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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Examine gene expression in maize pulvini in gravitropsim

ABSTRACT: A gradient cell elongation with maximum in the lower side of pulvini and minimum in the upper side of pulvini pushes a maize stem upwards from a horizontal to a vertical position during gravitropsim. A differentiated gene expression between lower and upper pulvini was examined at 1 h, 6 and 24 h. Gene expression levels were compared in control (not bending), lower and upper (bending) pulvini. The samples were harvested at 1 h, 6 h and 24 h gravitropsim and total RNA were extracted using for microarray experiment.

ORGANISM(S): Zea mays

SUBMITTER: Qisen Zhang

PROVIDER: E-GEOD-26071 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Examine gene expression in maize pulvini in gravitropsim

Project description:A gradient cell elongation with maximum in the lower side of pulvini and minimum in the upper side of pulvini pushes a maize stem upwards from a horizontal to a vertical position during gravitropsim. A differentiated gene expression between lower and upper pulvini was examined at 1 h, 6 and 24 h.

2011-07-31 | GSE26071 | GEO

Diurnal Regulation of Gene Expression in Leaves Over a 72-Hour Period

Project description:Background: Plant diurnal rhythms are vital environmental adaptations to coordinate internal physiological responses to alternating day-night cycles. A comprehensive view of diurnal biology has been lacking for maize (Zea mays), a major world crop. Methodology: A photosynthetic tissue, the leaf, and a non-photosynthetic tissue, the developing ear, were sampled under natural field conditions. Genome-wide transcript profiling was conducted on a high-density 105K Agilent microarray to investigate diurnal rhythms. The top-most fully expanded leaf from each plant collected. Plants were sampled every 4 hours over 3 days. Our sampling times were: 6 am (dawn), 10 am, 2 pm, 6 pm, 10 pm and 2 am. Tissues were collected from three field reps and within each field rep we collected samples from three individual plants

2010-09-02 | E-GEOD-23917 | biostudies-arrayexpress

Diurnal Regulation of Gene Expression in Immature Ear Over a 72-Hour Period

Project description:Background: Plant diurnal rhythms are vital environmental adaptations to coordinate internal physiological responses to alternating day-night cycles. A comprehensive view of diurnal biology has been lacking for maize (Zea mays), a major world crop. Methodology: A photosynthetic tissue, the leaf, and a non-photosynthetic tissue, the developing ear, were sampled under natural field conditions. Genome-wide transcript profiling was conducted on a high-density 105K Agilent microarray to investigate diurnal rhythms. The top-most immature ear, 4-5 cm in length, was collected. Plants were sampled every 4 hours over 3 days. Our sampling times were: 6 am (dawn), 10 am, 2 pm, 6 pm, 10 pm and 2 am. Tissues were collected from three field reps and within each field rep we collected samples from three individual plants

2010-09-02 | E-GEOD-23916 | biostudies-arrayexpress

Diurnal Regulation of Gene Expression in Leaves and Immature Ears Over a 72-Hour Period

Project description:This SuperSeries is composed of the following subset Series: GSE23916: Diurnal Regulation of Gene Expression in Immature Ear Over a 72-Hour Period GSE23917: Diurnal Regulation of Gene Expression in Leaves Over a 72-Hour Period Refer to individual Series

2010-09-02 | E-GEOD-23918 | biostudies-arrayexpress

Bulk cell RNAseq of putatative intestinal stem cell populations

Project description:A comparative bulk cell RNA-seq analysis of diverse intestinal stem cell populations was performed, for cells expressing the following markers: Lgr5-eGFPhi, Cd166+, Cd24lo, Grp78, upper side population (SP), Bmi1, mTert, Hopx, Dclk1, a lower side population (SP)

2017-07-10 | GSE99815 | GEO

Separated Pancreatic stellate cells (PSCs) by functional separation using modified Matrigel invasion assay

Project description:We separated PSCs by functional separation using moidfied Matrigel invasion assay our previously reported (Fujiwara, PLoS One, 2012). In this culture system, we evaluated two primary cultures of human PSCs. PSCs in the upper chambers were incubated for 72 hours in culture with SUIT-2 pancreatic cancer cells in the lower chambers, or as controls without pancreatic cancer cells in the lower chambers, and were collected from the top and bottom sides of the upper chambers separately. The top side-derived PSCs were cells that did not migrate toward the cancer cells, and the bottom side-derived PSCs were cells that migrated toward the pancreatic cancer cells. We then performed a DNA microarray analysis using these cells.

