title: Iron excess limits HHIPL2 gene expression and decreases osteoblastic activity in human MG-63 cells

status: Public on Sep 01 2012

city: RENNES

first: DOYARD

last: Mathilde

address: rue Henri Le Guilloux

institute: INSERM

summary: Our transcriptomic data shows that iron impact on human osteoblastic MG-63 cells  by decreasing HHIPL-2 gene expression (2 fold ratio). This impact is corrected in presence of deferoxamine. Additional biological experiments in the manuscript  suggest that the iron related modulation of HHIPL-2 gene expression could take place in the decrease of osteoblastic markers in the MG-63 cell line. Such mechanisms could  participate to the development of osteoporosis in iron overloaded patients.

overall_design: One-condition experiment, iron exposure using ferric ammonium citrate (FAC) at two concentrations (5 and 20µM) was compared to basal condition. Additional conditions include: deferoxamine (DFO) (iron chelator) 20µM alone or in addition to FAC 20µM. For each condition five biological replicates were performed (independent experiments).

first: Pascal

last: Guggenbuhl

first: Olivier

last: Loréal

first: Mathilde

last: Doyard


title: mRNA expression profile of dermal MSCs derived from psoriasis patients and normal control

status: Public on Nov 30 2012

city: Taiyuan

first: Ruixia

last: Hou

state: Shanxi

address: 1,Dong San Dao Xiang, Jiefang Road

department: Dermatology

country: China

institute: Taiyuan City Central Hospital

summary: Several studies have suggested that MSCs have pleiotropic immuno-modulatory effects,  including inhibition of T cell proliferation, suppression of NK cells proliferation, modulation of cytokine production, and inhibition of dendritic cell (DC) maturation etc. But the exactly mechanism are still largely unclear. We proposed to investigate the mRNA expression profile of psoriatic MSCs.

overall_design: 6 patients and 6 normal control were inrolled in the study, the mRNA expression profile of dermal MSCs were studied using the microarry.

first: Kaiming

last: Zhang


title: Gene expression analysis of human oral squamous cell carcinoma cell lines (HSC-4, OSC19)

status: Public on Oct 12 2012

city: Tokyo

first: Osamu

last: Nagano

state: DDS PhD

address: ３５　Shinanomachi

department: Institute for Advanced Medical Research

country: Japan

institute: Keio University School of Medicine

summary: As microarray based gene expression profiling is well suited to study the complex diseases such as cancer, we revealed gene expression changes of two different cell lines.

overall_design: Human oral squamous cell carcinoma (HSC-4, OSC-19) gene expression was measured.

first: Momoko

last: Yoshikawa

first: Hideyuki

last: Saya


title: The X-linked H3K27me3 demethylase Utx is required for embryonic development in a sex specific manner [Agilent array data]

status: Public on Aug 01 2012

city: Cambridge

first: Albert

middle: W

last: Cheng

state: MA

address: Room 453, 9 Cambridge Center

country: USA

institute: Whitehead Institute

summary:
Embryogenesis requires the timely and coordinated activation of developmental regulators.  It has been suggested that the recently discovered class of histone demethylases (UTX and JMJD3) that specifically target the repressive H3K27me3 modification play an important role in the activation of “bivalent” genes in response to specific developmental cues. To determine the requirements for UTX in pluripotency and development, we have generated Utx null ES cells and mutant mice. The loss of UTX had a profound effect during embryogenesis. Utx null embryos had reduced somite counts, neural tube closure defects and heart malformation which presented between E9.5 and E13.5. Unexpectedly, homozygous mutant female embryos were more severely affected than hemizygous mutant male embryos. In fact, we observed the survival of a subset of UTX-deficient males which were smaller in size and had reduced life-span. Interestingly, these animals were fertile with normal spermatogenesis. Consistent with a mid-gestation lethality, UTX null male and female ES cells gave rise to all three germ layers in teratoma assays although sex-specific differences could be observed in the activation of developmental regulators in embryoid body assays. Lastly, ChIP-seq analysis revealed an increase in H3K27me3 in Utx null male ES cells. In summary, our data demonstrate sex-specific requirements for this X-linked gene while suggesting a role for UTY during development.

Keywords: Expression profiling by array

overall_design:
Four-condition experiment, Wt (V6.5) ES vs. RA-treated Wt (V6.5) ES cells; UtxKO ES vs RA-treated UtxKO ES cells.

This Series represents the Agilent microarray data only (not ChIP-Seq).

first: Grant

last: Welstead

first: Rudolf

last: Jaenisch


title: oocyte miRNA profiling by array

status: Public on Sep 04 2012

city: Setagaya

first: Maki

last: Kusumi

state: Tokyo

department: Maternal-Fetal Biology

institute: National Research Institute for Child Health and Development

summary: This study compares miRNA expression profiles in mouse oocytes as young oocytes vs aged oocytes, and growing oocytes vs small oocytes from primordial follicles.

