title: A gene expression signature predicting the recurrence of tamoxifen-treated primary breast cancer.

status: Public on Mar 18 2008

city: Montpellier

first: Vincent

last: Negre

address: IRCM CRLC Val d'aurelle

institute: INSERM

summary:
A 36-gene classifier was constructed through expression profiling of 132 tumors  from tamoxifen-treated patients using 70-mer oligonucleotide microarrays. The robustness of the signature was demonstrated using expression data from 83 independent tumors. The 36-gene signature was (i) more efficient to predict disease-free survival than the traditional histo-pathological prognostic factors, (ii) as effective as the Nottingham Prognostic Index or the "Adjuvant!" software, and (iii) the only independent prognostic factor. Comparison with several already published signatures demonstrated that the 36-gene signature was among the best to classify tumors.
Keywords: Gene expression profiling; supervised analysis; molecular signature predictive of recurrence; univariate and multivariate analysis in relation to disease-free survival.

overall_design: In the study presented here, a cohort of 132 primary tumors from tamoxifen-treated patients followed up more than 5-years, was used to acquire expression profiles at the whole genome level by 70-mer oligonucleotide microarrays containing 22,680 probes (which represent 21,329 human specific genes). Supervised predictive analysis of microarrays allowed construction of a 36-gene molecular classifier whose robustness was assessed by using gene expression data from 83 independent tumors (including 23 tumors from our microarray platform and 60 tumors from the study by Ma et al., Cancer cell 2004; 5:607-616).

first: Maïa

last: Chanrion

first: Negre

last: Vincent

first: Hélène

last: Fontaine

first: Nicolas

last: Salvetat

first: Frédéric

last: Bibeau

first: Gaëtan

last: MacGrogan

first: Louis

last: Mauriac

first: Dionyssios

last: Katsaros

first: Franck

last: Molina

first: Charles

last: Theillet

first: Jean-Marie

last: Darbon


title: Tiling microarray of Oryza sativa japonica at 46nt resolution

status: Public on Feb 21 2007

city: New Haven

first: Rajkumar

last: Sasidharan

state: CT

address: 266 Whitney Avenue

department: MB & B

country: USA

institute: Yale University

type: Expression profiling by genome tiling array

summary:
This experiment was designed to identify transcribed regions of japonica subspecies of the rice genome. A series of high-density oligonucleotide tiling arrays that represent sense and antisense strands of the entire nonrepetitive sequence of all the 12 chromosomes were designed to measure genome-wide transcription. A total of 12253842 36mer oligonucleotide probes positioned every 46 nt on average were used for this purpose. The probes were synthesized via maskless photolithography at a feature density of approximately 389,000 probes per slide. The arrays were hybridized with fluorescence-labeled cDNA reverse-transcribed from equal amounts of four selected poly(A)+ RNA population (seedling root, seedling shoot, panicle, and suspension cultured cells).
Keywords: tiling array, genome-wide transcription

overall_design:
The arrays were hybridized with fluorescence-labeled cDNA reverse-transcribed from equal amounts of four selected poly(A)+ RNA population (seedling root, seedling shoot, panicle, and suspension cultured cells).

The four RNA population from seedling roots, seedling shoots, panicles, and suspension-cultured cells were pooled in equal amount and cDNAs were derived from the RNA mixture. Total RNA and mRNA were isolated using the RNeasy Plant Mini kit (Qiagen, Valencia, CA) and the Oligotex mRNA kit (Qiagen), respectively. First-strand cDNA was generated from 4 micro gram poly(A)+ RNA with SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA).

The cDNAs were precipitated in ethanol:isopropanol (1:1 v/v) and resuspended in 0.1 M NaHCO3 to facilitate coupling of Alexa Fluor 555 NHS esters (Molecular Probes, Eugene, OR) to the reactive groups of the amino-allyl dUTPs and were purified with CyScribe GFX glass fiber spin columns (Amersham Bioscience, Piscataway, NJ).

Microarrays were hybridized with 4 ¦Ìg labeled cDNA in 300 micro litre hybridization buffer (50 mM MES, 0.5 M NaCl, 10 mM EDTA, and 0.005% (v/v) Tween-20) for 16 hours at 50 deg C in disposable adhesive chambers (Grace BioLabs, Bend, OR) in a hybridization oven with constant agitation. Hybridized arrays were washed on an orbital Sample in non-stringent buffer (6¡Á SSPE, 0.01% [v/v] Tween-20) for 10 minutes at room temperature, then in stringent buffer (100 mM MES, 0.1 M NaCl, 0.01% Tween-20) for 30 minutes at 45 deg C. This was followed by a 5-minute wash in non-stringent buffer and a 2-minute wash in 0.1X SSC.

The arrays were dried with compressed nitrogen and scanned with an Axon 4000B laser scanner at 5 micro meter resolution.

The fluorescence intensity data were extracted with the NimbleScan software (NimbleGen Systems, Madison, WI).

first: Lei

last: Li

first: XiangFeng

last: Wang

first: Viktor

last: Stolc

first: Wei

last: Deng

first: Hang

last: He

first: Jan

last: Korbel

first: Xuewei

last: Chen

first: Waraporn

last: Tongprasit

first: Pamela

last: Ronald

first: Runsheng

first: Mark

last: Gerstein

first: XingWang


title: Effects of antimitotic drug benomyl on wild-type strain and strains with Yap1 or Pdr1 deletions

status: Public on Sep 06 2004

city: Paris

first: Gaëlle

last: Lelandais

address: 46, rue d'Ulm

department: Biologie

country: France

institute: Ecole Normale Supérieure

summary:
Time-course analyses of the modifications of the yeast gene expression program which immediately follows addition of the antimitotic drug benomyl. Parallel experiments were conducted in different genetic contexts using strains deleted in the Yap1 and Pdr1 genes.
Keywords: other

first: Anca

last: Lucau-Danila

first: Zuzana

last: Kozovska

first: Véronique

last: Tanty

first: Thierry

last: Delaveau

first: Frédéric

last: Devaux

first: Claude

last: Jacq


title: Microarrays analysis of SREBP-1a and SREBP-1c target genes identify new regulatory pathways.

status: Public on Jun 19 2008

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

summary:
In this study we have identified the target genes of SREBP1a and SREBP1c in primary cultures of human skeletal muscle cells using adenoviral vectors expressing the mature nuclear form of human SREBP1a or SREBP1c combined with oligonucleotide microarrays.
Keywords: comparison of human myotubes infected either by SREBP1a or 1C

overall_design:
Human myotubes were prepared from 3 different skeletal muscle biopsies. After 7 days of differentiation, myotubes were infected for 48 hours with recombinant adenovirus expressing either Renilla, nuclear SREBP1a or nuclear SREBP1c.
Each SREBP1a or SREBP1c infected myotubes culture was compared to Renilla infected myotubes culture. Renilla infected myotubes were considered as the control. Three biological replicates were processed.

first: Sophie

last: Rome

first: Virginie

last: Lecomte

first: Emmanuelle

last: Meugnier

first: Jennifer

last: Rieusset

first: Cyrille

last: Debard

first: Vanessa

last: Euthine

first: Hubert

last: Vidal

first: Etienne

last: Lefai


title: Global analysis of lipid metabolism regulation in Brassica napus developing seeds

