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Sample GSM3449734 Query DataSets for GSM3449734
Status Public on Jun 21, 2019
Title CS_seedlings_ Bisulfite_seq
Sample type SRA
 
Source name Triticum aestivum 12-days-old seedlings
Organism Triticum aestivum
Characteristics cultivar: Chinese Spring
tissue: 12-days-old seedlings
Treatment protocol No treatment applied.
Growth protocol 16h light, 8h dark, 22°C
Extracted molecule genomic DNA
Extraction protocol Chromatin or RNA was extracted from 12-days-old seedlingss, using standard protocols. 2 microgram mRNA, 2 microgram total RNA (rRNA depleted) were used to prepare mRNA-seq and lncRNA-seq. 2.2 microgram DNA extracted from the harvested seedlings were used to prepare ChIP-seq DnaseI-seq and Bisulfite-seq .
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China) using Illumina HiSeq 3000 following the manufacturer’s instructions (Illumina) to produce 150bp paired-end reads.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 3000
 
Description CS_seedlings_ Bisulfite_seq
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 and DNaseI-seq data, HISAT2 2.1.020 for RNA-seq data , Bismark_v0.19.0 for bisulfite-seq data , all with default settings.
For ChIP-seq and DNaseI-seq data, MACS1.3.7 was used to identify read-enriched regions (peaks) with combined criteria: P value < 1e–50 and fold-change >32. ChIP-seq data Target genes were defined as genes with a peak within or nearby the gene body (±2 kb).
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: In ChIP-seq, peak files were provided; In RNA-seq, read counts for genes (IWGSC RefSeq v1.0) were provided;In DNaseI-seq, peak files were provided; In Bisulfite-seq, BigWig files with position and methylation ratio were provided.
 
Submission date Oct 29, 2018
Last update date Jun 22, 2019
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 (2)
GSE121903 Distinct chromatin signitures of promoters, enhancers and transposons in allohexaploid wheat
GSE178372 Distinct chromatin signatures and transcriptional landscape of functional genetic elements in allohexaploid wheat
Relations
BioSample SAMN10340340
SRA SRX4947958

Supplementary file Size Download File type/resource
GSM3449734_CS_seedlings_Bisulfite_seq.CG.bw 633.3 Mb (ftp)(http) BW
GSM3449734_CS_seedlings_Bisulfite_seq.CHG.bw 674.8 Mb (ftp)(http) BW
GSM3449734_CS_seedlings_Bisulfite_seq.CHH.bw 1.8 Gb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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