histone marks H3K4me2 and H33K9me2. Each CENH3-, H3K4me2-, and H3K9me2-ChIPseq experiments was performed for two biological replicates.
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| Contributor(s) |
Kuo Y, Axel H, Houben A, Ishii T, Câmara AS, Schubert V, Neumann P |
| Citation(s) |
37311740 |
| |
| Submission date |
Mar 28, 2023 |
| Last update date |
Aug 07, 2023 |
| Contact name |
Anne Fiebig |
| E-mail(s) |
fiebig@ipk-gatersleben.de
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| Organization name |
IPK Gatersleben
|
| Department |
BIT
|
| Street address |
Correnstraße 3
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| City |
Seeland OT Gatersleben |
| ZIP/Postal code |
06466 |
| Country |
Germany |
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| Platforms (2) |
| GPL33287 |
Illumina NovaSeq 6000 (Chionographis japonica) |
| GPL33288 |
Illumina NovaSeq 6000 (Chionographis japonica; Secale cereale) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA949641 |
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