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| Status |
Public on Nov 05, 2018 |
| Title |
ST-10_S2_R1_001 |
| Sample type |
SRA |
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| Source name |
Control plantlets cultured for 10 days without MVOC exposure
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| Organism |
Nicotiana tabacum |
| Characteristics |
growth stage: 10 days after germination
mvoc exposure: None
cultivar: Samsun
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| Treatment protocol |
Tobacco seeds were surface-sterilized by immersion in 4% (w/v) sodium hypochlorite solution for 10 min followed by 3 x rinse with sterile water. Seeds were then placed on the surface of MS medium in petri dish and cultured for six days. Germinated seedlings were then transferred to Magenta GA7 vessels containing MS medium without exposure to microbial volatile organic compounds (MVOCs). There were three replicate seedling plants per vessel and four replicate vessels per treatment. After 10 days of cultivation, tissue samples including the apical meristem and 3 to 4 terminal leaves from all three seedling plants per vessel were collected, placed in a 1.5 ml microcentrifuge tube and immediately immersed in liquid nitrogen. Samples were pulverized into a fine powder using Geno/Grinder 2010 and stored at -80°C for RNA extraction use.
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| Growth protocol |
Premixed medium powder containing MS salts and vitamins (Murashige and Skoog, 1962, Physiol Plant 15,473) were acquired from Phytotechnology Laboratories (Cat No. M519, Overland Park, KS, USA). Culture medium was prepared by supplementing medium powder with 30 g/L sucrose with pH adjusted to 5.8 prior to autoclaving at 121°C for 20 min. Medium was distributed to Magenta GA7 vessel at 100 ml per vessel. After plants were inserted cultures were maintained at 25°C under a 16 h light and 8 h dark photocycle for 10 days prior to sample collection.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was then extracted from 100 mg tissue powder using the RNeasyR Plant Mini Kit per manufacturer’s instructions (Qiagen, Redwood City, CA, USA). There were four biological replicates from each treatment. RNA sequencing was performed by Genewiz via Illumina HiSeq platform (100bp paired end reads) (South Plainfield, NJ, USA).
Library preparation and 50bp single-end sequencing on the Illumina HiSeq system was performed by Genewiz (South Plainfield, NJ, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Raw reads were processed and analyzed by Genewiz. Trimmed sequences were imported into CLC Genomics Workbench (version v10.0.1, Qiagen, Redwood City, CA, USA) for de novo transcriptome assembly and mapping to Solanum lycopersicum genome assembly SL 3.0 (https://www.ncbi.nlm.nih.gov/genome/?term=tomato) using the CLC Genomics Workbench v10.0.1 RNA-seq analysis tool and default parameters (Mismatch cost 2, Insertion cost 3, Deletion Cost 3, Length fraction 0.8, Similarity fraction 0.8, Max hits for a read 10).
Genome_build: Solanum lycopersicum assembly SL 3.0 (2018 Solanaceae Genomics Project. https://www.ncbi.nlm.nih.gov/assembly/GCF_000188115.4/)
Supplementary_files_format_and_content: Tab-delimited text files include Gene ID-name, Region, TPM, Gene length, Unique gene reads, Total gene reads
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| Submission date |
Sep 24, 2018 |
| Last update date |
Nov 05, 2018 |
| Contact name |
Chris Dardick |
| E-mail(s) |
Chris.Dardick@ars.usda.gov
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| Phone |
1-304-725-3451
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| Organization name |
USDA-ARS
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| Department |
Appalachian Fruit Research Station
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| Street address |
2217 Wiltshire Road
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| City |
Kearneysville |
| State/province |
WV |
| ZIP/Postal code |
25430 |
| Country |
USA |
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| Platform ID |
GPL13760 |
| Series (1) |
| GSE120388 |
Tobacco transcriptomic changes induced by C. sph. MVOC |
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| Relations |
| BioSample |
SAMN10118525 |
| SRA |
SRX4733777 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3399612_ST-10_S2_R1_001_GE_-2.xlsx |
1.4 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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