|
| Status |
Public on Nov 08, 2023 |
| Title |
CD1 |
| Sample type |
SRA |
| |
|
| Source name |
Leaf
|
| Organism |
Phaseolus vulgaris |
| Characteristics |
plant: Red Hawk dark red kidney bean
sample group: CD
tissue: Leaf tissue
|
| Treatment protocol |
At the R2 stage, when at least 50% of the flower buds had opened, the plants were subjected to drought stress
|
| Growth protocol |
Red Hawk dark red kidney bean (Phaseolus vulgaris L.) was procured from Central Bean Co. Inc . The plants were maintained at 28/20°C in a greenhouse at Delaware State University, Dover, Delaware, with a 14/10 h photoperiod.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The nuclei were sonicated and purified using Phenol chloroform isoamyl alcohol. A library was prepared from purified FAIRE and input DNA to be sequenced with the Illumina HiSeqTM 2500
Illumina compatible FAIRE-Seq libraries were prepared using NEBNext Ultra DNA Library Preparation
|
| |
|
| Library strategy |
FAIRE-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The paired-end sequencing was done using Illumina HiSeqTM 2500
FastQC (v 0.11.7) was used to assess sequence quality for all samples
Quality trimmed reads were aligned to the reference genome of common bean (v 2.1) using Bowtie2 (v 2.3.5.1)
Quality of FAIRE-seq data was assessed using DeepTools (v 3.1.1)
The ChIPseeker (v 1.26.2) was used to characterize peaks.
Genome_build: v2.1
Supplementary_files_format_and_content: tdf
|
| |
|
| Submission date |
Nov 02, 2021 |
| Last update date |
Nov 08, 2023 |
| Contact name |
Shaojun Xie |
| E-mail(s) |
xie186@purdue.edu
|
| Phone |
7657140672
|
| Organization name |
Purdue University
|
| Street address |
3135 Decatur Street
|
| City |
WEST LAFAYETTE |
| State/province |
Indiana |
| ZIP/Postal code |
47906 |
| Country |
USA |
| |
|
| Platform ID |
GPL24868 |
| Series (1) |
| GSE187025 |
FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) analysis of chromatin accessibility in kidney bean under drought stress |
|
| Relations |
| BioSample |
SAMN22842855 |
| SRA |
SRX12906475 |
