|
Status |
Public on Jan 01, 2016 |
Title |
A. duranensis methylC-seq |
Sample type |
SRA |
|
|
Source name |
young unexpanded leaves
|
Organism |
Arachis duranensis |
Characteristics |
cultivar: V14167 tissue: young unexpanded leaves
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Leaves were ground in liquid nitrogen and DNA extracted using QIAGEN DNAeasy Plant Mini Kit (Cat. No. 69106). Libraries were constructed according to Urich et. al. MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nature Protocols 10, 475–483 (2015).
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|
|
Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
Whole Genome Bisulphite Sequencing of Arachis duranensis
|
Data processing |
Reads were trimmed, aligned, and methylation called using the methylpy pipeline Schultz et al. Human body epigenome maps reveal noncanonical DNA methylation variation Nature 523, 212–216 (2015). Genome_build: Aradu_v1.0_20140908 and Araip_v1.0_20140908 Supplementary_files_format_and_content: column 1 = chr = chromosome; column 2 = pos = coordinate for the cytosine position on the chromosome; column 3 = strand = + or - strand; column 4 = mc_class = context of the cytosine and the two following bases from the same strand; column 5 = mc_count = number of reads supporting a methylated cytosine; column 6 = total = total number of reads at that position; column 7 = methylated = cytosine is considered methylated if there is a 1 or unmethylated if there is a 0
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|
|
Submission date |
Jul 27, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Chad E. Niederhuth |
Organization name |
Michigan State University
|
Department |
Plant Biology
|
Street address |
612 Wilson Road
|
City |
East Lansing |
State/province |
M |
ZIP/Postal code |
48824 |
Country |
USA |
|
|
Platform ID |
GPL20737 |
Series (1) |
GSE71357 |
The genomes of the ancestral species of peanut - a remarkable case of living archaeology |
|
Relations |
BioSample |
SAMN03938701 |
SRA |
SRX1118858 |