overall_design: Oocytes were derived from the ovary of young (6-8 week-old) C57BL/6 mice and aged (41-43 week-old) mice and pooled according to whether they were 20 to 50 um or 60 to 80 um in diameter. Of oocytes with the diameter of more than 60um, oocyte from young mice are called ‘young oocytes’ and those from aged mice near the end of their reproductive life span are called ‘aged oocytes’ to analyze the miRNA profiling associated with aging. They were also each called ‘small oocytes’ or ‘large oocytes’ from the size of 60um so as to investigate miRNA profiling associated with growing. Total RNA from oocytes was isolated using mirVana miRNA Isolation Kit (Applied Biosystems). MiRNA expression was profiled using Agilent's Mouse miRNA Microarray Kit (G4472A) annotated against the Sanger miRBASE 10.1 database of miRNAs. This miRNA microarray was provided by Agilent Technologies (Santa Clara, CA). Each sample was run in duplicate.


title: Gene expression profiles in glucokinase activator (GKA)-treated pancreatic islets

status: Public on Oct 02 2012

city: Yokohama

first: Jun

last: Shirakawa

state: Kanagawa

address: 3-9, Fuku-ura, Kanazawa-ku

institute: Yokohama City university

summary: To identify the target genes of glucokinase activator (GKA) in islet, GKA-induced gene expression in mouse pancreatic islets was measured at 24 hours after treatment of 30 microM GKA or vehicle.


title: Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation

status: Public on Aug 03 2012

city: Rockville

first: Bryan

last: Frank

state: MD

address: 9704 Medical Center Drive

department: Dept of Infectious Diseases

institute: The J. Craig Venter Institute

summary: We used genome-scale modeling and multi-omics (transcriptomics, proteomics, and metabolomics) analysis to assess metabolic features that are critical for macrophage activation. We constructed a genome-scale metabolic network for the RAW 264.7 cell line to determine metabolic modulators of activation. Metabolites well-known to be associated with immunoactivation (glucose and arginine) and immunosuppression (tryptophan and vitamin D3) were among the most critical effectors. Intracellular metabolic mechanisms were assessed, identifying a suppressive role for de-novo nucleotide synthesis. Finally, underlying metabolic mechanisms of macrophage activation are identified by analyzing multi-omic data obtained from LPS-stimulated RAW cells in the context of our flux-based predictions.

overall_design: Two condition (flagellin and LPS) time course exposure of RAW 264.7 cell line at 1, 2, 4, and 24 hours. Two replicates for each condition and time point. All conditions compared to a pool of untreated cells at a 0 hour time point.

first: Aarash

last: Bordbar

first: Monica

middle: L

last: Mo

first: Ernesto

middle: S

last: Nakayasu

first: Alexandra

middle: C

last: Schrimpe-Rutledge

first: Young-Mo

last: Kim

first: Thomas

middle: O

last: Metz

first: Marcus

middle: B

last: Jones

first: Richard

middle: D

last: Smith

first: Scott

middle: N

last: Peterson

first: Daniel

middle: R

last: Hyduke

first: Joshua

last: Adkins

first: Bernhard

last: Palsson


title: LIN28A-mediated regulation of microRNA biogenesis in mouse embryonic stem cell (A3-1) [Agilent]

status: Public on Oct 25 2012

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

summary: LIN28A is a highly-conserved RNA-binding protein which is known to be involved in embryonic development, stem cell maintenance and proliferation. LIN28A is expressed in various types of cancer, and they are associated with advanced tumor malignancy. In embryonic stem cell, LIN28A specifically binds to let-7 precursors to suppress biogenesis of the let-7 microRNA family. In addition, LIN28A was reported to bind several mRNAs such as Oct4, cyclin A/B and histone H2A to activate their translation. For comprehensive understanding of the interaction between LIN28A and their target RNAs, we exploited UV-crosslinking and immunoprecipitation (CLIP) to capture their in vivo binding to target RNAs. LIN28A-binding RNAs were identified in a mouse embryonic stem cell line using multiple monoclonal and polyclonal antibodies. The result shows that LIN28 preferentially binds to let-7 precursors through GGAG binding motif, which is consistent with our previous results. We also identified that LIN28A binding is enriched in a certain subset of mRNAs. To understand the function of the novel LIN28A-mRNA binding, we carried out ribosome profiling from LIN28A-depleted mouse embryonic stem cells.

overall_design: Examination of miRNA level in embryonic stem cell treated with siRNA for GFP or for Lin28a

first: Minju

last: Ha

first: V


title: Phf19 links methylated lysine 36 of histone H3 to regulation of Polycomb activity

status: Public on Oct 04 2012

city: Barcelona

first: Luciano

last: Di Croce

address: Dr. Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation

summary: Gene expression profile in control (shCTR) and Phf19 depleted (sh4) mouse embryonic stem cell  untreated or treated 72 hr with 1 μM retinoic acid (72 RA).

overall_design: 4 samples, each one contains four biological replicas, except for ES-sh4_72hr RA which contains 3 replicas

first: Lluis

last: Morey


title: Tet2 facilitates the de-repression of myeloid target genes during C/EBPa induced transdifferentiation of pre-B cells

status: Public on Jul 27 2012

first: Eric

middle: M.