status: Public on Feb 26 2008

city: Shanghai

first: Hong-Wei

last: Xue

state: Shanghai

address: 300 Fenglin Road

department: molecular genetics

country: China

institute: Institute of Plant Physiology & Ecology

type:
Expression profiling by SAGE
Expression profiling by array

summary:
Gene expression profiles during seed development and fatty acid (FA) metabolism, as well as the relevant regulation, of Brassica napus were studied through multiple high-throughput genomic approaches. Serial Analysis of Gene Expression (SAGE) using seed materials obtained a total of 68,718 tags, of which 23,897 were unique and 503 tags were functionally identified, and revealed the transcriptome of approximately 35,000 transcripts in B. napus developing seeds. Further, ~22,000 independent ESTs were obtained by large-scale sequencing using immature embryos at different stages, and 8343 uni-ESTs and 3355 full-length cDNAs were identified respectively, resulting in the systemic identification of B. napus FA biosynthesis-related genes. Gene expression profiles were further studied employing cDNA chip hybridization to reveal the global regulatory network of FA metabolism in developing seeds. Together with the analysis on FA amounts and composition, it was shown that 17-21 days after pollination (DAP) was a crucial stage for transition of seed to sink tissue. High expressions of FA biosynthesis-related genes and transition of FA components are mainly at stages 21 DAP or 21-25 DAP respectively. In addition, compared to Arabidopsis, more critical roles of starch metabolism are detected for B. napus seed FA metabolism and storage components accumulation. Crucial effects of starch metabolism, carbon flux, oxidative pentose phosphate pathway (OPPP), photosynthesis, and other regulators in FA metabolism were discussed.
Keywords: Brassica napus, immature seed, SAGE, EST, cDNA microarray

overall_design: Brassica napus immature seeds at 5 and 9 days after pollination (DAP) were collected and used to construct SAGE library. Rapeseed embryos at different developmental stages were observed and two cDNA libraries were constructed using materials at 3-9 day after pollination(DAP) or 11-19 DAP. Gene expression profiles during seed development were further detailed studied via cDNA microarray. cDNA inserts of ESTs were PCR amplified and used to generate the glass-based cDNA chips. Immature seeds at different developmental(7, 9, 12, 17, 19, 21, 25, 31DAP) stages were used for hybridization, and the seed of 3 day after pollination was used as control.

first: Guo-Zhang

last: Wu

first: Ya

last: Niu

first: Rui

last: Ye

first: Wen-Hui

last: Lin

first: Qiu-Ming

last: Shi

first: Xiao-Dong

last: Xu

first: Rao

last: Li

first: Yu-Guang

last: Du


title: Hybrid wine yeast strains

status: Public on Jul 15 2008

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

summary:
This experiment is the analysis of the transcriptomes of several hybrid yeast strains obtained by crossing natural (from wine) isolates of S. cerevisiae and S. uvarum. All isolations have been done from hybrid strains growing in exponential phase in YPD.
Keywords: Strain comparison

sample_organism: Saccharomyces cerevisiae x Saccharomyces uvarum

overall_design: Transcriptomic analysis of three independent replicates of each yeast strain growing in exponential phase. Each replicate has been hybridized on a different macroarray (F19-F22-F24) as indicated in the sample files. A single DNA (S. cerevisiae 3002 wine strain) genomic hybridization, from the same labeling reaction, was done on the same macroarrays for normalization.

first: José

middle: E

last: Pérez-Ortín

first: Oreto

last: Antunez

first: Lisa

last: Solieri


title: Transcriptional Analysis of 1M Regions in Medicago truncatula Using Tiling Microarrays

status: Public on Jan 15 2008

first: Hang

last: He

address: 165 Prospect St

department: MCDB

summary:
We report here a transcriptonal analysis in six different organ types of a approximately 1 Mb region in legume plants barrel medic (Medicago truncatula) which is sytenic with soybean (Glycine max). We used oligonucleotide tiling microarrays to detecte transcription of over 80% of the predicted genes in both species. We detected differential gene expression in the six examined organ types.
Keywords: RNA

