|
| Status |
Public on Dec 14, 2018 |
| Title |
H3K27me3_ABA_0uM_4d_(Ctrl_for_100uM_4d) |
| Sample type |
SRA |
| |
|
| Source name |
10-d old seedlings treated with 0 μM ABA for 4 days
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Ws
tissue: the aerial parts of seedlings
age: 10-day-old
treatment: control
dose: 0 μM
time: 4 days
chip antibody: H3K27me3 (Upstate, USA, Cat. 07–449)
|
| Treatment protocol |
10-d old seedlings were transferred onto 1/2 Murashige and Skoog (MS) medium containing 50 μM ABA or 100 μM ABA for certain time.
|
| Growth protocol |
Arabidopsis thaliana seedlings were grown on 1/2 Murashige and Skoog (MS) medium without sucrose (2% agar, PH 5.8) under LDs conditions
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin or RNA was extracted from the treated seedlings, using standard protocols.
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China) using Illumina HiSeq 3000 following the manufacturer’s instructions (Illumina).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The sequencing reads were cleaned, including removing bases with low quality score (<20) and irregular GC content based on FastQC, cutting sequencing adaptor followed by filtering short reads.
The cleaned reads were mapped to Arabidopsis thaliana genome (TAIR10) using BOWTIE2.0 for DNA sequencing and TOPHATv2.0.8 for RNA sequencing, both with default settings.
The duplicated reads were removed, and only alignments with MAPQ score > 20 were kept for further analysis.
For ChIP-seq, SICER_V1.1 was used to identify read enriched regions (peaks) and MAnorm was applied to characterize the change of genome-wide H3K27me3 profile. For RNA-seq, HTSeq-count was used to preprocess the RNA-seq alignments and deseq was used to detect the differentially expressed genes.
Genome_build: TAIR10
Supplementary_files_format_and_content: In ChIP-seq, peak files was provided; In RNA-seq, read counts for genes (TAIR10) was provided.
|
| |
|
| Submission date |
Jun 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
yijing zhang |
| E-mail(s) |
zhangyijing@fudan.edu.cn
|
| Organization name |
Fudan University
|
| Department |
Biochemistry
|
| Lab |
Functional Epigenomics Group
|
| Street address |
2005 Songhu Road
|
| City |
shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
| |
|
| Platform ID |
GPL17639 |
| Series (1) |
| GSE98301 |
H3K27 tri-methyltransferases CLF and SWN redundantly buffer ABA-induced senescence |
|
| Relations |
| BioSample |
SAMN07221056 |
| SRA |
SRX2902554 |