last: Kallin

state: Barcelona

address: C/ Dr. Aiguader, 88

department: Differentiation and Cancer

institute: Center for Genomic Regulation

summary: Tet2 is an enzyme that hydroxylates methylated cytosines and has been implicated in hematopoietic differentiation and the formation of myeloid malignancies when mutated. An ideal system to study the role of Tet2 in myelopoeisis is C/EBPa induced transdifferentiation of pre-B cells into macrophages, where many myeloid genes become rapidly upregulated. Here we found that C/EBPa binds to upstream regions of Tet2 and that the gene becomes activated. Tet2 knockdowns impaired the upregulation of macrophage markers as well as phagocytic capacity, suggesting that the enzyme is required for both early and late stages of myeloid differentiation. A slightly weaker effect was seen in primary cells with a Tet2 ablation. Expression arrays of transdifferentiating cells with Tet2 knockdowns permitted the identification of a small subset of myeloid genes whose upregulation was blunted. Activation of these target genes was accompanied by a rapid increase of promoter hydroxy-methylation. Our observations indicate that Tet2 helps C/EBPa to rapidly de-repress myeloid genes during the conversion of pre-B cells into macrophages.

overall_design: Gene expression was measured in a control and Tet2kd mouse preB cell line (called Haftl) harboring an inducible form of C/EBPa. Expression was measured in starting cells and cells induced to transdifferentiate into macrophage-like cells for 24 hours. Technical duplicates for each treatment and time were assayed.

middle: M

last: Graf


title: Zebrafish whole embryos at 36 hpf treated with DMSO or 5uM 11,12-EET

status: Public on Jul 28 2012

city: Boston

first: Anthony

middle: Dominc

last: DiBiase

address: KFRB, 1 Blackfan St, Suite 8216

department: Hem/Onc

institute: Children's Hospital Boston

summary:
In our previous study, we found zebrafish embryos treated with 5uM 11,12-EET (epoxyeicosatrienoic acid) had increased stem cell marker, runx1, expression in the AGM. EET also induced ectopic runx1 expression in the tail. To systematically study how EET regulates gene expression, we performed microarray analysis on EET-treated embryos.
Zebrafish whole embryos were synchronized at fertilization. Embryos were grown at 28 degree overnight. 25 embryos per group were treated with DMSO or 5uM 11,12-EET starting from 24 hpf (hour post fertilization) until 36 hpf at 28 degree. The triplicates were from three different clutches of embryos, and split into DMSO v.s. EET for each clutch.

overall_design: EET vs. DMSO

first: P

last: Li

first: Yi

last: Zhou


title: Oxidative burden and mitochondrial dysfunction in a mouse model of Rett syndrome

status: Public on Aug 31 2012

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: To identify the detailed molecular causes of the mitochondrial dysfunction, oxidative burden and more vulnerable redox balance in Rett mouse hippocampus, we screened for differential gene expression in the hippocampal CA1 subfield of adult male mice. A whole mouse genome microarray was performed to assess, whether key enzymes of the mitochondrial respiratory chain or major cellular radical scavenging enzymes are affected in this MeCP2-deficient mouse model of Rett syndrome.

overall_design: Comparison of gene expression between male wildtype mice (Mecp2+/y) and mice lacking the MECP2 gene (Mecp2-/y) [B6.129P2(C)-Mecp2tm-1-1Bird (Guy et al. 2001, Nat. Genet. 27: 322-326)]. In total, 9 mice of each genotype were analyzed. The mRNA of groups of 3 animals was pooled to generate 3 independent biological samples, and finally three microarrays were run for each genotype.

first: Emanuel

last: Großer

first: Marc

last: Fischer

first: Belinda

last: Hildebrandt

first: Christiane

last: Menzfeld

first: Steffen

last: Vogelgesang

first: Till

middle: U

last: Manzke

first: Lennart

last: Opitz

last: Salinas-Riester

first: Michael

last: Müller


title: Gene expression induced by 5SA-Atoh1 in DLD1 cells

status: Public on Apr 11 2012

city: Bunkyo-ku

first: Kiichiro

last: Tsuchiya

address: 1-5-45 Yushima

institute: Tokyo Medical and Dental University

summary: To investigate the function of Atoh1 in colon cancer cells. We have employed whole genome microarray expression profiling as a discovery platform to iedntify the gene expression induced by Atoh1 in colon cancer cells.

overall_design: Mutated Atoh1 (5SA-Atoh1) replaced 5 serine residues to Alanin  for the protein stabilization were expressed in human colon cancer cellline; DLD1 cells. Triplicated RNAs were generated from GFP expressing DLD1 cells and 5SA-Atoh1 expressing DLD1 cell, respectively.


title: Comparison of Sox9-EGFP cell type transcriptomes during irradiation-induced crypt regeneration

status: Public on Jun 18 2012

city: Chapel Hill

first: P. Kay

last: Lund

state: NC

address: 6336 MBRB CB 7545 111 Mason Farm Road

department: Cell and Molecular Physiology

institute: UNC at Chapel Hill

summary: Transcriptional profiling of intestinal epithelial cells expressing either Negative, Sublow, Low or High levels of the Sox9-EGFP reporter transgene FACS-isolated from jejunum of non-irradiated mice or at 5 days after 14Gy abdominal irradiation.

