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| Status |
Public on Sep 30, 2021 |
| Title |
self-grafted RNA-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 |
Total RNA was extracted using the Spectrum Plant Total RNA Kit (Sigma, Saint Loius, USA) method according to the manufacturer’s instructions.
Libraries for RNA expression analysis were prepared in duplicates from 2 µg of total RNA using the TrueSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA) following the manufacturer’s instructions. Libraries quality and fragment sizes were checked with a TapeStation 2200 (Agilent technologies, Santa Clara, CA) instrument.
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| Library strategy |
RNA-Seq |
| Library source |
genomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
self-grafted
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| Data processing |
Reads were mapped with TopHat (Trapnell et al., 2009) on the eggplant genome (Barchi et al., 2019), using parameters–max-multihits 1–read-realign-edit-dist 0–no-mixed.
Mapped reads were subsequently counted using htseq-count (Anders et al., 2015) with parameters–order name–type = exon–stranded = reverse. As most of plant genomes are composed of transposable elements and LTRs are the most abundant, we used the LTRpred R tool (https://github.com/HajkD/LTRpred) to generate a new retrotransposon annotation file which was used as input for htseq-count.
Differential expression was assessed with DEseq (Anders and Huber, 2010), using as thresholds 1 Log2 fold change and a Benjamini-Hochberg’s FDR < 0.05.
Genome_build: 67/3 genome assembly, available at http://www.eggplantgenome.org/
Supplementary_files_format_and_content: For each genotype, the bigwig coverage file is provided, generated with samtools depth (Li et al 2009, Bioinformatics) from the the aligned reads.
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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) |
| GSE136784 |
Epigenetic bases of grafting-induced vigour in eggplant [RNA-Seq] |
| GSE136785 |
Epigenetic bases of grafting-induced vigour in eggplant |
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| Relations |
| BioSample |
SAMN12684631 |
| SRA |
SRX6794427 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4057872_Self-rep1.bw |
145.3 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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