|
| 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).
|
| |
|
| 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
|
| |
|
| 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 |
