title: Pax3 and Zic1 trigger the early neural crest gene regulatory network by the direct activation of multiple key neural crest specifiers [X_laevis_2]

status: Public on Dec 28 2013

city: Orsay

first: Anne-Helene

last: Monsoro-Burq

address: Bat 110

department: Université Paris Sud

institute: Institut Curie

summary:
Neural crest development is orchestrated by a complex and still poorly understood gene regulatory network. Premigratory neural crest is induced at the lateral border of the neural plate by the combined action of signaling molecules and transcription factors such as AP2, Gbx2, Pax3 and Zic1. Among them, Pax3 and Zic1 are both necessary and sufficient to trigger a complete neural crest developmental program. However, their gene targets in the neural crest regulatory network remain unknown. Here, through a transcriptome analysis of frog microdissected neural border, we identified an extended gene signature for the premigratory neural crest, and we defined novel potential members of the regulatory network. This signature includes 34 novel genes, as well as 44 known genes expressed at the neural border. Using another microarray analysis which combined Pax3 and Zic1 gain-of-function and protein translation blockade, we uncovered 25 Pax3 and Zic1 direct targets within this signature. We demonstrated that the neural border specifiers Pax3 and Zic1 are direct upstream regulators of neural crest specifiers Snail1/2, Foxd3, Twist1, and Tfap2b. In addition, they may modulate the transcriptional output of multiple signaling pathways involved in neural crest development (Wnt, Retinoic Acid) through the induction of key pathway regulators (Axin2 and Cyp26c1). We also found that Pax3 could maintain its own expression through a positive autoregulatory feedback loop. These hierarchical inductions, feedback loops, and pathway modulation provide novel tools to understand the neural crest induction network.
Transcriptomes of animal caps overexpressing Pax3+/-Zic1 in the presence/absence of cycloheximide, a translation inhibitor, were compared to control animal caps to identify direct Pax3 and Zic1 targets

overall_design: 2-4 cells stage embryos were injected with inducible Pax3-GR+/-Zic1-GR constructs. Animal caps were cut at stage 9. Cycloheximide (Chx, 0.1mg/ml) was then applied to the healed animal caps, from stage 10 to 10.5 (i.e. for 30 min at 23*C), then dexamethasone (Dex) was added at stage 10.5 to the cycloheximide-containing medium. Explants were rinced and lysed after two additional hours at 23*C, i.e. when sibling embryos reached stage 11.5-12. Total RNA was then extracted and hybridized on Affymetrix microarrays. Transcriptomes were compared to determine Pax3 and Zic1 targets.

first: Jean-Louis

last: Plouhinec

first: Daniel

last: Roche

first: Caterina

last: Pegoraro

first: Ana-Leonor

last: Figueiredo

first: Frédérique

last: Maczkowiak

first: Lisa

middle: J

last: Brunet

first: Jean-Philippe

last: Vert

first: Nicolas

last: Pollet

first: Richard

middle: M

last: Harland

first: Anne

middle: H


title: Pax3 and Zic1 trigger the early neural crest gene regulatory network by the direct activation of multiple key neural crest specifiers

country: France

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

overall_design: Refer to individual Series

middle: D


title: Chromatin Immunoprecipitation of E2A-PBX1 in the cell line 697

status: Public on Nov 23 2013

city: San Francisco

first: Joseph

middle: Leo

last: Wiemels

state: California

address: 1450 3rd Street, MC 0520

department: Epidemiology and Biostastics

country: USA

institute: UCSF

type: Genome binding/occupancy profiling by genome tiling array

summary:
Data from "Direct and indirect targets of the E2A-PBX1 leukemia-specific fusion protein" to be published in PLOS One, authors Christofer Diakos, Yuanyuan Xiao, Shichun Zheng, Leo Kager, Michael Dworzak, Joseph L. Wiemels
The experiment showed direct targets of the fusion protein.  In the manuscript, individual gene targets are explained, along with DNA motifs that the fusion protein bound to. Demonstrates the "direct" targets of the E2A-PBX1 leukemia fusion protein, which is a feature of about 5% of all chilldhood leukemia.

overall_design: Comparison of the ChIP pull-down from E2A antibody in an E2A-PBX1 positive cell line, compared to the input DNA.  There are 3 replicate experiments

first: Christofer

last: Diakos


title: Human esophageal dysplasia (16 cases) vs. esophageal squamous cell carcinoma (59 cases)

status: Public on Apr 29 2013

city: Beijing

first: Ming-Rong

last: Wang

address: 17 Panjiayuan Nanli, Chaoyang District, Beijing, China

country: China

institute: Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China

type: Genome variation profiling by genome tiling array

summary: Our aim is to identify frequent genomic aberrations both in ESCC and esophageal dysplasia, and to discover important copy number-driving genes and microRNAs in ESCC. We carried out array-based comparative genomic hybridization (array CGH) on 59 ESCC resection samples and 16 dysplasia biopsy samples. Expression of genes at 11q13.3 was analyzed by real-time PCR and immunohistochemistry (IHC). Integrated analysis was performed to identify genes or microRNAs with copy number-expression correlations.

overall_design: Two group experiment, esophageal dysplasia vs. esophageal squamous cell carcinoma. Biological replicates: 16 dysplasias vs. 59 carcinomas

first: Zhi-Zhou

last: Shi


title: Transcriptome analysis of rice infected with Rice black streak dwarf virus

status: Public on Dec 01 2012

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

country: Japan

institute: NARO/HARC

summary: Rice black streak dwarf virus (RBSDV) is the causal agent of rice black streak dwarf disease which causes severe loss of rice yield in Asia countries. In this study, we have analyzed the relationship between symptom and host gene responses by RBSDV infection.

overall_design: Comparison between RBSDV and mock infected rice. Biological replicates: 3 control, 3 infected, independently grown and harvested. 1 samples derived from 5 plants grown under same conditons

first: Takumi

last: Shimizu

first: Takahide

last: Sasaya

first: Hiroaki

last: Kondoh

first: Hiromi

first: Setsuko

last: Kimura

first: Toshihiro

last: Omura

first: Shoshi

last: Kikuchi


title: Human SCC-13 Cells: Control vs. Resitant populations to photodynamic therapy (PDT)

status: Public on Sep 06 2013

city: Madrid

first: Javier

last: Suela

state: M

address: Faraday 7

country: Spain

institute: NIMGenetics

summary: aCGH of control cells not subjected to PDT (Parental) and cells subjected to 5 or 10 sequential PDT treatments (5ºG and 10ºG, respectively).

overall_design: Three-condition experiment, cultures of SCC-13 cells not subjected to PDT (Parental) vs 5ºG and 10ºG generations of resistant cells.

first: Ángeles

last: Juarranz

first: Yolanda

last: Gilaberte


title: Transcriptome analysis of rice infected with Rice ragged stunt virus

summary: Rice ragged stunt virus (RRSV) is the causal agent of rice ragged stunt disease which causes severe loss of rice yield in Asia countries. In this study, we have analyzed the relationship between symptom and host gene responses by RRSV infection.

overall_design: Comparison between RRSV and mock infected rice. Biological replicates: 3 control, 3 infected, independently grown and harvested. 1 samples derived from 5 plants grown under same conditons


title: Transcriptome analysis of rice infected with Rice transitory yellow virus

summary: Rice transitory yellow (RTYV) is the causal agent of rice transitory yellow disease which causes severe loss of rice yield in Asia countries. In this study, we have analyzed the relationship between symptom and host gene responses by RGDV infection.

overall_design: Comparison between RTYV and mock infected rice. Biological replicates: 3 control, 3 infected, independently grown and harvested. 1 samples derived from 5 plants grown under same conditons


title: Suv4-20h Histone Methyltransferases Promote Neuroectodermal Differentiation by Silencing the Pluripotency-Associated Oct-25 Gene

status: Public on Feb 06 2013

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

summary: Post-translational modifications (PTMs) of histones exert fundamental roles in regulating gene expression. During development, groups of PTMs are constrained by unknown mechanisms into combinatorial patterns, which facilitate transitions from uncommitted embryonic cells into differentiated somatic cell lineages. Repressive histone modifications such as H3K9me3 or H3K27me3 have been investigated in detail, but the role of H4K20me3 in development is currently unknown. Here we show that Xenopus laevis Suv4-20h1 and h2 histone methyltransferases (HMTases) are essential for induction and differentiation of the neuroectoderm. Morpholino-mediated knockdown of the two HMTases leads to a selective and specific downregulation of genes controlling neural induction, thereby effectively blocking differentiation of the neuroectoderm. Global transcriptome analysis supports the notion that these effects arise from the transcriptional deregulation of specific genes rather than widespread, pleiotropic effects. Interestingly, morphant embryos fail to repress the Oct4-related Xenopus gene Oct-25. We validate Oct-25 as direct target of xSu4-20h enzyme-mediated gene repression, showing by chromatin immunoprecipitaton that it is decorated with the H4K20me3 mark downstream of the promoter in normal, but not in double-morphant, embryos. Since knockdown of Oct-25 protein significantly rescues the neural differentiation defect in xSuv4-20h double-morphant embryos, we conclude that the epistatic relationship between Suv4- 20h enzymes and Oct-25 controls the transit from pluripotent to differentiation-competent neural cells. Consistent with these results in Xenopus, murine Suv4-20h1/h2 double-knockout embryonic stem (DKO ES) cells exhibit increased Oct4 protein levels before and during EB formation, and reveal a compromised and biased capacity for in vitro differentiation, when compared to normal ES cells. Together, these results suggest a regulatory mechanism, conserved between amphibian and mammals, in which H4K20me3-dependent restriction of specific POU-V genes directs cell fate decisions, when embryonic cells exit the pluripotent state.

overall_design: Total RNA samples from Xenopus laevis embryos. Transcript levels were analyzed after injection of control or Suv420 morpholinos into blastomeres.

first: Dario

last: Nicetto

first: Matthias

last: Hahn

first: Julia

last: Jung

last: Schneider

first: Robert

last: David

first: Gunnar

last: Schotta

first: Ralph

middle: A

last: Rupp


title: Transcriptomic comparison of chemosensitive and chemoresistant cells

status: Public on Aug 23 2012

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: First, in a model of xenografts induced with HT-29 human colon cancer cells, we demonstrated that the transcription factor NF-kB was involved in the resistance to CPT-11. Then, from one tumor treated with CPT-11 plus a NF-kB inhibitor, we established a resistant cell line to CPT-11. The aim of this study was to compare the expression of genes involved in the signaling pathway of NF-kB between the sensitive and the resistant cell lines and to identify other genes (target or not of NF-kB) which the expression was modified when the resistant phenotype was acquired.

overall_design: Human colon cancer cells chemosensitive (HT-29) versus human colon cancer cells chemoresistant (RIV) in a dye-swap experiment.

