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E-MTAB-1009

ABSTRACT: Transcription profiling by array of the response of Arabidopsis cultivar Columbia etiolated seedlings and undifferentiated tissue culture cells to the spaceflight environment

PROVIDER: E-MTAB-1009 | ExpressionAtlas | 2017-03-27

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-MTAB-1009-analysis-methods.tsv	Tabular
	E-MTAB-1009-atlasExperimentSummary.Rdata	Rdata
	E-MTAB-1009-configuration.xml	Xml
	E-MTAB-1009-percentile-ranks.tsv	Tabular
	E-MTAB-1009.condensed-sdrf.tsv	Tabular

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Transcription profiling by array of the response of Arabidopsis cultivar Columbia etiolated seedlings and undifferentiated tissue culture cells to the spaceflight environment

Project description:transcriptome response of Arabidopsis cultivar Columbia etiolated seedlings and undifferentiated tissue culture cells to the spaceflight environment We address a key baseline question of whether gene expression changes are induced by the orbital environment, and then we ask whether undifferentiated cells, cells presumably lacking the typical gravity response mechanisms, perceive spaceflight. Arabidopsis seedlings and undifferentiated cultured Arabidopsis cells were launched in April, 2010, as part of the BRIC-16 flight experiment on STS-131. Biologically replicated DNA microarray and averaged RNA digital transcript profiling revealed several hundred genes in seedlings and cell cultures that were significantly affected by launch and spaceflight. The response was moderate in seedlings; only a few genes were induced by more than 7-fold, and the overall intrinsic expression level for most differentially expressed genes was low. In contrast, cell cultures displayed a more dramatic response, with dozens of genes showing this level of differential expression, a list comprised primarily of heat shock-related and stress-related genes. This baseline transcriptome profiling of seedlings and cultured cells confirms the fundamental hypothesis that survival of the spaceflight environment requires adaptive changes that are both governed and displayed by alterations in gene expression. The comparison of intact plants with cultures of undifferentiated cells confirms a second hypothesis: undifferentiated cells can detect spaceflight in the absence of specialized tissue or organized developmental structures known to detect gravity. This experiment was launched on STS-131 in 2010 and was supported by NASA grant NNX10AF45G - The Impact of Spaceflight on Arabidopsis: Deep Sequencing and DNA Arrays as Collaborative Readouts of the Transcriptome of Arabidopsis Seedlings and Undifferentiated Cells in Space to A-L. Paul and R.J. Ferl.

2014-04-10 | GSE56658 | GEO

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Project description:Transcription profiling by array of the response of Arabidopsis cultivar Columbia etiolated seedlings and undifferentiated tissue culture cells to the spaceflight environment

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E-MTAB-3011

Project description:Transcription profiling by array of etiolated Arabidopsis thaliana seedlings in response to microgravity

2014-10-15 | E-MTAB-3011 | ExpressionAtlas

E-GEOD-28297

Project description:Expression data from WT (Columbia) and pifq (pif1pif3pif4pif5) mutant Arabidopsis seedlings

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Identification of new full length Arabidopsis genes - pilot arrays

Project description:Identification of new and unpredicted full length Arabidopsis genes. Examination of cRNA prepared from Arabidopsis thaliana ecotype Columbia light grown 7-day old seedlings, light grown 7-day old seedlings treated at 4 degrees C for 24hrs, and etiolated 7-day old seedlings using pilot genome tiling arrays. Total RNA was isolated from seedlings with the TRIzol reagent procedure of Invitrogen, then poly(A)+ RNA was purified with Qiagen oligotex. One microgram poly(A)+ RNA was converted into ds-cDNA using T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions using ENZO labeling kit, fragmented and then 20 micrograms of fragmented cRNA were hybridized to the arrays according to Affymetrix instructions. Keywords: other

2003-10-30 | GSE604 | GEO

E-MTAB-5980

Project description:Transcription profiling by array of Arabidopsis thaliana columbia and DEWAX2 overexpression plants line stems

2017-08-16 | E-MTAB-5980 | ExpressionAtlas

E-MTAB-4245

Project description:Transcription profiling by high throughput sequencing of wheat cultivar Chinese Spring seedlings maintained without phosphate for 10 days

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E-MTAB-2845

Project description:Transcription profiling by array of influenza PR8 infected mouse lung tissue

2014-08-16 | E-MTAB-2845 | ExpressionAtlas

Transcription profiling by array of the response of Arabidopsis cultivar Columbia etiolated seedlings and undifferentiated tissue culture cells to the spaceflight environment

Project description:We address a key baseline question of whether gene expression changes are induced by the orbital environment, and then we ask whether undifferentiated cells, cells presumably lacking the typical gravity response mechanisms, perceive spaceflight. Arabidopsis seedlings and undifferentiated cultured Arabidopsis cells were launched in April, 2010, as part of the BRIC-16 flight experiment on STS-131. Biologically replicated DNA microarray and averaged RNA digital transcript profiling revealed several hundred genes in seedlings and cell cultures that were significantly affected by launch and spaceflight. The response was moderate in seedlings; only a few genes were induced by more than 7-fold, and the overall intrinsic expression level for most differentially expressed genes was low. In contrast, cell cultures displayed a more dramatic response, with dozens of genes showing this level of differential expression, a list comprised primarily of heat shock-related and stress-related genes. This baseline transcriptome profiling of seedlings and cultured cells confirms the fundamental hypothesis that survival of the spaceflight environment requires adaptive changes that are both governed and displayed by alterations in gene expression. The comparison of intact plants with cultures of undifferentiated cells confirms a second hypothesis: undifferentiated cells can detect spaceflight in the absence of specialized tissue or organized developmental structures known to detect gravity.

2012-03-08 | E-MTAB-1009 | biostudies-arrayexpress

The Arabidopsis spaceflight transcriptome: a comparison of whole plants to discrete root, hypocotyl and shoot responses to the orbital environment

Project description:transcriptome response of Arabidopsis cultivar Columbia and WS whole plants and plant tissue roots, hypocotyls and shoots to the spaceflight environment Arabidopsis thaliana was evaluated for its response to the spaceflight environment in three replicated experiments on the International Space Station. Two approaches were used; GFP reporter genes were used to collect gene expression data in real time within unique GFP imaging hardware, and plants were harvested on orbit to RNAlater for subsequent analyses of gene expression with using Affymetrix and SAGE transcriptome analyses. Three tissue types were examined (leaves, hypocotyls and roots) and compared to analyses conducted with whole plants. Transcriptome analyses with whole plants suggested that the spaceflight environment had little impact on the transcriptome of arabidopsis, however, closer examination of selected tissues revealed that there are a number of tissue-specific responses that arabidopsis employs to respond to this novel environment. This experiment was launched on STS-131 in 2010 and was supported by NASA grant NNX07AH27G - Transgenic Plant Biomonitors of Space Flight Exposure to R.J. Ferl and A-L. Paul.

2014-04-10 | GSE56659 | GEO

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