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| Status |
Public on Sep 30, 2021 |
| Title |
self-grafted BS-Seq rep1 |
| Sample type |
SRA |
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| Source name |
scion leaves
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| Organism |
Solanum virginianum |
| Characteristics |
ecotype: Ecavi
tissue: leaves
age: 5 months
rootstock: Solanum melongena
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| Treatment protocol |
Grafting was performed using the cleft methods (Lee et al., 1994, Gisbert et al., 2011)
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| Growth protocol |
Grafted plants were grown in in the experimental greenhouse of Carmagnola, Italy (44°53′N; 7°41′E) during the 2017 eggplant growing season.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the Qiagen Plant DNeasy kit (Qiagen).
Libraries were constructed starting from 120 ng of genomic DNA bisulfite-converted using the EZ DNA Methylation-Gold Kit (Zymo Research, Irvine, CA). Converted samples were immediately used to prepare bisulfite libraries employing the TrueSeq DNA Methylation Kit (Illumina, San Diego, CA) accordingly to the protocol’s instruction
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
self-grafted
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| Data processing |
Whole genome bisulfite sequencing (WGBS) and RNA-seq raw reads were trimmed using Trimmomatic (Bolger et al., 2014) to remove adapter sequences
High-quality trimmed sequences (on average 90,7 % of raw reads) were aligned against the eggplant genome (Barchi et al., 2019) using Bismark (Krueger & Andrews, 2011). Duplicated reads were collapsed into one read.
Not repeated chloroplast sequences (mappability = 1) retrieved from Ding et al., 2016 were used to estimate the bisulfite conversion. The mappability was computed on eggplant genome, with the gem‐mappability tool from the Gem library (Derrien et al., 2012), with a k-mer size of 75 bp and allowing a maximum of one mismatch.
To account for non-converted DNA, we applied a correction according to (Catoni et al. 2017, EMBO Journal). Briefly, the number of methylated reads were decreased as: m*= max(0, m – nc) (where m* is the corrected number of methylated reads, m is the raw number of methylated reads, n is the total number of reads and c is the conversion rate).
Genome_build: 67/3 genome assembly, available at http://www.eggplantgenome.org/
Supplementary_files_format_and_content: For each genotype, the CX_Report generated by Bismark is reported (Krueger et al. 2011, Bioinformatics), after correction for non-converted DNA has been applied.
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| Submission date |
Sep 03, 2019 |
| Last update date |
Sep 30, 2021 |
| Contact name |
Marco Catoni |
| Organization name |
University of Birmingham
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| Department |
School of Biosciences
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| Street address |
Edgbaston
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| City |
Birmingham |
| ZIP/Postal code |
B15 2TT |
| Country |
United Kingdom |
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| Platform ID |
GPL27419 |
| Series (2) |
| GSE136783 |
Epigenetic bases of grafting-induced vigour in eggplant [Bisulfite-Seq] |
| GSE136785 |
Epigenetic bases of grafting-induced vigour in eggplant |
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| Relations |
| BioSample |
SAMN12684620 |
| SRA |
SRX6794435 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4057864_Ecavi_Self_rep1_corrected.CX_report.txt.gz |
1.6 Gb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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