first: Jean-Francois

last: PEYRON

first: Patricia

last: Lagadec

first: Sebastien

last: Grosso

first: Pascal

last: Barbry


title: Transcriptomics comparisons of Mac-T cells versus mammary tissue during late pregnancy and peak lactation

status: Public on Apr 30 2013

city: Corvallis

first: Massimo

last: Bionaz

state: OR

address: 316A Withycombe Hall

department: Animal and Rangeland Sciences

institute: Oregon State University

summary: The bovine mammary epithelial cell line Mac-T has been used to study mammary gland in vitro. The reliability of this system to study mammary gland has not been tested using genomics approaches. In the present experimetn a direct transcriptomics comparison between Mac-T cells and mammary tissue at -30 and at 60 day in milk (DIM) is performed. Data indicated that Mac-T cells and mammary tissue had a substantially different transcriptome with a larger difference between Mac-T cells and lactating mammary tissue (i.e., 60 DIM) compared to non-lactating mammary tissue (i.e., -30 DIM). In addition, data indicated that the Mac-T cells substantially differ with mammary tissue in lactation-specific functions.

overall_design: cDNA from Mac-T cells induced in vitro into lactation for 36h (addition of prolactin) was directly hybridize in the microarray chip with cDNA from mammary tissue at -30 or 60 day in milk from 3 cows.

first: Afshin

last: Hosseini

first: Rekha

last: Sharma

first: Juan

last: Loor


title: Microarray data Ptf1a gain-of-function Xenopus pancreas development

status: Public on Nov 01 2012

city: Woods Hole

first: Cassandra

middle: Kathryn

last: Bilogan

state: MA

address: 7 MBL St

department: Eugene Bell Center for Regenerative Biology and Tissue Engineering

institute: Marine Biology Laboratory

summary:
The Ptf1a gene has essential functions during several stages of pancreas development. It is expressed in the naïve endoderm and required pancreas cell fate specification; it is also required later in the differentiation and maintenance of acinar cells. To identify the regulatory genetic program downstream of Ptf1a required for early pancreatic fate acquisition, we used microarrays to perform a comprehensive gene expression analysis of Ptf1a overexpressing endodermal tissue at NF32 and NF36.
The results revealed an up-regulation on 1142 probe sets over 2-fold. Additional analyses, by in situ hybridizations, identified 9 genes that were endodermally expressed after the onset of endogenous Ptf1a; STXBP1, putative transmembrane protein TA-2, C25H, IGFBP1, IRF1, HALPN3, Hey1, sestrin 1, syndecan-4. These results provide insight into the regulatory network activated by Ptf1a during early pancreas development.

overall_design: In order to identify downstream targets of Ptf1a, two microarrays were performed at different time-points. The two microarrays compared control pancreatic tissue (GFP) and pancreatic tissue over-expressing Ptf1a (Ptf1a+GFP). The first microarray was performed at NF32, hence renamed MA32, 8 hours after the initial expression of endogenous Ptf1a. A second microarray was performed at NF36 (MA36), 8 hours after the first one.   Ptf1a+gfp mRNA or gfp mRNA alone was injected into the two dorso-vegetal blastomeres of eight-cell embryos, targeting the anterior endoderm, and 40/48 hours later the anterior endoderm was dissected out. Approximated 15 endoderm explants were pooled for each RNA preparation, and both control and experimental samples were collected from the same batch of embryos; this was done in triplicate at NF32 and in quadruplicate at NF36 (Fig. 1A). For the NF32 microarray, we used the Affymetrix 3’ Xenopus laevis Genome 2.0 GeneChip, whereas for the NF36 microarray we used the Affymetrix 3’ Xenopus laevis Genome 1.0 GeneChip; the NF36 microarray was performed prior to the release of the 2.0 GeneChip.

middle: K

first: Marko

middle: E

last: Horb


title: The protein kinase MLTK Is a key regulator for chondrogenesis.

status: Public on Sep 04 2012

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

institute: Graduate School of Biostudies, Kyoto University

summary:
Sox9 acts together with Sox5 or Sox6 as a master regulator for chondrocyte differentiation; however, how these transcription factors functionally interact and collaborate to regulate chondrogenesis remains unclear. Here we show that the protein kinase MLTK plays an essential role in the onset of chondrogenesis through triggering the induction of Sox6 by Sox9. Knockdown of MLTK in Xenopus embryos results in drastic loss of craniofacial cartilages without defects in neural crest formation. We also find that Sox6 is specifically induced during craniofacial chondrogenesis and this induction is inhibited by MLTK knockdown. Remarkably, Sox6-knockdown embryos display essentially the same phenotype as the MLTK-knockdown embryos; the drastic loss of cartilages and the marked down-regulation of genes involved in chondrogenesis. Microarray analysis reveals a remarkable similarity between Sox6-depleted and MLTK-depleted embryos in their gene expression pattern. Moreover, we find that ectopic expression of MLTK can induce Sox6 expression in a Sox9-dependent manner. These results identify a novel, key regulator for chondrogenesis.
We used microarrays to describe the genome-wide gene expression profiles of xMLTK-depleted and xSox6-depleted embryos.

overall_design: CoMO, xMLTK-MO, or xSox6-MO was injected into the animal pole of all blastomeres (10 ng/cell) at the four-cell stage. The heads of embryos were cut out and harvested at 72 hours after fertilization (corresponding to about stage 41). Total RNA was extracted using TRIsol reagent, treated with DNase (TURBO DNase, Ambion), and then purified using RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instruction. The quality of total RNA was assessed using the Agilent 2100 BioAnalyzer. Reverse transcription to synthesize first-strand cDNA, second-strand cDNA synthesis, in vitro transcription to synthesize Biotin-modified aRNA, aRNA purification and fragmentation of the labeled aRNA were performed using the GeneChip 3’ IVT Express Kit and hybridization to the Affymetrix GeneChip Xenopus laevis Genome 2.0 Array was performed using the GeneChip Hybridization Wash and Stain Kit according to the manufacturer’s instruction. Hybridized arrays were scanned using an Affymetrix GeneChip Scanner. Scanned Chip images were analyzed with GeneChip operating Software v.1.4 (GCOS) and GeneSpring GX 11.0.2. (Agilent technologies).

first: Toshiyasu

last: Suzuki

first: Morioh

last: Kusakabe


title: DNA copy number gain at 1q23.3 is associated with poor survival in metastatic bladder cancer

status: Public on Jul 07 2013

city: Boston

first: Markus

last: Riester

address: 3 Blackfan Circle

department: Biostatistics & Computational Biology

institute: Dana-Farber Cancer Institute


title: Comparison of animal-blastomeres' RNA content to vegetal-most half of vegetal blastomeres' RNA content at the 8-cell stage of Xenopus laevis embryos to identify animal-enriched transcripts

status: Public on Dec 21 2013

city: Washington

first: Sally

middle: A.

last: Moody

state: DC

address: 2300 I St. NW

department: Anatomy and Regenerative Biology

institute: The George Washington University School of Medicine and Health Sciences

summary:
In Xenopus laevis, a number of studies identified vegetal factors that specify the germ line, endoderm and dorsal axis, but there are few studies demonstrating roles for animal-enriched maternal mRNAs.
Therefore, we carried out a microarray analysis to identify novel maternal transcripts enriched in animal blastomeres.

overall_design: We sought to maximize differences between animal and vegetal samples. To that end, we dissected 8-cell embryos into animal blastomeres and vegetal blastomeres, and further dissected the vegetal blastomeres into vegetal-most halves (VP) and equatorial regions (discarded).

first: Paaqua

last: Grant

first: Bo

middle: X

last: Yan


title: miRNA reponse to bleomycin instillation

status: Public on Feb 01 2013

first: Kevin

last: Lebrigand

summary: Comparison of C57BL/6 (sensitive) and BALB/c (resistant) mice challenged by intratracheal bleomycin instillation: miRNA expression profiles were established from lungs derived from the two strains, following a 7- or 14-days PBS or bleomycin administration.

overall_design: One color -experiment with 2 strains of mice (C57BL/6 and BALB/c) following a 7- or 14-days PBS or bleomycin administration (n=3), corresponding to a total of 24 samples.

first: nicolas

last: Pottier

first: Bernard

last: Mari


title: Expression profiling of soybean genes in response to drought (reproductive stage)

status: Public on Nov 10 2012

city: Yokohama

first: Dung

middle: Tien

last: Le

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Plant Science Center

institute: RIKEN Yokohama Institute

summary: Drought-responsive genes in soybean leaves were successfully identified using Affymetrix Soybean Gene 1.0 ST arrays on leaves samples of reproductive-stage soybean plants. R1 soybean plants planted in pots were imposed drought by withholding water for 5 days until the soil moisture content dropped to 5%, and 3rd trifoliates (now at the R2 stage) were collected for expression profiling.

overall_design: Soybean plants were grown in pots. When the plants reached the R1 stage (started flowering), drought treatment was imposed by withholding water. The soil moisture content was monitored during the process until the 5th day of water withholding, when soil moisture content reached 5%. The 3rd trifoliate (counting from shoots), now at the R2 stage, was collected for total RNA extraction, while other 3rd trifoliates of similar chlorophyl index were collected for leaves water content determination to identify the severity of the stress. Total RNA from 3rd trifoliates were used for expression profiling using Affymetrix Soybean Gene 1.0 ST arrays. Four biological repeats per treatment were performed, three biological repeats were chosen for expression profiling.


title: DNA copy number gain at 1q23.3 is associated with poor survival in metastatic bladder cancer [Agilent]

summary: Metastatic urothelial carcinoma (UC) of the bladder is associated with multiple somatic copy number alterations (SCNAs). We evaluated SCNAs to identify predictors of poor survival in patients with metastatic UC treated with platinum chemotherapy.

overall_design:
We obtained overall survival (OS) and DNA copy number data from UC patients in a Spanish discovery cohort and three validation cohorts.
GISTIC was used to identify altered regions, and associations between copy number gains/losses and OS were determined by a Cox proportional hazard model adjusting for performance status and visceral disease
The output files of the GISTIC 2.0 software are linked as supplementary files on Series record along with readme.txt file describing the contents of each file/column.


title: “Seed-milarity” confers to hsa-miR-210 and hsa-miR-147b similar functional activity

status: Public on Aug 20 2012

summary: Specificity of interaction between a microRNA (miRNA) and its targets crucially depends on the seed region located in its 5’-end. It is often implicitly considered that two miRNAs sharing the same biological activity should display similarity beyond the strict six nucleotide region that forms the seed, in order to form specific complexes with the same mRNA targets. We have found that expression of hsa-miR-147b and hsa-miR-210, though triggered by different stimuli (i.e. lipopolysaccharides and hypoxia, respectively), induce very similar cellular effects in term of proliferation, migration and apoptosis. Hsa-miR-147b only shares a “minimal” 6-nucleotides seed sequence with hsa-miR-210, but is identical with hsa-miR-147a over 20 nucleotides, except for one base located in the seed region. Phenotypic changes induced after heterologous expression of miR-147a strikingly differ from those induced by miR-147b or miR-210. In particular, miR-147a behaves as a potent inhibitor of cell proliferation and migration. These data fit well with the gene expression profiles observed for miR-147b and miR-210, which are very similar, and the gene expression profile of miR-147a, which is distinct from the two others.  Bioinformatics analysis of all human miRNA sequences indicates multiple cases of miRNAs from distinct families exhibiting the same kind of similarity that would need to be further characterized in terms of putative functional redundancy. Besides, it implies that functional impact of some miRNAs can be masked by robust expression of miRNAs belonging to distinct families.

