 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 18, 2023 |
| Title |
HZ62_leaf_H3K4me3_BHCS-054 |
| Sample type |
SRA |
| |
|
| Source name |
seedling
|
| Organism |
Brassica napus |
| Characteristics |
tissue: seedling
cell type: 2 weeks
chip antibody: H3K4me3 antibody (Abclonal, A2357)
genotype: WT
treatment: a day/night cycle of 16h/8h and a temperature of 22/18℃
|
| Treatment protocol |
a day/night cycle of 16h/8h and a temperature of 22/18℃
|
| Growth protocol |
a day/night cycle of 16h/8h and a temperature of 22/18℃
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Materials of HZ62 were collected and cross-linked using 1% formaldehyde (Sigma, F8775) and quenched with 0.2M glycine (Sigma, G7126) at room temperature. About 1g of samples were used for each library. After grinding into fine powder with liquid nitrogen, cell lysis by 1% SDS (Sigma, AM9822) at 4°C.
The chromatin was fragment by sonication using a Bioruptor (Diagenode) into 200-600 bp. ChIP was performed using H3K4me3 and H3K27me3 antibody (Abclonal, A2357, A2363). Then, the protein-DNA complexes were reversed cross-linking using proteinase K (Invitrogen, AM2546) at 55°C. ChIP-DNA was extracted using phenol:chloroform:isoamyl alcohol (Sigma, P3803). ChIP-DNA libraries were constructed by using NEBNext Ultra II DNA library prep kit for Illumina (New England BioLabs, E7645) according to the manufacturer’s guidelines.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Fastp with default parameters was used to trimmed adaptors and low-quality reads in raw reads
Clean reads were mapped to the Brassica napus ZS11 genome by BWA-MEM with default parameters
SAMtools was used to remove the low mapping quality reads with parameters “-q 30 -f 2”，GATK MarkDuplicates was used to rm duplicated reads
ChIP-seq narrow peaks were called by MACS2, with parameters “-f BAMPE -B -g 921913538 -q 1e-5”
Assembly: Brassica napus ZS11 （Chen et al., 2021）
Supplementary files format and content: tab-delimited text files , peak file
|
| |
|
| Submission date |
Nov 22, 2022 |
| Last update date |
Jul 18, 2023 |
| Contact name |
Wenying Zhong |
| E-mail(s) |
[email protected]
|
| Organization name |
Huazhong Agricultural University
|
| Street address |
Lion Rock Street
|
| City |
Wuhan |
| ZIP/Postal code |
430072 |
| Country |
China |
| |
|
| Platform ID |
GPL26378 |
| Series (2) |
| GSE218583 |
Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrids [ChIP-seq] |
| GSE218592 |
Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrids |
|
| Relations |
| BioSample |
SAMN31840793 |
| SRA |
SRX18352948 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6752846_BHCS-054_HZ62_leaf_H3K4me3_peaks.xls.gz |
1.5 Mb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
