Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of indole-3-acetic acid at physiological concentrations (IAA) treatment of Arabidopsis seedlings

ABSTRACT: To demonstrate the analysis of differential expression using CATMA v1 arrays, Arabidopsis seedlings were treated with indole-3-acetic acid at physiological concentrations. The seedlings were germinated in liquid medium, and treated with indole-3-acetic acid for 30, 120 or 240 minutes. Changes in expression patterns were monitored using a complete loop design including an untreated sample (0 minutes). Reciprocal labelling was used rendering a total of eight hybridisations. An additional self-to-self hybridisation for time-point 0 was included. The statistical analysis was based an ANOVA model and indicated that 1123 GSTs were differentially expressed (p < 2.37 x 10-6) in at least one of the three time points following treatment.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Ian Small

PROVIDER: E-MEXP-65 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications.

Hilson Pierre P Allemeersch Joke J Altmann Thomas T Aubourg Sébastien S Avon Alexandra A Beynon Jim J Bhalerao Rishikesh P RP Bitton Frédérique F Caboche Michel M Cannoot Bernard B Chardakov Vasil V Cognet-Holliger Cécile C Colot Vincent V Crowe Mark M Darimont Caroline C Durinck Steffen S Eickhoff Holger H de Longevialle Andéol Falcon AF Farmer Edward E EE Grant Murray M Kuiper Martin T R MT Lehrach Hans H Léon Céline C Leyva Antonio A Lundeberg Joakim J Lurin Claire C Moreau Yves Y Nietfeld Wilfried W Paz-Ares Javier J Reymond Philippe P Rouzé Pierre P Sandberg Goran G Segura Maria Dolores MD Serizet Carine C Tabrett Alexandra A Taconnat Ludivine L Thareau Vincent V Van Hummelen Paul P Vercruysse Steven S Vuylsteke Marnik M Weingartner Magdalena M Weisbeek Peter J PJ Wirta Valtteri V Wittink Floyd R A FR Zabeau Marc M Small Ian I

Genome research 20041001 10B

Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization between complementary nucleic acid strands, inciting us to create a collection of gene-specific sequence tags (GSTs) representing at least 21,500 Arabidopsis genes and which are compatible with both approaches. The GSTs were carefully selected to ensure that each of them shared no significant similari ...[more]

PMID: 15489341

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Project description:The purpose of this experiment was to do investigatge the transcriptional effect of anti-TNF treatment in patients suffering from rheumatoid arthritis. Two series of hybridizations were performed. Each hybridization was done with a technical replicate (the same amount of RNA taken from the same amplified RNA aliquot labeled in two separate reactions and hybridized onto two separate arrays). In the first series of hybridizations RNA exptracted from biopsies taken before treatment was hybridized in a common reference design to enable comparisons between patients. In the second series RNA from biopsies taken after and before treatment were hybridized on the same chip in a direct design to enable investigation of the effect of treatment. 10 patients (8 females and 2 males, median age 54, range 25-69) meeting the American College of Rheumatology (ACR) criteria for RA were recruited for this study. All patients received infliximab (an antibody directed against TNF-alpha) infusions 3mg/kg at week 0 and than after 2 weeks and 6 weeks. Five of these patients were receiving prednisolon and all ten patients were treated with methotrexate to a maximum of 20 mg per week. Synovial biopsies were obtained during arthroscopy from all patients before and after a median of 9 weeks of treatment (with one exception, patient 7 where the second biopsy was obtained during open surgery). Biopsies were taken at the site of inflammation close to cartilage (cc) or not close to cartilage (ncc), defined as less or more than 1.5 cm away from cartilage, respectively. One biopsy was taken before and after treatment from patient 5, 7, 9 and 10. Multiple biopsies were retrieved before and/or after treatment from patient 1, 2, 3, 4, 6 and 7. Due to small amounts of RNA available for patient 9 it was only used in the second series of hybridizations. The average biopsy weight was 22 mg. The ethical committee at the Karolinska Hospital approved all experiments on human cells and tissues. Informed consent was obtained from all study subjects.

Dataset Information

Transcription profiling of indole-3-acetic acid at physiological concentrations (IAA) treatment of Arabidopsis seedlings

Publications

Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications.

Similar Datasets

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