|
| Status |
Public on Aug 02, 2011 |
| Title |
FHY3_Far-Red |
| Sample type |
SRA |
| |
|
| Source name |
FHY3_Far-Red
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
developmental stage: seedling
age: 4 days
antibody: FLAG (Sigma-Aldrich)
genotype/variation: 35S:3FLAG-FHY3-3HA fhy3-4 transgenic line
|
| Growth protocol |
The homozygous 35S:3FLAG-FHY3-3HA fhy3-4 seedlings grown in D or continuous FR light for 4 d were used for ChIP assays following the procedure described previously
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
5 g of seedlings were first cross-linked with 1% formaldehyde under vacuum, and then the samples were ground to powder in liquid nitrogen. The chromatin complexes were isolated and sonicated and then incubated with monoclonal FLAG antibodies (Sigma-Aldrich). The precipitated DNA was recovered and used to generate Illumina sequencing libraries according to the manufacturerâs instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Sequencing reads from D and FR libraries were mapped to TAIR9 genome release of Arabidopsis thaliana using the MAQ software, allowing for up to two mismatching nucleotides and no gaps. Only uniquely mapped reads were retained for further analyses. The output of the analysis pipeline was converted to browser extensible data (BED) files for viewing the data in the Integrative Genomics Viewer (IGV) genome browser. Numerous peak detection algorithms have been proposed recently for analyzing the ChIP-seq datasets, and they provide more or less similar results. In this study, MACS software with default parameters (bandwidth, 300 bp; mfold, 32; p-value of 1.00e-05) was used to call peaks representing enriched binding sites.
|
| |
|
| Submission date |
Jul 15, 2011 |
| Last update date |
Sep 04, 2019 |
| Contact name |
Bosheng Li |
| E-mail(s) |
libs@sustc.edu.cn
|
| Organization name |
SUSTC (current, may different with previous institution )
|
| Department |
MCDB
|
| Street address |
SUStech Huiyuan #1 406
|
| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
581055 |
| Country |
China |
| |
|
| Platform ID |
GPL9062 |
| Series (2) |
| GSE30711 |
ChIP-Seq data from Arabidopsis thaliana under dark and far-red light |
| GSE30713 |
Genome-wide Binding Site Analysis of FAR-RED ELONGATED HYPOCOTYL 3 Reveals Its Novel Function in Arabidopsis Development |
|
| Relations |
| Reanalyzed by |
GSE136843 |
| SRA |
SRX083215 |
| BioSample |
SAMN00668254 |
