|
| Status |
Public on Aug 06, 2019 |
| Title |
M-1-105 |
| Sample type |
SRA |
| |
|
| Source name |
Columbia-0
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
replicate type: biological rep 3
tissue: rosette leaves
|
| Treatment protocol |
Five memory plants, four non-memory plants, and four Col-0 wild-type plants were sequenced were used. Leaves at bolting were flash freezed in liquid nitrogen. Tissues were ground by motor and pestle in liquid nitrogen.
|
| Growth protocol |
Seeds were sown on peat mix in square pots in reach-in chambers at 12hrs daylenght (22 °C, 120-150 μmol/(m^2*s) light)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA extraction using DNeasy Plant kit (Qiagen, Germany).
Genomic DNA Sonicated to 100-300 bp fragments and purified with MiniElute PCR Purification Kit (Qiagen, Germany), incubated at 20 ℃ after add End Repair Mix. Then purified and added a single ‘A’ nucleotide to the 3’ ends of the blunt fragments, purified again and add Methylated Adapter to the 5’ and 3’ ends of each fragment. Then fragments with 300bp-400bp size-range were purified with QIAquick Gel Extraction kit (Qiagen, Germany) and subjected to bisulfite treatment by using Methylation-Gold kit (ZYMO). Followed with PCR and gel purification (350bp-400bp range fragments were selected). Qualified libraries sequenced pair end on the HiSeq X-ten system.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
memory line
|
| Data processing |
Illumina for basecalling
The sequences were trimmed using trim_galore 0.4.1 and cutadapt 1.9.1 with cutoff 20
The sequences were aligned using Erne-meth 2.1.1 with default options and set the output as a bismark coverage file
tab-delimited file generated with bismark2bedGraph with options -CX --ample_memory
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited file, 1-based genomic coords with <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count non-methylated> fields
|
| |
|
| Submission date |
Aug 21, 2018 |
| Last update date |
Aug 07, 2019 |
| Contact name |
Hardik Kundariya |
| E-mail(s) |
hsk13@psu.edu
|
| Organization name |
The Pennsylvania State University
|
| Street address |
361 N. Frear
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16801 |
| Country |
USA |
| |
|
| Platform ID |
GPL23157 |
| Series (1) |
| GSE118874 |
Bisulfite (methylome) sequencing of msh1 memory line and non-memory (normal looking) sibling plants with isogenic Col-0 wild-type control in Arabidopsis |
|
| Relations |
| BioSample |
SAMN09873038 |
| SRA |
SRX4589938 |