overall_design:
To compare the set of transcripts targeted by hsa-miR-147a, hsa-miR-147b and hsa-miR-210, we overexpressed these miRNAs in human lung adenocarcinoma A549 cells by transfecting them with synthetic pre-miRNAs or a synthetic “negative” pre-miRNA as a control (miR-Neg). RNA samples were harvested at 48 hours post-transfection and 3 independent experiments were carried out.
48 hours post-transfection, 3 independent experiments were performed in dye-swap: hsa-miR-147a versus miR-Neg; hsa-miR-147b versus miR-Neg; hsa-miR-210 versus miR-Neg.

first: Thomas

last: Bertero

first: Pascal

last: Barbry


title: A validated microarray platform for Mycobacterium tuberculosis

status: Public on Jun 01 2013

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary: The new microarray described for Mycobacterium tuberculosis in our study has a more complete reprensentation of the genome than any other array design reported till date. Further, protocols for sample preparation, labelling and hybridisation for accurate gene expression profiling of M.tuberculosis have been optimised.

overall_design: Whole genome expression profiling on Mycobacterium tuberculosis H37Rv (OD600 0.4-0.5) was performed using exponential phase cultures after 0 and 6 Hrs in presence and absence of drug (Isoniazid) by using PolyA-dT and WT method. The exponential culture after 24 and 72 Hrs were used for validating the specific hybridization with or without formamide. All time points had two biological replicates with two technical replicates.

first: Amita

last: Gupta

first: Balaji

last: Venkataraman

first: Madavan

last: Vasudevan


title: Expression profiling of soybean genes in response to drought

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

overall_design: Refer to individual Series


title: Early downstream targets of Notch signaling which contribute to multiciliate cell fate

status: Public on Mar 01 2012

city: San Diego

first: Chris

last: Kintner

state: CA

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute

summary:
Analysis of epithelial explants injected with the intracellular domain of Notch (ICD) to block the formation of multi-ciliate and proton secreting cells or with dominant negative human Mastermind (HMM) or a DNA binding mutant of Mastermind (DBM) to induce the formation of ectopic multi-ciliate and proton secreting cells.  Results show which genes are up or down-regulated when DBM/HMM are compared to ICD.
Epithelial cells projecting hundreds of motile cilia are prominent in the respiratory system, brain ependyma and female reproductive tract where they generate a vigorous fluid flow along luminal surfaces.  Despite their importance for organ function, how multiciliate cells arise developmentally in diverse epithelia is poorly understood.  Notch signaling has been shown in a variety of tissues, including the Xenopus epithelium, to regulate the formation of multiciliate cell precursors.  In order to identify early downstream targets of Notch signaling which contribute to multiciliate cell fate we blocked or activated Notch signaling in explants of Xenopus epithelium and looked at changes in gene expression to identify candidates that regulate multiciliate cell fate. Here we identify a novel coiled-coil protein, called multicilin (MCI), whose expression is Notch-regulated and restricted to epithelia where multiciliate cells forms in Xenopus embryos.  Inhibiting MCI activity blocks the formation of multiciliate cell precursors while ectopic MCI activity is sufficient to induce multiciliate cell differentiation within epithelial progenitors.

overall_design: 2-cell stage Xenopus embryos were injected with synthetic mRNA encoding ICD, DBM or HMM.  At stage 9/10 the presumptive ectoderm was cut off the embryo and cultured on a fibronectin coated coverslip.  At stage 12 RNA was harvested from explants and used as the starting material for arrays.

first: Jennifer

middle: L

last: Stubbs

first: Eszter

last: Vladar

first: Jeffrey

last: Axelrod


title: Multicilin promotes centriole assembly and ciliogenesis during multiciliate cell differentiation.

summary:
Analysis of epithelial explants injected with the intracellular domain of Notch (ICD) alone, to block the formation of multiciliate cells, or with Dexamethasone inducible Multicilin (MCI-HGR) to induce the formation of ectopic multiciliate cells.  MCI-HGR plus ICD injected samples were compared to ICD alone to identify candidate genes whose expression changes when MCI is active.
Epithelial cells projecting hundreds of motile cilia are prominent in the respiratory system, brain ependyma and female reproductive tract where they generate a vigorous fluid flow along luminal surfaces.  Despite their importance for organ function, how multiciliate cells arise developmentally in diverse epithelia is poorly understood. We identified a novel coiled-coil protein, we have termed multicilin (MCI), whose expression is Notch regulated and restricted to epithelia where multiciliate cells form in Xenopus embryos. In order to identify early downstream targets of multicilin we blocked the formation of endogenous multiciliate cells by injecting ICD mRNA.  In a subset of samples we then misexpressed a dexamethasone inducible form of MCI (MCI-HGR) to identify specific targets of MCI in explants of Xenopus epithelium. In explants expressing MCI-HGR genes specifically expressed in ciliated cells such as FoxJ1 and alpha-tubulin were highly upregulated along with various genes known to be required for ciliogenesis, and a large number of genes likely to be part of the ciliome based on homology of potential structural motifs.

overall_design: 2-cell stage Xenopus embryos were injected with synthetic mRNA encoding ICD or ICD along with MCI-HGR.  At stage 9/10 the presumptive ectoderm was cut off the embryo and cultured on a fibronectin coated coverslip.  At stage 11.5 dexamethasone was added to all conditions to induce MCI.  Explants were harvested 5 hours after adding dexamethasone (approximately stage14) and used as the starting material for arrays.


title: Human monocyte-derived macrophages polarized by GM-CSF or M-CSF

status: Public on Apr 13 2012

first: Angel

last: Corbí

state: Madrid

address: Ramiro de Maeztu 9

department: Molecular Microbiology and Infection Biology

institute: Consejo Superior de Investigaciones Científicas

summary: Identification of genes differentially expressed between human monocyte-macrophages generated in the presence of either GM-CSF (termed M1) or M-CSF (termed M2)

overall_design: Human peripheral blood monocytes from three independent healthy donors (#1, #2 and #3) were isolated by anti-CD14-labeled magnetic microbeads. CD14+ monocytes were cultured for 7 days in RPMI 10% FCS containing either GM-CSF or M-CSF. Total RNA from each condition was extracted and purified using the RNeasy kit (Qiagen). Labelled RNA was used as hybridization probes on human Codelink Whole genome Bioarray. All experimental procedures were performed following manufacturer instructions. Microarrays were scanned with a GenePix 4000B (Axon Instruments) scanner. Scanned images and raw data were processed using the Codelink Expression Software.

last: Corbi

first: Miguel

last: Vega


title: Expression data from Xenopus laevis liver

status: Public on Oct 11 2011

city: Mainz

first: Marianne

last: Mathäs

address: Obere Zahlbacherstraße 67

institute: Universitätsmedizin Mainz

summary: Pregnane X receptor (PXR) is generally considered the most important sensor of natural and anthropogenic xenobiotics in vertebrates. In Xenopus, however, PXR plays a role in neural development and it is irresponsive to xenobiotics. We report a first broad-spectrum amphibian xenobiotic receptor, which is an ortholog of the mammalian constitutive androstane receptor (CAR). The low basal activity and pronounced responsiveness to activators such as drugs and steroids displayed by the Xenopus CAR resemble PXR, which both trace back to a common ancestor early in the divergence of land vertebrates. The constitutive activity of CAR emerged first in Sauropsida (reptiles and birds) and it is common to all fully terrestrial land vertebrates (Amniota). This activity can be mimicked by humanizing just two amino acids of the Xenopus CAR. These results demonstrate a remarkable plasticity of CAR which enabled its employment as Xenopus xenosensors. They open way to toxicogenomic and bioaugmentation studies in amphibians, a critically endangered taxon of land vertebrates. Taken together, we provide evidence for a much earlier origin of CAR, for its conservation in tetrapods which exceeds that of PXR, and for its remarkable functional plasticity which enabled its role as a PXR-like xenosensor in Amphibia.

overall_design:
We used microarrays to detect global transcriptional changes in Xenopus laevis livers following pregnenolone and artemisinin treatment in order to identify target genes of xlCAR.
Arteminisin or pregnenolone were injected intraperitoneally into three frogs on two consecutive days. The control group received in parallel two DMSO injections. All frogs were sacrificed 24 h after the second injection by decapitation, and livers were immediately frozen in liquid nitrogen. After RNA isolation, specimens within the same experimental group were pooled.

first: Shiwei

last: Deng


title: Effect of histone deacetylase inhibitors on miRNA expression in thyroid cancer cells

status: Public on Dec 06 2011

first: Kevin

last: Lebrigand

summary: BCPAP papillary thyroid carcinoma cells were cultured in the presence or the absence of TSA (330nM) for 16h in fresh complete medium. Three independent experiments were performed and total RNA was extracted.

overall_design: Three independent experiments performed in dye-swap (TSA versus control).

first: Paul

last: Hofman

first: Patrick

last: Brest

last: Mari


title: Expression data from Xenopus endoderm at stage 15 following four hours of Ngn3-GR overexpression

status: Public on Apr 01 2012

first: Marko

last: Horb

address: 7 MBL Street

institute: Marine Biological Laboratory

summary: Ngn3 is a master regulator of pancreatic endocrine development. It is necessary for the creation of all endocrine cells in mice. Little is known about the genes that act downstream of the transcription factor Ngn3 in pancreas endocrine development to specify each of the endocrine lineages. As a consequence, little is known about the genes involved in early development and the specification of the beta cell. We used microarrays to identify Ngn3 downstream genes that are involved in early and ectopic beta cell development in Xenopus laevis. We overexpressed Ngn3 in the Xenopus early endoderm and analyzed the genes that are upregulated four hours after.

overall_design: Xenopus laevis embryos were injected with Ngn3-GR mRNA at the eight-cell stage in the two dorsal vegetal blastomeres. Embryos at stage 12 were either treated with dexamethasone (+DEX) for four hours or no DEX (-DEX). The endoderm was dissected at stage 15. We looked for genes upregulated in the +DEX samples compared to the -DEX samples.


title: A Multi-loop, Double-cube Microarray Design Applied to Prostate Cancer Cell Lines with Variable Sensitivity to Histone Deacetylase Inhibitors

status: Public on Dec 17 2011

city: Baltimore

first: Luigi

last: Marchionni

state: MD

address: 1550 Orleans St., CRB2, Room 1M52

department: Oncology

institute: Johns Hopkins University

summary: Implementation of a complex design for a microarray experiment on resistance mechanisms of histone deacetylase inhibitors (HDACI).

overall_design: To improve our understanding of the underlying mechanism of HDACI resistance in prostate cancer cells, we designed a novel ‘‘multiple-loop, double-cube’’ cDNA microarray experiment. In the experiment DU-145 and PC3 cells were treated with two different HDACIs (vorinostat and valproic acid) and incubation periods (48 and 96 hours). Preprocessing included exploratory analyses of the quality of the arrays and intensity-dependent within-array Loess normalization. An ANOVA model was used for inference. The results were validated by Western blot analysis of known treatment targets.

last: Aiyetan

first: Madeleine

last: Kortenhorst

first: Marianna

last: Zahurak

first: Shabana

last: Shabbeer

first: Nathan

last: Galloway

first: Giovanni

last: Parmigiani

first: Henk

last: Verheul

first: Michael

last: Carducci


title: Overexpression of miR-483-3p in human keratinocytes

status: Public on Jun 29 2011

summary: HaCaT human keratinocytes were transfected with pre-miR-483-3p or pre-miR-NC. RNA samples were harvested 48h post-transfection and mRNA profiles were determined with pan genomic arrays. Two biological replicates were performed for each comparison. Data were normalized using a dye-swap method.