2014-02-25 | GSE55300 | GEO

Separated Pancreatic stellate cells (PSCs) by functional separation using modified Matrigel invasion assay

2014-02-25 | E-GEOD-55300 | biostudies-arrayexpress

Transcription profiling of maize pulvinus after gravity treatment

Project description:Not much is known about the molecular processes involved during gravitropism in monocot plants such as maize. A microarray based study on the expression of genes after a gravity stimulating the maize pulvinus will provide us with valuable information and a better understanding of the underlying molecular processes involved in monocot gravitropism. Objectives for this study included the identification of genes that were regulated at the transcriptional and translation level during gravitropism in the maize pulvinus. This was achieved by microarray analysis of total RNA versus polyribosome associated RNA during a time-course of gravity stimulation of the maize pulvinus. Experiment Overall Design: Six week old maize plants were gravity stimulated by 90Âº reorientation. Upper (slow elongation) and lower (fast elongation) halves of the most gravity competent pulvini were harvested over a time course ranging from 2 minutes up to one hour (2min, 5 min, 15min, 30min, 60min). Pulvini samples from control (vertical, no gravity stimulation) plants were harvested and labeled as left and right. For each time point, total mRNA and polyribosome-associated mRNA were purified and the transcript profiles analyzed using Affymetrix GeneChipÂ® Maize Genome Arrays. The experiment was repeated twice (two growing seasons) and represent two biological repetitions.

2008-10-18 | E-GEOD-8320 | biostudies-arrayexpress

Arabidopsis inflorescence stems: upper flanks vs lower flanks after gravi-stimulation at 10 min and 30 min

Project description:Transcriptional profiling of upper flanks and lower flanks of Arabidopsis inflorescence stems after gravistimulation. Candidate genes which were up-regulated in the lower flanks relative to the upper falanks after gravi-stimulation at 30 min were identified. Two time-points experiments, at 10 min and 30 min. Biological replicates: 2 replicates for each experiments (as color swapped data)

2014-06-12 | E-GEOD-58417 | biostudies-arrayexpress

Expression data from leaf tissues of 35S:AtHMA4 and wild-type tomato plants grown in the presence of Zn

Project description:Arabidopsis HMA4 transformation facilitates Zn root-to-shoot translocation, but in Zn-supply dependent manner. It implies that distinct effects of HMA4 expression on Zn root:shoot distribution in transgenics grown under different Zn supply regimes results from the interaction between the transgene activity and the molecular background of the host plant. Microarray analysis was performed to compare expression profiles in leaves of transgenic and WT-plants grown in the presence of 5 µM Zn to identify the molecular mechanism underlying the difference in Zn root:shoot distribution between 35S:AtHMA4-expressing and wild-type tomato. To recognize tissue specific alterations in gene transcription in tomato leaves invoked by AtHMA4 expression, spongy paerenchyma + lower epidermis and palisade paerenchyma + upper epidermis were isolated using LCM technique. Understanding the interplay between the transgene and the endogens is crucial for planning genetic modification for Zn-biofortification purpose. 10-day old tomato plant (35S:AtHMA4 expressing and WT) were subjected to 5 µM Zn (added as ZnSo4) for 15 days. Three independent experiments were performed. At the end of each experiment the 3rd and 4th leaf (counting upwards) were collected, 1-2 mm long and 2-3 mm wide fragments were cut out from between the vascular bundles in the middle part of each leaf, embedded in NEG-50 Frozen Section Medium (Thermo Scientific), and frozen in liquid nitrogen. Total RNA isolated from three batches of leaves was amplified and used for three independent microarray analysis.

2015-05-08 | E-GEOD-68640 | biostudies-arrayexpress

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