|
| Status |
Public on Nov 28, 2015 |
| Title |
H3K27me3 ChIP-seq, seedling |
| Sample type |
SRA |
| |
|
| Source name |
H3K27me3 ChIP-seq, seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
tissue: seedling
developmental stage: 14-day old
molecule: genomic DNA
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Arabidopsis ecotype Col-0 was surface steriled and planted on 1/2 MS medium. The culture condition was: 16 hour with light at 23℃, 70% humity, 8 hours without light at 18℃, 70% humity. 2 weeks old seedlings were harvested. The rest were transferred to soil medium for addtional two weeks and the inflorescence was harvested.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified by using DNeasy Plant Mini Kit (Qiagen,Cat. No. 69104) with its standard protocol. Co-immunoprecipitated DNAs were ligated to adaports and followed by PCR amplification. ChIP-seq: Anti-trimethyl-Histone H3 (Lys27), Cat. # 07-449, Millipore
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Illumina Casava1.7 software was used for basecalling.
Adaptor sequences in the sequencing reads were removed using Cutadapt v1.0 with default parameters.
Trimmed reads were aligned to Arabidopsis genome using Bowtie v0.12.7 with parameters '-m 1 -v 3 --best --strata'.
BCP (version 1.1) was used to call peaks for H3K27me3 modification in no control model.
Target genes/lncRNAs were indentified by at least 200bp/100bp overlapped regoin with the peak regions.
genome build: TAIR10
processed data files format and content: wig files include the H3K27me3 signial intensity for each sample
|
| |
|
| Submission date |
Dec 03, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Yijun Qi |
| E-mail(s) |
qiyijun@biomed.tsinghua.edu.cn
|
| Organization name |
National Institute of Biological Sciences
|
| Lab |
Yijun Qi's lab
|
| Street address |
#7 Science Park Road, Zhongguancun Life Science Park
|
| City |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
| |
|
| Platform ID |
GPL11221 |
| Series (1) |
| GSE42695 |
Genome-wide profiling of long non-coding RNAs in Arabidopsis |
|
| Relations |
| SRA |
SRX208116 |
| BioSample |
SAMN01822148 |