overall_design: HaCaT transfection of pre-miR-483-3p (3p) or pre-miR-NC (NC) at 48h in a dye-swap experiment.

first: Roger

last: Rezzonico

first: Bernard

first: Gilles

last: Ponzio

first: Pascal

last: Barbry


title: Differential gene expression analysis between Miltefosine resistant and sensitive leishmania donovani

status: Public on Sep 30 2011

city: New Delhi

first: Poonam

last: Salotra

state: Delhi

address: Safdarjung Hospital Campus

department: National Institute of Pathology

institute: Indian Council of Medical Research

summary: Gene expression analysis was carried out between experimental miltefosine resistant L.donovani (adapted to 30ug/ml miltefosine drug pressure) and its corresponding wild type miltefosine senstive parasite

overall_design: 3 biological replicates of lab generated miltefosine resistant Leishmania donovani (K417 M30) were compared with corresponding wild type sensitive parasite (K417WT)

first: Marc

last: Ouellette

first: Arpita

last: Kulshrestha


title: Microarray analysis of mediastinal lymph node of pigs naturally affected by postweaning multisystemic wasting syndrome

status: Public on Apr 30 2012

city: Bellaterra, Barcelona

first: Lana

middle: Teixeira

last: Fernandes

state: Catalunya

address: Campus de la UAB, Edifici cresa

department: Virology

institute: CReSA

summary: Postweaning multisystemic wasting syndrome (PMWS) is one of the pig diseases with major economic impact worldwide. Clinical, pathologic and some immunologic aspects of this disease are well-known, but the molecular mechanisms underlying pathogenic mechanisms of the disease are still poorly understood. The objective of the present study was to investigate the global changes in gene expression in the mediastinal lymph nodes from pigs naturally affected by PMWS and healthy counterparts, using the Affymetrix Porcine Genechip®.  This is the first study on gene expression in pigs naturally affected by PMWS. The present results allowed identifying potential mechanisms underlying the inflammation, lymphocyte depletion in lymphoid tissues and immune suppression, which are key features of PMWS.

overall_design: A total of twenty-five conventional 13 to 15-week-old pigs were used in this study. Animals were selected from three farms with historical records of PMWS and free of Porcine reproductive and respiratory syndrome virus (PRRSV) and Pseudorabies virus (PRV) infections. Twelve out of the 25 pigs fulfilled the PMWS diagnosis and were selected as cases, and the remaining thirteen pigs were selected as healthy control animals. At least one case and one control were used from each farm. 25 microarrays were used in the experiment, corresponding to the RNAs from mediastinal lymph nodes of 12 PMWS-affected pigs and 13 healthy controls.

middle: T

first: Anna

last: Tomás

first: Albert

last: Bensaid

first: Marina

last: Sibila

first: Armand

last: Sánchez

first: Joaquim

last: Segalés


title: Overexpression of miR-129-5p in thyroid carcinoma cells

first: Kevin

last: Lebrigand

summary: TCP1 papillary thyroid carcinoma cells were plated at 100,000 cells/well in a 6-well plate and transfected with 10nM of a synthetic pre-miR-129-5p or a negative pre-miRNA using Lipofectamine RNAiMAX reagent. RNA samples were harvested at 24 and 48 hours post-transfection.

overall_design: Three independent experiments performed in dye-swap: miR-129-5p versus miR-Neg.

first: Paul

last: Hofman

first: Patrick

last: Brest

last: Mari


title: Expression profiling of soybean genes in response to drought (vegetative stage)

status: Public on Apr 03 2012

first: Dung

last: Le

summary: Drought-responsive genes in soybean leaves were successfully obtained using soybean gene 1.0 ST array. Leaf samples from the vegetative stage of soybean plants were used.

overall_design: V6 soybean plants planted in the pots were imposed drought by withholding water for 6 days until the soil moisture content drop to 5% and trifolium 4th were collected for expression profiling

first: Motoaki

last: Seki

first: Son

last: Tran


title: RIP-Chip Analysis of hnRNP K in Xenopus juvenile brain

status: Public on Jul 06 2011

city: Albany

first: Ben

middle: Gregory

last: Szaro

state: NY

address: 1400 Washington Avenue

department: Biological Sciences

institute: University at Albany, State University of New York

summary: Cells use their wide variety of RNPs to integrate the expression of functionally inter-related proteins by forming RNP complexes with cis-elements that are shared among co-regulated RNAs. In this study, we identified the the associated mRNAs that co-precipitated with hnRNP K in developing juvenile frog brain.

overall_design: three replicates of immunoprecipitation experiments for both hnRNP K and beta-galactosidase(control)

first: Yuanyuan

last: Liu

middle: G


title: Identification of quantitative trait loci controlling gene expression during the innate immunity response of soybean

status: Public on Oct 06 2011

city: Columbia

first: Md Shakhawat

last: Hossain

state: Missouri

address: 201 Life Science Center 1201 Rollins Road

department: Plant Sciences

institute: University of Missouri

summary:
Microbe associated molecular pattern (MAMP)-responsive genes were identified in leaves of four different genotypes. The genotypes used in this study were: LD0-2817P; LDX01-1-65; Ripley and EF59. Leaves from three-weeks old plants were used in this study
We used microarray to identified the MAMP-responsive genes in leaves of four soybean genotypes trated with 1 uM flg22 and 50 ug/ml chitin for 30 minutes

overall_design: Trifoliolate leaves from three-week-old plants were detached and then vacuumed infiltrated with ddiH2O for 2 min. Water-infiltrated trifoliolate leaves from five different plants of each genotype were pooled and cut into approximately 1 cm2 slices. Equal amount of leaf slices (~30 slices) were transferred into two different Petri dishes and then floated overnight on autoclaved ddiH2O. Water was removed from both Petri dishes and was replaced with 5 ml of MAMP solution [1 mM flagellin 22 (flg22) and 50 mg of crab shell chitin (called in this study as chitin)], or 5 ml of mock solution [autoclaved ddiH2O plus equivalent amount of dimethyl sulfoxide (DMSO). DMSO was included since it was contained in the solution used to dissolve the flg22 peptide]. After a 30 min treatment, mock- and MAMP-treated leaf slices were harvested into different tubes and immediately frozen in liquid nitrogen. Samples were stored at -80 until use. All procedures described above were performed under dark conditions.

first: Oswaldo

last: Valdés-López

first: Sandra

last: Thibivilliers

first: Jing

last: Qiu

first: Wayne

middle: W

last: Xu

first: Tran

last: Nguyen

last: Libault

first: Brandon

first: Robert

middle: B

last: Goldberg

first: Curtis

last: Hill

first: Glen

last: Hartman

first: Brian

last: Diers

first: Gary

last: Stacey


title: Transcriptome analysis of rice infected with three RDV strains

status: Public on Jul 02 2011

city: Sapporo

first: Kouji

last: Satoh

address: Hitsujigaoka 1

institute: NARO/HARC

summary:
Rice dwarf virus (RDV) is the causal agent of rice dwarf disease which causes severe loss of rice yield in northern Asia countries. The disease symptoms are stunting of plant growth, chlorosis specks on leaves, and delayed and incomplete panicle exertion. Symptom severity  was different among three strains (RDV-O, –D84, and -S),  and was in the rank order RDV-O < -D84, < -S. In this study, we have analyzed the relationship between symptom severity and host gene responses by the gene expression analysis through the 60-mer oligo microarray.

Keywords: virus infection, disease response

overall_design: Comparison between RDV and mock infected rice. Biological replicates: 3 control, 3 infected, independently grown and harvested., 3 strain (RDV-O, -D84, -S). 1 samples derived from 5 plants grown under same conditons

first: Takumi

last: Shimizu

first: Takahide

last: Sasaya

first: Hiroaki

last: Kondoh

first: Hiromi

first: Setsuko

last: Kimura

first: Toshihiro

last: Omura

first: Shoshi

last: Kikuchi


title: Atorvastatin effect on SaOS2 osteosarcoma cells

status: Public on Feb 22 2011

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary:
SaOS2 osteosarcoma cells were cultured with or without atorvastatin (10 µM) for 6, 15 or 24h (2 biological replcates). RNA were isolated and hybridized to RNG microarrays.

Background
Osteosarcoma is the most common primary tumor of bone. The rapid development of metastatic lesions and resistance to chemotherapy remain major mechanisms responsible for the failure of treatments and poor survival rate for patients.

Methods
We previously showed that the HMGCoA reductase inhibitors statins exhibit anti-tumoral effects on osteosarcoma cells. Here, using microarray analysis, we identify cyr61/CCN1 as a new target of statins. Modulations of expression of cyr61 were performed in human and murine osteosarcoma cell lines to investigate in vitro cell viability, migratory potential and invasiveness. Cyr61 expression was evaluated in 231 tissue cores from osteosarcoma patients using tissue microarray. Tumor behavior and metastases occurence were analysed by IM injection of modified osteosarcoma cells to BALB/c mice.

Results
Transcriptome comparisons revealed that statins down-regulate cyr61 expression in SaOS2 cells. Cyr61 silencing in human and murine osteosarcoma cell lines enhanced cell death, but reduced cell migration and cell invasion compared to parental cells whereas cyr61 overexpression had opposite effects. Tissue microarray analysis demonstrated that cyr61 protein expression is higher in human osteosarcoma compared to normal bone tissue and is further increased in metastatic tissues. In vivo, cyr61 overexpression in osteosarcoma cells enhanced lung metastases development whereas cyr61 silencing strongly reduced metastases in mice.

Conclusion
The results reveal that cyr61 expression increases with tumor grade in human osteosarcoma and demonstrate that cyr61 silencing inhibits in vitro osteosarcoma cell invasion and migration as well as in vivo lung metastases in mice. These data provide a novel molecular target for therapeutic intervention in metastatic osteosarcoma.

overall_design: Dye balance-experiment comparing atorvastatin versus untreated cells at 6, 15 and 24 hours using 2 biological replicates.

first: Olivia

last: Fromigue

first: Bernard

last: Mari

first: Pascal

last: Barbry


title: Protease profiling of liver fibrosis reveals the ADAM metallopeptidase with thrombospondin type 1 motif, 1 as a central activator of transforming growth factor beta

status: Public on Jan 05 2012

summary: During chronic liver disease, tissue remodeling leads to dramatic changes and accumulation of matrix components. Matrix metalloproteases and their inhibitors have been involved in the regulation of matrix degradation. However, the role of other proteases remains incompletely defined. We undertook a gene-expression screen of human liver fibrosis samples using a dedicated gene array selected for relevance to protease activities, identifying the ADAMTS1 (A Disintegrin And Metalloproteinase [ADAM] with thrombospondin type 1 motif, 1) gene as an important node of the protease network. Up-regulation of ADAMTS1 in fibrosis was found to be associated with hepatic stellate cell (HSC) activation. ADAMTS1 is synthesized as 110-kDa latent forms and is processed by HSCs to accumulate as 87-kDa mature forms in fibrotic tissues. Structural evidence has suggested that the thrombospondin motif-containing domain from ADAMTS1 may be involved in interactions with, and activation of, the major fibrogenic cytokine, transforming growth factor beta (TGF-β). Indeed, we observed direct interactions between ADAMTS1 and latency-associated peptide-TGF-β (LAP-TGF-β). ADAMTS1 induces TGF-β activation through the interaction of the ADAMTS1 KTFR peptide with the LAP-TGF-β LKSL peptide. Down-regulation of ADAMTS1 in HSCs decreases the release of TGF-β competent for transcriptional activation, and KTFR competitor peptides directed against ADAMTS1 block the HSC-mediated release of active TGF-β. Using a mouse liver fibrosis model, we show that carbon tetrachloride treatment induces ADAMTS1 expression in parallel to that of type I collagen. Importantly, concurrent injection of the KTFR peptide prevents liver damage. CONCLUSION: Our results indicate that up-regulation of ADAMTS1 in HSCs constitutes a new mechanism for control of TGF-β activation in chronic liver disease.

overall_design: Total RNA from 32 patients with hepatic fibrosis associated with hepatitis C virus (HCV) infection (n=15) or alcohol abuse (n=17) versus a common pooled control liver sample, inverting the cy3 and cy5 labelling for each sample.

first: Nathalie

last: Theret


title: Effect of HdIV or MdBV injection on the Spodoptera frugiperda fat body transcriptome

status: Public on Apr 05 2011

city: Sophia Antipolis cedex

first: frederique

last: hilliou

address: 400 route des chappes, BP167

department: SPE

institute: INRA

summary: Comparison of the effects of 2 polydnaviruses (HdIV vs MdBV) injection on L5 Spodoptera frugiperda larvae fat body transcriptome.

overall_design: The experimental design is as follows: 3 biological replicates with dye swap. Each treatment (HdIV or MdBv) is compared to control treatment (PBS).

first: Bertille

last: PROVOST

first: Frederique

last: Hilliou


title: VEGFB treated macrophage

status: Public on Mar 01 2011

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

summary:
VEGFB effect in resting and active macrophage.
The goal of this study was to investigate the effects of Vascular Endothelial Growth Factor B (VEGFB) on gene expression in resting and active macrophages. Resting macrophages were obtained from peripheral blood of healthy volunteers. A part of macropahges were activated by Lipopolysaccharides (LPS). Both types of cells were treated by VEGFB. Total RNA was extracted using conventional Trizol extraction, quantified by Nanodrop and analyzed by Bioanalyzer. 1microg of RNA was amplified using AminoAllyl MessageAmp kit. 5µg amino allyl-coupled RNA was labeled with Cy3 or Cy5 dyes. Dye coupling yield >5% was a prerequisite for further analysis. 750ng of labeled RNA was hybridized on 25K gene microarrays for 17 hours at 60°C. 4 arrays per sample were hybridized and scanned with the Genepix 4000B Scanner (Molecular Devices). Microarray data quantification and pre-processing was performed with the MAIA software . The SAM tool was applied to identify differentially expressed genes.

overall_design: Macrophages from 2 different volunteers were treated by vehicle, or VEGFB, or LPS, or LPS and VEGFB

first: Lu

last: Zhang

first: Celine

last: Jeanty


title: Gene expression profiling in peripheral blood cells of patients with rheumatoid arthitis in response of anti-TNF-alpha

status: Public on Jul 13 2011

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

summary:
The goal of  this study was to characterize the effects of anti-TNF-alpha treatments on gene expression in peripheral blood mononuclear cells.
8 women were submitted to a 12 weeks treatments with Etanercept or Adalimumab. Peripheral blood mononuclear cells were taken before and after the treatment.
The samples from the same patients (obtained before and after the 12 weeks of treatment) were compared on the same microarray. Sample taken before the treatment was considered as the control.

overall_design: Blood mononuclear cells from 8 women suffering from rheumatoid arthritis were used in this study. The samples from the same patients (obtained before and after the 12 weeks of treatment) were compared on the same microarray. Mononuclear cells taken before the treatment was considered as the control.

first: Emmanuelle

last: Meugnier

first: Fabienne

last: Coury

first: Jacques

last: Tebib

first: Carole

last: Ferraro-Peyret

first: Sophie

last: Rome

last: Bienvenu

first: Hubert

last: Vidal

first: Nicole

last: Fabien


title: Effect of HdIV or MdBV injection on the Spodoptera frugiperda hemocyte transcriptome

summary: Comparison of the effects of 2 polydnaviruses (HdIV vs MdBV) injection on L5 Spodoptera frugiperda larvae hemocytes transcriptome.

last: Barbry

first: Kevin

last: Lebrigand


title: Sf9 induction with methoxyfenozide and methoprene

status: Public on Oct 10 2011

last: hilliou

summary:
published at http://dx.plos.org/10.1371/journal.pone.0025708

Effect of hormone agonists on Sf9 cells : methoxyfenozide (Mtfz) and methoprene (Mtp)

overall_design: We have 12 microarrays corresponding to 6 dye swaps , there is 3 biological replicates for each comparison. 6 microarrays: dye swap of 3 biological replicates corresponding to the comparison between Sf9 cell lines treatment with methoprene (Mtp) versus DMSO control treatment. And 6 microarrays: dye swap of 3 biological replicates corresponding to the comparison between Sf9 cell lines treatment with methoxyfenozide(mtfz) versus DMSO control treatment

first: Gaëlle

last: Le Goff

first: Pascal


title: Autoantibody Epitope Spreading in the Pre-Clinical Phase Predicts Progression to Rheumatoid Arthritis [ANALYTE: Cytokine or chemokine]

status: Public on Sep 10 2011

city: Stanford

first: William

last: Robinson

address: 269 Campus Dr

institute: Stanford University

summary: Rheumatoid arthritis is a prototypical autoimmune arthritis affecting nearly 1% of the world population and is a significant cause of worldwide disability. Though prior studies have demonstrated the appearance of RA-related autoantibodies years before the onset of clinical RA, the pattern of immunologic events preceding the development of RA remains unclear. To characterize the evolution of the autoantibody response in the preclinical phase of RA, we used a novel multiplex autoantigen array to evaluate development of the anti-citrullinated protein antibodies (ACPA) and to determine if epitope spread correlates with rise in serum cytokines and imminent onset of clinical RA. To do so, we utilized a cohort of 81 patients with clinical RA for whom stored serum was available from 1-12 years prior to disease onset. We evaluated the accumulation of ACPA subtypes over time and correlated this accumulation with elevations in serum cytokines. We then used logistic regression to identify a profile of biomarkers which predicts the imminent onset of clinical RA (defined as within 2 years of testing). We observed a time-dependent expansion of ACPA specificity with the number of ACPA subtypes. At the earliest timepoints, we found autoantibodies targeting several innate immune ligands including citrullinated histones, fibrinogen, and biglycan, thus providing insights into the earliest autoantigen targets and potential mechanisms underlying the onset and development of autoimmunity in RA. Additionally, expansion of the ACPA response strongly predicted elevations in many inflammatory cytokines including TNF-α, IL-6, IL-12p70, and IFN-γ. Thus, we observe that the preclinical phase of RA is characterized by an accumulation of multiple autoantibody specificities reflecting the process of epitope spread. Epitope expansion is closely correlated with the appearance of preclinical inflammation, and we identify a biomarker profile including autoantibodies and cytokines which predicts the imminent onset of clinical arthritis.

overall_design: A total of 556 human sera were profiled using multiplex cytokine and chemokine assays. The cohort was comprised of 80 patients with clinical RA for whom stored serum was available from 1-10 years prior to disease onset and 78 control subjects without RA matched to cases based on age, gender, race, region of assignment, and time of serum sampling.

first: Jeremy

last: Sokolove

first: Reuven

last: Bromberg

first: Ryan

middle: J

last: Tibshirani

last: Deane

first: Lauren

last: Lahey

first: Lezlie

last: Derber

first: Piyanka

last: Chandra

first: Jess

last: Edison

middle: R

last: Gilliland

first: Robert

first: Jill

middle: M

last: Norris

first: V

last: Holers

middle: H


title: Expression data from Xenopus anterior gut RFX6 knockdown

status: Public on Jan 24 2011

city: Montreal

first: Esther

last: Pearl

state: Quebec

address: 110 Pine Avenue West

country: Canada

institute: Clinical Research Institute of Montreal

summary: Recently a new neonatal diabetes syndrome, Mitchell-Riley syndrome, was discovered.  To identify the genetic cause of the syndrome homozygosity mapping was used, several chromosomal regions were linked to Mitchell-Riley syndrome.  In situ hybridization of genes from one such region using model organism Xenopus laevis identified RFX6 as a potential candidate gene; mutant forms of RFX6 were subsequently found in Mitchell-Riley patients.  Analysis of the expression pattern of RFX6 in Xenopus development shows it is expressed broadly in the endoderm early in development, and later RFX6 becomes restricted to the endocrine cells of the gut and pancreas.  Morpholino knockdown of RFX6 in Xenopus caused a loss of pancreas marker gene expression.  Injection of exogenous wild type RFX6 rescued the morpholino phenotype in Xenopus tadpoles.  Attempts to rescue the loss-of-function phenotype using mutant forms of RFX6 found in Mitchell-Riley patients were unsuccessful suggesting the changes lead to loss-of-function and could be the cause of Mitchell-Riley syndrome.  Microarray analysis of gene expression in knockdown tissue suggested a downregulation in marker genes for lung, stomach and heart, ambiguous results for the liver, and an upregulation in kidney marker gene expression.  RT-PCR and in situ hybridization confirms a loss of lung, stomach and heart gene expression, no change in liver marker hex and an upregulation in kidney marker KcnJ1.  The fact that the morpholino phenotype affects multiple organs suggests that RFX6 has a broad role early in endoderm development.

overall_design: Xenopus laevis embryos were injected with morpholinos, either mismatch control (MM) or RFX6 start site (MO1), at the 8-cell stage.  The foreguts of the resulting tadpoles were dissected at 3 different stages of development, NF30, NF40 and NF44.

first: Zeina

last: Jarikji

first: Marko

last: Horb


title: Hepatic Gene Expression Profiles of Growing Beef Steers Grazing High vs. Low Endophyte-Infected Tall Fescue Grass

status: Public on Nov 30 2010

city: Lexington

first: Shengfa

middle: F

last: Liao

state: KY

address: 214 WP Garrigus Bldg

department: Dept of Animal & Food Sciences

institute: University of Kentucky

summary:
Neotyphodium coenophialum is an endophytic fungus that infects most tall fescue (Festuca arundinacea) pastures that are commonly used in animal grazing systems in the United States. Beef cattle grazing such pastures are impaired in health and production performance, resulting in a large economic loss in US food-animal production systems. Based on the clinical symptoms and laboratory analyses of blood, it was hypothesized that such affected cattle display liver-specific changes in the expression of gene transcripts that are associated with the metabolic enzymes and transporters critical for beef health and performance.
Microarray analysis using the GeneChip Bovine Genome Array (Affymetrix, Inc., Santa Clara, CA) was conducted to determine if grazing endophyte-infected tall fescue pastures affects the liver gene expression profiles of growing beef steers.

overall_design: Nineteen steers were assigned to graze either a low toxic endophyte tall fescue-mixed grass (LE treatment, 5.7 ha, n = 9) or a high toxic endophyte infected tall fescue (HE treatment, 5.7 ha, n = 10) pasture located in the University of Kentucky Agricultural Research Center. All steers had ad libitum access to fresh water and an industry standard mineral-vitamin supplement. 88 days grazing on pasture. Approximately 2 g of tissue from the right lobe of the liver of each steer were collected for RNA extraction and microarray analysis.

