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Series GSE115554 Query DataSets for GSE115554
Status Public on Oct 29, 2018
Title Comparative gene expression analysis in the Arabidopsis thaliana root apex using RNA-seq and microarray transcriptome profiles [RNA-seq]
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary The root apex is an important section of the plant root, involved in environmental sensing and cellular development. Analyzing the gene profile of root apex in diverse environments is important and challenging, especially when the samples are limiting and precious, such as in spaceflight. The feasibility of using tiny root sections for transcriptome analysis was examined in this study.To understand the gene expression profiles of the root apex, Arabidopsis thaliana Col-0 roots were sectioned into Zone-I (0.5 mm, root cap and meristematic zone) and Zone-II (1.5 mm, transition, elongation and growth terminating zone). Gene expression was analyzed using microarray and RNA seq.Both the techniques, arrays and RNA-Seq identified 4180 common genes as differentially expressed (with > two-fold changes) between the zones. In addition, 771 unique genes and 19 novel TARs were identified by RNA-Seq as differentially expressed which were not detected in the arrays.
Single root tip zones can be used for full transcriptome analysis; further, the root apex zones are functionally very distinct from each other. RNA-Seq provided novel information about the transcripts compared to the arrays. These data will help optimize transcriptome techniques for dealing with small, rare samples.
Overall design Arabidopsis thaliana var. Columbia (COL-0) seedlings were grown on sterile solid media plates containing 0.5 % phytagel. The plates were vertically placed in growth chambers with continuous light (80-100 µmol m -2) at a constant temperature of 19° C. Eight day old seedlings were harvested into RNA-later solution in a 50 mL centrifuge tubes and stored at -20 °C freezer. The root tips were dissected into zone-I: 0.5mm from the tip including the root cap and root division zones, and zone-II: 1.5mm sections including root elongation and root hair zone. Microarray and sequencing experiments were performed.
Contributor(s) Krishnamurthy A, Ferl RJ, Paul A
Citation(s) 30473943
Submission date Jun 11, 2018
Last update date Dec 03, 2018
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 (6)
GSM3181995 ROOT ZONE I (0.5mm) REP 1 [RNA-seq]
GSM3181996 ROOT ZONE I (0.5mm) REP 2 [RNA-seq]
GSM3181997 ROOT ZONE I (0.5mm) REP 3 [RNA-seq]
This SubSeries is part of SuperSeries:
GSE115555 Comparing RNA-Seq and microarray gene expression data in two zones of the Arabidopsis root apex relevant to spaceflight
BioProject PRJNA475464
SRA SRP150181

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Supplementary file Size Download File type/resource
GSE115554_RNAseq_Genediff_pilot.xlsx 3.2 Mb (ftp)(http) XLSX
GSE115554_RNAseq_Isoformsdiff_pilot.xlsx 6.0 Mb (ftp)(http) XLSX
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