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| Status |
Public on Mar 29, 2022 |
| Title |
ctr10_1 |
| Sample type |
SRA |
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| Source name |
ctr10_green stem
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| Organism |
Vitis vinifera |
| Characteristics |
cultivar: Touriga Nacional
age: post inoculation day 10
tissue: Green stem
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Stem tissue samples were ground in liquid nitrogen and total RNA was extracted using CTAB-based extraction protocol according to Gambino et al. (2008) followed by a DNase I treatment (RNase-Free DNase Set, Qiagen). Concentration and quality of the total extracted RNA were checked using the 'Quant-it ribogreen RNA assay' (Life Technologies, Grand Island, NY, USA) and the RNA 6000 nano chip (Agilent Technologies, Santa Clara, CA, USA), respectively.
Illumina mRNA sequencing libraries were made from 200 ng of total RNA of each sample using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen, Vienna, Austria) according to manufacturer's protocol using 15 cycles for the enrichment PCR step. Libraries were quantified by qPCR on a Lightcycler 480 (Roche, Basel, Switzerland), according to Illumina's protocol 'Sequencing Library qPCR Quantification protocol guide', version February 2011. A High Sensitivity DNA chip (Agilent Technologies, Santa Clara, CA, US) was used to control the library's size distribution and quality. The libraries were equimolarly pooled and sequenced at the NXTGNT massively parallel sequencing facility (www.nxtgnt.ugent.be, Ghent University) on an Illumina NextSeq 500 high throughput flow cell, generating single-end 75bp reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
RUN345-AC-20_S13
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| Data processing |
Adequate sequencing quality was confirmed using FastQC version 0.11.5 (Andrews, 2010).
Afterward, these reads were trimmed using cutadapt (Martin, 2011) version 1.11 to remove the “QuantSEQ FWD” adaptor sequence. . Potential contamination was checked using FastQ Screen version 0.7.0 (Wingett and Andrews, 2018).
The trimmed reads were mapped to the combined annotated reference genome of V. vinifera (NCBI Reference Sequence: GCF_000003745.3) and L. theobromae strain LA-SOL3 (SUB3910116, Félix et al., unpublished) using the STAR aligning software version 2.5.3a (Dobin et al., 2013).
Following the mapping step, the RSEM software version v1.2.31 (Li and Dewey, 2011), was used to generate the count tables for both V. vinifera and L. theobromae. Please note that the reference genome from Vitis vinifera was combined with the genome of Lasiodiplodia theobromae to have a joined reference genome to characterize the mixed samples of both organisms (VitisVinifera_V3.gff.gz).
Genome_build: V. vinifera GCF_000003745.3; L. theobroma SUB3910116
Supplementary_files_format_and_content: tab-delimited text files include gene_id, transcirpt_id(s), gene length, effective_length, expected_counts, TPM an FPKM for each sample
Genome_build: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/003/745/GCF_000003745.3_12X/GCF_000003745.3_12X_genomic.gff.gz
Genome_build: VitisVinifera_V3.gff.gz
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| Submission date |
Apr 01, 2019 |
| Last update date |
Mar 29, 2022 |
| Contact name |
Laurentijn Tilleman |
| Organization name |
Ghent University
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| Street address |
Ottergemsesteenweg 460
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| City |
Gent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
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| Platform ID |
GPL24368 |
| Series (1) |
| GSE129109 |
Dual RNA-Sequencing of Vitis vinifera During Lasiodiplodia theobromae Infection Unveils Host-Pathogen Interactions |
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| Relations |
| BioSample |
SAMN11298955 |
| SRA |
SRX5611564 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3693424_20.genes.results.txt.gz |
592.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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