|
| Status |
Public on Aug 19, 2022 |
| Title |
mature_leaves_met1-3_RNAPII_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
mature leaves met1-3
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: mature leaves
development stage: mature leaves from five-week old
genotype: met1-3
chip antibody: RNAPII
|
| Treatment protocol |
Tissues were cross-linked with 1% formaldehyde for 10 min and quenched with 0.2 M glycine at room temperature.
|
| Growth protocol |
Plants were grown at 22 °C under a 16 h light/8 h dark photo-period, and two- and five-week-old plants were used for all experiments.
|
| 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 |
Trimmomatic fitered the raw reads
ChIP-seq reads were aligned to the TAIR10 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: TAIR10
Supplementary_files_format_and_content: bigWig by deepTools bamCoverage
|
| |
|
| Submission date |
Sep 11, 2021 |
| Last update date |
Aug 19, 2022 |
| Contact name |
Qiangwei Zhou |
| E-mail(s) |
qwzhou@mail.hzau.edu.cn
|
| Organization name |
Huazhong Agricultural university
|
| Street address |
Hongshan district, shizishan #1
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL23157 |
| Series (2) |
| GSE183957 |
DNA Methylation shapes histone modification landscape for transcription regulation in Arabidopsis [ChIP-Seq] |
| GSE183987 |
DNA methylation underpins the epigenomic landscape regulating genome transcription in Arabidopsis |
|
| Relations |
| BioSample |
SAMN21396512 |
| SRA |
SRX12144840 |
