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| Status |
Public on Mar 08, 2023 |
| Title |
EE501F2_093_C_T2_R2 |
| Sample type |
SRA |
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| Source name |
leaf tissue
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| Organism |
Solanum chacoense |
| Characteristics |
genotype: EE501F2_093
condition: Control
time: T2-48 hours after beetle placement
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| Treatment protocol |
For each genotype, two cages received adult Colorado potato beetles (treatment) and one cage did not receive beetles (control). Adult Colorado potato beetles were collected from untreated foliage of the commercial cultivar S. tuberosum ╘Atlantic╒ at the Michigan State University Montcalm Research Center (Lakeview, MI) on July 16th, 2019. Adult beetles were starved for 6 hours prior to being put on the experimental plants. When plants were 15-weeks old, 50 beetles were applied to treatment cages and leaf tissue was harvested for RNA isolation in the following time course: T0 = immediately preceding beetle placement; T1 = 24 hours after beetle placement; T2 = 48 hours after beetle placement. At each of the three timepoints, two biological replicates were prepared by pooling equal quantities of tissue from the third fully expanded leaf each genotype and condition (treatment or control) (N = 24). Total percent defoliation was visually determined for each treatment plant at T2
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| Growth protocol |
Six in vitro plantlets of each genotype (80-1 and EE501F2_093) (N = 12 plantlets) with good roots were transplanted to 6╙ pots in SUREMIXTM media (Michigan Grower Products Inc., Galesburg, MI). Two plants of each genotype were placed in individual RESTCLOUDTM mesh insect cages (15.3╙ wide x 15.3╙ deep x 23.6╙ long) (N = 6 cages) in a growth chamber maintained under 60% relative humidity, a 16 hr photoperiod, 16íC night and 20íC day temperature and 250 mE of light intensity. After two weeks, plants received 20-20-20 Peters Professional General Purpose Fertilizer (ICL-SF USA, Summersville, SC) at a rate of 500mg/l twice weekly.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the Qiagen RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). Samples were Turbo DNase (Thermo Fisher Scientific, Waltham, MA, USA) treated, and RNA quantity and quality was assessed using an Agilent 4200 TapeStation (Agilent Technologies Inc., Santa Clara, CA).
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit and approximately 30,000,000 50nt single-end Illumina reads were generated for each sample on the Illumina HiSeq 4000 platform.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Raw reads were processed with Trimmomatic (v0.35) (MINLEN = 36, LEADING = 20, TRAILING = 20) to remove low-quality bases, adapters, and primers (Bolger et al., 2014).
Cleaned reads were aligned to the potato doubled monoploid S. tuberosum clone DM1-3 516 R44 (DM) pseudomolecules (PGSC Version 6.1) using STAR (v2.7.3a) (Dobin et al., 2013).
Alignments for each sample generated from separate Illuminia lanes were merged using the Picard tool MergeSamFiles (v2.18.27-Java-1.8) (broadinstitute.github.io/picard).
Reads aligning to annotated DM reference genes were counted using HTSeq in union mode (v0.11.2) (Anders et al., 2015).
Genome_build: Spud DB http://solanaceae.plantbiology.msu.edu/index.shtml
Supplementary_files_format_and_content: text file containing Htseq counts
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| Submission date |
Mar 22, 2021 |
| Last update date |
Mar 09, 2023 |
| Contact name |
Natalie Kaiser |
| E-mail(s) |
[email protected]
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| Organization name |
Michigan State University
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| Department |
PSM
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| Street address |
1066 Bogue Street
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| City |
East Lansing |
| State/province |
MI |
| ZIP/Postal code |
48824 |
| Country |
USA |
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| Platform ID |
GPL27550 |
| Series (1) |
| GSE169331 |
Expression profiling of Solanum chacoense in response to Colorado potato beetle herbivory |
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| Relations |
| BioSample |
SAMN18420470 |
| SRA |
SRX10410786 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5195919_EE501F2_093_C_T2_R2.REVERSE.htseqcounts.txt.gz |
147.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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