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| Status |
Public on Jul 08, 2024 |
| Title |
100 varieties, mix |
| Sample type |
SRA |
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| Source name |
leaf
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| Organism |
Triticum aestivum |
| Characteristics |
tissue: leaf
develomental stage: 2-leaf-seedling
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
1cm-long-leaves of the plants were harvested, mixed together and fixed with 1% formaldehyde in HEPES buffer (50 mM HEPES, 1 mM EDTA, pH 8.0, 0.1 M NaCl, and 1 mM PMSF). The fixed leaves were ground to a fine powder in liquid nitrogen. Wheat 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). The extracted nuclei were purified with H1B buffer supplemented with 0.5% Triton X-100. The purified nuclei were washed once with RSB buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, and 3 mM MgCl2). The pelleted nuclei were resuspended with 2 ml RSB buffer and then divided equally into five 1.5-ml Eppendorf tubes. The aliquoted nuclei were digested with DNase I (0, 0.01, 0.03, 0.05, and 0.08 units). The resulting digested nuclei were extracted using 1 volume of phenol, phenol:chloroform, and chloroform, after which the DNA from each digestion was resuspended in 2 volumes of cold ethanol and then pelleted.
A DNase-sequencing library was prepared from 0.03 U DNase I-digested nuclei. Approximately 2 µg DNA was separated by 1.5% agarose gel electrophoresis, and DNA fragments (50-300 bp) were cut and purified to prepare the DNase-sequencing library with the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB).
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| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Trimmomatic version 0.39 and Sickle version 1.33 were used to trim adaptors and eliminate bases with low quality scores (<20) and/or short read lengths (<20 bp).
The Burrows–Wheeler Aligner version 1.2.3 was used to align the remaining clean reads to the International Wheat Genome Sequencing Consortium reference genome (v1.0).
Use bcftools mpileup version 1.8 to generate the initial vcf file, then use bcftools call to perform variant detection on vcf, and output variant site information.
Bcftools filter retains site information with QUAL greater than 20 and DP value greater than 10.
VCFtools version 0.1.16 was used to calculate the pi value.
Assembly: International Wheat Genome Sequencing Consortium (IWGSC) reference sequence (version 1.0)
Supplementary files format and content: txt, pi-value of whole genome computed from DHS data.
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| Submission date |
Jul 11, 2022 |
| Last update date |
Jul 08, 2024 |
| 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 |
GPL25409 |
| Series (1) |
| GSE207939 |
Wheat-RegNet: An encyclopedia of common wheat hierarchical regulatory network |
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| Relations |
| BioSample |
SAMN29634802 |
| SRA |
SRX16117998 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6323625_pi_5000.windowed.pi.txt.gz |
3.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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