 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 31, 2021 |
| Title |
B409_root_H3K4me3_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
B409_root_H3K4me3
|
| Organism |
Brassica napus |
| Characteristics |
cultivar: B409
developmental stage: one-week roots after planting
tissue: root
chip antibody: H3K4me3
|
| Treatment protocol |
Tissues were cross-linked with 1% formaldehyde for 10 min and quenched with 0.2 M glycine at room temperature.
|
| Growth protocol |
Germinating seeds were obtained by placed on moist paper for 7 d at 22 °C. For roots and young leaves, the germinated seeds were grown in a phytotron with the day/night cycle set at 16 h/8 h and a temperature of 22 °C/18 °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 described. 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. flower bud buds and siliques were harvested.
|
| 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).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Raw reads were filtered for adapter and low quality reads by Trimmomatic
Clean reads mapped to the reference genome with bwa mem
The reads with mapping quality lower 30 and duplication were filtered by samtools
MACS2 were used to call the peak
Genome_build: Download the genome from www.genoscope.cns.fr/brassicanapus
Supplementary_files_format_and_content: bogWig file by deepTools bamCoverage
|
| |
|
| Submission date |
Jan 08, 2020 |
| Last update date |
Jan 31, 2021 |
| Contact name |
Guan Peng Peng |
| E-mail(s) |
[email protected]
|
| Organization name |
Huazhong Agricultural University
|
| Department |
college of informatics
|
| Street address |
shizishan street
|
| City |
WuHan |
| State/province |
HuBei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL26378 |
| Series (2) |
| GSE143283 |
Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. [ChIP-seq] |
| GSE143287 |
Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. |
|
| Relations |
| BioSample |
SAMN13761772 |
| SRA |
SRX7520616 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4256156_B409_root_H3k4me3_rep1.bw |
32.6 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