first: James

middle: A

last: Boling

middle: C

last: Matthews


title: [E-MTAB-369] Transcription profiling by array of Xenopus laevis embryos at 15 different stages

city: Kobe

first: Naoki

last: Irie

state: Hyogo

address: 2-2-3 Minatojima-minami Chuo-ku

institute: RIKEN Center for Developmental Biology

summary:
Transcription profiling of X.laevis development.
The experiment were perfomed as a part of our Vertebrate Evo-Devo project. The aim of the project is to compare transcription profiles of normal (unmanipulated, wild-type, whole embryo) vertebrate embryos.

overall_design: Total RNA was collected from wild type X.laevis whole embryos at 15 different stages (Stages:2, 5, 9, 11, 13, 17, 19, 21, 23, 26, 28, 31, 37/38, 43, 48), and hybridized to  Affymetrix Xenopus laevis Genome 2.0 Array. All the stages contains data from 2 biological replications. Each staged-samples consists of pooled total RNA from several whole embryos.


title: Early Multipotent Cardiovascular Progenitors Derived from Pluripotent Stem Cells Engraft in Postmyocard Infarted Primate

status: Public on Feb 08 2011

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

summary: During embryogenesis, the cardiac cell fate is acquired as early as gastrulation. There is compelling evidence that embryonic stem cells (ESC) can recapitulate early steps in cardiogenesis. Identification from human pluripotent stem cells of early cardiovascular cell progenitors, at the origin of the first cardiac lineage, would shed light on human normal and pathological cardiogenesis and would pave the way toward cell therapy for cardiac degenerative diseases. Here, we report the isolation, and a phenotypic characterisation of an early Oct-4+, SSEA-1+, Mesp1+ population of cardiovascular progenitors derived from human pluripotent stem cells. This multipotential progenitor features the capability to generate cardiomyocytes as well as smooth muscle and endothelial cells. We further bring a proof of concept that these progenitors can be used in cardiac regenerative medicine as allografted in infarcted non human primate myocardium, they differentiate in ventricular myocytes without any adverse effect.

overall_design:
One RNA sample from HUESC-POU5F1 was compared in dye-swap to undifferentiated HUESC.
Three distinct RNA samples from BMP2-induced SSEA1+ cells were compared in dye-swap to paired remaining SSEA1-.
Reference samples correspond to undifferentiated HUESC and to SSEA1 negative cells, respectively.
population respectivement.

first: michel

last: PUCEAT

first: Pascal

last: Barbry


title: Adenosine-treated endothelial progenitor cells

status: Public on Jan 29 2011

first: Yvan

last: Devaux

summary: The goal of this study was to investigate the effects of the cardioprotective nucleoside adenosine on gene expression in early and late endothelial progenitor cells. Adenosine mod

overall_design:
Early outgrowth endothelial progenitor cells were obtained by adhesion of peripheral blood mononuclear cells of healthy volunteers. Late endothelial progenitor cells were obtained by purification of CD34+ peripheral blood cells and were cultured and amplified in endothelial-specific medium containing growth factors.
Both cell types were treated by adenosine (10micromol/L) for 6 hours. Total RNA was extracted using conventional Trizol extraction, quantified by Nanodrop and analyzed by Bioanalyzer.
1microg of RNA was amplified using AminoAllyl MessageAmp kit. 5µg amino allyl-coupled RNA was labeled with Cy3 or Cy5 dyes. Dye coupling yield >5% was a prerequisite for further analysis. 750ng of labeled RNA was hybridized on 25,000 gene microarrays for 17 hours at 60°C. 4 arrays per sample were hybridized and scanned with the Genepix 4000B Scanner (Molecular Devices). Six independent experiments were performed.
Microarray data quantification and pre-processing was performed with the MAIA software and intensity values were log-transformed. Gene expression values were standardized across experiments with mean = 0 and standard deviation = 1. The SAM tool was applied to identify differentially expressed genes.


title: Dual-species microarray for assessing gene expression in stromal microenvironment, cancer cells and their interactions (v2 array)

status: Public on Aug 04 2010

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

summary:
Design a human-mouse dual-species microarray to provide a technology for investigation of cancer-stromal interaction in xenograft model.

The 2 reference RNA were used to evaluate and identify probes with potential the cross-species hybridization, so that we can label these probes and exclude them before analysis of biological samples/data.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Reference RNA from human and mouse were labeled using Cy3. Samples were hybridized on customized-commercial array with Agilent probes and user-designed species-specific probes (Human-mouse dual-species array HomoMus_v2). This array is designed and improved from hte first version GPL10714

first: Xinan

last: Yang

first: Younghee

last: Lee

first: Rosie

last: Xing

first: Yves

last: Lussier


title: DNA copy number data from the CE01 clinical study

status: Public on Oct 25 2010

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

summary: Patients with cervical cancer were treated with external beam radiotherapy (EBRT) at a dose of 45Gy in 25 fractions over five weeks, with weekly cisplatin. Biopsies were taken pre-, during and post-treatment and analysed for copy number changes.

overall_design: Cervical cancer patients were treated with chemoradiotherapy and disease response was followed by array CGH profiling.

first: Susanna

last: Cooke

first: Stewart

last: MacArthur

middle: D

last: Brenton


title: Microarray analysis of BHLHB2 and BHLHB3 target genes in human skeletal muscle cells

status: Public on Apr 11 2010

first: emmanuelle

last: meugnier

summary: In this study we have identified the target  genes of BHLHB2 and BHLHB3 in primary cultures of human skeletal muscle cells using adenoviral vectors expressing either BHLHB2 or BHLHB3, and oligonucleotide microarrays.

overall_design: Human myotubes were prepared from 4 different skeletal muscle biopsies. After 7 days of differentiation, myotubes were infected for 48 hours with recombinant adenovirus expressing either GFP, BHLHB2 or BHLHB3. Each BHLHB2- or BHLHB3-infected myotubes culture was compared to GFP-infected myotubes culture. GFP-infected myotubes were considered the control. Four biological replicates were processed.

first: Emmanuelle

last: Meugnier

first: Virginie

last: Lecomte

first: Vanessa

last: Euthine

first: Etienne

last: Lefai


title: A human-like fat diet is sufficient to induce transgenerational obesity

status: Public on Jun 01 2010

first: Kevin

last: Lebrigand

summary: The prevalence of obesity has steadily increased since decades. In the meantime, in line with the exposition of populations of from industrialized countries have been exposed to fat-rich diet with high exaggerated ù6/ù3 ratio of ù6- over ù3-polyunsaturated fatty acids. To assess the contribution of dietary fatty acids, male and female mice fed a human-like fat diet were mated randomly and maintained after breeding on the same diet for successive generations. Offspring showed over 4 generations a gradual enhancement in fat mass due to combined hyperplasia and hypertrophy with no change in energy intake. Transgenerational alterations in adipokine levels were accompanied by hyperinsulinemia. When switched to a standard diet, the obese phenotype (termed revHF4) reversed partially. Offspring of revHF4 mice exhibited higher birth weight and faster gain weight compared to control mice. Gene expression analyses of the stromal vascular fraction of adipose tissue over generations revealed i) underexpression of genes favoring angiogenesis and controlling oxidative stress and ii) overexpression of genes involved in inflammation, and in adipogenesis .and in insulin resistance. Thus, under conditions of genome stability, our results show that metabolic imprinting induced by a human-like fat diet is accompanied by a gradual fat mass enhancement, in accordance with the increasing prevalence of obesity observed in humans over generations.

overall_design: 2 independent experiments. Experiment 1 = 12 microarrays, corresponding to the 6 possible comparisons between STD, HF0, HF3 and HF4, in dye-swap. Experiment 2 = 22 microarrays, corresponding to the 6 possible comparisons between HF0, HF1, HF3 and HF4, in dye-swap, plus a dye-swap comparison between HF0 and STD (2 times), HF1 and HF1-REV (one time), HF3 and HF3-REV (one time), HF4 and HF4-REV (one time). (HF0 = outcome of STD, fed with a high fat diet. STD = fed with a normal diet. HF1 = outcome of HF0, fed with a high fat diet. HF1-REV = outcome of HF0, fed with a normal diet. HF3 = outcome of HF2, fed with a high fat diet. HF3-REV = outcome of HF2, fed with a normal diet. HF4 = outcome of HF3, fed with a high fat diet. HF4-REV = outcome of HF3, fed with a normal diet).

first: Florence

last: Massiéra


title: MicroRNA Regulation by Phorbol-ester and cytokines in Human Lung Fibroblasts

status: Public on Nov 01 2009

summary: Human Fetal pulmonary Fibroblasts (CCL153) were treated by PMA, IL1, TGFbeta and TNFalpha for 24 hours and compared for microRNA expression with control cells.

overall_design: Dye-swap-experiment in which each stimulated (PMA,IL1,TGFbeta,TNFalpha) condition is compared with control cells.

first: Bernard

last: Mari

first: Pascal

last: Barbry

last: Le Brigand


title: A Novel Dominant Mesomelic Dysplasia Associated with A 1.0-Mb Microduplication of HOXD Gene Cluster at 2q31.1

status: Public on Mar 09 2010

city: Seoul

first: Woong Yang

last: Park

address: 28 Yongondong, Chongnogu

department: Biochemistry and Molecular Biology

country: South Korea

institute: Seoul National University

summary: A three-generation family with four patients affected by a mesomelic dysplasia was investigated for genome-wide DNA copy number variation profiles. This revealed a microduplication of a 1.0-Mb chromosomal segment at 2q31.1 spanning nine Homeo box D (HOXD) genes that co-segregated with the phenotype. Quantitative PCR analysis of a gene within this duplicated region showed consistent results. A phenotypically similar condition, mesomelic dysplasia Kantaputra type (MDKa; MIM 156232)[1], has also been mapped to this chromosomal region[2], raising the possibility that MDKa and the condition observed in this family may be allelic.

overall_design: three-generation family including four affected individuals and two unaffected individuals

first: Woong-Yang

first: Tae-Joon

last: Cho


title: Gene expression profiling of Imatinib and PD166326 resistant cell lines

status: Public on Jun 01 2009

summary:
A comparison between parental K562 cells (CML) and two clones derived from this cell line : ImaR and PDR which are resistant against Imatinib mesylate and PD166326 respectively , two inhibitors of BCR-ABL.
Keywords: gene expression, comparison

overall_design: Six dual channel Samples compared in all combinations, PDR vs. K562, K562 vs. ImaR, ImaR vs K562, PDR vs ImaR, ImaR vs PDR, K562 vs PDR.

