|
| Status |
Public on Jul 27, 2013 |
| Title |
prr7-3 IP (ExpII) |
| Sample type |
SRA |
| |
|
| Source name |
whole seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: prr7-3 IP
chip antibody: anti-HA
age: 15 days
experiment: Experiment 2 (ExpII)
tissue: whole seedlings
|
| Growth protocol |
Plants were grown on Murashige and Skoog medium with 0.8% agar and 2% sucrose under 70 µmol m-2s-1 and a 12 h light/12 h dark regime for two weeks before analysis.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were extracted from cross-linked cells, sonicated, and immunoprecipitated with antibodies.
Libraries were contructed for Illumina sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
IP using anti-HA antibody
|
| Data processing |
FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) to filter out adapter sequences (fastx_clipper) and low quality reads (fastq_quality_trimmer) with minimum read length set at 30bp and minimum quality threshold at 20
Bowtie alignment to Arabidopsis TAIR10 genome with -m to exclude reads that can align more than once to the genome
QuEST to identify binding sites and determine false discovery rates, with the type of experiment specified as a transcription factor, calling parameter set to relaxed, and peak shift lower threshold set to 10
Python scripts to define common binding sites as those located within 500bp
In Experiment II, python scripts were used to randomly discard immunoprecipitated reads until their total number closely matched the total number of negative control reads in order for QuEST to estimate FDR values
The binding sites determined by QuEST were compared to TAIR10 genes to associate binding sites to putative target genes using a python script (genes were associated to binding sites located 1000bp upstream of the transcriptional start site to 1000bp downstream of the transcriptional stop)
Flanking sequences around each binding site were acquired using a publicly available script (http://www.stanford.edu/%7evalouev/QuEST/output_genomic_regions_from_calls.pl.gz) for input into MEME and Weeder
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: <file name>_peak_caller.ChIP.out.accepted was used to determine corresponding genes in reference to the TAIR10 genome. Binding sites were visualized from the <file name>_normalized.profile.wig file.
|
| |
|
| Submission date |
Jul 26, 2013 |
| Last update date |
Sep 04, 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 |
GPL9302 |
| Series (1) |
| GSE49282 |
Identification of Arabidopsis thaliana PRR7 regulated clock components and circadian outputs through genome-wide binding sites analysis |
|
| Relations |
| Reanalyzed by |
GSE71397 |
| Reanalyzed by |
GSE136843 |
| BioSample |
SAMN02265605 |
| SRA |
SRX328354 |
