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| Status |
Public on Aug 30, 2021 |
| Title |
G1812_Bisulphiteseq_DNAmeth |
| Sample type |
SRA |
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| Source name |
seedling
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| Organism |
Triticum urartu |
| Characteristics |
tissue: seedling
accession: G1812 (PI428198)
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| Treatment protocol |
Regarding the cold and heat stress treatments, 7-day-old seedlings grown in soil were transferred to 4 °C for 5 hours, 40 °C for 7 hours, respectively. To assess the effects of drought, 7-day-old seedlings were cultivated in soil for another 2 weeks without watering. For the NaCl and ABA treatments, 7-day-old seedlings grown in soil were treated with 250 mM NaCl for 7 hours, 100 μm ABA for 2 weeks. For wounding stress, 7-day-old seedlings were injured on leaves by scissors and samples were taken 2.5 hours later.
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| Growth protocol |
16h light, 8h dark, 22°C
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
2.2 μg DNA extracted from the harvested seedlings were used to prepare ChIP-seq, DNase-seq and Bisulphite-seq. RNA was extracted using TRIzol and 2μg total RNA were used to prepare RNA-seq. Nuclei were extracted with H1B buffer(20 mM Tris-HCl, pH 8.0, 50 mM EDTA, 5 mM spermidine, 0.15 mM spermine, 40% glycerol, and 0.1% mercaptoethanol) for DNase-seq.
Libraries were prepared for sequencing using standard Illumina protocols.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Sequencing reads were cleaned with the Trim Galore, Trimmomatic, and Sickle programs.
The cleaned reads were mapped to WheatTu IGDBv1.0 using BWA for ChIP-seq and DNase-seq. HISAT2 for RNA-seq data. Bismark program for Bisulphite-seq.
For ChIP-seq and DNase-seq, MACS was used to identify read-enriched regions (peaks) with P value < 1e–10. The MAnorm package was used for the quantitative comparison of signals between samples with the following criteria: |M value| > 1 and P < 0.05.
For RNA-seq, featureCount program of the Subread package was used to determine the RNA-seq read density for the genes. The DEseq2 program was used for detecting differentially expressed genes based on the following criteria: |log2 fold-change| > 1 and P < 0.05.
For Bisulphite-seq, the extent of the cytosine methylation was determined with the bismark_methylation_extractor implemented in the Bismark program. Next, the methylation ratio of a cytosine was calculated as the number of mCs divided by the number of reads covering the position. Bases covered by fewer than three reads were considered low-confidence positions whose methylation ratios were not recorded.
Genome_build: IGDBv1.0
Supplementary_files_format_and_content: peak files and bigwig files
Supplementary_files_format_and_content: FPKM values for each sample
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| Submission date |
Feb 22, 2021 |
| Last update date |
Aug 30, 2021 |
| 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 |
GPL29754 |
| Series (2) |
| GSE167228 |
Evolutionary rewiring of wheat abiotic stress responsive network by lineage-specific transposable elements I |
| GSE167229 |
Evolutionary rewiring of wheat abiotic stress responsive network by lineage-specific transposable elements |
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| Relations |
| BioSample |
SAMN18026063 |
| SRA |
SRX10149523 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5100026_G1812_DNAmeth.mC.bw |
4.6 Gb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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