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Sample GSM4159749 Query DataSets for GSM4159749
Status Public on Apr 01, 2020
Title Tomato_Neg_Ctrl1
Sample type RNA
 
Source name non-spiked tomato RNA
Organism Solanum lycopersicum
Characteristics treatment(s): no virus spiked tomato
infection: none
virus strain: none
virus genotype: none
Treatment protocol HAV/18f culture supernatant was collected and used for inoculation. NoV GII.4 Minerva stool sample was suspended in 10% phosphate-buffered saline (PBS), centrifuged at 9000 ×g for 3 min, and the supernatant was collected and used for inoculation.
Growth protocol Confluent culture of FRhK-4 cells in 75 cm2 flasks (5 x 106 cells) were infected with 5-10 pfu/cell of HAV/18f in 1.5 ml of MEM containing 1% heat inactivated FBS. After 1 hr of adsorption, 13.5 ml of the same medium was added to each flask and Incubation continued for 5-6 days.
Extracted molecule total RNA
Extraction protocol HAV/18f was spiked onto tomatoes, and the samples were shaked in TGBE buffer and homogenized. The eluate was collected and clarified by centrifugation to remove food particulates. The supernatant was recovered, and RNA was precipitated with 70% ice cold isopropanol. The RNA pellet was collected by centrifugation and re-suspended in the lysis buffer following the instructions of RNAqueous Kit. Potassium acetate was added to precipitate any remaining polysaccharides. The extracted RNA samples were further treated with DNase and Dynabeads mRNA Purification Kit. For virus-spiked green onions and celery, material was eluted using either Glycine Buffer or TGBE buffer supplemented with pectinase, respectively, then virus particles were concentrated by ultracentrifugation and RNA was extracted with commercial kits.
Label biotin
Label protocol Samples were prepared and hybridized to FDA-EVIR GeneChip Tiling Array according to Affymetrix specifications.
 
Hybridization protocol Samples were prepared and hybridized to FDA-EVIR GeneChip Tiling Array according to Affymetrix specifications.
Scan protocol The tiling arrays were scanned using an Affymetrix GeneChip scanner with a scanning resolution of 1.56 µm pixelsize according to manufacturer's instruction.
Description total RNA: polyA enrichment
Data processing The probe intensities were extracted with Affymetrix PowerTools software (APT 2.10.2.2), and then exported to Excel for further processing.
 
Submission date Nov 13, 2019
Last update date Apr 03, 2020
Contact name Christine Fang Yu
E-mail(s) Christine.Yu@fda.hhs.gov
Phone 1-301-796-0643
Organization name US Food and Drug Administration
Department Center for Food Safety and Applied Nutrition
Lab Office of Applied Research and Safety Assessment
Street address 8301 Muirkirk Rd.
City Laurel
State/province MD
ZIP/Postal code 20708
Country USA
 
Platform ID GPL27751
Series (1)
GSE140351 Capability of FDA-EVIR Microarray for Detection of Norovirus and Hepatitis A Virus in Inoculated Tomatoes, Green Onions, and Celery

Data table header descriptions
ID_REF
VALUE normalized to the negative controls

Data table
ID_REF VALUE
15689 1
15688 1
23523 1
106854 1
20196 1
97128 1
97127 1
45765 1
7778 1
40359 1
40358 1
30804 1
72396 1
72393 1
109472 1
100109 1
23309 1
21116 1
9818 1
9817 1

Total number of rows: 105527

Table truncated, full table size 824 Kbytes.




Supplementary file Size Download File type/resource
GSM4159749_tomato_neg1.CEL.gz 472.3 Kb (ftp)(http) CEL
Processed data included within Sample table

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