NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE95582 Query DataSets for GSE95582
Status Public on Jun 07, 2019
Title During development, the Sku6 mutant roots engage different genes than wild type Col-0 roots, either on the ground or in spaceflight.
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary The wild type Col-0 plants and the Sku-6 mutant plants of the Col-0 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 Sku6 gene (At2g03680) codes for a protein that localizes to microtubule within the cortical array and putatively acting as an intramolecular linker. The development of Col-0 and Sku-6 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 Sku-6 mutant plants also differs from Col-0 at either age and in either environment, suggesting the role of the genetic background in these developmental decisions. The 4 days old Sku-6 roots in orbit engaged more genes than the 4 days old Col-0 roots in orbit but also more than the 4 days old Sku-6 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.
 
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 01, 2017
Last update date Jun 07, 2019
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)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (32)
GSM2516735 Ground Control, 4 days old, Col0 Rep1
GSM2516736 Ground Control, 4 days old, Col0 Rep2
GSM2516737 Ground Control, 4 days old, Col0 Rep3
Relations
BioProject PRJNA377558
SRA SRP100938

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
GSE95582_FLT_4d_Col-0_to_FLT_8d_Col-0.xlsx 157.9 Kb (ftp)(http) XLSX
GSE95582_FLT_4d_Col-0_to_GC_4d_Col-0.xlsx 167.2 Kb (ftp)(http) XLSX
GSE95582_FLT_4d_Sku6_to_FLT_4d_Col-0.xlsx 51.2 Kb (ftp)(http) XLSX
GSE95582_FLT_4d_Sku6_to_FLT_8d_Sku6.xlsx 190.2 Kb (ftp)(http) XLSX
GSE95582_FLT_4d_Sku6_to_GC_4d_Sku6.xlsx 103.8 Kb (ftp)(http) XLSX
GSE95582_FLT_8d_Col-0_to_GC_8d_Col-0.xlsx 97.6 Kb (ftp)(http) XLSX
GSE95582_FLT_8d_Sku6_to_FLT_8d_Col-0.xlsx 38.6 Kb (ftp)(http) XLSX
GSE95582_FLT_8d_Sku6_to_GC_8d_Sku6.xlsx 62.3 Kb (ftp)(http) XLSX
GSE95582_GC_4d_Col-0_to_GC_8d_Col-0.xlsx 256.6 Kb (ftp)(http) XLSX
GSE95582_GC_4d_Sku6_to_GC_4d_Col-0.xlsx 71.5 Kb (ftp)(http) XLSX
GSE95582_GC_4d_Sku6_to_GC_8d_Sku6.xlsx 215.6 Kb (ftp)(http) XLSX
GSE95582_GC_8d_Sku6_to_GC_8d_Col-0.xlsx 39.0 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