first: Patrick

last: Auberger

first: Sebastien

last: Grosso


title: MicroRNA signature of thyroid tumors of uncertain malignancy

status: Public on Aug 22 2011

summary: Well-differentiated tumours (WDT) of the thyroid gland can be difficult to diagnose. Focal nuclear clearing can be suggestive of a papillary thyroid carcinoma (PTC), while questionable vascular or capsular penetration may raise the possibility of diagnosis of a follicular thyroid carcinoma (FTC). The recently proposed term “thyroid tumours of uncertain malignant potential” (TT-UMP) defines cases showing inconclusive morphological evidence of malignancy. We use microRNA (miRNA) expression profiling to analyze 42 well differentiated thyroid tumours including 7 follicular tumours of uncertain malignant potential (FT-UMP), 6 well differentiated tumours of uncertain malignant potential (WDT-UMP), 7 follicular thyroid adenomas (FTA), 5 follicular variant of papillary thyroid carcinoma (FV-PTC) 6 follicular thyroid carcinoma (FTC), and 11 conventional papillary thyroid carcinoma (C-PTC) with 6 C-PTC mutated for BRAFV600E (C-PTC-mut) and 5 not mutated: wild type (C-PTC-wt). Comparison of these 13 tumours of uncertain malignant potential (7 FT-UMP and 6 WDT-UMP) with those obtained from 16 PTC (11 C-PTC and 5 FV-PTC), 6 FTC and 7 FTA is performed in order to clarify the relationships between TT-UMP and the morphologically well characterized categories of thyroid tumours (i.e. C-PTC, FV-PTC, FTC and FTA). In first, each pathological sample (“L” for Lesional tissue) is compared with its matched control (“S” for Safe tissue) for the 42 patients (84 miRNA microarray slides). This control was taken from the same patient at a large distance from the tumour. Secondly, the perilesional tissue from the same patients but 2 (1 PTC and 1 adenoma, without enough RNA left) is compared to normal thyroid tissue (safe tissue reference) obtained from a patient who underwent total thyroidectomy for a laryngeal carcinoma that partially invaded the thyroid gland, to search for microRNA signatures of perilesional tissues (80 miRNA microarray slides).Experiments is performed with a miRNA microarray, referenced in GEO under the accession number GPL4717 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL4717).

overall_design: 42 Patients: 7 FT-UMP, 6 WDT-UMP, 7 FTA (+1 duplicate sample), 5 FV-PTC, 6 FTC (+ 2 duplicate samples), and 11 C-PTC.  44 dye-swap pairs and 1 with no dye swap pair for a total of 89 samples.

first: Paul

last: Hofman

first: Sandra

last: Lassalle


title: Comparison between stromal vascular fraction of adipose tissue, testis and epididymis in mouse

summary: An experiment was performed in order to compare directly profiles of stromal vascular fraction of adipose tissue, testis and epidydimis, in order to rule out a possible contamination of the stromal vascular fraction of adipose tissue (SVF) by adjacent tissues (i.e. epididymis and testis). This led to the identification of a list of 2358 SVF-specific probes, which was subsequently used for further investigations.

overall_design: 3 dye-swap pairs, comparing 3 distinct samples of total RNA prepared from: (1) stromal vascular fraction of adipose tissue, (2) testis and (3) epidydimis.


title: Transcription rate analysis of wild type strain subjected to osmotic stress

status: Public on Apr 23 2009

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

summary:
Transcription rate (TR) analysis of W303-1a yeast strain growing in exponential phase in YPD subjected to osmotic stress

Keywords: time course

overall_design: Transcription rate analysis by means of GRO of three independent replicates the yeast strain growing in exponential phase. Each time point replicate has been hybridized on a different macroarray (F11-F17).


title: mRNA amount analysis of wild type strain subjected to osmotic stress

summary:
mRNA amount (RA) analysis of W303-1a yeast strain growing in exponential phase in YPD subjected to osmotic stress

Keywords: time course

overall_design: Transcriptomic analysis of three independent replicates the yeast strain growing in exponential phase. Each time point replicate has been hybridized on a different macroarray (F11-F17).


title: MiRNA and lung cancer (INCA project) - 26 RNG25k microarrays

status: Public on Oct 01 2010

summary: Gene expression analysis in 13 pairs of primary lung cancers and their corresponding non cancerous lung tissues. These specimens were obtained from the Nice Hospital Tumor Bio Bank, France.

overall_design: Dye swap-experiment comparing cancerous tissue versus adjacent normal lung tissue.

first: Marie-pierre

last: Puissegur


title: MiRNA and lung cancer (INCA project) - 40 miRNAs microarrays

summary: MicroRNA expression pattern in 20 pairs of primary lung cancers and their corresponding non cancerous lung tissues. These specimens were obtained from the Nice Hospital Tumor Bio Bank, France.


title: Osmotic stress on yeast S. cerevisiae

summary:
mRNA amount (RA) and Transcription rate (TR) analysis of W303-1a (wt) and hog1 mutant yeast strains growing in exponential phase in YPD subjected to osmotic stress

This SuperSeries is composed of the SubSeries listed below.

overall_design:
Refer to individual Series

Transcriptomic and transcription rate analysis by means of GRO of three independent replicates the yeast strain growing in exponential phase. Each time point replicate has been hybridized on a different macroarray (F11-F24). A single DNA genomic hybridization from the same labeling reaction was done on the same microarrays for normalization.


title: mRNA profiling of mir-155-overexpressing fibroblasts

status: Public on Dec 22 2009

summary: To identify putative fibroblasts-specific targets of mir-155, we overexpressed mir-155 in lung fibroblasts by transfecting them with a synthetic pre-mir-155 or a synthetic “negative” pre-miRNA as control (miR-Neg). RNA samples were harvested at 24 and 48 hours post-transfection and 2 independent experiments were carried out.

overall_design: 24 and 48 hours post-transfection, 2 independent experiments performed in dye-swap: miR-155 versus miR-Neg


title: ARGONAUTE-small RNA Interactions in Arabidopsis thaliana Identified by High-Throughput Sequencing

status: Public on Aug 16 2008

city: Saint Louis

first: James

last: Carrington

state: MO

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

type: Non-coding RNA profiling by high throughput sequencing

summary:
The goal of this study was to identify small RNA-ARGONAUTE interactions in Arabidopsis. Co-immunoprecipitation assays followed by high-throughput sequencing were done to identify small RNA associated with HA-AGO2 and HA-AGO7.

Keywords: small RNA - ARGONAUTE interactions

overall_design:
Sequencing-by-synthesis technology was used to sequence small RNA from input and co-immunoprecipitation fractions from cell lysates of inflorescence  tissue from Arabidopsis plants transformed with HA epitope-tagged AGO2 or AGO7 constructs. Meaningful intepretation requires comparison between the input and co-immunoprecipitation datasets.

Fastq files are not available for this series as only ELAND output files were provided by the sequencing facility at the time of sequencing (2007).

first: Taiowa

last: Montgomery


title: MiRNA and lung cancer (INCA Project) - 16 RNG25k microarrays

summary: To identify putative novel specific targets of mir-210, we overexpressed miR-210 as well as miR-34a and a siRNA targeted against E2F3 in A549 human adenocarcinoma cells by transfecting them with  synthetic pre-miRNAs or a synthetic “negative” pre-miRNA as control (miR-Neg). RNA samples were harvested at 48 hours post-transfection and 2 independent experiments were carried out.

overall_design: 48 hours post-transfection, 2 independent experiments performed in dye-swap: miR-210 versus miR-Neg ; miR-34a versus miR-Neg ; si-E2F3 versus miR-Neg ; si-control versus miR-Neg.

first: marie-pierre

last: puissegur


title: RNA pol II ChIP on chip (RPCC)

status: Public on Aug 24 2009

summary:
Adaptation of the ChIP-on-chip protocol, to calculate genomic transcription rates in S. cerevisiae.

Keywords: ChIP-chip

overall_design: There are 3 different experimental conditions: -Yeast cell growing exponentially  in YPD. -Yeast cell stopped after 2 h of changing them to YPGal. -Yeast cell growing exponentially after 14.5 h of changing them to YPGal.  We have used 3 different IP protocols: -total RNA pol II using a Myc tagged RNA pol (RPB1-Myc) -RNA pol II CTD using the Ab 8WG16 (Covance) -RNA pol II CTD Phosphorylated on Ser5 (David Bentley\'s lab)  There are 3 independent biological replicates of each experiment.

first: Vicent

last: Pelechano

middle: E


title: Hela hsa-miR-34a, b-5p, and c transcriptomes

status: Public on May 13 2009

first: Kevin

last: Lebrigand

summary: Comparative transcriptome analysis of Hela cells transfected with hsa-miR-34a,b-5p or c.

overall_design: Hela cells transfected with hsa-miR-34a,b-5p or c versus two distincts negative miR controls (mirNeg1 and mirNeg2) in a dye swap experiment.

first: Brice

last: Marcet

first: Bruno

last: Cardinaud


title: Functional cooperation between AAA-ATPase domain and a bromodomain.

status: Public on Oct 01 2009

summary: A functional cooperation between an AAA type ATPase domain and a bromodomain has been evidenced. These two domains were identified and their activity tested in a yet uncharacterized factor, named Atad2, whose two-domain configuration remained highly conserved during evolution. In human and mouse, Atad2 is most abundantly expressed in testis and in the mouse. It has also been detected in post-meiotic stages and in mature spermatozoa. The AAA-ATPase domain was found necessary for protein multimerization and high affinity binding to acetylated nucleosomes by its bromodomain. The binding was found specific to acetylated histone H4 tail with a critical role for the acetylated K5 position. In vivo studies show that Atad2 behaves as a general repressor of transcription and possesses a chromatin “freezing” activity. Finally, we demonstrate that the induction of apoptosis leads to an early degradation of Atad2, which probably facilitates the action of apoptotic factors by increasing chromatin dynamics.

overall_design: The experimental design includes 6 slides, corresponding to 3 experimental comparisons, in dye-swap. Each comparison corresponds is done on a specific cell line (A549, SAOS or H1299), treated with a siRNA against Atad2 or against a control siRNA.

first: Cécile

last: Caron

first: Pascal

last: Barbry


title: Characterization of retinoic acid-regulated microRNAs

status: Public on Nov 18 2008

summary:
The aim of this study is to identify microRNAs (miRNAs) transcriptionnally regulated by retinoic acid (RA). For that purpose we have used the RA-based treatment of the Acute Promyelocytic Leukemia (APL) as a model. This malignancy is characterised by a differentiation arrest of granulopoiesis at the promyelocytic stage. APL is molecularly associated with reciprocal translocations that always involve the retinoic acid receptor a (RARa). In the vast majority of APL cases, a t(15;17) chromosomal translocation fuses the genes encoding the promyelocytic leukemia protein PML and RARa. The resulting PML-RARa is a transcriptional repressor that impedes the expression of RA-regulated genes notably through an aberrant recruitment of transcriptional repressors and histone deacetylases. Consequently, these genes become insensitive to physiological doses (nanoM) of all-trans-retinoic acid (ATRA) but pharmacological doses (microM), overcome the PML-RARa-mediated repression and restore normal transcription and granulocytic differentiation. The restorative effects of RA can be reproduced in vitro in the NB4 cells, which were derived from an APL patient. These cells provide an excellent model to study the transcriptional deregulations that arise in APL and the molecular effects of the anti-cancerous RA-based treatment. We also used in this study the RA-resistant cells, namely NB4-LR1 and NB4-LR2 cells. The NB4-LR1 cells do transcriptionally respond to ATRA but do not maturate. In contrast, the NB4-LR2 cells show a clear defect in RA signaling, as they harbor a truncated form of PML-RAR protein that is not sensitive to pharmacological doses of RA.
First, we plan to characterize miRNAs-repressed by PML-RAR. We reasoned that if some miRNAs are repressed by this protein, then pharmacological doses of RA should abolish this repression and lead to an increase in the level of expression of the corresponding miRNAs. NB4, NB4-LR1 and NB4-LR2 cells will thus be treated for 16h with ATRA (1 microM), and miRNAs profiles will be compared. We anticipate that, the expression of a potential miRNA-repressed by PML-RAR should be up-regulated by ATRA in both NB4 and NB4-LR1 cells but remain unchanged in NB4-LR2 cells. This expression pattern should in fact be similar to those observed for known RA-regulated genes, such as RARb, a well characterized target of the RARa and PML-RAR proteins. Importantly, this experimental procedure was already validated with the identification of a miRNA repressed by PML-RAR (patent Lecellier et al. #WO 2006/048553). MiRNAs candidates obtained will then be validated by chromatin immunoprecipitation using anti-RARa and anti-PML antibodies, followed by luciferase assays in presence or absence of ATRA.
Keywords: retinoic acid-mediated gene regulation

overall_design: To characterize miRNAs regulated by PML-RAR.

