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| Status |
Public on Nov 23, 2023 |
| Title |
WGBS, Colfax, 4 hpi, control1 |
| Sample type |
SRA |
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| Source name |
shoot
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| Organism |
Glycine max |
| Characteristics |
tissue: shoot
genotype: Colfax
treatment: control
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated using the modified CTAB method.
Library construction was performed at Novogene.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
WGBS_cf_4_c1
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| Data processing |
The raw reads were quality controlled by FastQC and trimmed using Trimmomatic.
The resulting clean reads were then mapped to the soybean reference genome v4.0 (Wm82.a4) using Bismark with the following parameters (-n 2, -I 50, -N 1).
To eliminate PCR duplicates, the deduplication package under Bismark was utilized.
Additional packages including Bismark methylation extractor, bismark2bedGraph and coverage2cytosine under Bismark were employed to extract the methylated cytosines and count methylated and unmethylated reads.
Assembly: Williams 82 genome assembly v4.0 (Wm82.a4)
Supplementary files format and content: Tab-delimited txt file including the number of methylated reads and unmethlyated reads per each of cytosine contexts for each sample
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| Submission date |
Aug 16, 2023 |
| Last update date |
Nov 23, 2023 |
| Contact name |
Meixia Zhao |
| Organization name |
University of Florida
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| Street address |
1355 Museum Dr
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| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32611 |
| Country |
USA |
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| Platform ID |
GPL28801 |
| Series (2) |
| GSE240965 |
Transcriptomic and epigenetic responses unveil resistance mechanisms to Phytophthora sansomeana in soybean [WGBS] |
| GSE240966 |
Transcriptomic and epigenetic responses unveil resistance mechanisms to Phytophthora sansomeana in soybean |
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| Relations |
| BioSample |
SAMN37006472 |
| SRA |
SRX21382623 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7713071_cf_4_c1_cytosine_20chrs.txt.gz |
1.3 Gb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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