overall_design:
Both the barrel medic and soybean tiling arrays were produced on the Maskless Array Synthesizer platform. Briefly, tiling-paths consisting of 36-mer oligonucleotides offset by five nucleotides were designed to represent both DNA strands of the selected barrel medic and soybean genome sequence. Probes were synthesized at a feature-density of 390,000 probes per array in a “chess board” design. Microarray production and storage were carried out.
Total RNA and mRNA were sequentially isolated using the RNeasy Plant Mini kit (Qiagen, Valencia, CA) and the Oligotex mRNA kit (Qiagen) according to the manufacturer’s recommendations, respectively. mRNA from different organ types was reverse transcribed using a mixture of oligo(dT)18 and random nonamer primers, during which amino-allyl-modified dUTP (aa-dUTP) was incoporated. The aa-dUTP decorated cDNA was fluorescent labeled by conjugating the monofunctional Cy3 dye (GE Healthcare, Piscataway, NJ) to the amino-allyl functional groups in the cDNA. Two μg dye-labeled targets were used for hybridization.

first: Lei

first: Juan

last: Zhang

first: Xiangfeng

last: Wang

first: Viktor

last: Stolc

first: Waraporn

last: Tongpraist

first: Oliver

last: Yu

first: XingWang

last: Deng


title: Identification of a stable gene signature of tolerance to renal allograft by meta-analysis.

status: Public on Oct 06 2015

city: Nantes

first: Daniel

last: BARON

state: Loire-Atlantique (44)

address: 30 Bd Jean Monnet

department: UMR1064 - Centre de Recherche en Transplantation & Immunologie

institute: Institut national de la santé et de la recherche médicale-INSERM

type:
Third-party reanalysis
Expression profiling by array

summary:
This study corresponds to a re-analysis and meta-analysis of the five transcriptomic studies related to spontaneous tolerance to renal allograft in human. It examines the transcriptome of peripheral blood samples from six distinct clinical groups: healthy volunteers (HV); tolerant patients (TOL); stable patients on minimal immunosuppression (MIS) or maintained on classical immunosuppressive therapy (STA); patients showing either signs of chronic rejection (CR) or acute rejection (AR). The initial studies are the following:   -Study 1 from Braud C. et al. (J Cell Biochem., 2008) published under GEO accession number GSE47755 and comprising 250 unique samples (8 HV; 21 TOL; 190 STA; 31 CR).  -Study 2 from Brouard S.  et al. (Proc Natl Acad Sci U S A., 2007) published under GEO accession number GSE47683 and comprising 67 unique samples (8 HV; 12 TOL; 10 MIS; 12 STA; 11 CR; 14 AR).   - Study 3 from Lozano JJ. et al. (Am J Transplant., 2011) published under GEO accession number GSE22707 and comprising 42 unique samples (6 HV; 12 TOL; 12 STA; 12 CR).  - Study 4 from Newell KA. et al. (J Clin Invest., 2010) published under GEO accession number GSE22229 and comprising 58 unique samples (12 HV; 19 TOL; 27 STA).  - Study 5 from Sagoo P. et al. (J Clin Invest. 2010) published under GEO accession number GSE14655 and comprising two distinct cohorts of patients. The IOT (“Indices of Tolerance”) cohort (5a) corresponds to a European group of patients and totalizes 74 unique samples (8 HV; 10 TOL; 11 MIS; 36 STA; 9 CR). The ITN (“Immune Tolerance in Transplantation”) cohort (5b) corresponds to an American group of patients and totalizes 105 unique samples (20 HV; 22 TOL; 11 MIS; 34 STA; 18 CR).
The final data matrix corresponds to the combination of the data from the five independent studies and examines the expression of 1846 meta-genes (MG) across 596 unique blood samples. The 1846 meta-genes correspond to the genes being measured across the five datasets and form a virtual microarray platform (TOL-HUMAN-G1846). The 596 examined samples can be divided into 62 HV, 96 TOL, 32 MIS, 311 STA, 81 CR, and 14 AR.

overall_design: expression of 1846 meta-genes (MG) across a panel of 596 blood samples

last: Baron

first: Gérard

last: Ramstein

first: Sophie

last: Brouard

first: Rémi

last: Houlgatte