|
| Status |
Public on Dec 06, 2020 |
| Title |
pie1-6_input |
| Sample type |
SRA |
| |
|
| Source name |
Seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: pie1-6
antibody: none
|
| Growth protocol |
Plants were grown at 22°C in a growth chamber with 16 h of light and 8 h of darkness on 1/2 MS medium with 0.8% glucose and were harvested at 14-days old.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed according to a previously published protocol (Wierzbicki et al., 2008).
ChIP samples were sent to the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) for library construction and Illumina sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Low-quality sequences (q < 20) and adapters were trimmed using trimmomatic.
The paired-end reads were mapped to the TAIR10 genome of Arabidopsis thaliana with BWA(0.7-13) with defauilg parameter
To remove potential PCR duplicates, rmdup from SAMtools (Li et al., 2009) was used
Regions of H2A.Z enrichment were defined by computing the log2 ratios of the output of H2A.Z to input genomic DNA
Genome_build: TAIR10
Supplementary_files_format_and_content: tdf
|
| |
|
| Submission date |
Dec 06, 2017 |
| Last update date |
Dec 06, 2020 |
| Contact name |
Huang Huan |
| E-mail(s) |
ahuanghuan@163.com
|
| Organization name |
Chinese Academy of Sciences
|
| Department |
Shanghai Center for Plant Stress Biology
|
| Street address |
No. 3888 Chenhua Road
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL17639 |
| Series (2) |
| GSE107750 |
H2A.Z ChIP-seq of WT, ros1-14, idm1-9, arp6-4 and pie1-6 |
| GSE107752 |
35S-SUC2 WT and antisilencing mutants |
|
| Relations |
| BioSample |
SAMN08136768 |
| SRA |
SRX3447380 |