overall_design: 4 distinct cell populations, FACS-isolated based on expression levels of the Sox9-EGFP reporter transgene (Sox9-EGFP Negative, Sublow, Low and High cells); 2 conditions: Non-irradiated vs Irradiated; Biological replicates: 7 independent non-irradiated mice and 3 independent irradiated (studied at day 5 post-irradiation) mice

middle: K

first: Laurianne

last: Van Landeghem

first: Amanda

middle: T

last: Mah


title: Investigation of the gene expression pattern of human hepatocellular carcinoma (HCC) infiltrating γδT cells

status: Public on Jun 05 2012

city: Shanghai

first: Yong

last: Yi

address: 180 Fenglin Road

institute: Liver Cancer Institute

summary: Fresh human HCC tissue and paired pertumor liver tissue were acquired, isolation of the infiltrating lymphocytes was conducted by discontinous density gradient centrifugation in Percoll. After removal of dead cells and incubation with components of TCRγ/δ isolation kit (Mitenyi Biotec), γδ T cells were positively selected from the single-cell suspension using autoMACS Separator (Miltenyi Biotec) with recommended programs. Then we employed whole genome microarray expression profiling as a discovery platform to indentify genes which are differentially expressed between HCC-derived and paired peritumor-derived γδT cells.

overall_design: Ten paired fresh HCC tissue and peritumor liver tissue were acquired and subjected to γδT cells isolation.

first: Shuang-jian

last: Qiu


title: Array-based transcriptional analysis of Clostridium sporogenes during germination, cell outgrowth and vegetative life

status: Public on Jun 13 2012

city: Cremona

first: Daniela

last: Bassi

state: CR

address: via Milano 24

department: Istituto di Microbiologia

country: Italy

institute: Università Cattolica del Sacro Cuore

summary:
The members of the genus Clostridium, such as the other spore-forming anaerobic bacteria, have a complex and strictly regulated life-cycle but very little is known about genetic pathways involved at different stages. Clostridium sporogenes, Gram positive bacterium usually involved in food spoilage and frequently isolated from late blowed cheese is genetically indistinguishable from proteolytic Clostridium botulinum and is the non-neurotoxigenic counterpart often used as exemplar for the toxic subtypes. In this work we have performed a microscopy study combined with a custom array-based analysis of C. sporogenes cycle, from dormant spores to early stationary phase.
 We identified in spores a total of 211 transcripts validating the ipothesis that mRNAs are abundant and strikingly different from those present in growing cells. The spores transcripts included genes responsible of different life-sustaining functions, suggesting the theory of transcripts entrapment or of a basic poly-functional genes activation for future steps. In addition, after three hours from the beginning of the germination process, a 20% of the total up-regulated genes were temporally expressed in germinating spores. The vegetative condition appears to be the more active in terms of gene transcription and protein synthesis and also genes for germination and sporulation factors seem to be expressed at this point. These results suggest that spores are not silent entities and a wider knowledge about genetic pathways involved in Clostridium life cycle could be of help for a better understanding also of pathogenic clostridia types.

overall_design: RNA was isolated from spores, germinating spores (3h), outgrowth/transitional mid-log vegetative cells and early stationary cells of Clostridium sporogenes UC9000 previously isolated from milk. There were 3 biological replicates (independent cultures) for each condition. Probes corresponding to 3400 genomic CDSs of C. botulinum A  ATCC 3502 were synthesized in three replicates randomly distributed on the chip.

first: Fabrizio

last: Cappa

first: Piersandro

last: Cocconcelli


title: Brain transcriptome variation among behaviorally distinct strains of zebrafish (Danio rerio)

status: Public on Jun 15 2012

city: N. Dartmouth

first: Robert

last: Drew

address: 285 Old Westport Road

department: Biology

institute: University of Massachusetts Dartmouth

summary:
Domesticated animal populations often show profound reductions in predator avoidance and fear-related behavior compared to wild populations.  These reductions are remarkably consistent and have been observed in a diverse array of taxa including fish, birds, and mammals.  Experiments conducted in common environments indicate that these behavioral differences have a genetic basis.  In this study, we quantified differences in fear-related behavior between wild and domesticated zebrafish strains and used microarray analysis to identify genes that may be associated with this variation.
Compared to wild zebrafish, domesticated zebrafish spent more time near the water surface and were more likely to occupy the front of the aquarium nearest a human observer.  Microarray analysis of the brain transcriptome identified high levels of population variation in gene expression, with 1,749 genes significantly differentially expressed among populations.  Genes that varied among populations belonged to functional categories that included DNA repair, DNA photolyase activity, response to light stimulus, neuron development and axon guidance, cell death, iron-binding, chromatin reorganization, and homeobox genes.  Comparatively fewer genes (112) differed between domesticated and wild strains with notable genes including gpr177 (wntless), selenoprotein P1a, synaptophysin and synaptoporin, and acyl-CoA binding domain containing proteins (acbd3 and acbd4).
Microarray analysis identified a large number of genes that differed among zebrafish populations and may underlie behavioral domestication.  Comparisons with similar microarray studies of domestication in rainbow trout and canids identified sixteen evolutionarily or functionally related genes that may represent components of shared molecular mechanisms underlying convergent behavioral evolution during vertebrate domestication.  However, this conclusion must be tempered by limitations associated with comparisons among microarray studies and the low level of population-level replication inherent to these studies.

