|
| Status |
Public on Dec 03, 2015 |
| Title |
prr9-1 PRR9::HA-PRR9 CCR2::LUC #109 Input |
| Sample type |
SRA |
| |
|
| Source name |
whole seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: whole seedlings
collection time: ZT4
age: Two weeks
growth: Cycling 12 h light/12 h dark
|
| Treatment protocol |
Plants were collected at ZT4.
|
| Growth protocol |
Plants were grown in cycling 12 h light/12 h dark for two weeks.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
See Liu et al., “Direct regulation of abiotic responses by the Arabidopsis circadian clock component PRR7” (2013) for ChIP-seq extract protocol
Illumina compatible libraries were prepared using the Rubicon Genomics ThruPLEX-FD Prep Kit for multiplexing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Anti-HA antibody used to immunoprecipitate HA-tagged PRR9
|
| Data processing |
Quality filtering using Fastx Toolkit fastq_quality_trimmer with -t 20 -l 30
Alignment to Arabidopsis genome using Bowtie with -m 1
Binding site identification using MACS2 with –broad
Binding sites were associated with the nearest transcriptional start site using ChIPpeakAnno
Genome_build: TAIR10
Supplementary_files_format_and_content: bed format for MACS2 broad_peaks and summits, text files for annotated binding sites
|
| |
|
| Submission date |
Jul 27, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Tiffany L Liu |
| E-mail(s) |
liutiff1@msu.edu
|
| Organization name |
Michigan State University
|
| Department |
Plant Biology
|
| Lab |
Farre
|
| Street address |
3260 Molecular Plant Sciences Building
|
| City |
East Lansing |
| State/province |
Michigan |
| ZIP/Postal code |
48824 |
| Country |
USA |
| |
|
| Platform ID |
GPL17639 |
| Series (1) |
| GSE71397 |
Identification of Arabidopsis thaliana PRR9 regulated clock components and circadian outputs through genome-wide binding sites analysis |
|
| Relations |
| BioSample |
SAMN03939919 |
| SRA |
SRX1121728 |
