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Sample GSM7333164 Query DataSets for GSM7333164
Status Public on Jul 22, 2024
Title ATAC-Seq Leaf_rep1
Sample type SRA
 
Source name Leaf
Organism Triticum aestivum
Characteristics tissue: Leaf
Growth protocol Wheat (Triticum aestivum; BBAADD, 2n = 6x = 42) cultivar AK58 was used in our study. Materials with no vernalization were taken from plants grown 2 weeks (day for 16h at 22°C, night for 8h at 19°C) after germination. Materials with vernalization were taken from plants planted in greenhouse after vernalization for 1 mouth in cold chamber (4℃, 16 h light/8 h dark) and grew in green house (day for 16h at 22°C, night for 8h at 19°C) for 1 day.
Extracted molecule genomic DNA
Extraction protocol none provided
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing We used fastp v0.21.0 for data quality control and Bowtie v2.3.5.1 to align reads to wheat reference genome (bowtie2 -X 1000 --very-sensitive).
SAMtools v1.3.1 was used to sort and filter bam (samtools -q 10), Picard v2.16.0 to remove clonal duplicate, and MACS2 v 2.2.6 to call peak(macs2 --keep-dup all --nomodel --extsizes 150 --shift -75).
All the raw peaks were split into 150 bp bins with 50 bp overlapping, filtered by Tn5 integration site density, and merged by bedtools with “-d 200”.
Peaks overlapped with input and aligned to plant chloroplast DNA (NCBI) were discard, which guaranteed ACRs we identified were high-quality ACRs.
Assembly: ChineseSpring v1.1
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
 
Submission date May 12, 2023
Last update date Jul 22, 2024
Contact name Zefu Lu
E-mail(s) luzefu@live.com
Organization name Institute of Crop Sciences
Street address No.12 Zhongguancun South St.,Haidian District, Beijing, P.R.China
City Beijing
State/province Haidian
ZIP/Postal code 100081
Country China
 
Platform ID GPL25409
Series (2)
GSE232424 Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat (ATAC-Seq)
GSE232430 Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat
Relations
BioSample SAMN35063625
SRA SRX20313527

Supplementary file Size Download File type/resource
GSM7333164_Leaf.peak.bed.gz 1.0 Mb (ftp)(http) BED
GSM7333164_Leaf_rep1.bw 222.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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