Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Comparison of the transcriptomes of tfIIs vs Col-0

ABSTRACT: Testing the consequences of the absence of the transcript elongation factor TFIIS on the transcriptome in Arabidopsis. Keywords: Comparison of mutant and wildtype Four replicate RNA extractions were performed of each genotype using independent pools of plants. Samples were hybridized in two dye-swaps. tfIIs1#1 (Cy5) vs. Col-0#1 (Cy3) Col-0#2 (Cy5) vs. tfIIs1#2 (Cy3) dye-swap tfIIs1#3 (Cy5) vs. Col-0#3 (Cy3) Col-0#5 (Cy5) vs. tfIIs1#4 (Cy3) dye-swap Samples were hybridized in two dye-swaps. The data were normalized over all 4 hybridizations to obtain one, single log-ratio(Sample/Reference). The raw data files of all four of the hybridizations are attached to the Sample.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Marion Grasser

PROVIDER: E-GEOD-10663 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Transcript elongation factor TFIIS is involved in arabidopsis seed dormancy.

Grasser Marion M Kane Caroline M CM Merkle Thomas T Melzer Michael M Emmersen Jeppe J Grasser Klaus D KD

Journal of molecular biology 20090103 3

Transcript elongation factor TFIIS promotes efficient transcription by RNA polymerase II, since it assists in bypassing blocks during mRNA synthesis. While yeast cells lacking TFIIS are viable, inactivation of mouse TFIIS causes embryonic lethality. Here, we have identified a protein encoded in the Arabidopsis genome that displays a marked sequence similarity to TFIIS of other organisms, primarily within domains II and III in the C-terminal part of the protein. TFIIS is widely expressed in Arabi ...[more]

PMID: 19150360

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Project description:Sample groupings for this project are as follows: Cauline leaf vs Cultured Cell : - Cauline leaf, p1; Exp:Red; Ref: Green (Cy5:Cy3) - Cauline leaf, p2; Exp:Red; Ref: Green (Cy5:Cy3) - Cauline leaf, p3; Exp:Red; Ref: Green (Cy5:Cy3) Cotyledon light vs Cotyledon dark : - Cotyledon, CP1; Exp:Red; Ref: Green (Cy5:Cy3) - Cotyledon, CP2; Exp:Red; Ref: Green (Cy5:Cy3) Cotyledon light vs Cultured cell : - Cotyledon, cn1; Exp:Green; Ref: Red (Cy3:Cy5) - Cotyledon, cn2; Exp:Green; Ref: Red (Cy3:Cy5) Cotyledon dark vs Cultured cell : - Cotyledon dark, n1; Exp:Green; Ref: Red (Cy3:Cy5) - Cotyledon dark, n2; Exp:Green; Ref: Red (Cy3:Cy5) - Cotyledon dark, n3; Exp:Green; Ref: Red (Cy3:Cy5) Germinating seed vs Cultured cell : - Germinating seed, gn1; Exp:Green; Ref: Red (Cy3:Cy5) - Germinating seed, gn2; Exp:Green; Ref: Red (Cy3:Cy5) - Germinating seed, gn3; Exp:Green; Ref: Red (Cy3:Cy5) Hypocotyl light vs Hypocotyl dark : - Hypocotyl, hldn1; Exp:Red; Ref: Green (Cy5:Cy3) - Hypocotyl, hldn2; Exp:Red; Ref: Green (Cy5:Cy3) Hypocotyl light vs Cultured cell : - Hypocotyl light, hln1; Exp:Green; Ref: Red (Cy3:Cy5) - Hypocotyl light, hln2; Exp:Green; Ref: Red (Cy3:Cy5) Petal vs Cultured cell : - Petal, pn1; Exp:Green; Ref: Red (Cy3:Cy5) - Petal, pn2; Exp:Green; Ref: Red (Cy3:Cy5) - Petal, pn3; Exp:Green; Ref: Red (Cy3:Cy5) 1DBP vs Cultured cell : - Pistil 1DBP, pin1; Exp:Green; Ref: Red (Cy3:Cy5) - Pistil 1DBP, pin2; Exp:Green; Ref: Red (Cy3:Cy5) - Pistil 1DBP, pin3; Exp:Green; Ref: Red (Cy3:Cy5) Pistil 1DPP vs Cultured cell : - Pistil 1DPP, psn1; Exp:Green; Ref: Red (Cy3:Cy5) - Pistil 1DPP, psn2; Exp:Green; Ref: Red (Cy3:Cy5) - Pistil 1DPP, psn3; Exp:Green; Ref: Red (Cy3:Cy5) - Pistil 1DPP, psn4; Exp:Green; Ref: Red (Cy3:Cy5) Root dark vs Cultured cell : - Root dark, rdn1; Exp:Green; Ref: Red (Cy3:Cy5) - Root dark, rdn2; Exp:Green; Ref: Red (Cy3:Cy5) Root light vs Cultured cell : - Root light, rln1; Exp:Green; Ref: Red (Cy3:Cy5) - Root light, rlp1; Exp:Red; Ref: Green (Cy5:Cy3) Root light vs Root dark : - Root light vs dark, rldp1; Exp:Red; Ref: Green (Cy5:Cy3) - Root light vs dark, rldp2; Exp:Red; Ref: Green (Cy5:Cy3) Rosette leaf vs Cultured cell : - Rosette leaf, rfp1; Exp:Red; Ref: Green (Cy5:Cy3) - Rosette leaf, rfp2; Exp:Red; Ref: Green (Cy5:Cy3) - Rosette leaf, rfp3; Exp:Red; Ref: Green (Cy5:Cy3) Sepal vs Cultured cell : - Sepal, sn1; Exp:Green; Ref: Red (Cy3:Cy5) - Sepal, sn2; Exp:Green; Ref: Red (Cy3:Cy5) Silique 3DPP vs Cultured cell : - Silique 3DPP, s3n1; Exp:Green; Ref: Red (Cy3:Cy5) - Silique 3DPP, s3n2; Exp:Green; Ref: Red (Cy3:Cy5) - Silique 3DPP, s3n3; Exp:Green; Ref: Red (Cy3:Cy5) Silique 8DPP vs Cultured cell : - Silique 8DPP, s8n1; Exp:Green; Ref: Red (Cy3:Cy5) - Silique 8DPP, s8n2; Exp:Green; Ref: Red (Cy3:Cy5) - Silique 8DPP, s8n3; Exp:Green; Ref: Red (Cy3:Cy5) Stamen vs Cultured cell : - Stamen, smn1; Exp:Green; Ref: Red (Cy3:Cy5) - Stamen, smn2; Exp:Green; Ref: Red (Cy3:Cy5) - Stamen, smn3; Exp:Green; Ref: Red (Cy3:Cy5) Hypocotyl dark vs Cultured cell : - Hypocotyl dark, hn1; Exp:Green; Ref: Red (Cy3:Cy5) - Hypocotyl dark, hn2; Exp:Green; Ref: Red (Cy3:Cy5) Stem vs Cultured cell : - Stem, stp1; Exp:Red; Ref: Green (Cy5:Cy3) - Stem, stp2; Exp:Red; Ref: Green (Cy5:Cy3) - Stem, stp3; Exp:Red; Ref: Green (Cy5:Cy3) Keywords: other

Project description:In Western countries, colorectal cancer (CRC) is the third most common cancer in both men and women and the second leading cause of cancer-related deaths (approximately 500,000 deaths annually). For CRC, the tumor stage is the main prognostic factor for survival or relapse after surgery. Current staging is based on the AJCC classification which takes into account tumor size/depth, lymph node involvement and distant metastases. Surgical intervention can cure a significant portion of the patients, especially those that are presented in stages I, II or III (around 75% of patients). Patients in stage II undergo surgery only, whereas stage III patients receive adjuvant chemotherapy. However, a major fraction of these patients either have no need for adjuvant treatment (40% stage III) or would benefit when they were given adjuvant therapy in stage II. Therefore, in the current practice, the majority of patients receive not the optimal treatment. An accurate and reliable method that identifies patients with low and high risk for recurrence could improve the selection for adjuvant therapies in these groups, reducing over- or under-treatment. Molecular profiling of mRNA expression by microarray is an approach to identify relevant genes and gene signatures and has been used already for different types of cancer, like breast and HCC. Most studies, however, resulted in their own classification with a specific separation into groups. Most of these microarray studies show remarkably little overlap and it is difficult to find a clear correlation between the molecular classes and prognosis. The results of the studies seem to be center-dependent because of the different microarray techniques used, the small heterogeneous cohorts that are studied and the different clinical parameters used for the evaluation. Recently, we used a mechanism-driven approach to find a correlation between gene expression in HCC and prognosis in which we tried to overcome most shortcomings (van Malenstein et al. CCR 2010). In this study, we want to apply the approach which we used for HCC now in CRC with the aim to improve the prognosis prediction for patients in AJCC stage II and III. We determined the gene expression by microarray in the colon cancer cell line Caco2 and identified the genes that are differentially expressed under hypoxia (72 hours, 2% O2). Using a bioinformatic approach, we used 5 sets of expression data with corresponding clinical information (training: 3 sets, 234 patients and validation: 2 sets, 322 patients). This resulted in a unique 21 gene set with good performance in retrospective analysis. A second improvement we wanted to achieve is the development of a method that can be applied on FFPE material, which would expand the use of the technique to samples outside the university or research setting. We used the nCounter technique that uses hybridization of labeled probes and quantification without an amplification step. We tested our 21 genes on a cohort of 384 well-characterized patients that were collected between 2004 and 2006 at the University Hospitals of Leuven. We compared cells under hypoxia 2% O2 versus 20% O2 conditions. This was done for two cell lines (Caco2 human colorectal adenocarcinoma cell line and HPAC pancreas adenocarcinoma cell line). Each sample has a biological replicate. Samples are hybridized in dye-swap, resulting in 4 hybridizations per cell line.

Dataset Information

Comparison of the transcriptomes of tfIIs vs Col-0

Publications

Transcript elongation factor TFIIS is involved in arabidopsis seed dormancy.

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