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Series GSE81442 Query DataSets for GSE81442
Status Public on Sep 01, 2017
Title Arg1 functions in the physiological adaptation of undifferentiated plant cells to spaceflight
Organism Arabidopsis thaliana
Experiment type Expression profiling by array
Summary Scientific access to spaceflight and especially the International Space Station has revealed that physiological adaptation to spaceflight is accompanied or enabled by changes in gene expression that significantly alter the transcriptome of cells in spaceflight. A wide range of experiments have shown that plant physiological adaptation to spaceflight involves gene expression changes that alter cell wall and other metabolisms. However, while transcriptome profiling aptly illuminates changes in gene expression that accompany spaceflight adaptation, mutation analysis is required to illuminate key elements required for that adaptation.
In this study transcriptome profiling was used to gain insight into the spaceflight adaptation role of Altered response to gravity-1 (Arg1), a gene known to affect gravity responses in plants on Earth. The study compared expression profiles of cultured lines of Arabidopsis thaliana derived from wild type (WT) cultivar Col-0 to profiles from a knock-out line deficient in the gene encoding (ARG1 KO), both on the ground and in space. The cell lines were launched on SpaceX CRS-2 as part of the Cellular Expression Logic (CEL) experiment of the BRIC17 spaceflight mission. The cultured cell lines were grown within 60mm Petri plates in Petri Dish Fixation Units (PDFUs) that were housed within the Biological Research In Canisters (BRIC) hardware. Spaceflight samples were fixed on orbit. Differentially expressed genes were identified between the two environments (spaceflight and comparable ground controls) and the two genotypes (WT and ARG1 KO). Each genotype engaged unique genes during physiological adaptation to the spaceflight environment, with little overlap. Most of the genes altered in expression in spaceflight in WT cells were found to be Arg1-dependent, suggesting a major role for that gene in the physiological adaptation of undifferentiated cells to spaceflight.
 
Overall design The CEL (Cellular Expression Logic) experiment setup and organization was a modification of a previous Arabidopsis cell culture experiment in BRIC16 (Paul, Zupanska et al. 2012). The CEL BRIC17 experiment was launched on board the Dragon capsule of SpaceX-3 CRS mission to the International Space Station (ISS) on the 1st of March 2013. The cultured cell lines (both the ground control and the spaceflight samples) were grown within 60mm Petri plates in Petri Dish Fixation Units (PDFUs) that were housed within the Biological Research In Canister (BRIC) hardware. Two BRIC containers (A and B) were assigned to CEL within the BRIC17 payload. Each chamber housed 5 PDFUs, each PDFU holding one 60mm Petri plate. In each BRIC container there were 2 plates with wild type (WT) cells and 3 plates with knock-out cells of two genotypes. The exact same PDFU composition was recapitulated in BRICs on the ground in the ISS Environmental Simulator (ISSES) chamber at Kennedy Space Center (KSC) as Ground Controls. The Ground Controls were initiated with a 48 hrs delay so that the precise temperature environment of the ISS could be recreated for the ground controls in the ISSES chamber. Cells were fixed in-flight in RNAlater on the 10th day on orbit, and the ground controls were fixed 48 hours later. RNAlater fixation was initiated by the crew using an activation tool that moves RNAlater from a storage container in the PDFU into the Petri Plate. Twenty four hours after fixation, the entire BRIC was moved to the MELFI (Minus Eighty-degree Laboratory Freezer for ISS) where it resided until cold stowage transport back to Earth within the Dragon capsule. After returning to Earth the samples were reclaimed at KSC, and then transported to the University of Florida (UF) laboratories. The total RNA was extracted from spaceflight samples and corresponding Ground Control samples and subjected to microarrays.
 
Contributor(s) Zupanska AK, Shultz E, Yao J, Sng N, Zhou M, Callaham JE, Ferl RJ, Paul A
Citation(s) 29088549
Submission date May 13, 2016
Last update date Apr 13, 2021
Contact name Robert J. Ferl
E-mail(s) ferllabuf@gmail.com
Phone 352-273-8030
Organization name University of Florida
Department Horticultural Sciences
Lab Ferl's lab
Street address 1301 Fifield Hall PO Box 110690
City Gainesville
State/province Florida
ZIP/Postal code 32611
Country USA
 
Platforms (1)
GPL198 [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array
Samples (18)
GSM2152569 FLIGHT BRIC A PDFU-1 300 WT Rep1
GSM2152570 FLIGHT BRIC A PDFU-1 300 WT Rep2
GSM2152571 FLIGHT BRIC A PDFU-2 302 WT
Relations
BioProject PRJNA321540

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE81442_RAW.tar 28.7 Mb (http)(custom) TAR (of CEL)
GSE81442_Statistical_analysis_dataset.xlsx 8.5 Mb (ftp)(http) XLSX
Processed data included within Sample table
Processed data are available on Series record

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