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| Status |
Public on Aug 16, 2018 |
| Title |
Small leaf - Biorep 2 |
| Sample type |
SRA |
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| Source name |
Leaf
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| Organism |
Vitis riparia |
| Characteristics |
infection: NA
leaf size: Small
genotype: Wild type
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| Treatment protocol |
Ungalled control leaves vs. leaves naturally infected by Daktulosphaira vitifoliae gall-inducing insect.
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| Growth protocol |
Samples were collected in the field in Rocheport (Missouri, USA; 38° 58' 16.424" N, 92° 32' 54.118" W).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were dissected on ice, and flash frozen in liquid nitrogen. RNA was extracted and DNase1 treated, on column, using the Spectrum Plant Total RNA Kit (Sigma #STRN50-1KT; Sigma-Aldrich, St. Louis, MO, USA; protocol A and Appendix). The resulting RNA was further purified and concentrated with the RNeasy MinElute Cleanup Kit (Qiagen #74204; Qiagen, Hilden, Germany) and eluted with pure water. The quality of the resulting RNA was assessed using the Agilent 2100 BioAnalyzer (www.genomics.agilent.com; Agilent, Santa Clara, CA, USA), and all RNA integrity number values were found to be above 8.
The Illumina libraries were constructed using the RNA TruSeq Kit (Illumina, Inc., San Diego, CA, USA), barcoded (TACT ungalled; GTAT galled), and sequenced single-end with 100bp reads on the Illumina HiSeq-2000 platform at the University of Missouri DNA core (http://dnacore.missouri.edu ).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Wild grapevine ungalled control (small) leaf
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| Data processing |
A custom Perl script was used to parse the libraries and remove barcode sequences resulting in approximately 40.9 million reads for the ungalled library and 40.3 million reads for the galled library.
NextGENe V2.3.3.1 (SoftGenetics, LLC., State College, PA, USA) was used to quality filter the fastq data, remove reads with a median quality score of less than 22, trim reads at positions that had 3 consecutive bases with a quality score of less than 20, and remove any trimmed reads with a total length less than 40 bp.
Genome-wide syntenic analyses were performed to identify Arabidopsis thaliana – Vitis vinifera orthologs using CoGe (http://genomevolution.org/CoGe/).
Arabidopsis – Vitis orthologs were identified using reciprocal BLASTp analyses (protein database) with a 0.00001 p-value cutoff resulting in the annotation of ~86.7 % of all coding sequences in the Vitis vinifera V2 genome.
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample.
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| Submission date |
Aug 15, 2018 |
| Last update date |
Aug 16, 2018 |
| Contact name |
William G. Spollen |
| E-mail(s) |
[email protected]
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| Phone |
573-884-8151
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| Organization name |
University of Missouri-Columbia
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| Department |
Informatics Research Core Facility
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| Lab |
Scott A. Givan
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| Street address |
113 Bond Life Sciences Center
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| City |
Columbia |
| State/province |
MO |
| ZIP/Postal code |
65211 |
| Country |
USA |
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| Platform ID |
GPL24498 |
| Series (1) |
| GSE118569 |
A galling insect activates plant reproductive programs during gall development |
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| Relations |
| BioSample |
SAMN09837301 |
| SRA |
SRX4554088 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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