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| Status |
Public on Jun 21, 2019 |
| Title |
CS_seedlings_H3K4me1_ChIP_seq_rep2 |
| 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
chip antibody: H3K4me1
chip antibody manufacturer: Upstate
chip antibody catalog #: 07–436
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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 |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
CS_seedlings_H3K4me1_ChIP_seq_rep2
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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 |
SAMN10340349 |
| SRA |
SRX4947949 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3449725_macs_CS_seedlings_H3K4me1_ChIP_seq_rep2_peaks.bed.gz |
3.1 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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