|
| Status |
Public on Aug 04, 2014 |
| Title |
FHY1-GFP_1_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis thaliana seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: 35S: GFP-FHY1, fhy1-1
developmental stage: 4 day old seedling
antibody: anti-GFP
antibody manufacturer: Clontech
catalog number: 632592
|
| Growth protocol |
To determine whether phyA and FHY1 associate with the same genes upon FR irradiation, four-day old etiolated 35S: GFP-FHY1 fhy1-1 transgenic seedlings were exposed to 3hr FR. The treated plants were utilized for ChIP-seq analysis with an anti-FHY1 antibody that exhibits high specificity in the detection of FR-induced FHY1-association events. FHY1 associated-DNA samples from three distinct biological replicates and an input DNA sample (as a negative control) were subjected to high-throughput Solexa (Illumina) sequencing.
|
| 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 antibodies. The precipitated DNA was recovered and used to generate Illumina sequencing libraries according to the manufacturer’s instructions.
standard Illumina ChIP-seq protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Bowtie for alignment, v1, default parameter
MACS for peak-calling, v1.4.4, default parameter
Genome_build: TAIR10
Supplementary_files_format_and_content: BED, peaks called by MACS, Table head: chr start end length summit tags -10*LOG10(pvalue) fold_enrichment FDR(%); FHY1_chipseq_.bed contains the overlapping peaks in each sample.
|
| |
|
| Submission date |
May 29, 2014 |
| Last update date |
May 15, 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 |
GPL13222 |
| Series (2) |
| GSE58083 |
The photoreceptor chaperone FHY1 has an independent role in gene modulation and plant development under far-red light [ChIP-seq] |
| GSE58084 |
The photoreceptor chaperone FHY1 has an independent role in gene modulation and plant development under far-red light |
|
| Relations |
| BioSample |
SAMN02803814 |
| SRA |
SRX555089 |
