GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE95620 Query DataSets for GSE95620
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
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.
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.
Contributor(s) Paul A, Zupanska AK, Ferl RJ
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Mar 02, 2017
Last update date Mar 01, 2020
Contact name Robert J. Ferl
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)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (32)
GSM2519300 Ground Control, 4 days old, Sku5 Rep1
GSM2519301 Ground Control, 4 days old, Sku5 Rep2
GSM2519302 Ground Control, 4 days old, Sku5 Rep3
BioProject PRJNA377717
SRA SRP101274

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
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 SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap