title: Lamin A/C is required for SHSY5Y neuroblastoma cell differentiation and its expression is linked to a less malignant phenotype.

status: Public on Jul 11 2013

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

summary: The main scientific objective of the project was to investigate whether Lamin A/C could be involved in neuroblastoma differentiation. Moreover, taking into account the significance of differentiation stage in the neuroblastoma tumor progression we have also studied a possible role of Lamin A/C in the tumorigenesis of this neuronal cancer. As differentiating stimulus we used the all-trans retinoic acid (RA), the most effective compound which has been shown to induce differentiation in neuroblastoma cells. To get insight into the impairment of cell differentiation produced by the LMNA  (Lamin A/C) silencing in SHSY5Y cells, we compared the gene expression profile of control and silenced cells both in Retinoic Acid treated and untreated samples, using the one-color Agilent microarray platform.

overall_design: Four condition experiment: cells infected with a mock vector (Mock cells), treated and untreated with retinoic acid (RA); cells infected with a silencing vector for LMNA (LMNA-KD cells), treated and untreated with retinoic acid.

first: Giovanna

last: Maresca

first: Manuela

last: Natoli

first: Daniela

last: Trisciuoglio

first: Rossella

last: Brandi

first: Simona

last: D'Aguanno

first: Mara

last: D'Onofrio

first: Andrea

last: Urbani

first: Donatella

last: Del Bufalo

first: Armando

last: Felsani

first: Igea

last: D'Agnano


status: Public on Jun 01 2016

city: Gif sur Yvette

first: Véronique

last: BRUNAUD

address: avenue des sciences

country: France

institute: INRAE

type: Expression profiling by high throughput sequencing

summary:
NGS2013-04: Transcriptomic response to Nod Factor treatments on Medicago
Role of the root hair in water and nutrient uptake and the establishment of the nitrogen-fixing symbiotic interaction with rhizobia.

overall_design: The RNA was extracted from root hairs of Medicago: control vs treated by nod factors (2 biological replicates)

first: Sandrine

last: Balzergue

first: Stéphanie

last: Huguet

last: Brunaud

first: Isabelle

last: Gaillard

first: Nicolas

last: Pauly


title: Expression profiling in silencing suppressor plants or in mirna mutants-Transcriptional and post-transcriptional changes in Arabidopsis plants that constitutively express suppressors of RNA silencing

status: Public on Aug 23 2011

summary:
gen107_ptgs - gene profiling in silencing suppressor plants or in mirna mutants - What are the genes that are differentially regulated in various tissues derived from silencing suppressor plants or miRNA mutants? - HcPro, P15, P19, CHS-RNAi (control), were grown on MS solid medium, and tissues were harvested at different developmental stages. dcl1-9, hen1-1 and La-er (control) were grown on MS solid medium, and tissues harvested at different developmental stages.
Keywords: gene knock in (transgenic),gene knock out

overall_design: 40 dye-swap - Chromochip Arabidopsis thaliana 21.7K CHROMO4_1

first: Vincent

last: Colot

first: Agnes

last: Yu


title: Gene expression profiling of de novo diffuse large B-cell lymphoma samples

status: Public on Feb 05 2019

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

country: Denmark

institute: Aalborg University Hospital

type:
Expression profiling by array
Third-party reanalysis

summary:
Gene expression profiling was performed for 7 DLBCL primary clinical samples and assignment of activated B-cell-like(ABC)/germinal center B-cell-like (GCB) DLBCL classes, B-cell-associated gene signature (BAGS), and a probability of response to vincristine was performed for each sample.
Diffuse large B-cell lymphoma (DLBCL) is a very heterogeneous malignant disease with diverse clinical presentation, outcome, and pathogenic mechanism. In order to better risk stratify patients there is a current need to find and validate new biomarkers of the disease.  An alternatively spliced transcript of NOTCH3 missing exon 16 was identified and displayed prognostic and predictive biomarker potential.

overall_design: In total, 75 primary DLBCL samples were included in this study. Gene expression profiles were determined using Affymetrix GeneChip HG-U133 Plus 2.0 arrays. Gene expression of 7 samples were normalized together with expression from 68 DLBCL primary clinical samples that have been included in GSE74266 (n=47) and GSE109027 (n=21) and additional 16 other primary DLBCL samples, which has not been used further in this study.

first: Ditte

middle: S

last: Jespersen

first: Anna

middle: A

last: Schönherz

first: Hanne

last: Due

first: Hans

last: Johnsen

first: Martin

last: Bøgsted

first: Karen

last: Dybkær


title: Expression data from primary and hereditary pheochromocytomas (PHEOs) and paragangliomas (PGLs)

status: Public on Dec 31 2013

city: Bethesda

first: Uma

middle: T

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

country: USA

institute: NIH

summary:
Genotype specific differences in expression profiles have been evaluated using human HuGene1.0-ST Gene Chips. In this dataset we include expression data for 7 PHEOs/PGLs patient samples with HIF2A or PHD2 mutation.
Viable appearing tissue from the center of the lesions was collected and snap frozen for RNA extraction. Each of the 7 PHEO/PGL samples was examined by pathologist upon resection.

overall_design: Microarray analysis was performed on normal and tumor samples.

first: Stephanie

last: Fliender

first: Karel

last: Pacak


title: Insights into electrosensory organ development, physiology and evolution from a lateral line organ-enriched transcriptome

status: Public on Mar 27 2017

city: Cambridge

first: Clare

last: Baker

address: Anatomy Building, Downing Street

department: PDN

country: United Kingdom

institute: University of Cambridge

summary: The anamniote lateral line system, comprising mechanosensory neuromasts and electrosensory ampullary organs, is a useful model for investigating the developmental and evolutionary diversification of different organs and cell types. Zebrafish neuromast development is increasingly well understood, but neither zebrafish nor Xenopus is electroreceptive and our molecular understanding of ampullary organ development is rudimentary. We have used RNA-seq to generate a lateral line-enriched gene-set from late-larval paddlefish (Polyodon spathula). Validation of a subset reveals expression in developing ampullary organs of transcription factor genes critical for hair cell development, and genes essential for glutamate release at hair cell ribbon synapses, suggesting close developmental, physiological and evolutionary links between non-teleost electroreceptors and hair cells. We identify an ampullary organ-specific proneural transcription factor, and candidates for the voltage-sensing L-type Cav channel and rectifying Kv channel predicted from skate (cartilaginous fish) ampullary organ electrophysiology. Overall, our results illuminate ampullary organ development, physiology and evolution.

overall_design: mRNA profiles of pooled opercular and fin tissue (3 biological replicates each), manually dissected from stage 46 larval paddlefish (Polyodon spathula), were generated by deep sequencing using the Illumina HiSeq 2500 platform (multiplex paired-end, 2x100 bp).


title: Gene expression profiling of oral squamous cell carcinoma (OSCC)

status: Public on May 02 2013

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

summary: According to epidemiological studies, a vast majority, approximately 80%~90% of male OSCC patients in Taiwan habitually drink alcohol (A), and chew betel quid (B), and use cigarette (C). To assess the impact of these dietary factors on the transcriptom, we conduct a high-throughput screen survey in an oral cancer cohort with exposure of A, B, and C. Results indicate several potential oncogenes and tumor suppressor genes are dysregulated in OSCC patients with ABC risk factors.

overall_design: Total RNA was collected from tumor and non-tumor pair-wise samples. These biopsies were obtained from 40 male OSCC patients who regularly drink alcohol, chew areca nut and smoking.

first: C

middle: H

middle: Y

last: Chang

first: J

middle: R

last: Hsiao

first: Shih-Sheng

last: Jiang


title: Transcriptional and post-transcriptional changes in Arabidopsis plants that constitutively express suppressors of RNA silencing

first: Véronique

last: BRUNAUD

type: Genome binding/occupancy profiling by genome tiling array

type: Expression profiling by genome tiling array

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: cgh_colvscvi_wg-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions

status: Public on May 17 2011

type: Genome variation profiling by genome tiling array

summary: a2e_heterosis - cgh_colvscvi_wg - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - Comparative genome hybridization between Arabidopsis thaliana accessions Col-0 and CVi.

overall_design: 2 dye-swap - cgh; technical replicate - extract: 6487002,7357902; technical replicate - extract: 6487602,7355302.

first: Vincent

last: Colot

first: Francois

last: Roudier

first: Ali

last: Banaei

first: Michael

last: Seifert

first: Raheleh

last: Karimi

first: Andreas

last: Houben

first: Florian

last: Mette

first: Marie-Laure

last: Martin-Magniette


title: cgh_colvsc24_wg-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions

summary: a2e_heterosis - cgh_colvsc24_wg - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - Comparative genome hybridization between Arabidopsis thaliana accessions Col-0 and C24.

overall_design: cgh; technical replicate - extract: 6486702, 6487302


title: chip in silencing suppressor plants or in mirna plants-Transcriptional and post-transcriptional changes in Arabidopsis plants that constitutively express suppressors of RNA silencing

summary: gen107_ptgs - chip in silencing suppressor plants or in mirna plants - What are the genes that are differentially regulated in various tissues derived from silencing suppressor plants or miRNA mutants? - How are the histone modifications and the chromatin structure in miRNA mutants or in silencing suppressor plants?

overall_design: 12 dye-swap - CHROMO4_2 arrays - ChIP-chip

first: Agnes

last: Yu

first: Olivier

last: Voinnet

first: Jean-Pierre

last: Renou


title: NOVEL POTENTIAL MARKERS OF TUMOR-INITIATING CELLS IN COLON CANCER

status: Public on Jan 04 2011

first: Nathalie

last: Saulnier

address: Largo Francesco Vito,1

institute: Università Cattolica del Sacro Cuore di Roma

summary:
BACKGROUND: Several in vitro assays have been used to identify “cancer stem cells” (CSC), including expression of cell surface markers and Hoechst dye efflux properties. However, each of these methods has potential pitfalls that complicate interpretation of the results. Focusing on colon cancers (CC), the CD133 antigen has been proposed as a marker of colon CSC. However, conflicting results have been reported in the literature indicating the need of a systematic analysis of CSC within CC and a complete validation of markers for the isolation of these cells.
AIMS: Aim of this study was to confirm that CD133 expression is a valid method for isolating CSC in CC and verify if other antigens can increase the specificity of this marker for isolating CSC in CC.
METHODS: CD133+ and CD133- cells were isolated from different human CC lines (CaCo-2, HT29, LOVO, HCT-116) by FACS sorter and the tumor-initiating potential of CD133+ cells was assessed in vitro, by soft-agar colony formation assay, and in vivo, upon transplantation into nude mice. Furthermore, the gene expression profile of CD133+ versus CD133- CaCo-2 cells was compared by the means of microarray analysis. Then, in the effort to identify a common “tumor stem cell” signature for CC, the most relevant transcripts resulting from gene expression profiling on CD133+ cells was assessed by real-time PCR on SP-fraction isolated by FACS sorter from the same CC cell lines. Finally, we deplete CD133 expression in the CaCo-2 cell line by the means of siRNA and verified by Western Blot analysis whether there was a functional correlation between CD133 and the target genes. Moreover, CaCo-2 and HCT116 cells were exposed to sodium butyrate (NaBu) for 72h. Colon cells differentiation was assessed by Alkaline phosphatase activity and expression of CD133 and target genes was tested by western blot.
RESULTS:  We confirmed that only CD133+ cells have a tumor-initiating potential in vitro and in vivo. Furthermore, microarray analysis of CD133+ versus CD133- CaCo-2 cells revealed a significant overexpression of various transcripts involved in cell proliferation, invasion and stemness in CD133+ cell fraction. Comparison of the transcripts by real-time PCR revealed that the genes of Endothelin-1 (END-1) and NR4A2 are highly expressed in both CD133 + cells and in SP fractions. Finally, when we deplete CD133 expression in Caco-2cells by siRNA, we observed a significant attenuation of END-1 and NR4A2 expression, thus demonstrating that CD133 is involved in the transcriptional regulation of  these genes. Interestingly, we also showed that the expression of all three genes was inversely correlated with cell differentiation status as demonstrated by the fact that their expression decreases in a time- and dose-dependent manner after differentiation induced by NaBu.
CONCLUSION:  Overall, this study confirms the role of CD133antigen as CSC marker and  showed for the first time the existence of a functional relationship between CD133, END-1 and NR4A2 expression, hypothesizing that CD133 is involved in the transcriptional regulation of these gene.

overall_design: Microarray analysis was performed on CD133+ and CD133- sorted CACO-2 cells. For both fractions, cells were sorted three independent times. Sample preparation was performed according to Affymetrix recommendations. A total of 6 arrays were hybridized, including 3 CD133+ replicates and 3 CD133- replicates.

first: Maria

last: Puglisi

first: Alessandro

last: Sgambatto

first: Marta

last: Barba

first: M

middle: F

last: Errico

first: E

last: Giorda

first: A

last: Boninsegna

first: Anna

middle: C

last: Piscaglia

first: R

last: Carsetti

last: Cittadini

first: Antonio

last: Gasbarrini


title: cgh_colvsc24_chr4-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions

first: Véronique

last: BRUNAUD

summary:
a2e_heterosis - cgh_colvsc24_chr4 - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - Comparative genome hybridization between Arabidopsis thaliana accessions Col-0 and C24

Keywords: cgh,chip-chip

overall_design: 2 dye-swap - Tiling arrays Chromosome IV Arabidopsis

first: Vincent

last: Colot

first: Francois

last: Roudier


title: Genome Wide Gene Expression Study of Circulating Monocytes in human with extremely high vs. low bone mass

status: Public on Mar 01 2008

city: Changsha

first: Shu-Feng

last: Lei

state: Hunan

address: Lushan Road 36

department: College of Life Science

country: China

institute: Hunan Normal University

summary:
Peak bone mass (PBM) is an important determinant of osteoporosis. Circulating monocytes may serve as early progenitors of osteoclasts and produce important molecules for bone metabolism. To search for genes functionally important for osteoclastogenesis, we performed a whole genome gene differential expression study of circulating monocytes in human subjects with extremely low vs. high peak bone mass.
Keywords: Circulating monocyte, Gene expression, Peak bone mass, DNA microarray

overall_design: We first recruited 878 healthy Chinese females aged 20-45 y with an average of 27.3 y when PBM is attainted and maintained. Then, we distributed the total sample according to the hip Z-score of PBM. From the bottom 100 and top 100 subjects of the PBM phenotypic distribution, we selected 12 subjects (Low-PBM 1-12) and 14 (High-PBM 1-14) with extremely low and high PBM for further DNA microarray experiments.Total RNA was extracted from monocytes

first: Hong-Wen

last: Deng


title: water stress-Identification of targets of the transcription factor hahb-4 in relation to abiotic stress

status: Public on Aug 31 2007

summary:
rs04-09_hahb4 - water stress - We want to know which genes are over-expressed or down regulated in Arabidopsis plants transformed with the sunflower hahb-4 homeodomain transcription factor with respect to non transformed ones in control and water stress conditions. This gene, hahb4, confers drought tolerance to transgenic Arabidopsis plants. - Overexpression of the hahb4 gene vs vector transformed control
Keywords: gene knock in (transgenic),treated vs untreated comparison

overall_design: 3 dye-swap - CATMA arrays

first: Frederique

last: Bitton

middle: P

last: Renou

first: Martin

last: Crespi

first: Marie-Laure

middle: L

last: Martin-Magniette


title: potyvirus-Transcriptional analysis of Arabidopsis thaliana infected by a potyvirus.

summary:
ra03-02_potyvirus - potyvirus - Identification of genes involved in plant/virus interactions. - In this experiment, Arabidopsis plants infected by a virus, Tobacco etch virus (TEV), a potyvirus, were compared with healthy plants to identify genes for which the expression is modified by the viral infection. Analysis of both inoculated leaves and upper young leaves were performed 7 days after the inoculation with the virus (or with only buffer for the healthy plants).
Keywords: normal vs disease comparison

overall_design: 6 dye-swap - CATMA arrays

first: Ludivine

last: Taconnat

first: Jean-Pierre

first: Frederic

last: Revers


title: dml6-Lignin mutants and UV stress

status: Public on Jun 20 2007

summary:
af09_lignin - dml6 - Transcriptome analysis of lignin mutants and UV stress effect on secondary wall synthesis - DML6 vs S DML6+UV vs S+UV S vs S+UV DML6 vs DML6+UV
Keywords: normal vs disease comparison,treated vs untreated comparison

overall_design: 2 dye-swap - CATMA arrays

first: caroline

last: Proux

first: Lise

last: Jouanin


title: dex-gvg-Transcriptome alterations by the 6b oncogene of Agrobacterium

summary:
rs03-01_onc6b - dex-gvg - The oncogene 6b affects the plant growth at the leaf, root, stem and flower level. The protein is localized in the nucleus and is suspected to modify transcription. - Observation of the effect of Dex-GFP expression on the transcriptome (control)
Keywords: gene knock in (transgenic)

overall_design: 1 dye-swap - CATMA arrays

first: Leon-

last: Otten


title: club root response-Deciphering the Arabidopsis mechanisms of resistance to clubroot (Plasmodiophora brassicae)...

summary:
ra03-05_clubroot - club root response - Characterisation of the transcriptional changes (host genes up- and down-regulated) during the P. brassicae / A. thaliana interaction. - The objective of the study was to identify the genes up and down-regulated during the interaction of P. brassicae with a partial resistant genotype of Arabidopsis. The transcriptome pattern of inoculated and non-inoculated plants of Arabidopsis was compared at three time points after inoculation (24 hours, 48 hours and one-week ai). Sixty plants were studied by comparison (inoculated-non inoculated) and by kinetic point. RNAs of the 30 inoculated plants and the RNAs of the 30 non-inoculated plants were pooled to eliminate variability between individual plants and thus to target for genes for which differences in expression were linked to the inoculation by the pathogen. Five comparisons have been performed: inoculated-non inoculated at 24 hours ai; inoculated-non inoculated 48 hours ai; inoculated-non inoculated one-week ai; inoculated 24h ai-inoculated 48h ai; inoculated 48h ai- inoculated one-week ai. The entire experiment was repeated (biological repetition) and each comparison was performed in two independent hybridisations (technical repetition).
Keywords: normal vs disease comparison,time course

overall_design: 10 dye-swap - CATMA arrays

first: Maria

last: Manzanares


title: Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions


title: stem developement-Lignin mutants and UV stress

summary:
af09_lignin - stem developement - Transcriptome analysis of lignin mutants and UV stress effect on secondary wall synthesis - transcription frofiling of stem developement in Arabidopsis thaliana. time course with 3 points: 2cm, 10 cm and 25cm (maturation)
Keywords: time course


title: della-regulation of salt stress responses-DELLAs contribute to salt stress responses

status: Public on Jul 01 2008

summary:
rs06-07_della - della-regulation of salt stress responses - Identification of DELLA-dependent dowtream targets in response to salt stress - Aim was to determine downstream target of DELLA proteins involved in salt stress tolerance. Wt, ga1-3, penta seeds were sterilized, sown on MS agar plates then put for stratification for 3 days at 4degreeC. Plates were placed in growth cabinet for 9 days. Seedlings were transferred to 24 well-plates, with 2 seedlings per well (0.5 ml MS liquid per well). Plates were placed in the same condition for 3 days. Finally, NaCl were added (final concentration 200 mM), except for the control. The salt treatment was applied for 30 min and 1h. Treatment was stopped by freezing in liquid nitrogen.
Keywords: dose response,gene knock out,time course

overall_design: 12 dye-swap - CATMA arrays

first: Pascal

last: Genschik

first: Richard

last: Berthome


title: cdt1-Characterization of the AtCDT1a and AtCDT1b by RNAi

first: Véronique

last: BRUNAUD

summary:
rs04-06_cdt1 - cdt1 - CDT1 is a protein of the pre-replication complex, and accumulates during the G1-S transition, thus play a major role in S-phase entry - Comparison of 3 independant RNAi lines
Keywords: normal vs rnai mutant comparaison

first: Catherine-

last: Bergounioux


title: ntr-Transcriptomic study of a thioredoxin reductase knock-out mutant.

summary:
rs04-02_ntr - ntr - Thioredoxins are small redox proteins implicated in crucial pathways of cell life. They are reduced by a conserved flavoprotein named NADPH-dependent thioredoxin reductase (NTR). In order to give an insight into the functions of the NTR/thioredoxin pathway in Arabidopsis, we have used a reverse genetic approch. Both NTR genes (NTRA and NTRB) have been inactivated in the double ntra ntrb mutant. T-DNA lines have been provided by the SALK library. Surprisingly, this mutant shows a limited phenotype suggested that some additional redox pathways are involved in compensating the inactivation of the NTR/thioredoxin pathway. In order to isolate compensatory genes that would be transcriptionally induced in the ntra ntrb mutant, we have performed this CATMA project.  - Comparison of the transcript profile of the ntra ntrb knock-out mutant vs Col-0 wild-type ecotype. Seeds of the wild-type Col-0 ecotype and of the ntra ntrb homozygote double mutant were sowed in soil. Three replicates of lines were made (Col-0 1, 2 and 3 ntra ntrb 1, 2 and 3) : plants were put at different places of the greenhouse and grown at different times. Germination was synchronized by 4 days at 4degreeC and plants were grown during 17 days, until they reached a 6 rosette leaves stage. Entire plants (30 plants per sample) were harvested, frozen in liquid nitrogen and stored at 80degreeC until extraction.
Keywords: gene knock out,wt vs mutant comparison

first: Jean-Philippe

last: Reichheld


title: antimycine a-The cytochrome pathway and cytochrome C biogenesis

summary:
rs04-01_cytc - antimycine a - Is there a retrograde regulation of mitochondrial cytochrome pathway ? - Presence of an inhibitor of the cytochrome pathway (antimycine A). This treatment induces the expression of a gene coding for an alternative oxydase (AOX1a) and one of the two genes coding for apocytochrome c (CYTc-a).
Keywords: treated vs untreated comparison

first: Geraldine

last: Bonnard


title: oncogene_effect-Transcriptome alterations by the 6b oncogene of Agrobacterium

summary:
rs03-01_onc6b - oncogene_effect - The oncogene 6b affects the plant growth at the leaf, root, stem and flower level. The protein is localized in the nucleus and is suspected to modify transcription. - Effects of the activation of the oncogene 6b on the transcriptome
Keywords: gene knock in (transgenic)


title: translatome-cd-Analysis of the translatome of Arabidopsis in response to Cadmium stress

summary:
cea03-02_translatome-cd - translatome-cd - Is there a change in the translation in Cadmium stress condition ? - Comparison between translated RNA (polysomes) and total RNA or non translated RNA (monosomes) in cadmium stress conditions.
Keywords: transcribed vs translated,treated vs untreated comparison

first: Christophe

last: Robaglia


title: profiling of the root architecture response to phyllobacterium-Arabidopsis thaliana transcriptome analysis in ...

summary:
ra04-07_pgpr - profiling of the root architecture response to phyllobacterium - Experiment 1 : Which genes are up- or down-regulated in Arabidopsis thaliana cultivated in vitro with increased lateral root development in response to Phyllobacterium STM196 inoculation. Experiment 2 : Which genes are up- or down-regulated during the ISR triggered by a rhizobacteria, in comparison with those affected by a pathogenic interaction. Experiment 3 : which genes are specifically induced or repressed in Arabidopsis thaliana by inoculation of the soil with a PGPR vs a bacteria that has the ability to trigger nodule formation in a Legume.  - Seeds of wild-type Arabidopsis thaliana (ecotype Columbia) were surface-sterilized and sawn on agar mineral medium (see below). 4 days after storage in the dark at 4degreeC, seedling were cultivated 6 days in a growth chamber (16 h daily, 20-22degreeC) and then transferred on a fresh agar mineral medium inoculated or not with Phyllobacterium STM196 (2.108 cfu/ml). 6 days later, root and leaves were collected, froze on liquid nitrogen and stored at -80degreeC.
Keywords: treated vs untreated comparison

first: Bruno

last: Touraine


title: profiling of the pgpr induced systemic resistance (isr)-Arabidopsis thaliana transcriptome analysis in respons...

summary:
ra04-07_pgpr - profiling of the pgpr induced systemic resistance (isr) - Experiment 1 : Which genes are up- or down-regulated in Arabidopsis thaliana cultivated in vitro with increased lateral root development in response to Phyllobacterium STM196 inoculation. Experiment 2 : Which genes are up- or down-regulated during the ISR triggered by a rhizobacteria, in comparison with those affected by a pathogenic interaction. Experiment 3 : which genes are specifically induced or repressed in Arabidopsis thaliana by inoculation of the soil with a PGPR vs a bacteria that has the ability to trigger nodule formation in a Legume.  - Seeds were sawn on 0.8% (W/V) agar mineral medium (see below). 4 days after storage in the dark at 4degreeC, seedling were cultivated 6 days in a growth chamber (16 h daily, 20-22degreeC) and then transferred on soil inoculated or not with 107 cfu.g-1 of Bradyrhizobium strain ORS278. Three weeks later, 3 leaves per plant were infiltrated with a suspension of Pseudomonas syringae pv. tomato (2.105 cfu.ml-1) or with MgSO4 10 mM alone for control plants. Infiltrated leaves were collected 24h later.
Keywords: normal vs rnai mutant comparaison,treated vs untreated comparison

overall_design: 5 dye-swap - CATMA arrays

last: Renou


title: endothelium-Transcriptome analysis of the tannin-producing cells in Arabidopsis

summary:
ra03-06_seed_endothelium - endothelium - Identification of all tannin metabolism functions. - Comparisons between wild type seeds and seed that have no endothelium, thus no tannin producing cells. This phenotype is obtained by specifically expressing the Barnase gene under the BANYULS promoter.
Keywords: gene knock out

overall_design: 8 dye-swap - CATMA arrays

first: Frederique

last: Bitton

first: Isabelle

last: Debeaujon


title: msil-Identification of genes induced by fertilization

summary:
ra04-01_msil - msil - Trying to identify genes induced during parthenogenetic development of the seed - control S4 vs mutant msil2 technical repeat
Keywords: wt vs mutant comparison

last: Berger

first: Marie-Laure

last: Martin-Magniette


title: ago-Transcriptome of the argonaute (ago) mutant

summary:
ra04-02_ago - ago - Identification of the regulation pathways implied in adventitious root formation control in Arabidopsis - Transcription analisys of 2 different AGO1 mutants
Keywords: gene knock out

overall_design: 4 dye-swap - CATMA arrays

first: Jean-Pierre

first: Catherine

last: Bellini


title: trancriptional response to 3 rhizobacteria-Arabidopsis thaliana transcriptome analysis in response to plant gr...

summary:
ra04-07_pgpr - trancriptional response to 3 rhizobacteria - Experiment 1 : Which genes are up- or down-regulated in Arabidopsis thaliana cultivated in vitro with increased lateral root development in response to Phyllobacterium STM196 inoculation. Experiment 2 : Which genes are up- or down-regulated during the ISR triggered by a rhizobacteria, in comparison with those affected by a pathogenic interaction. Experiment 3 : which genes are specifically induced or repressed in Arabidopsis thaliana by inoculation of the soil with a PGPR vs a bacteria that has the ability to trigger nodule formation in a Legume.  - Seeds of wild-type Arabidopsis thaliana (ecotype Columbia) were surface-sterilized and sawn on agar mineral medium. Four days after storage in the dark at 4degreeC, seedlings were cultivated 6 days in a growth chamber (16 h daily, 20-22degreeC) and then transferred on soil inoculated or not with 108 cfu.g-1 of Mesorhizobium loti, or 108 cfu.g-1 of Phyllobacterium STM196, or 107 cfu.g-1 of Bradyrhizobium ORS278.
Keywords: treated vs untreated comparison

first: Ludivine

last: Taconnat


title: ccme-The cytochrome pathway and cytochrome C biogenesis

summary:
rs04-01_cytc - ccme - Is there a retrograde regulation of mitochondrial cytochrome pathway ? - The homozygote arabidopsis line 9S9 overproducing AtCCME-HIS (At3g1790), a mitochondrial heme chaperon involved in c-type cytochrome maturation will be compared with the corresponding wild type (Wassilievskjia).
Keywords: gene knock in (transgenic)


title: myb-Functional analysis of two Eucalyptus xylem MYB transcription factors overexpressed in Arabidopsis.

summary:
rs04-03_myb - myb - Xylogenesis is a fundamental developmental process that is specific of vascular plants. It allows the formation of xylem, also called wood in trees, a complex tridimensional tissue composed of different cell types. This process occurs through the control of fundamental cell mechanisms like cell division and differentiation, secondary cell wall synthesis, lignin deposition and programmed cell death. Xylogenesis is controlled spatially and temporally by specific genetic programs that involve hundreds of genes. For instance, lignin biosynthetic genes, CAD and CCR, are specifically expressed during xylogenesis through MYB transcription factor binding sites, a process that seems to be common to all vascular plants. We have cloned two xylem specific MYB transcription factors, EgMYB1 et EgMYB2, in Eucalyptus. Interestingly, they are able to bind MYB consensus sequences of CAD and CCR promoters in vitro and to modulate CAD and CCR expression in vivo. When overexpressed in Arabidopsis or tobacco, they affect xylem structure by changing cell wall structure and quality. To follow expression changes of Arabidopsis genes in transgenic plants overexpressing Eg MYB1 and EgMYB2 should help us to find out which genes might be target of those transcription factors. This should help us to decipher the actual role of those two MYBs in xylogenesis, two new members of a large family of transcription factors in plants.  - Xylogenesis is a fundamental developmental process that is specific of vascular plants. It allows the formation of xylem, also called wood in trees, a complex tridimensional tissue composed of different cell types. This process occurs through the control of fundamental cell mechanisms like cell division and differentiation, secondary cell wall synthesis, lignin deposition and programmed cell death. Xylogenesis is controlled spatially and temporally by specific genetic programs that involve hundreds of genes. For instance, lignin biosynthetic genes, CAD and CCR, are specifically expressed during xylogenesis through MYB transcription factor binding sites, a process that seems to be common to all vascular plants. We have cloned two xylem specific MYB transcription factors, EgMYB1 et EgMYB2, in Eucalyptus. Interestingly, they are able to bind MYB consensus sequences of CAD and CCR promoters in vitro and to modulate CAD and CCR expression in vivo. When overexpressed in Arabidopsis or tobacco, they affect xylem structure by changing cell wall structure and quality. To follow expression changes of Arabidopsis genes in transgenic plants overexpressing Eg MYB1 and EgMYB2 should help us to find out which genes might be target of those transcription factors. This should help us to decipher the actual role of those two MYBs in xylogenesis, two new members of a large family of transcription factors in plants.
Keywords: gene knock in (transgenic)

first: Jacqueline

last: Grima-Pettenati


title: time course-Transcriptome analysis of the hypocotyl growth switch

summary:
ra03-04_elongation_isoxaben - time course - 1. Study the molecular basis of the growth acceleration observed in hypocotyl cells. We previously have observed that cell elongation takes place in two distinct phases (Refregier et al., 2004). A slow growth phase during which a thick polylamellated wall is deposited and a rapid growth phase during which cell wall polymers are extensively remodelled. In dark-grown hypocotyls the slow growth phase takes place during the first 48h after seed-imbibition synchronously in all cells. At 48h after imbibition, cells at the basis of the hypocotyl undergo a growth acceleration, this acceleration follows an acropetal gradient along the hypocotyl. In this experiment, we investigated the changes in transcript abundance that accompany this sudden increase in growth rate. 2. Study the feed-back mechanisms involved in the coordination between cellulose synthesis and the cell elongation. The inhibition of cellulose using chemical inhibitors also inhibits cell elongation. In the same study (Refregier et al., 2004), we have observed that the effect of the cellulose synthesis inhibitor isoxaben on cell elongation is different dependent on the growth stage. When applied during the slow growth phase, cells continue to elongate slowly and do not show the growth acceleration at 48h after imbibition. Surprisingly, when applied after the growth acceleration, isoxaben does not inhibit subsequent growth. In this study we compared the effects of isoxaben on the transcript profiles before and after the growth acceleration. This should inform us about the response of the hypocotyl cells to the inhibition of cellulose and should provide insights into the molecular events that underly the observed coupling between cellulose synthesis and cell elongation. - 1- Time course from 45h until 55h after seed-imbibition, comparisons respectively between: 45h - 48h, 48h - 52h, 52h - 55h
Keywords: time course

first: Gaetan

last: Lemonnier

first: Herman

last: Hofte


title: isoxaben treatment-Transcriptome analysis of the hypocotyl growth switch

summary:
ra03-04_elongation_isoxaben - isoxaben treatment - 1. Study the molecular basis of the growth acceleration observed in hypocotyl cells. We previously have observed that cell elongation takes place in two distinct phases (Refregier et al., 2004). A slow growth phase during which a thick polylamellated wall is deposited and a rapid growth phase during which cell wall polymers are extensively remodelled. In dark-grown hypocotyls the slow growth phase takes place during the first 48h after seed-imbibition synchronously in all cells. At 48h after imbibition, cells at the basis of the hypocotyl undergo a growth acceleration, this acceleration follows an acropetal gradient along the hypocotyl. In this experiment, we investigated the changes in transcript abundance that accompany this sudden increase in growth rate. 2. Study the feed-back mechanisms involved in the coordination between cellulose synthesis and the cell elongation. The inhibition of cellulose using chemical inhibitors also inhibits cell elongation. In the same study (Refregier et al., 2004), we have observed that the effect of the cellulose synthesis inhibitor isoxaben on cell elongation is different dependent on the growth stage. When applied during the slow growth phase, cells continue to elongate slowly and do not show the growth acceleration at 48h after imbibition. Surprisingly, when applied after the growth acceleration, isoxaben does not inhibit subsequent growth. In this study we compared the effects of isoxaben on the transcript profiles before and after the growth acceleration. This should inform us about the response of the hypocotyl cells to the inhibition of cellulose and should provide insights into the molecular events that underly the observed coupling between cellulose synthesis and cell elongation. - 1- 45 hours, transfer to medium +/-isoxaben, harvest at 48 hours: comparison 48 hours + /- isoxaben. 2- 52 hours, transfer on + /-isoxaben, harvest 55 hours: comparison 55 hours + /-isoxaben (after transition: inhibition synthesis of cellulose, no inhibition of cellular elongation).
Keywords: treated vs untreated comparison


title: sade-catma-A functional study of genes that might play a role in DNA repair/recombination and in the response ...

summary:
af51_atm - sade-catma - which Arabidopsis thaliana genes are induced by ionising radiations? Comparison of SADE transcriptome data (Af1999083) and micro-arrays transcriptome data.  - gamma rays irradiated vs non irradiated 4 days old seedlings
Keywords: treated vs untreated comparison

first: caroline

last: Proux

first: Marie-helene

middle: h

last: Montane


title: open stomata2-Open stomata 2 mutant

first: Véronique

last: BRUNAUD

summary:
af73_ost2 - open stomata2 - transcription profiling of the open stomata 2 mutant hypersensitive to drought - Ler vs OST (Open STomata mutant), Ler drought vs OST drought Ler vs Ler drought OST vs OST drought
Keywords: wt vs mutant comparison

first: Jeff

last: Leung


title: nitrogen starvation and re-supply-Improving the nitrogen use efficiency : from model plant to crop species.

summary:
gnp3-b4_nitrogen_starvation - nitrogen starvation and re-supply - What are the transcriptomic short- and long-term plant responses to nitrogen starvation and nitrogen re-supply?  - WS Arabidopsis ecotype were grown on 6mM nitrate as sole nitrogen source during 35 days under short days . At T0, plants were then starved for nitrate for 10 days and root and shoot samples were harvested separately 2 and 10 days after treatment (T2, T10). Then, nitrate (6 mM) was re-supplied for 1 and 24 hours (T+1, T+24).
Keywords: time course

sample_organism:
Arabidopsis thaliana
Brassica napus

overall_design: 36 dye-swap - CATMA arrays

first: Francoise

last: Vedele


title: comparison ws vs de and dy-Impact of a plastidial redox perturbation on Arabidopsis transcriptome

summary:
af47_thioredoxins - comparison ws vs de and dy - Knock-out mutants of the ferredoxin-thioredoxin reductase were used to evaluate the impact of the redox perturbation of the plastidial thioredoxins on Arabidopsis transcriptome. - Wild-type (WS) and two T-DNA mutant lines for the variable subunit of ferredoxin:thioredoxin reductase ( DY and DE from INRA of Versailles collection) were compared
Keywords: wt vs mutant comparison

first: Emmanuelle

last: Issakidis-bourguet


title: comparison ws vs crb (cul3a)-Study of the function of SCF complexes in Arabidopsis.

summary:
af01_cul3a2_cul3b - comparison ws vs crb (cul3a) - Cullin proteins belong to a multigene family that includes at least three members in budding yeast, six in human, five in C. elegans and five in Arabidopsis thaliana. All cullins analyzed so far directly interact with RBX1/HRT1/ROC1, a RING finger protein, thereby forming the core module of different ubiquitin ligase complexes, which specifically recruit substrate proteins for ubiquitylation and subsequent degradation by the proteasome. CULLIN1, the only cullin protein studied so far in plants, has been shown to be essential for plant development and to play a role in multiple signalling cascades. Here, we report on the first molecular and genetic characterisation of a plant Cullin 3. In contrast to fungi and animals, the genome of the model plant Arabidopsis thaliana contains two related CULLIN 3 genes, called CUL3A and CUL3B. We found that CUL3A is ubiquitously expressed in plants and that the CUL3A protein is also able to interact with RBX1 and certain Arabidopsis BTB-domain proteins. In order to determine the role of CUL3A in plant development, we used a reverse genetic approach and identified T-DNA insertion mutants. cul3a null mutants flower slightly latter than the control plants and their hypocotyls exhibit a reduced sensitivity to far red light. The viability of the cul3a mutant plants suggests functional redundancy between both CUL3 genes in plants.  - Comparaison of mutant AtCul3a (T-DNA mutant of Versailles collection) and WS.
Keywords: wt vs mutant comparison

first: Pascal

last: Genschik


title: comparison col0 vs 003d-Study of the function of SCF complexes in Arabidopsis.

summary:
af01_cul3a2_cul3b - comparison col0 vs 003d - Cullin proteins belong to a multigene family that includes at least three members in budding yeast, six in human, five in C. elegans and five in Arabidopsis thaliana. All cullins analyzed so far directly interact with RBX1/HRT1/ROC1, a RING finger protein, thereby forming the core module of different ubiquitin ligase complexes, which specifically recruit substrate proteins for ubiquitylation and subsequent degradation by the proteasome. CULLIN1, the only cullin protein studied so far in plants, has been shown to be essential for plant development and to play a role in multiple signalling cascades. Here, we report on the first molecular and genetic characterisation of a plant Cullin 3. In contrast to fungi and animals, the genome of the model plant Arabidopsis thaliana contains two related CULLIN 3 genes, called CUL3A and CUL3B. We found that CUL3A is ubiquitously expressed in plants and that the CUL3A protein is also able to interact with RBX1 and certain Arabidopsis BTB-domain proteins. In order to determine the role of CUL3A in plant development, we used a reverse genetic approach and identified T-DNA insertion mutants. cul3a null mutants flower slightly latter than the control plants and their hypocotyls exhibit a reduced sensitivity to far red light. The viability of the cul3a mutant plants suggests functional redundancy between both CUL3 genes in plants.  - Comparaison of AtCul3b (mutant of Gabi collection) and Col0.
Keywords: wt vs mutant comparison

last: Renou


title: atm time course-A functional study of genes that might play a role in DNA repair/recombination and in the resp...

summary:
af51_atm - atm time course - which Arabidopsis thaliana genes are induced by ionising radiations? Comparison of SADE transcriptome data (Af1999083) and micro-arrays transcriptome data.  - which Arabidopsis thaliana genes are induced by ionising radiations ? time course: 0.75h, 1.5h, 3h, 5h dose: Gamma rays irradiated vs non irradiated 4-days old seedlings
Keywords: time course


title: iron response-Transcriptomic response to iron signaling

summary:
no27_iron_signaling - iron response - Effect of exceed of Iron - Time course experiment, star design and 3 biological repeats.
Keywords: time course

overall_design: 18 dye-swap - CATMA arrays

last: Bitton

first: Michel

last: Rossignol


title: double mutant sbe-The impact of some genes mutations implicated in the amidon metabolism

summary:
af30_starch_circadian_rythm - double mutant sbe - The scientific aim is to study the impact of some genes mutations implicated in the amidon metabolism on the expression profils of other genes and in particular those of the carbonated metabolism. Those analyses will be done from RNAs (total or messenger) extracted from leaves at various time of the day and the night - Biological question : what is the impact of the absence of both branching enzymes II on the expression of the genes involved in carbon metabolism in the Arabidopsis leaves?
Keywords: gene knock out

first: Christophe

last: D Hulst

first: Samira

last: Elftieh


title: transcriptome profiling from a protoplast culture of arabidopsis thaliana-From protoplast to plant : transcrip...

summary:
ra03-03_protoplats - transcriptome profiling from a protoplast culture of arabidopsis thaliana - transcriptome profiling and comparison of 6 status of differentiation - protoplasts were extracted from plantlet cultivated during 2 weeks then placed in a culture midium which stimulate cell division. Protoplasts were harvested after 0, 24, 48, 96 or 168 hours of culture. Biological repeat has been done (experiments A and C)
Keywords: time course

overall_design: 16 dye-swap - CATMA arrays

first: Olivier

last: Pichon

first: Valerie

last: Gaudin

first: Marie-Laure

last: Martin-Magniette


title: circadian cycle-The impact of some genes mutations implicated in the amidon metabolism

summary:
af30_starch_circadian_rythm - circadian cycle - The scientific aim is to study the impact of some genes mutations implicated in the amidon metabolism on the expression profils of other genes and in particular those of the carbonated metabolism. Those analyses will be done from RNAs (total or messenger) extracted from leaves at various time of the day and the night - The first experiments will deal with the wild reference plant (WS) . The RNAm of leaves would be harvested according to day and night hours. Some harvesting will be done every 3 hours during a 24H period (so 10 different points ). This correspond to a total of 20 slides ( 2 samples and 1 swap per point). This account have been done according to the informations obtained from JJ Leguay in dec 2002
Keywords: time course

last: Lemonnier

first: Jean-Pierre


title: tor-Transcriptome analysis of TOR (Target of Rapamycin) mutant.

summary:
ra03-07_tor - tor - Study of 2 TOR mutants (7817 Strong, 7846 weak)  - Mutant vs wild type on different nitrogen conditions (10mM=control and 100uM)
Keywords: treated vs untreated comparison,wt vs mutant comparison

first: Christian

last: Meyer


title: atm-root-A functional study of genes that might play a role in DNA repair/recombination and in the response to...

summary:
af51_atm - atm-root - which Arabidopsis thaliana genes are induced by ionising radiations? Comparison of SADE transcriptome data (Af1999083) and micro-arrays transcriptome data.  - Gamma rays irradiated vs non irradiated 3 or 4-days old seedlings
Keywords: treated vs untreated comparison

last: Proux


title: No-Transcriptional impact of Cd-induced nitric oxide synthesis

status: Public on May 31 2007

summary:
rs05-08_no - no - Cadmium treatment induces slow but long lasting nitric oxide production in plant tissues. This NO production can be suppressed using the commonly used Nitric Oxide Synthase inhibitor L-NAME. This inhibitor tends to partially alleviate Cd toxicity. This effect is correlated with a strong diminution of Cd content in roots of plants treated both with Cd and L-NAME compared to roots from plants treated with Cd only. The main goal of this study is the identification of transcriptionnal changes caused by Cd-induced nitric oxide, and that could potentially result in enhanced Cd root accumulation.  - Germination of surface sterilized seeds was performed on solid MS/2 medium. After 2 weeks, the young plantlets were placed on sand for an additional 3 week period in a controlled environment (8 h photoperiod of 300 umol m-2 s-1, 22degreeC, 70% relative humidity) . Plants of similar rosette diameters were then transfered to an hydroponic culture using the nutritive solution described in [Gravot et al. 2004 FEBS Letters 561:22-28] for an acclimation of 3 days. L-NAME and cadmium treatments were respectively started 1 and 2 hours after the start of illumination and root tissues were collected 24 h later and immediatly frozen in liquid nitrogen before RNA extraction. Treatments were : 1 : control 2 : L-NAME 5 mM 3 : Cd 30 uM 4 : L-NAME 5mM + Cd 30 uM 5 : Cd 15 uM For each condition, 3 independent biological repetitions were conducted. RNA were extracted separatly and checked for quality before pooling together.
Keywords: treated vs untreated comparison

first: Ludivine

last: Taconnat

first: Alain

last: Pugin


title: analysis of atnuc-l1 mutant line-Characterization of a nucleolin gene in Arabidopsis thaliana mutant line

last: BRUNAUD

summary:
rs05-07_nucleolin - analysis of atnuc-l1 mutant line - To establish if nucleolin plays a role in controlling gene expression of genes involved in ribosome biogenesis - transcriptome analysis of the Atnuc-L1 mutant line
Keywords: gene knock out

first: Julio

last: Saez-Vasquez


title: NRT2.4 NO3 transport mutant

summary:
Transcriptome of the AtNRT2.4 mutant - Mutants have no phenotype
Keywords: gene knock out

first: Frederique

last: Vedele

first: Frank

last: Chopin


title: Nitrate control of Arabidopsis seed dormancy

first: Véronique

summary:
Freshly harvested Arabidopsis seeds (ecotype Col0 obtained under 10 mM nitrate nutrition, referred to as C10) are dormant and do not germinate when sown on an agarose-based medium. This experiment was performed to analyze the genes that are differentially expressed in freshly harvested C10 seeds sown on agarose (dormant) versus freshly harvested C10 dry seeds (dormant) to analyze differential expression of genes during the first 6 hrs of imbibition of dormant seeds. Reference: Alboresi et al. Plant Cell Environ (2005) 28 : 500-512  - 16 DAP siliques were harvested from Col 0 plants grown on 10 or 50 mM nitrate or from G4 3 mutant grown on 10 mM nitrate in growth chambers.
Keywords: treated vs untreated comparison

last: Renou

first: Hoai-Nam

middle: N

last: Truong


title: Nickel_root-effect of nicotianamine over-accumulation in standard condition and in response to nickel treatment

summary:
rs04-05_nickel - nickel_root - Nicotianamine is a known metal chelator (of Mn, Fe, Zn, Ni, Cu) suspected to be involved in metal delivery and/or circulation in planta. This project aim at understanding the effect of the modulation of the nicotianamine content on the transcriptome of Arabidopsis thaliana in control hydroponic condition and in response to nickel treatment both at the root and at the leaf level. - After germination, plants were grown hydroponically for 6 weeks in classical nutrient solution (Marques et al, New Phytol, 2004, vol 164, pp 289-95) and then treated for 48 hours with 50 uM NiSO4 or with no nickel added for control.
Keywords: gene knock in (transgenic)

last: Lebrun


title: Time course h2o2 treatment-involvement of small non coding RNAs in Arabidopsis responses to oxidative stress

summary:
rs04-10_oxydative--stress - time course h2o2 treatment - Effect of an hydrogen peroxide treatment on gene regulation in arabidopsis cells - Arabidopsis cells (5 days after subculturing) were cultured at 21degreeC, 8 h photoperiod under agitation. H2O2 2.5 uM was added to cells 5 days after subculturing and 2 hours after the beginning of the light period. Treated and control cells were collected 15 min, 1 h, 5 h and 12 h after treatment.
Keywords: treated vs untreated comparison

first: Caroline

last: Hartmann


title: CKI role in plant development

summary:
rs04-08_ntkis - nt-kis - Transcription profiling of NtKIS overexpressing lines - 35S NtKIS (CDK inhibitor) versus Col0
Keywords: gene knock in (transgenic)

last: Bitton

first: Catherine-

last: Bergounioux


title: Effect of atrazine and sucrose on xenobiotic tolerance in Arabidopsis

summary:
rs05-05_atrazine - effect of atrazine and sucrose on arabidopsis transcriptome - Growth in the presence of sucrose was shown to confer to Arabidopsis thaliana seedlings, under conditions of in vitro culture, a very high level of tolerance to the herbicide atrazine and to other photosynthesis inhibitors (Sulmon et al., 2004). The CATMA investigation will be useful to reveal the gene networks implicated in the mechanisms of xenobiotics tolerance.  - Seeds of Arabidopsis thaliana (ecotype Columbia) were surface-sterilized inbayrochlore/ethanol (1:1, v/v), rinsed in absolute ethanol and dried overnight. Germination and growth were carried out under axenic conditions in square Petri dishes. After seeds were sowed, Petri dishes were placed at 4degreeC for 48 h in order to break dormancy and homogenize germination, and then transferred to a control growth chamber at 22degreeC under a 16-h light period regime at 4500 lux for 4 weeks. Growth medium consisted of 0.8% (w/v) agar in 1x Murashige and Skoog (MS) basal salt mix (Sigma, St. Louis, MO, USA) adjusted to pH 5.7. After 4 weeks of cultivation on vertical plates plantlets were transferred on fresh medium complemented or not with atrazine 10 uM and with sucrose 80mM or mannitol 80 mM which were directly added during preparation of agar-MS media prior to sterilisation. Atrazine was sterilized by microfiltration through 0.2 um cellulose acetate filters (Polylabo, Strasbourg, France) and then axenically added to melted agar-MS medium prior to pouring into Petri dishes. Then plantlets were harvested after 24 hours of transfer and extracted for RNA.
Keywords: treated vs untreated comparison

first: Gwenola

last: Gouesbet-Jan


title: Transcriptome analysis of two mutants rdr6/sgs2 and sgs3 impaired in post-transcriptional gene silencing (PTGS)

summary:
Identification of new genes regulated by RDR6 and SGS3 (two genes involved in PTGS) by analysis of the transcriptome of rdr6-1 and sgs3-1 mutants compared to wild-type plants in different tissues (flower and leaves). The comparison between transcriptome of rdr6-1 and sgs3-1 mutant alleles impaired in PTGS and development (juvenile-to-adult transition) and transcriptome of rdr6-5 and sgs3-3 alleles impaired only in PTGS would allowed identification of genes involved in the developmental default (zip phenotype) of the null alleles (rdr6-1 and sgs3-1 mutants). - Transcriptome of rdr6 and sgs3 mutants will be compared to the transcriptome of wild-type plants in flower and leaves. Further-more the comparison between transcriptome of rdr6-1 and sgs3-1 mutant alleles impaired in PTGS and development (juvenile-to-adult transition) and transcriptome of rdr6-5 and sgs3-3 alleles impaired only in PTGS will be done for flowers and leaves.
Keywords: gene knock in (transgenic)

first: Herve

last: Vaucheret

last: Martin-Magniette


title: Effect of nicotianamine over-accumulation in standard condition and in response to nickel treatment

summary:
rs04-05_nickel - nickel_leaf - Nicotianamine is a known metal chelator (of Mn, Fe, Zn, Ni, Cu) suspected to be involved in metal delivery and/or circulation in planta. This project aim at understanding the effect of the modulation of the nicotianamine content on the transcriptome of Arabidopsis thaliana in control hydroponic condition and in response to nickel treatment both at the root and at the leaf level. - After germination, plants were grown hydroponically for 6 weeks in classical nutrient solution (Marques et al, New Phytol, 2004, vol 164, pp 289-95) and then treated for 48 hours with 50 uM NiSO4 or with no nickel added for control.
Keywords: gene knock in (transgenic),organ comparison

first: Michel


title: Identification of genes involved in cell wall integrity signalling in Arabidopsis dark-grown hypocotyls

summary:
Inhibition of cellulose synthesis by chemical inhibitors or in a mutant background leads to rapid inhibition of cell elongation. This inhibition appears to be an active process, which involves feedback signalling from the cell wall. We have isolated two loci THE1 and THE2, which are identified by mutations that partially suppress the dark-grown hypocotyl phenotype in a mutant background for cellulose synthase catalytic subunit CESA6/PROCUSTE1. THE1 encodes a receptor kinase and may play a role in this feedback signalling process. To identify genes that are regulated by THE1 and THE2, we compared the transcript profiles of 5 day-old dark-grown seedlings of the1-1/prc1-1 with prc1-1 ; the1-3/prc1-8 with prc1-8 ; prc1-8 or the1-3 with WS and the2-1/prc1-1 with prc1-1.  - We have isolated two loci THE1 and THE2, which are identified by mutations that partially suppress the dark-grown hypocotyl phenotype in a mutant background for cellulose synthase catalytic subunit CESA6/PROCUSTE1. THE1 encodes a receptor kinase and may play a role in this feedback signalling process. To identify genes that are regulated by THE1 and THE2, we compared the transcript profiles of 5 day-old dark-grown seedlings of the1-1/prc1-1 with prc1-1 ; the1-3/prc1-8 with prc1-8 ; prc1-8 or the1-3 with WS and the2-1/prc1-1 with prc1-1.
Keywords: gene knock out

overall_design: 7 dye-swap - CATMA arrays

first: Sandrine

last: Balzergue

first: Herman

last: Hofte


title: Which genes are expressed in Arabidopsis pollen.- Comparison between Columbia and WS pollen RNAs.

status: Public on Jan 31 2007

summary:
RNAs of Pollen from Columbia and WS were compared
Keywords: ecotype comparison

first: Frederic

last: Berger

first: Marie-Laure


title: The study of ethylene response in cellular elongation of Arabidopsis roots

summary:
The goal of the experiments is to identify differential genes between the roots of Arabidopsis thaliana and roots treated for 3 h with 1-aminocyclopropane-1-carboxylic acid (ACC). ACC blocks the maximal cell elongation of the root cells. - Arabidopsis plants are grown for 5 days on MS medium and then we transfer them to a medium supplemented with ACC (5uM) or without ACC. After 3 h of growth, we isolate the RNA of the roots.
Keywords: treated vs untreated comparison

last: Taconnat

first: Jean-Pierre

first: Tinne

last: De Cnodder


title: gene profiling in silencing suppressor plants or in mirna mutants-Transcriptional and post-transcriptional changes in Arabidopsis plants that constitutively express suppressors of RNA silencing

last: BRUNAUD

summary:
gen107_ptgs - gene profiling in silencing suppressor plants or in mirna mutants - What are the genes that are differentially regulated in various tissues derived from silencing suppressor plants or miRNA mutants? - HcPro, P15, P19, CHS-RNAi (control), were grown on MS solid medium, and tissues were harvested at different developmental stages. dcl1-9, hen1-1 and La-er (control) were grown on MS solid medium, and tissues harvested at different developmental stages.
Keywords: gene knock in (transgenic),gene knock out

overall_design: 60 dye-swap - CATMA arrays

first: Agnes

last: Yu

first: Florence

last: Jay

first: Ludivine

first: Sandra

last: Pelletier

first: Yu

last: Wang

first: Olivier

last: Voinnet

first: François

last: Roudier

first: Vincent

last: Colot


title: Malignant Germ Cell Tumors Display Common microRNA Profiles Resulting in Global Changes in Expression of mRNA Targets

status: Public on Mar 15 2010

first: Matthew

middle: Jonathan

last: Murray

address: Box 197, Hills Road

department: MRC/Hutchison Research Centre

institute: MRC Cancer Cell Unit

type:
Expression profiling by array
Non-coding RNA profiling by array
Third-party reanalysis

summary:
Comparison of miRNA expression profiles in malignant germ cell tumors compared to non-malignant control group.
Use of bioinformatic algorithm Sylamer to interrogate mRNA expression profiles from malignant germ cell tumors for enrichment or depletion of binding sites for differentially expressed miRNAs.
Use of Gene Ontology (GO) analysis to demonstrate functional significance of differentially expressed miRNAs in malignant germ cell tumors.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design:
mRNA profiling:
Analyzed global mRNA expresion profiles from 21 pediatric samples (17 malignant germ cell tumors, 1 benign germ cell tumor and 3 gonadal controls) using Sylamer (van Dongen et al, Nature Methods 2008, PMID 18978784) to study functional significance of differentially expressed miRNAs in malignant germ cell tumors. 16 of these files previously published - Palmer et al, Cancer Research 2008, PMID 18519683; GEO Accession Number GSE10615.
Similarly, re-analyzed published global mRNA expresion profiles from 25 adult samples (20 malignant germ cell tumors and 5 testis controls) using Sylamer (van Dongen et al, Nature Methods 2008, PMID 18978784) to study functional significance of differentially expressed miRNAs in malignant germ cell tumors. These files previously published - Korkola at al, Cancer Research 2006, PMID 16424014; GEO Accession Number GSE3218.

miRNA profiling:
Analyzed global miRNA expression files from 48 samples including 32 pediatric gonadal and extragonadal germ cell tumors, 2 adult testicular seminomas, 8 gonadal and developmental control samples and 6 germ cell tumor cell lines.
Re-analyzed published data (TaqMan MicroRNA Assays) from study of miRNA expression in adult gonadal germ cell tumors (Gillis et al, J Pathol 2007, PMID 17893849) and compared with pediatric findings. Re-analyzed data linked below as supplementary file.

middle: J

first: Roger

middle: D

last: Palmer

first: Harpreet

middle: K

last: Saini

first: Stijn

last: van Dongen

first: Cei

last: Abreu-Goodger

first: Balaji

last: Muralidhar

first: Mark

last: Pett

first: Claire

middle: M

last: Thornton

first: James

last: Nicholson

first: Anton

last: Enright

first: Nicholas

last: Coleman


title: atnin7-1 in two different nitrogen conditions

first: Véronique

last: BRUNAUD

summary:
Does the ko of NIN7 leads to a differential expression in comparison to the wildtype and is this dependent on the nitrogen regime? Can we repeat the results from the first experiment, and is there a difference between the two alleles?  - Plants were harvested during the first 3 hours of light after 42 growth on 0.2mM and 6mM nitrate in hydroponic condition (short day, 170 uE). 42 DAYS of growth
Keywords: gene knock out

first: Ludivine

last: Taconnat

first: Jean-Pierre

last: Renou

first: Anne

last: Krapp

first: Marie-Laure

last: Martin-Magniette


title: comparison ws vs haf2_gcn5-histone acetylation required for gene expression during germination

summary:
af31_haf2_gcn5 - comparison ws vs haf2_gcn5 - Genes whose expression during seed germination is affected by the mutation of two histone acetyltransferase genes GCN5 and HAF2 (the later encodes TAF1).  - mRNA extraxted from 72h germinating seed of the mutants gcn5 and haf2 were used for comparison with Ws seed at the same satge. 2 repetitions techniques + 1 repetition biologique.
Keywords: wt vs mutant comparison

first: Gaetan

last: Lemonnier

first: Dao-xiu

middle: x

last: Zhou