|
| Status |
Public on May 22, 2018 |
| Title |
Methylome Medicago HM085 |
| Sample type |
SRA |
| |
|
| Source name |
plant
|
| Organism |
Medicago truncatula |
| Characteristics |
ecotype: HM085
tissue: mature leaves
age: 45 days
|
| Treatment protocol |
the plant was grown in the greenhouse under long day conditions during the winter
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
MethylC-seq: MethylC-seq analysis was performed as described in (Schmtiz et al. 2013)
RNA-seq: RNA-seq was performed using TopHat v2.0.13 and Cufflinks v2.2.1
small RNAseq was performed using Illumina small RNA TruSeq library prep kit,and using bowtie for sequence mapping
Genome_build: Mtruncatula_285_Mt4.0
Supplementary_files_format_and_content: tab delimited text file, see "allc_header_descriptions.txt", "smallRNA.processedfile_description.txt" and "RNA_column_header_descriptions.txt" for column headers
|
| |
|
| Submission date |
May 21, 2018 |
| Last update date |
May 22, 2018 |
| Contact name |
Robert J Schmitz |
| E-mail(s) |
schmitz@uga.edu
|
| Organization name |
University of Georgia
|
| Department |
Genetics
|
| Street address |
B416 Davison Life Sciences
|
| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
| |
|
| Platform ID |
GPL17491 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN09233961 |
| SRA |
SRX4109091 |
