|
| Status |
Public on Jan 19, 2021 |
| Title |
L1 line without expression of Mn-superoxide dismutase and deficient production of H2O2. - L1_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
L1 transgenic line tobacco
|
| Organism |
Nicotiana tabacum |
| Characteristics |
tobacco line: L1
cultivar: Xanthi
genotype: CchGLP-
group: H2O2 deficient production
|
| Growth protocol |
All plants were kept at room temperature under a 16 h light/8 h dark photoperiod. After three weeks the seedlings were transferred into individual pots with Mixture 3 Peat Moss Sunshine as substrate and kept inside a glass chamber at room temperature with humidity of 70% for three days. They were kept in a greenhouse until sampling. The plants were watered daily.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from 200 mg of leaf tissue of each sample, which was pulverised with liquid nitrogen. Extractions were carried out by the cetyltrimethylammonium bromide (CTAB) method described by Clarke 2009
The library preparation was done by BGI according to their standard directional WGBS pipeline. The WGBS consisted of a 150 pb paired-end sequencing with coverage of 12X on a NovaSeq 6000 system (Illumina, Inc.).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Bisulfite-treated genomic DNA
|
| Data processing |
Raw reads were pre-processed with the Fastp v0.20.0 using -c -x -y options for polyX trimming in 3' ends, base correction in overlapped regions and low complexity filtering, respectively.
Clean reads were aligned to the N. tabacum reference genome (Nitab4.5) using Bismark aligner v0.22.3 under the parameters –N 1 -L 20 –bowtie2 --nondirectional.
Differential methylation analysis was performed using Methylkit v1.14.2 in R v4.0.0 as follows: Methylated cytosines were extracted from aligned reads using processBismarkAln function. In order to filter bases above the background expected from inefficiencies in the bisulfite conversion reaction and sequencing errors, filterByCoverage function was used to discards bases that have coverage below 10X and also discards the bases that have more than 99.9th percentile of coverage in each sample. The parameters for calculated DiffMeth function were slim = TRUE, weighted. mean = TRUE. Differential methylated cytosines (DmC) were defined as bases that had q-value < 0.01 and methylation difference > 25 %.
Genome_build: GCA_002210045.1
Supplementary_files_format_and_content: bedGraph files was obtained with bismark_methylation_extractor
|
| |
|
| Submission date |
Nov 10, 2020 |
| Last update date |
Jan 20, 2021 |
| Contact name |
Luis F. Garcia-Ortega |
| E-mail(s) |
luis.garcia@cinvestav.mx
|
| Organization name |
Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav)
|
| Department |
Department of Genetic Engineering
|
| Lab |
Laboratory for research and learning in biological computing
|
| Street address |
Km 9.6 Libramiento Norte
|
| City |
Irapuato |
| State/province |
Guanajuato |
| ZIP/Postal code |
36824 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL29390 |
| Series (1) |
| GSE161166 |
Whole-genome DNA methylation analysis in hydrogen peroxide overproducing transgenic tobacco |
|
| Relations |
| BioSample |
SAMN16722356 |
| SRA |
SRX9468633 |
