NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4057864 Query DataSets for GSM4057864
Status Public on Sep 30, 2021
Title self-grafted BS-Seq rep1
Sample type SRA
 
Source name scion leaves
Organism Solanum virginianum
Characteristics ecotype: Ecavi
tissue: leaves
age: 5 months
rootstock: Solanum melongena
Treatment protocol Grafting was performed using the cleft methods (Lee et al., 1994, Gisbert et al., 2011)
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.
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
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina NextSeq 500
 
Description self-grafted
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.
 
Submission date Sep 03, 2019
Last update date Sep 30, 2021
Contact name Marco Catoni
Organization name University of Birmingham
Department School of Biosciences
Street address Edgbaston
City Birmingham
ZIP/Postal code B15 2TT
Country United Kingdom
 
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
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap