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| Status |
Public on Feb 26, 2024 |
| Title |
Bd21-3_H3_rep1 |
| Sample type |
SRA |
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| Source name |
Bd21-3
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| Organism |
Brachypodium distachyon |
| Characteristics |
cell line: Bd21-3
cell type: leaf
genotype: Bd21-3
chip antibody: anti-H3
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| Growth protocol |
The seedlings grown to the 4th leaf stage under 20h (20h light/4h dark) photoperiods, and the samples were harvested at ZT10.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Seedlings were harvested and fixed with the buffer containing 0.4 M sucrose, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 1% formaldehyde, and 1 mM PMSF.Chromatin was sonicated into DNA fragments around 200~500-bp in size using lysis buffer containing 50 mM HEPES (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM PMSF, 1% SDS, 0.1% Na deoxycholate, 1% Triton X-100 and Protease Inhibitor cocktail.
The ChIP-seq libraries were constructed by following the manufacturer’s instructions of VAHTSTM Universal DNA Library Prep Kit (Vazyme).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Cutadapt was used to trim the raw ChIP-seq reads to obtain high sequencing qualiyt reads.
Bowtie2 was used to map cleaned reads to the genome of Brachypodium distachyon.
Using SAMtools to sort reads and remove duplicate reads.
MACS2 was utilized to find peaks, and MAnorm was used to find different peaks in mutant compared with WT.
Reads were normalized using the bamCoverage tool in deepTools and using heatmap to exhibit by plotHeatmap tool in deepTools.
Assembly: Brachypodium distachyon (genome version is 3.0, download from http://plants.ensembl.org/)
Supplementary files format and content: bigwig
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| Submission date |
Sep 14, 2023 |
| Last update date |
Feb 26, 2024 |
| Contact name |
Wenhao Xie |
| E-mail(s) |
[email protected]
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| Phone |
18005879367
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| Organization name |
Fudan University
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| Department |
School of Life Science
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| Street address |
No. 2005, Songhu Road
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| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
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| Platform ID |
GPL33763 |
| Series (1) |
| GSE243212 |
ChIP-seq to test histone methylation in Bd21-3 and the jmj1-1 mutant. |
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| Relations |
| BioSample |
SAMN37395678 |
| SRA |
SRX21780248 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7780734_Bd21-3_H3_rep1.bigwig |
108.2 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
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