|
| Status |
Public on Jun 30, 2018 |
| Title |
Rutgers WT [1-P1] |
| Sample type |
SRA |
| |
|
| Source name |
cultivar Rutgers
|
| Organism |
Solanum lycopersicum |
| Characteristics |
genotype: WT
background cultivar: Rutgers
tissue: leaf
|
| Treatment protocol |
The top three leaves from each tomato plant (four weeks old) were collected and freeze in liquid nitrogen immediately and put into -80 ℃
|
| Growth protocol |
Wild-type tomato (Solanum lycopersicum, cultivar Rutgers) and the corresponding, MSH1-RNAi segregate out (msh1 memory line) were germinated on MetroMix 200 medium (SunGro) and maintained at 26°C to 28°C with a 15-h day length and at 20°C to 22.8°C with a 9-h dark period.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA extraction using DNeasy Plant kit (Qiagen, Germany). Genomic DNA from three individual plants for both WT and msh1 memory line were used for subsequent Bisulfite methylome sequencing experiment.
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 |
1-P1
|
| 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: SL250 - Solanum_lycopersicum.SL2.50
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 |
Oct 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Sally A Mackenzie |
| E-mail(s) |
sam795@psu.edu
|
| Phone |
814-863-8324
|
| Organization name |
Penn State University
|
| Department |
Biology
|
| Lab |
Mackenzie
|
| Street address |
362 North Frear
|
| City |
State College |
| State/province |
PA |
| ZIP/Postal code |
16803 |
| Country |
USA |
| |
|
| Platform ID |
GPL24124 |
| Series (1) |
| GSE105008 |
Bisulfite methylome sequencing of msh1 memory line in tomato |
|
| Relations |
| BioSample |
SAMN07788259 |
| SRA |
SRX3287345 |
