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| Status |
Public on Apr 10, 2024 |
| Title |
YFP_YFP_rep4, ChIP-seq |
| Sample type |
SRA |
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| Source name |
14-day-old seedlings
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| Organism |
Oryza sativa Japonica Group |
| Characteristics |
tissue: 14-day-old seedlings
cultivar: Nipponbare
genotype: pUbi::YFP
treatment: no treatment
antibody: YFP
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| Growth protocol |
Rice were grown in artificial growth chambers under an SD photoperiod for 14 days.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Rice 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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| Description |
Oryza sativa Nipponbare
YFP_YFP_rep4
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| Data processing |
Raw reads were trimmed to remove the adapters and take out the reads with low sequencing quality score using Cutadapt.
The reads with high quality score were aligned to the rice reference genome (MSU7) using Bowtie2.
Reads mapped to the nuclear genome were preserved and SAMtools was used to obtain high quality alignments.
After deduplication, SICER was used to call peaks by comparing the IP and the input.
Reads were normalized as reads per kilobase per million mapped reads (RPKM) in windows of 10 bp using the bamCoverage tool in deepTools. To obtain the enrichment signal around the gene body, TSS and TTS, computeMatrix tool in deepTools was employed.
Assembly: MSU7
Supplementary files format and content: bigWig
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| Submission date |
Apr 05, 2024 |
| Last update date |
Apr 10, 2024 |
| Contact name |
Wenhao Xie |
| E-mail(s) |
20210700089@fudan.edu.cn
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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 |
GPL27860 |
| Series (2) |
| GSE225484 |
ChIP-seq for OsINO80 location using YFP antibody, and ChIP-seq for WT and osino80 using H3, H2A, H2A.Z, H2Aub, H3K9me2, H3K4me2, H3K4me3, H3K27me3, and H3K36me3 antibodies |
| GSE263341 |
ChIP-seq, RNA-seq and BS-seq for WT and osino80 |
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| Relations |
| BioSample |
SAMN40786188 |
| SRA |
SRX24173432 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8189889_YFP_YFP_rep4.bigwig |
108.7 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
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