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Sample GSM8148567 Query DataSets for GSM8148567
Status Public on Apr 28, 2024
Title 60d_soybean_seeds_IgG_aChIP-seq_rep1
Sample type SRA
 
Source name 60d seeds
Organism Glycine max
Characteristics tissue: 60d seeds
cell line: Williams 82
cell type: 60d seeds cells
chip antibody: IgG
Growth protocol For the collection of economically important plant organs, the plants were planted and managed under normal agricultural conditions on the experimental farm of Huazhong Agricultural University, Wuhan, China. For the collection of vegetativetissues, the plants were planted in greenhouses.
Extracted molecule genomic DNA
Extraction protocol Tissues were evenly cut into small pieces, crosslinked with 1% formaldehyde in vacuum for 10 min, and then quenched with 0.2 M glycine for 5 min at room temperature.
Libraries were prepared using an NEBNext® Ultra™ II DNA library prep kit for Illumina® sequencing (New England BioLabs, E7645) and sequenced using an Illumina Novaseq 6000 platform (paired-end 150 bp reads).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing Evaluated the quality of sequencing data using FastQC.
Fastp with “-l 15 -f 0 -t 0” parameters to was used to filter out adaptors and low-quality reads from raw reads, resulting in clean reads.
bwa mem algorithm43 with “-k 19 -T 30” parameters to map trimmed reads to the corresponding reference genomes.
SAMtools with parameters “-q 30 -f 2” to remove low-quality mapping and removed PCR-duplicated reads and redundant reads using the GATK MarkDuplicates.
Narrow peaks were called by MACS2, with parameters “-B -q 1e-5 -f BAMPE”
Assembly: Brassica napus : GWHANRE00000000, Solanum tuberosum L : DM v4.03, Glycine max : ZH13 v2.0, Zea mays : GCF_902167145.1, Solanum lycopersicum : GCF_000188115.4, Dianthus caryophyllus : v1, Citrus sinensis : GCF_000317415.1, Arabidopsis thaliana : TAIR10, Saccharum officinarum : AP85-441 v20190103, Cucumis melo : GCF_000313045.1, Oryza sativa : GCF_001433935.1,Populus:sPta717 v2
Supplementary files format and content: Narrowpeak and broadpeak
Supplementary files format and content: \
 
Submission date Mar 15, 2024
Last update date Apr 28, 2024
Contact name Wenying Zhong
E-mail(s) [email protected]
Organization name Huazhong Agricultural University
Street address Lion Rock Street
City Wuhan
ZIP/Postal code 430072
Country China
 
Platform ID GPL28801
Series (2)
GSE243804 aChIP: efficient, sensitive, robust ChIP-seq for economically important plant organs [ChIP-Seq]
GSE243806 aChIP: efficient, sensitive, robust ChIP-seq for economically important plant organs
Relations
BioSample SAMN40467841
SRA SRX23957571

Supplementary file Size Download File type/resource
GSM8148567_MXCS-182_peaks.narrowPeak.gz 154 b (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA

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