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| Status |
Public on Aug 17, 2016 |
| Title |
Sorghum bicolor methylC-seq |
| Sample type |
SRA |
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| Source name |
Sorghum bicolor methylC-seq
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| Organism |
Sorghum bicolor |
| Characteristics |
tissue: leaf
genotype: wild-type
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| Treatment protocol |
N/A
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| Growth protocol |
N/A
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (gDNA) was purified from 0.5 g of leaves by using DNeasy Plant MiniKit (Qiagen, Valencia, CA), according to the manufacturer’s instructions. MethylC-Seq libraries were constructed according to Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR. (2015) MethylC-seq: Base resolution whole genome bisulfite sequencing library preparation. Nature Protocols Feb(10):475–483
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
MethylC-seq analysis were performed as described in Schultz et al. (2015). Human body epigenome maps reveal noncanonical DNA methylation variation. Nature 523:212–216.
Genome_build: JGI v2.0 (B. distachyon); Brassica database v1.0 (B. oleracea); JGI v2.0 (M. guttatus); JGI v3.0 (P. trichocarpa); JGI v2.0 (S. bicolor)
Supplementary_files_format_and_content: Tab delimited text file, column headers
Supplementary_files_format_and_content: Column1: chromosome
Supplementary_files_format_and_content: Column2: cytosine position
Supplementary_files_format_and_content: Column3: strand
Supplementary_files_format_and_content: Column4: CNN (N = A, T, C, G)
Supplementary_files_format_and_content: Column5: methylated cytosines at this site
Supplementary_files_format_and_content: Column6: total detected cytosines at this site
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| Submission date |
Aug 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Adam James Bewick |
| E-mail(s) |
bewickaj@uga.edu
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| Organization name |
University of Georgia
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| Department |
Genetics
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| Lab |
Schmitz
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| Street address |
120 East Green Street
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| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30605 |
| Country |
USA |
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| Platform ID |
GPL20818 |
| Series (1) |
| GSE72155 |
FASTmC: predictive models for non-reference-based estimations of DNA methylation |
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| Relations |
| BioSample |
SAMN03998607 |
| SRA |
SRX1156640 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1856261_allc_Sbicolor.tsv.gz |
877.7 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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