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| Status |
Public on Apr 25, 2020 |
| Title |
W306_young_leaf_H3K4me3_rep1 |
| Sample type |
SRA |
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| Source name |
W306
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| Organism |
Oryza sativa |
| Characteristics |
tissue: young leaf
development stage: young leaves from two-week old seedlings
cultivar: BASMATI 385
chip antibody: H3K4me3
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| Treatment protocol |
Tissues were cross-linked with 1% formaldehyde for 10–15 min and quenched with 0.2 M glycine at room temperature.
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| Growth protocol |
Germinating seeds were obtained by soaking dry seeds in water for 72 h at 37 °C. For roots and young leaves, the germinated seeds were grown in a phytotron with the day/night cycle set at 14 h/10 h and a temperature of 32 °C/28 °C. Roots were obtained 7 d after planting on moist filter paper, and young leaves were obtained from 2-week-old plants cultured hydroponically as described34. Approximately 20-d-old seedlings were transplanted to the field and managed under normal agricultural conditions on the experimental farm of Huazhong Agricultural University, Wuhan, China. Mature leaves at the floral induction phase and young panicles were harvested.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-DNA was extracted with phenol:chloroform:isoamyl alcohol (Sigma–Aldrich, P3803), precipitated with ethanol, and resuspended in TE buffer. ChIP DNA libraries were prepared using an NEBNext® Ultra™ II DNA library prep kit for Illumina® (New England BioLabs, E7645). Briefly, ChIP DNA was end-repaired, ligated with an adaptor, and followed by 6–10 cycles of PCR amplification, per the manufacturer’s guidelines. Next, library fragments of 250–650 bp were selected using AMPure XP beads (Beckman, A63881). Finally, the DNA fragments were sequenced using an Illumina HiSeq X Ten system (paired-end 150-bp reads)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Trimmomatic fitered the raw reads
ChIP-seq reads were aligned to the MSU.7.0/MH63 genome assembly using bwa mem
Data were filtered using the SAMTOOLS MAPQ30 and filter the duplication reads
peaks were called using MACS.2.2.1 with narrow(H3K4me3,H3K27ac,PII)/broad(H3K27me3,H3K4me1,H3K9me2) parameters
Genome_build: MSU.7.0,MH63
Supplementary_files_format_and_content: bigWig by deepTools bamCoverage
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| Submission date |
Dec 20, 2019 |
| Last update date |
Apr 27, 2020 |
| Contact name |
Liang Xie |
| E-mail(s) |
lxie@webmail.hzau.edu.cn
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| Phone |
+8615827364128
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| Organization name |
Huazhong Agricultural University
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| Street address |
No.1,Shizishan Street
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| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
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| Platform ID |
GPL24468 |
| Series (2) |
| GSE142462 |
Integrative analysis of reference epigenomes in rice [ChIP-seq] |
| GSE142570 |
Integrative analysis of reference epigenomes in rice |
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| Relations |
| BioSample |
SAMN13662610 |
| SRA |
SRX7426545 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4228115_W306_young_leaf_H3K4me3_rep1.bw |
18.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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