overall_design: RNA was extracted from the brains of fish from four behaviorally distinct strains of zebrafish and hybridized on Affymetrix microarrays.  Brains from 2-5 individual fish of the same sex were pooled and homogenized together, for a total of two biological replicate pools per sex per strain (16 microarrays total).

middle: E

first: Matthew

last: Settles

first: Erin

middle: J

last: Churchill

first: Shayna

last: Williams

first: Soniya

last: Balli

first: Barrie

last: Robison


title: JMJD3 is needed to regulate TGF beta responsive genes.

status: Public on May 01 2012

first: Conchi

last: EI

address: Baldiri Reixac 15

institute: IBMB

summary: Neural development requires crosstalk between signaling pathways and chromatin. In this study, we demonstrate that neurogenesis is promoted by an interplay between the TGFβ pathway and the H3K27me3 histone demethylase (HDM) JMJD3. Genome-wide analysis showed that JMJD3 is targeted to gene promoters by Smad3 in neural stem cells (NSCs) and is essential to activate TGFβ-responsive genes. In vivo experiments in chick spinal cord revealed that the generation of neurons promoted by Smad3 is dependent on JMJD3 HDM activity. Overall, these findings indicate that JMJD3 function is required for the TGFβ developmental program to proceed

overall_design: Mouse neural stem cells (NSC) control and JMJD3 knock down (shctrl and shJMJD3) were treated with the vehicle (-TGFb) or TGFbeta 5ng/ml (+TGFb) for 2.5h. Three replicates were performed for each point. And all of them were use it to posterior analysis.

first: Conch

last: Estaras

first: Marian

last: Martinez-Balbas


title: Gene expression profile of zebrafish renal collecting ducts

status: Public on Aug 24 2012

city: Shinjuku-ku

first: Isao

last: Kobayashi

address: 35 Shinanoma-chi

department: Cell Differentiation

institute: Keio University

summary: The kidney is the main hematopoietic organ in teleost fish. Various stages of hematopoietic cells were observed in the interstitial tissue of the kidney. We recently demonstrated that zebrafish hematopoietic stem cells (HSCs) expressing jam1a were specifically localized along the renal collecting ducts in the adult kidney. Interestingly, most of HSCs invaded into the intracellular spaces of the epithelium in collecting ducts, suggesting that collecting ducts provide a specific microenvironment for HSCs. In order to identify niche factors in collecting ducts, we performed microarray analysis in collecting ducts isolated from the Tg(jam1a:EGFP) zebrafish kidney.

overall_design: Collecting ducts were isolated from Tg(jam1a:EGFP) zebrafish under a fluorescent microscope. To examine the effect of X-ray irradiation on the niche, collecting ducts were isolated from the fish irradiated with 25Gy. The whole kidney tissues were also used for a comparison analysis. Two independent replicates consisting of five zebrafish were prepared for each sample.

first: Jingjing

first: Toshio

last: Suda


title: The class-specific BCR tonic signal modulates lymphomagenesis in a transgenic model of c-myc transgene deregulation.

status: Public on Feb 01 2012

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: c-myc-3'RR mice developed Burkitt like lymphoma (IgM and IgD positive cells). We wished to study lymphomagenesis in mice carrying a modified B cell receptor with a higher level of tonic signal. The c-myc-3'RR transgene was introduced in a background with an IgH mutation that replaces IgM with IgA expression. Lymphoma arising in double mutant animals mostly carried the phenotype of activated cells, often expressing CD43, and in 10% of cases carrying a plasma cell phenotype. BCR tonic signal appears as a direct modulator of B cell malignancy phenotype.

overall_design: Burkitt lymphoma (BL) from 4 c-myc-3'RR mice, anaplastic (ANA) lymphoma from 4 c-myc-3'RR mice, CD43 negative lymphoma from 4 c-myc-IgA mice and CD43 positive lymphoma from 4 c-myc-IgA mice were investigated.

first: Yves

last: Denizot

first: P

last: Barbry

first: K


title: LPS treatment of RAW2647 macrophages

status: Public on Jan 24 2012

first: John

last: Braisted

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

summary: Macrophages are central players in the immune response and manifest divergent phenotypes to control inflammation and innate immunity. Signaling factors are traditionally recognized as the stimuli governing macrophage functions. In recent years, metabolism’s importance has been reemphasized as critical signaling and regulatory pathways of human diseases and processes, ranging from cancer to aging, often converge on metabolic responses. In this study, we assessed metabolic features that play critical roles in macrophage function. We constructed a genome-scale metabolic network for the RAW 264.7 cell line, an oft-used in vitro model. We determined immunomodulators of activation. Metabolites well-known to be associated with immunoactivation (e.g., glucose and arginine) and immunosuppression (e.g., tryptophan and vitamin D3) were amongst the most critical effectors. Intracellular metabolic mechanisms linked critical suppressive effectors were assessed, identifying a suppressive role for nucleotide synthesis. Furthermore, we demonstrate how metabolic mechanisms of macrophage activation can be identified by analyzing multi-omic data of LPS-stimulated RAW cells in the context of our predictions. Our study demonstrates metabolism’s role in regulating macrophage activation may be greater than previously anticipated.

