|
| Status |
Public on May 02, 2017 |
| Title |
sldml2-1-46dpa_BS_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
sldml2-1-46dpa_BS
|
| Organism |
Solanum lycopersicum |
| Characteristics |
genotype/variation: sldml2-1
tissue: fruit
day after anthesis: 46 dpa
|
| Growth protocol |
All plant materials used in this study are first generation (T0) of regenerated plants from callus. Tomato cultivar Micro-Tom used in this study were ordered from Ball (Illinois, USA). Tomato plants were grown in a greenhouse located on Purdue University campus. Tomato tissue culture was performed accroding to the established protocol (Sun, 2006). All tissue culture steps were conducted at room temperature with a photoperiod of 16 h light and 8 h dark.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tomato genomic DNA was extracted using a modified cetyltrimethylammonium bromide-based method (Clarke, 2009) or by using the QIAGEN DNeasy Plant Maxi Kit following the prodcut manual. Totol RNA were extracted using Trizol reagent (Ambion, 15596)
Genomic DNA was extracted from the tomato fruit and sent to Genomics Core Facility of Shanghai Center for Plant Stress Biology for bisulfite treatment, library preparation, and sequencing. Bisulfite sequencing libraries were prepared using standard Illumina protocols.
Total RNA were extracted from the tomato fruit using methods described above. Library construction and deep sequencing were performed by the Core Facility of Genomics in Shanghai Plant Stress Biology Center, China.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
treated with bisulfite
|
| Data processing |
MethylC-Seq:Reads were mapped to SL2.50 using BRAT-BW with parameters -m 2 -i 0 -a 1000. Copy-duplicates were remove using remove-dupl command of BRAT-BW. acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each cytosine of forward and reverse strands of the reference
mRNA-Seq: RNA-Seq reads were trimmed using the fastx_trimmer command FASTX-Toolkit ( http://hannonlab.cshl.edu/fastx_toolkit/index.html ) with parameter “-f 14 -l 80“ before alignment. Trimmed reads were mapped to SL2.50 by TopHat2, allowing up to two mismatches.
Genome_build: tomato genome build 2.50 (SL2.50)
Supplementary_files_format_and_content: For MethylC-Seq: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (unconverted_C / ( converted_C+ unconverted_C ) ).
Supplementary_files_format_and_content: For mRNA-Seq: The bedGraph files were generated using genomeCoverageBed from bedtools with parameter -bga -split
|
| |
|
| Submission date |
Feb 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian-Kang Zhu |
| E-mail(s) |
zhu132@purdue.edu
|
| Organization name |
Purdue University
|
| Department |
Department of Horticulture and Landscape Architecture
|
| Street address |
625 Agriculture Mall Dr.
|
| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
| |
|
| Platform ID |
GPL19694 |
| Series (1) |
| GSE94903 |
Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit |
|
| Relations |
| BioSample |
SAMN06335086 |
| SRA |
SRX2563606 |
