|
| Status |
Public on Feb 03, 2017 |
| Title |
AT2G46270_GBF3_ABA_ChIP_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
whole seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
accession: Col-0
age: 3 day
light condition: dark
treatment: 10 uM abscisic acid, 4 hours
chip antibody: GFP (ThermoFisher #A11122)
|
| Treatment protocol |
10 uM ABA treatment or ethanol mock treatment for 4 hours.
|
| Growth protocol |
Recombineering tagging of YPet to TF genes was carried out as described previously (Zhou et al., The Plant Journal 2011; PMID 21294796). Seedling were germinated and grown on nylon mesh in hydroponics for 3 days in dark before ABA or mock treatment.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After formaldehyde crosslink and nuclei isolation, chromatin was sonicated to 100-500 bp fragments. YPet-tagged TF of interest was immunoprecipitated by a rabbit polyclonal GFP antibody (cat #A11122, Thermo Fisher USA). Mock ChIP was carried out by immunoprecipitating Col-0 with the same GFP antibody. Detailed ChIP protocol is described in Song et al. Curr. Protoc. plant Biol. 2016.
Libraries were prepared according to Illumina's instructions accompanying TruSeq DNA sample prep kit and sequenced by Illumina HiSeq 2500 according to the manufacturer's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
AT2G46270_GBF3_ABA_optimal_narrowPeak_p16.bed
|
| Data processing |
Base-calling were performed by Illumina Real-Time Analysis software v1.17.20 to v1.18.61.
Reads were aligned by bowtie version 0.12.7 against the Arabidopsis TAIR10 genome assembly with parameters " -m 1 --best --strata -S --chunkmbs 256" for 100 bp reads or "-m 1 --best --strata -S -3 30 --chunkmbs 256" for 130 bp reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: Peak regions in narrowPeak format were created by the Irreproducible Discovery Rate (IDR) pipeline using initial peak calls from MACS2 version 2.0.10, with q-value thresholds of 0.05, 0.01, and 0.001 for replicate consistency. The resulting optimal set of peaks were then filtered by a p-value cutoff of 1e-16.
|
| |
|
| Submission date |
Apr 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Joseph R Ecker |
| E-mail(s) |
ecker@salk.edu
|
| Phone |
8584534100
|
| Organization name |
HHMI-Salk-Institute
|
| Department |
Genomic Analysis Laboratory
|
| Lab |
Ecker lab
|
| Street address |
10010 North Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL17639 |
| Series (2) |
| GSE80564 |
ChIP-seq of abscisic acid-reponsive transcription factors |
| GSE80568 |
ChIP-Seq and RNA-Seq of abscisic acid-reponsive transcription factors |
|
| Relations |
| BioSample |
SAMN04884779 |
| SRA |
SRX1719979 |
