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Sample GSM5667202 Query DataSets for GSM5667202
Status Public on Nov 08, 2023
Title DDW3
Sample type SRA
 
Source name Leaf
Organism Phaseolus vulgaris
Characteristics plant: Red Hawk dark red kidney bean
sample group: DDW
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 SAMN22842870
SRA SRX12906488

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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