overall_design:
The RAW 264.7 (ATTC) cell line was stimulated for 24 hours with LPS. Treated cells were washed twice with Dulbecco’s PBS and harvested for high-throughput analyses.
Labeled cDNA was prepared as described (Jones et al. 2010). A mixture Cy3-labeled control cDNA and Cy5-labeled were hybridized to Agilent Mouse GE 4x44K v2 Microarray (Agilent Technologies) and processed. Image analysis and intra-chip normalization were performed with Feature Extraction 9.5.3.1 (Agilent). Data were analyzed with MeV (tm4.org) or with custom python scripts

first: Marcus

last: Jones

first: Scott

last: Peterson

first: Joshua

last: Adkins

first: Bernhard

last: Palsson

first: Aarash

last: Bordbar


title: Expression data from early zebrafish embryos

status: Public on Apr 09 2012

first: Ting

last: Xu

address: No. 1239 Road Siping

institute: Tongji University

summary: In the early zebrafish embryo, the developing genome profile can be interfered with by exposure to pentachlorophenol, and some specific sets of genes are up-regulated or down-regulated. We used microarrays to detail the global program of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: Zebrafish embryos were selected at successive stages of early development for RNA extraction and hybridization on Affymetrix microarrays. We selected embryos exposed to 20 ug/L pentachlorophenol (C1), 50 ug/L pentachlorophenol (C2),  and deionized water control (C3) at the gastrula stage (about 8hpf).

first: Jing

last: Zhao


title: mRNA microarray analysis on young adult zebrafish exposed to benzene, toluene, formaldehyde and a BTF mix

status: Public on Dec 31 2011

city: seoul

first: jinhee

last: choi

address: 90 Jeonnong-dong, Dongdaemun-gu

department: College of Urban Science

institute: University of Seoul

summary: In order to evaluate the identification of genes and pathways, the global gene expression profiles were assessed in response to three chemicals (benzene (B), toluene (T), formaldehyde (F)) individually and as a BTF mix  on zebrafish. We performed whole genome DNA microarray experiments with subsequent quantitative analysis conducted on selected genes.

overall_design: We used synchronized zebrafish populations exposed to B, T, F or a BTF mix, and whole genome microarrays to screen for global changes in zebrafish transcription profiles. Young adults of zebrafish were selected  for RNA extraction and hybridization on Affymetrix microarrays.

first: Jinhee

last: Choi

first: Myung-Chul

last: Lee

first: Tae-Soo

last: Chon


title: Regulation of gene expression by mir-493

status: Public on Apr 01 2012

city: Chuo-ku

first: koji

last: okamoto

address: 5-1-1 Tsukiji

department: Division of Cancer Differentiation

institute: National Cancer Center Research Institute

summary: To identify genes that are inhibited by mir-493, we have employed whole genome microarray expression profiling as a discovery platform to identify genes that are down-regulated after expression of mir-493.   HCT116 colon cancer cells were transfected with control or mir-493 mimic for 24 hrs, and total RNA extracted from the transfected cells were labeled with Cy3 and used for microarray analyses with Agilent Whole Human Genome Oligo Microarrays.

overall_design: gene expression in HCT116 cells was measured after transfection of control or mir-493.  Three independent experiments were performed for each transfection.

first: Koji

last: Okamoto


title: Expression data from Ezh2-null erythrocyte/megakaryocyte progenitor (MEP)

status: Public on Dec 27 2011

city: Chiba

first: ATSUSHI

last: IWAMA

address: 1-8-1 Inohana, Chuo-ku

department: Department of Cellular and Molecular Medicine

institute: Graduate School of Medicine, Chiba University

summary: The polycomb group (PcG) proteins function in gene silencing through histone modifications. They form chromatin-associated multiprotein complexes, termed polycomb repressive complex (PRC) 1 and PRC2. These two complexes work in a coordinated manner in the maintenance of cellular memories through transcriptional repression of target genes. EZH2 is a catalytic component of PRC2 and trimethylates histone H3 at lysine 27 to transcriptionally repress the target genes. PcG proteins have been characterized as general regulators of stem cells, but recent works also unveiled their critical roles in cancer.

overall_design: Wild type and Ezh2 null MEP from fetal liver and adult bone marrow

first: Atsushi

last: Iwama

first: Makiko

last: Mochizuki-Kashio


title: Changes in gene expression from postnatal (3 wk and 4 wk) to young adult (8 wk) male and female mouse liver (Mus musculus)

status: Public on Apr 04 2012

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: Microarray analysis of male and female CD-1 mouse liver was carried out at 3, 4, and 8 wk of age to elucidate developmental changes in gene expression from the pre-pubertal period to young adulthood.  A large number of sex-biased and sex-independent genes showed significant changes during this developmental period.  Notably, sex-independent genes involved in cell cycle, chromosome condensation, and DNA replication were down regulated from 3 wk to 8 wk, while genes associated with metal ion binding, ion transport and kinase activity were up regulated.  A majority of genes showing sex differential expression in adult liver did not display sex differences prior to puberty, at which time extensive changes in sex-specific gene expression were seen, primarily in males.  Thus, in male liver, 76% of male-specific genes were up regulated and 47% of female-specific genes were down regulated from 3 to 8 wk of age, whereas in female liver 67% of sex-specific genes showed no significant change in expression.  In both sexes, genes up regulated from 3 to 8 wk were significantly enriched (p < E-76) in the set of genes positively regulated by the liver transcription factor HNF4α, as determined in a liver-specific HNF4α knockout mouse model, while genes down regulated during this developmental period showed significant enrichment (p < E-65) for negative regulation by HNF4α. Significant enrichment of the developmentally regulated genes in genes subject to positive and negative regulation by pituitary hormone was also observed. Nine sex-specific transcription factors showed pubertal changes in expression and may contribute to the developmental changes that onset after 3-4 wk.  Overall, the observed changes in gene expression during postnatal liver development reflect the deceleration of liver growth and the induction of specialized liver functions, with widespread changes in sex-specific gene expression primarily occurring in male liver.

overall_design: Liver RNA isolated from the following six groups of CD-1 mice was used in the present study:  3 wk old male (M) mice (n = 10; 5 per each pool) and female (F) mice (n = 10; 5 per each pool); 4 wk old male mice (n = 12; 6 per each pool) and female mice (n = 12; 6 per each pool); 8 wk old male mice (n = 12; 6 per each pool) and female mice (n = 12; 6 per each pool).  These RNA pools were used in seven separate sets of competitive hybridization experiments: 1) 3 wk M vs. 3 wk F; 2) 4 wk M vs. 4 wk F; 3) 8 wk M vs. 8 wk F; 4) 3 wk M vs. 8 wk M; 5) 4 wk M vs. 8 wk M; 6) 3 wk F vs. 8 wk F; 7) 4 wk F vs. 8 wk F.  Fluorescent labeling of RNA and hybridization of the Alexa 555-labeled (green) and Alexa 647-labeled (red) aRNA samples to Agilent Mouse Gene Expression 4x44k v2 microarrays (Agilent Technology, Palo Alto, CA; catalog # G4846A-026655) were carried out, with dye swapping for each of the seven hybridization experiments to eliminate dye bias.  Two microarrays, one for each mixed cDNA sample, were hybridized for each of the seven fluorescent reverse pairs, giving a total of 14 microarrays.

first: Tara

last: Conforto


title: Non-Overlapping Functions of the Polycomb group Cbx Family of Proteins in Embryonic Stem Cells

status: Public on Jan 06 2012

first: Luciano

last: Di Croce

address: Dr. Aiguader, 88

institute: Centre for Genomic Regulation

summary: Gene expression profile in control and Cbx7 depleted (shRNA#33) mouse embryonic stem cells and embryoid bodies at day 9

overall_design: 4 samples, each one contains four biological replicas, except for ES-shCtr which contains 3 replicas

first: Lluis

last: Morey


title: MicroRNA profiles of four developmentally related hematopoietic cell types isolated from the BM of B6 and D2 mice.

status: Public on Dec 15 2011

city: Groningen

first: Leonid

last: Bystrykh

state: Groningen

address: A. Deusinglaan 1

department: European Research Institute for the Biology of Ageing - ERIBA

country: Netherlands

institute: University Medical Center Groningen

summary: performed a genetic screen for microRNAs that are differentially expressed between LSK, LS−K+, erythroid and myeloid cells isolated from C57BL/6 and DBA/2 mice. This analysis identified 131 microRNAs that were differentially expressed between cell types and 15 that were differentially expressed between mouse strains. Of special interest was an evolutionary conserved miR-cluster located on chromosome 17 consisting of miR-99b, let-7e and miR-125a. All cluster members were most highly expressed in LSKs and down-regulated upon differentiation. In addition, these microRNAs were higher expressed in DBA/2 cells compared to C57BL/6 cells, and thus correlated with HSPC frequency. To functionally characterize these microRNAs, we overexpressed the entire miR-cluster 99b/let-7e/125a and miR-125a alone in BM cells from C57BL/6 mice. Overexpression of the miR-cluster or miR-125a dramatically increased day-35 CAFC activity and caused severe hematopoietic phenotypes upon transplantation. We showed that a single member of the miR-cluster, namely miR-125a, is responsible for the majority of the observed miR-cluster overexpression effects. Finally, we performed genome-wide gene expression arrays and identified candidate target genes through which miR-125a may modulate HSPC fate.

overall_design: Microarray-based microRNA profiling study was peformed of four developmentally related hematopoietic cell types isolated from the BM of B6 and D2 mice. Total RNA isolated from purified LSK multilineage cells, committed LS−K+ cells, erythroid TER-119+ cells and myeloid Gr-1+ cells was hybridized to Agilent microRNA arrays. Triplicates were generated for each of the 8 conditions (4 cell types, 2 mouse strains). From the final anaysis one replicate for B6 LS-K+ cells was removed based on PCA, therefore B6 Prog group consist of only 2 biological replicates.

first: Alice

last: Gerrits

first: Marta

middle: A

last: Walasek

first: Sandra

last: Olthof

first: Ellen

last: Weersing

first: Martha

last: Ritsema

first: Erik

last: Zwart

first: Ronald

last: van Os

middle: V

first: Gerald

last: de Haan


title: c-myc-3'RR/p53+/- mice lymphomas

status: Public on Jan 05 2012

first: Kevin

last: Lebrigand

summary: c-myc-3'RR mice prone to develop Burkitt lymphoma (BL) were crossed with p53+/- mice in order to obtain c-myc-3'RR/p53+/- mice. These mice develop a wider spectrum of lymphoma including BL, mantle cell lymphoma (MCL) and plasma cell lymphoma (PCL). Transcriptoma analysis of these lymphomas is investigated in these arrays.

