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| Status |
Public on Mar 01, 2020 |
| Title |
During development, the Sku5 mutant roots engage different genes than wild type WS roots, either on the ground or in spaceflight. |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The wild type WS plants and the Sku5 mutant plants in the WS background were germinated on ISS or on the ground and the gene expression profiles in roots at 4 days or 8 days were established. The Sku5 gene (AT4G12420) codes for a multi-copper oxidase-like protein SKU5 protein that is involved in directed root tip growth. The Sku5 protein is glycosylated, GPI-anchored and localizes to the plasma membrane and the cell wall. The Sku5 gene is expressed most strongly in expanding tissues. The development of WS and Sku5 plants on orbit differs from that on the ground as demonstrated by the comparison of the gene expression profiles between 4 days old to 8 days old plant in the two environments. However the development of Sku5 mutant plants also differs from WS at either age and in either environment, suggesting the role of the genetic background in these developmental decisions. The 4 days old Sku5 roots in orbit engaged substantially more genes than the 4 days old WS roots in orbit but also more than the 4 days old Sku5 roots on the ground. Overall the 4 days old roots differentially expressed more genes in spaceflight relative to ground than the 8 days old roots of either genotype. Finally, the 4 days old Sku5 roots in orbit differ in 862 genes from the 8 days Sku5 roots in orbit while on the ground there is merely half of the number of genes differentially expressed between the 4 days and 8 days developmental stages of the Sku5 roots.
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| Overall design |
APEX03-2 (Advanced Plant Experiment 03-2) also identified as TAGES-Isa (Transgenic Arabidopsis Gene Expression System—Intracellular Signaling Architecture) was launched on SpaceX mission CRS-5 on 10 January 2015. Dry, sterilized Arabidopsis seeds were planted aseptically on the surface of 10-cm2 solid media plates and remained dormant until removed from cold stowage and exposed to light at the initiation of the experiment on the ISS (International Space Station). The plates were grown in the Vegetable Production System (VPS/Veggie) hardware on the Columbus Module of the ISS with the overhead LED lighting of the VPS. At four or for the second experimental set at eight days, seedlings were harvested by an astronaut into KFT (Kennedy Fixation Tube) containing RNAlater solutions. Upon return to Earth, the harvested material was used to compare the transcriptomes of each genotype and each age using RNAseq technology. The patterns of gene expression was compared between treatments (spaceflight versus ground control) within each genotype of same age or between two ages within same genotype and within same treatment. For 4 day old roots 5-8 roots were combined to serve as one biological replica. For 8 day old roots 2-3 roots were used to form one biological replica. In each case the four biological replicas were used for the transcriptomic analysis.
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| Contributor(s) |
Paul A, Zupanska AK, Ferl RJ |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Mar 02, 2017 |
| Last update date |
Mar 01, 2020 |
| Contact name |
Robert J. Ferl |
| E-mail(s) |
ferllabuf@gmail.com
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| Phone |
352-273-8030
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| Organization name |
University of Florida
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| Department |
Horticultural Sciences
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| Lab |
Ferl's lab
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| Street address |
1301 Fifield Hall PO Box 110690
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| City |
Gainesville |
| State/province |
Florida |
| ZIP/Postal code |
32611 |
| Country |
USA |
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| Platforms (1) |
| GPL19580 |
Illumina NextSeq 500 (Arabidopsis thaliana) |
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| Samples (32)
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| GSM2519303 |
Ground Control, 4 days old, Sku5 Rep4 |
| GSM2519304 |
Spaceflight, 4 days old, Sku5 Rep1 |
| GSM2519305 |
Spaceflight, 4 days old, Sku5 Rep2 |
| GSM2519306 |
Spaceflight, 4 days old, Sku5 Rep3 |
| GSM2519307 |
Spaceflight, 4 days old, Sku5 Rep4 |
| GSM2519308 |
Ground Control, 4 days old, Wassilewskija Rep1 |
| GSM2519309 |
Ground Control, 4 days old, Wassilewskija Rep2 |
| GSM2519310 |
Ground Control, 4 days old, Wassilewskija Rep3 |
| GSM2519311 |
Ground Control, 4 days old, Wassilewskija Rep4 |
| GSM2519312 |
Spaceflight, 4 days old, Wassilewskija Rep1 |
| GSM2519313 |
Spaceflight, 4 days old, Wassilewskija Rep2 |
| GSM2519314 |
Spaceflight, 4 days old, Wassilewskija Rep3 |
| GSM2519315 |
Spaceflight, 4 days old, Wassilewskija Rep4 |
| GSM2519316 |
Ground Control, 8 days old, Sku5 Rep1 |
| GSM2519317 |
Ground Control, 8 days old, Sku5 Rep2 |
| GSM2519318 |
Ground Control, 8 days old, Sku5 Rep3 |
| GSM2519319 |
Ground Control, 8 days old, Sku5 Rep4 |
| GSM2519320 |
Spaceflight, 8 days old, Sku5 Rep1 |
| GSM2519321 |
Spaceflight, 8 days old, Sku5 Rep2 |
| GSM2519322 |
Spaceflight, 8 days old, Sku5 Rep3 |
| GSM2519323 |
Spaceflight, 8 days old, Sku5 Rep4 |
| GSM2519324 |
Ground Control, 8 days old, Wassilewskija Rep1 |
| GSM2519325 |
Ground Control, 8 days old, Wassilewskija Rep2 |
| GSM2519326 |
Ground Control, 8 days old, Wassilewskija Rep3 |
| GSM2519327 |
Ground Control, 8 days old, Wassilewskija Rep4 |
| GSM2519328 |
Spaceflight, 8 days old, Wassilewskija Rep1 |
| GSM2519329 |
Spaceflight, 8 days old, Wassilewskija Rep2 |
| GSM2519330 |
Spaceflight, 8 days old, Wassilewskija Rep3 |
| GSM2519331 |
Spaceflight, 8 days old, Wassilewskija Rep4 |
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| Relations |
| BioProject |
PRJNA377717 |
| SRA |
SRP101274 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE95620_FLT_4d_Sku5_to_FLT_8d_Sku5.xlsx |
206.0 Kb |
(ftp)(http) |
XLSX |
| GSE95620_FLT_4d_Sku5_to_GC_4d_Sku5.xlsx |
118.7 Kb |
(ftp)(http) |
XLSX |
| GSE95620_FLT_4d_WS_to_FLT_8d_WS.xlsx |
127.1 Kb |
(ftp)(http) |
XLSX |
| GSE95620_FLT_4d_WS_to_GC_4d_WS.xlsx |
22.1 Kb |
(ftp)(http) |
XLSX |
| GSE95620_FLT_8d_Sku5_to_FLT_8d_WS.xlsx |
164.5 Kb |
(ftp)(http) |
XLSX |
| GSE95620_FLT_8d_Sku5_to_GC_8d_Sku5.xlsx |
191.4 Kb |
(ftp)(http) |
XLSX |
| GSE95620_FLT_8d_WS_to_GC_8d_WS.xlsx |
106.4 Kb |
(ftp)(http) |
XLSX |
| GSE95620_GC_4d_Sku5_to_GC_4d_WS.xlsx |
50.2 Kb |
(ftp)(http) |
XLSX |
| GSE95620_GC_4d_Sku5_to_GC_8d_Sku5.xlsx |
121.0 Kb |
(ftp)(http) |
XLSX |
| GSE95620_GC_4d_WS_to_GC_8d_WS.xlsx |
130.0 Kb |
(ftp)(http) |
XLSX |
| GSE95620_GC_8d_Sku5_to_GC_8d_WS.xlsx |
66.0 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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