|
| Status |
Public on May 15, 2019 |
| Title |
wt Col - rep1 [MethylC-seq] |
| Sample type |
SRA |
| |
|
| Source name |
inflorescence (stage 1-12) immature flower buds
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype/background: Columbia
genotype/variation: wt
tissue: inflorescence (stage 1-12) immature flower buds
|
| Growth protocol |
Plants were grown under 16-hour day conditions at 22ºC in a growth chamber. All tissue is inflorescence (stage 1-12) immature flower buds.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated from each sample using fractional precipitation followed by phenol-chloroform extraction and RNaseA treatment.
1 µg of isolated DNA was used to prepare libraries as previously described in Urich et al., PMID: 25692984.
Single-end Illumina sequencing of 150 bp was performed at the University of Georgia Genomics Facility.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
MethylC-seq
|
| Data processing |
Sequencing reads were processed to remove adapters and low-quality reads as in Panda et al., PMID: 27506905. PCR duplicated reads were removed, and only uniquely mapping reads were used to assay methylation.
The weighted methylation level of genomic features (TE, gene, or DMR) was calculated as described previously in Schultz et al., PMID: 23131467.
Genome_build: TAIR10
Supplementary_files_format_and_content: *tsv: Tab-delimited text files showing total number of reads (total) and reads reporting methylation (mc_count) for each cytosine in the genome.
|
| |
|
| Submission date |
Aug 17, 2018 |
| Last update date |
May 15, 2019 |
| Contact name |
R. Keith Slotkin |
| E-mail(s) |
kslotkin@danforthcenter.org
|
| Organization name |
Donald Danforth Plant Science Center
|
| Street address |
975 North Warson Road
|
| City |
St. Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63132 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (2) |
| GSE118695 |
Methylome of the Arabidopsis mRNA export mutant aly1 and associated controls |
| GSE118709 |
Methylome, transcriptome, RIP-seq and small RNA-seq of the Arabidopsis mRNA export mutant aly1 and associated controls |
|
| Relations |
| Alternative to |
GSM2101949 |
| BioSample |
SAMN09847897 |
| SRA |
SRX4563050 |
