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Status |
Public on Jun 21, 2019 |
Title |
CS_seedlings_ Bisulfite_seq |
Sample type |
SRA |
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Source name |
Triticum aestivum 12-days-old seedlings
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Organism |
Triticum aestivum |
Characteristics |
cultivar: Chinese Spring tissue: 12-days-old seedlings
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Treatment protocol |
No treatment applied.
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Growth protocol |
16h light, 8h dark, 22°C
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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.
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Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina HiSeq 3000 |
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Description |
CS_seedlings_ Bisulfite_seq
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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.
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Submission date |
Oct 29, 2018 |
Last update date |
Jun 22, 2019 |
Contact name |
yijing zhang |
E-mail(s) |
zhangyijing@fudan.edu.cn
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Organization name |
Fudan University
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Department |
Biochemistry
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Lab |
Functional Epigenomics Group
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Street address |
2005 Songhu Road
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City |
shanghai |
ZIP/Postal code |
200438 |
Country |
China |
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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 |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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