NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4560903 Query DataSets for GSM4560903
Status Public on Feb 04, 2021
Title CS_seedlings_H3K27me3_ChIP_seq_Rep2
Sample type SRA
 
Source name Triticum aestivum 14-days-old seedlings
Organism Triticum aestivum
Characteristics tissue: 14-days-old seedlings
cultivar: Chinese Spring
chip antibody: H3K27me3
chip antibody manufacturer: Upstate
chip antibody catalog #: 07–449
Treatment protocol For hormone and NaCl treatments, germinated seeds were grown in Hoagland solution at 22 °C under long-days conditions for 7 days. The 7-day-old seedlings in Hoagland were treated with 100μm ABA, 100μm MeJA, 500μm SA and 150mM NaCl, respectively, followed by incubation for 7 days.
Growth protocol 16h light, 8h dark, 22°C
Extracted molecule genomic DNA
Extraction protocol Chromatin or RNA was extracted from 14-days-old seedlingss, using standard protocols. 2μg total RNA (rRNA depleted) were used to prepare lncRNA-seq,2.2 μg DNA extracted from the harvested seedlings were used to prepare ChIP-seq. For DAP-seq, genomic DNA was extracted from leaves (14-days-old). 5μg gDNA was used to prepare DAP-seq library.
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China) using Illumina HiSeq 2000/2500 system (Illumina) to produce 150-bp paired-end reads.
For DAP-seq, genomic DNA was extracted from wheat leaves using Plant DNAzol Reagent (invitrogen) and fragmented. DNA was then end repaired using the End-It kit (Lucigen) and A-tailed using Klenow (3′–5′ exo-; NEB). Truncated Illumina Y-adapter was ligated to DNA using T4 DNA Ligase (Promega).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 3000
 
Data processing Sequencing reads were cleaned with Trim Galore v0.4.4, Trimmomatic v0.36 and sickle, including removing bases with low quality score (<25) and irregular GC content, and cutting sequencing adaptors followed by filtering short reads.
The cleaned reads were mapped to International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v1.0 using BWA 0.7.5a-r405 for ChIP-seq, HISAT2 2.1.020 for RNA-seq data, all with default settings.
For ChIP-seq, MACS1.3.7 was used to identify read-enriched regions (peaks) with combined criteria: P value < 1e–5 and fold-change >32. ChIP-seq data Target genes were defined as genes with a peak within or nearby the gene body (±2 kb).
For DAP-seq, MACS2.2.6 was used to identify protein binding sites (peaks). TF peaks which overlap with Halo peaks were removed. The top 6,000 peaks, ranked first by -log10(qvalue), then by fold enrichment, were used to discover novel DNA-binding motifs by MEME-ChIP in MEME software toolkit.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: In ChIP-seq, peak files were provided; In lncRNA-seq, read counts for genes (IWGSC RefSeq v1.0) were provided. In DAP-seq, peak files were provided.
 
Submission date May 20, 2020
Last update date Feb 04, 2021
Contact name yijing zhang
E-mail(s) zhangyijing@fudan.edu.cn
Organization name Fudan University
Department Biochemistry
Lab Functional Epigenomics Group
Street address 2005 Songhu Road
City shanghai
ZIP/Postal code 200438
Country China
 
Platform ID GPL24354
Series (1)
GSE139019 An atlas of wheat epigenetic regulatory elements reveals subgenome-divergence in the regulation of development and stress responses
Relations
BioSample SAMN14981202
SRA SRX8368153

Supplementary file Size Download File type/resource
GSM4560903_CS_seedlings_H3K27me3_ChIP_seq_Rep2.bw 765.7 Mb (ftp)(http) BW
GSM4560903_macs_CS_seedlings_H3K27me3_ChIP_seq_Rep2_peaks.bed.gz 1.8 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap