|
| Status |
Public on Jul 22, 2016 |
| Title |
ddm1 |
| Sample type |
SRA |
| |
|
| Source name |
stage 1-9 inflorescence tissue
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: ddm1
|
| Growth protocol |
All mutants used in this study are in the Col-0 ecotype background of Arabidopsis thaliana. Plants were grown in long-day (18 hour light) conditions at 23℃ and stage 1-12 inflorescence tissue was used for all experiments and sequencing.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated using fractional precipitation followed by phenol-chloroform extraction and RNase A treatment. 1ug of DNA was used to prepare libraries as previously described (Urich et al. 2015).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
library strategy: MethylC-seq
|
| Data processing |
Data were mapped to the TAIR10 reference genome
MethylC-seq analysis were performed as described in Schmtiz et al. Epigenome-wide inheritance of DNA methylation variants in a recombinant inbred population. Genome Research (2013).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab delimited text file, see metafile for column headers
|
| |
|
| Submission date |
Mar 30, 2016 |
| Last update date |
May 15, 2019 |
| 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 |
GPL19580 |
| Series (1) |
| GSE79746 |
Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation |
|
| Relations |
| BioSample |
SAMN04594645 |
| SRA |
SRX1671721 |