first: charles

last: lecellier

last: Le Brigand


title: Androgen dependent gene expression profiling of the urogenital sinus

status: Public on Dec 04 2008

city: Baltimore

first: Luigi

last: Marchionni

address: 1550 Orleans St., CRB2, Room 1M52

institute: Johns Hopkins University

summary:
Cancer cells differentiate along specific lineages that largely determine their clinical and biologic behavior. Distinct cancer phenotypes from different cells and organs likely result from unique gene expression repertoires established during lineage commitment in the embryo and maintained after malignant transformation. We used comprehensive gene expression analysis to examine this concept in the prostate, an organ with a readily manipulable developmental program and a high propensity for cancer. We focused on gene expression changes in the murine prostate rudiment (Urogenital Sinus, UGS) at three time points during the first 48 hours of exposure to androgen, which initiates proliferation and invasion of prostate epithelial buds into surrounding mesenchyme.

Keywords: time course, prostate gland development

overall_design:
Differential gene expression was assessed by direct comparisons  of labeled moieties, using dye-swaps as technical replicates. Hybridizations were performed  on the Agilent (Santa Clara, CA) Whole Mouse Genome DNA microarray (mgug4122a). Three  different time points were analyzed using RNA pooled from different embryos:

• UGS of female embryos upon 6 hours of androgen treatment compared to UGS of vehicletreated  mice (H6 comparison, 8 different slides);

• UGS of female embryos upon 12 hours of androgen treatment compared to UGS of vehicletreated  mice (H12 comparison, 6 different slides);

• UGS of male embryos compared to UGS of female embryos (MvsF comparison, 10 different  slides). Pools from male tissues were hybridized against pools from female litter-mates;

first: Edward

last: Schaeffer

first: Zhenhua

last: Huang

first: Brian

last: Simons

first: Amanda

last: Blackford

first: Wayne

last: Yu

first: Giovanni

last: Parmigiani

first: David

last: Berman


title: Aortic gene expression profile of rats exposed in utero to maternal diabetes

status: Public on Feb 01 2010

city: Angers

first: Celine

last: Fassot-Lucht

address: Rue Haute de Reculée

department: BNMI

institute: INSERM U1083

summary: Epidemiologic studies have clearly identified modifications of fetal environment as a risk factor for the development of cardiovascular diseases and of metabolic syndrome in adulthood. In our experimental model, rats exposed to maternal diabetes develop a volume-dependent hypertension as early as 6 month of age. In order to determine if the development of hypertension results from an abnormal vascular fetal programming, gene expression profile of thoracic aorta were studied in adult rats exposed in utero to maternal hyperglycemia.

overall_design: 10 samples total (including 5 dye swaps)

last: FASSOT-LUCHT


title: Validation of Ehrlichia ruminantium micro-array using genomic DNA of Gardel (Gp40) and Welegevonden (Wp11) strains

status: Public on Dec 01 2009

last: Lebrigand

summary: In order to study the transcriptome of the pathogen, Ehrlichia ruminantium, specific microoarray was designed and validated using genomic DNA of Gardel and Welgevonden strains. Gardel strain was isolated in Guadeloupe and Welgevonden strain in South Africa. DNA from Ehrlichia ruminantium was extracted from cell culture infected with Gardel passage 40 and Welgevonden passage 11, using QIAmp kit (Qiagen). Ehrlichia ruminantium DNA was labeled using BioPrime array CGH labeling system kit (Invitrogen) and Cy3-dCTP (Amersham).  Arrays were incubated at 60°C for 20 hours in hybridization chamber. After hybridization, arrays were washed according to the Agilent protocol. Arrays were scanned and the signal intensity of all spots were quantified by Genepix pro 6.0 (Molecular Device Corporation) and data were saved for further analysis.

overall_design: A one color two microarrays preliminary experiment from genomic DNA extraction.

first: Nathalie

last: Vachiery

first: Loic

last: Emboule

first: Bernard

last: Mari


title: MicroRNA expression pattern in Human normal pulmonary fibroblast and lung adenocarcinoma

first: Kevin

summary: MicroRNA expression pattern in a Human fetal normal pulmonary fibroblast (CCL153) and a lung adenocarcinoma cell line (A549).

overall_design: Dye swap-experiment comparing CCL-153 and A549 cells.

last: Barbry


title: Comparison of natural yeast hybrids

first: Jose

last: Perez-Ortin

summary: Analysis of genomic variation in several Saccharomyces cerevisiae x S. kudriavzevii natural hybrids

overall_design:
S. cerevisiae and S. kudriavzevii yeasts have been described among wine strains. These strains exhibit enological properties of interest for the wine industry. A preliminary characterization of these hybrids showed a trend to reduce the S. kudriavzevii fraction of the hybrid genome. As a first approach to understand the mechanisms involved in the genome changes occurred after hybridization that may account for differences in their enological properties, we characterized the genomic constitution of several wine S. cerevisiae x S. kudriavzevii strains by using a combined approach based on the RFLP analysis of gene regions, comparative genome hybridizations with S. cerevisiae DNA arrays, ploidy analysis and gene dose determination by quantitative real-time PCR.

Genomic DNA hybridizations of w27, w46, SPG1691 and 441 hybrids were compared against the laboratory strain FY1679. Hybridizations were performed by triplicate in order to obtain the final CGH ratio.

first: J

last: Garcia-Martinez


title: Gene expression profiling of liver injury during human orthotopic liver transplantation.

status: Public on Mar 01 2008

summary:
The purpose of this study was to identify the main genes involved in liver I/R using a transcriptomic approach.
Keywords: Normal vs transplanted human liver comparison, stress response, clinical analysis.

overall_design: Twenty one liver transplant biopsies (sample= T1-T21) taken after graft reperfusion were compared with 7 normal control livers (sample= control1-control7). Transplanted samples are divided into two groups based on the peak levels of serum aspartate amino transferase (AST) in the patient serum and the histologic score of the biopsy (suzuki score): group 1 (14 patients, ALT=1500 U/l), mild to moderate injury; group 2, (7 patients, AST>1500 U/l) severe injury. Control samples include 5 liver biopsies from patients undergoing tumour surgical resection and 2 commercial RNA from Stratagene. Two technical replicates were performed for each transplanted and normal patient inverting cye dye (dye-swap), and 6 replicates were carried out for commercial RNA (3 cy3 and 3 cy5 for each). This experimental design involves 32 slides.

first: Virginie

last: Defamie

first: Raffaele

last: Cursio

first: Pascal

last: Le Brigand


title: Global mapping of epigenetic modifications of histone H3 Lysine 4 di- and trimethylation in Rice

status: Public on Jan 04 2008

city: New Haven

first: Hang

last: He

state: CT

address: 165 Prospect St

department: MCDB

institute: Yale University

type: Methylation profiling by genome tiling array

summary:
We present high-resolution maps of DNA methylation and H3K4 di- and tri-methylation of two entire chromosomes and two fully sequenced centromeres in rice shoots and cultured cells. Most transposable elements have highly methylated DNA but no H3K4 methylation whereas over half of protein-coding genes have both methylated DNA and  di- and/or tri-methylated H3K4. Methylation of DNA but not H3K4 correlates with suppressed transcription. In contrast, if both DNA and H3K4 are methylated transcription is only slightly reduced.  Transcriptional activity was positively correlated with H3K4Me3/H3K4Me2 within the gene body: genes with predominantly H3K4Me3 were actively transcribed whereas genes with predominantly H3K4Me2 were transcribed at moderate levels. Both H3K4Me2 and H3K4Me3 exhibited two peaks in long rice genes; a minor peak correlated with putative transcription start sites and a major peak downstream, implying possible roles in transcriptional initiation and elongation.
Keywords: whole genome profiling, DNA methylation, ChIP

overall_design:
Plant Materials and Growth Conditions
All plants used in this study were rice strain Oryza sativa ssp japonica cv Nipponbare. Dehusked seeds were surface sterilized and sown on solidified Murashige and Skoog medium with 3.0% sucrose. Plants were grown in chambers at 28°C with continuous white light for 7 days, and the entire shoots were harvested. Suspension cultured cells were derived from the same rice strain and maintained as described previously (Su et al., 2007).

Isolation of epigenetically modified genomic DNA fragments
Methylated DNA was isolated from total genomic DNA prepared using the Plant DNeasy Mini Kit (QIAGEN) by the McrBC-digestion method (Lippman et al., 2004).  DNA bearing modified was isolated by chromatin immunoprecipitation (ChIP) with antibodies that specifically recognize H3K4Me2, H3K4Me3 and CenH3.

Tiling Microarray Design, Hybridization, Scanning and Data analysis
Tiling probes were selected by the NASA Oligonucleotide Selection Algorithm (NOPSA) (Stolc et al., 2005). Microarrays were hybridized with Cy3 or Cy5 labeled DNA for 16-20 hours at 50°C, then washed each 10 min at room temperature. Hybridization images were generated by a GenePix 4200A scanner (Axon). Raw data was sequentially processed by LOESS normalization and Quantile normalization.

first: Xueyong

last: Li

first: Xiangfeng

last: Wang

first: Kun

first: Yeqin

last: Ma

first: Ning

last: Su

first: Viktor

last: Stolc

first: Waraporn

last: Tongprasit

first: Weiwei

last: Jin

first: Jiming

last: Jiang

first: Songgang

first: XingWang

last: Deng


title: Hat mutants

status: Public on Jul 23 2005

first: Jose

summary:
Transcriptomes from the hat1, hat2 and hat1 hat2 mutants in S288C yeast background.
Keywords: parallel sample

first: Oreto

last: Antúnez

first: José

last: Pérez-Ortín


title: SUS1

status: Public on Jan 02 2004

last: Perez-Ortin

summary:
Transcriptome analysis of sus1 mutant in reference to its parental wild type reference. Iterative global median method was used for between sample normalization.
z-test was performed to evaluate differential gene expression.
Keywords: repeat sample

last: Antunez


title: GRX5, PET117 and MLP1 yeast mutants

status: Public on Dec 29 2003

summary:
Transcriptome comparisons between grx5, pet117 and mlp1 mutants. All of them are referenced to the same parental wild type sample using three independent samples and three independent nylon macroarrays. Each replicate pair (wt/mutant), hybridized on the same membrane, was normalized by lowess method.
z-tests were performed to evaluate differential gene expression.
Keywords = yeast
Keywords = GRX5
Keywords = PET117
Keywords: other

last: Garcia-Martinez