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| Status |
Public on Jul 22, 2019 |
| Title |
Z-4: Salt_IP_rep3 |
| Sample type |
SRA |
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| Source name |
Soybean root cells
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| Organism |
Glycine max |
| Characteristics |
tissue: Soybean root cells
chip antibody: Anti-H3K27me3 (Millipore, #07-449)
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| Treatment protocol |
For the salt stress treatment, the uniformly growing plants were kept in 0 mM/L, 50 mM/L, 75 mM/L, 100 mM/L, 150 mM/L and 200 mM/L of NaCl solutions for 30 hours.
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| Growth protocol |
The Glycine line, Glycine max Williams 82, was used in this study. Seeds were sterilized with 75% ethanol and then germinated in pots filled with coconut fiber. Soybean seedlings were grown in soil in an incubator with 25℃/20℃ (light/dark) and 16h/8h (light/dark) cycles until the second trifoliate leaves started expand. As a control, the untreated seedlings (0 mM/L) were planted and harvested at the same time with the stress-treated plants. The 100 mM/L salt treated seedlings were used for RNA-seq and ChIP-seq analysis since the phenotypic differences were clear at this concentration which is also commonly used for salinity test on soybean.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP assay was performed from approximately 2 g of soybean roots as previously described (Kim et al., 2012b; Xu et al., 2018).
Library construction and deep sequencing were performed as described previously (Wang et al., 2016; Xu et al., 2018).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
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| Data processing |
ChIP DNA samples described above were prepared for high throughput Illumina sequencing (one hundred and fifty pair-end read sequencing).
The ChIP-seq data was analyzed as described previously (Wang et al., 2016; Xu et al., 2018). The first 30 base pairs from the 5' end containing primer or adapter sequences were trimmed. The 3' end of the sequencing reads were trimmed based on base-call quality using the BWA quality trim algorithm (Li and Durbin, 2009).
The sequencing reads were aligned Glycine max reference genome (Glycine max Wm82.a2.v1). Only uniquely mapped reads that mapped to one location of the genome only (as opposed to those that mapped to multiple reads) were retained for peak calling.
Three biological replicates were performed for each sample. Each input was used as a control for peak calling for each sample using MACS 1.4 (Zhang et al., 2008). The statistical identification of peaks was performed for each sample using MACS with the default 10-5 p-value cutoff.
Genome_build: Glycine max Wm82.a2.v1
Supplementary_files_format_and_content: The three replicates results were overlapped using BedTools (Quinlan and Hall, 2010). The resulting BED format files that contain the peak location were visualized with the Integrated Genome Viewer (Robinson et al., 2011; Thorvaldsdottir et al., 2013).
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| Submission date |
Jul 01, 2019 |
| Last update date |
Jul 22, 2019 |
| Contact name |
guoweijun guoweijun |
| E-mail(s) |
guoweijun01@163.com
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| Phone |
13126571191
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| Organization name |
Chinese Academy of Agricultural Sciences
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| Department |
Biotechnology Research Institute
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| Lab |
LI PU lab
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| Street address |
No. 12, Zhongguancun South Street
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| City |
Beijing |
| ZIP/Postal code |
100081 |
| Country |
China |
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| Platform ID |
GPL21309 |
| Series (2) |
| GSE133573 |
Dynamic changes in genome-wide histone methylation and gene expression of soybean roots in response to salt stress (ChIP-seq dataset) |
| GSE133575 |
Dynamic changes in genome-wide histone methylation and gene expression of soybean roots in response to salt stress |
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| Relations |
| BioSample |
SAMN12172109 |
| SRA |
SRX6385187 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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