overall_design: Four different plasma cell lymphoma (PCL1-4), three different mantle cell lymphoma (MCL1-4) and four different Burkitt lymphoma (BL1-4) were compared.

first: Yves

last: Denizot

first: P

last: Barbry

first: K


title: ARX transcription factor implicated in mental retardation and epilepsy

status: Public on Dec 22 2011

city: Brest

first: Gaelle

last: Friocourt

address: 46 rue Félix Le Dantec, CS51819

department: Molecular Genetics

institute: Inserm U613

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Comparison of gene expression between Arx-transfected N2a cells and cells transfected by the corresponding empty vector

summary: Genetic investigations of X-linked intellectual disabilities have implicated the ARX (Aristaless-related homeobox) gene in a wide spectrum of disorders extending from phenotypes characterised by severe neuronal migration defects such as lissencephaly, to mild or moderate forms of mental retardation without apparent brain abnormalities but with associated features of dystonia and epilepsy. Analysis of Arx spatio-temporal localisation profile in mouse revealed expression in telencephalic structures, mainly restricted to populations of GABAergic neurons at all stages of development. Furthermore, studies of the effects of ARX loss of function in humans and animal models revealed varying defects, suggesting multiple roles of this gene during brain development. However, to date, little is known about how ARX functions as a transcription factor and the nature of its targets. To better understand its role, we combined chromatin immunoprecipitation and mRNA expression with microarray analysis and identified a total of 1006 gene promoters bound by Arx in transfected neuroblastoma (N2a) cells and in mouse embryonic brain. Some of these promoters were enriched for a sequence very similar to a motif previously identified as Arx-binding motif and approximately 24% of Arx-bound genes were found to show expression changes following Arx overexpression or knock-down. Several of the Arx target genes we identified are known to be important for a variety of functions in brain development, including axonal guidance and synaptic plasticity and some of them suggest new functions for Arx. Overall, these results identified multiple new candidate targets for Arx and should help to better understand the pathophysiological mechanisms of intellectual disability and epilepsy associated with ARX mutations.

overall_design: N2a cells were transfected with either Arx or the corresponding empty vector. Eight different independent experiments were performed. The 16 samples were randomly distributes on the 2 expression microarrays.

first: Marie-Lise

last: Quillé

first: Edouard

last: Hirchaud

first: Solenne

last: Carat

first: Daniel

last: Baron

first: Rémi

last: Houlgatte

first: Gaëlle


title: The human Ewing's Sarcoma oncoprotein EWS-FLI1 causes Ewing's-type tumors in zebrafish

status: Public on Nov 01 2011

city: Dallas

first: James

middle: F

last: Amatruda

state: TX

address: 5323 Harry Hines Boulevard

department: Pediatrics and Molecular Biology

institute: University of Texas Southwestern Medical Center

summary:
The  fusion oncoprotein EWS-FLI1 arises from a t(11;22)(q24;q12) chromosomal translocation and causes Ewing's Sarcoma, a malignant bone tumor.  The mechanism whereby EWS-FLI1 transforms cells is unknown.  Somatic, mosaic expression of human EWS-FLI1 in zebrafish from the heat shock promoter [Tg(HSP:EWS-FLI1)] caused small round blue cell tumors (SRBCTs) similar to human Ewing's sarcoma.
We performed microarray studies comparing zebrafish SRBCTs to another tumor type, zebrafish malignant peripheral nerve sheath tumors (MPNSTs).  The results identify a conserved set of EWS-FLI1-regulated genes,and provide insight into the pathogenesis of Ewing's Sarcoma tumors.

overall_design: Zebrafish SRBCTs arising from somatic insertions of the EWS-FLI1 transgene were collected.  MPNSTs from non-transgenic fish of the same genetic background were collected in parallel.  RNA was prepared from all samples and hybridized to zebrafish-specific Affymetrix arrays.

first: Stefanie

last: Leacock


title: miRNA expression profile of follicular (FO) and marginal zone (MZ) B cells

city: Madrid

first: Almudena

last: Ramiro

state: Madrid

address: Calle Melchor Fernandez Almagro 3

institute: CNIO

summary: We have analyzed miRNA expression profile in FO and MZ B cells to identified differentially expressed miRNAs between this two subsets that could be potencially involved in the regulation of terminal B cell differentiation

overall_design: Spleens from CD19-Creki/+Dicerfl/+ and CD19-Creki/+Dicerfl/fl mice were collected and after erythrocyte lysis, splenocytes were stained with anti-B220, anti-CD21 and anti-CD23 antibodies. B220+CD21brightCD23+ (MZ) and B220+CD21+CD23bright (FO) B cell populations were sorted and total RNA of purified populations was extracted with TRIzol. miRNA microarray hybridations were performed on Mouse miRNA Microarray platform (Agilent Technologies).

first: L

last: Belver

first: V

middle: G

last: de Yebenes

first: A


title: Microarray analysis of 2,3,7,8-Tetrachlorodibenzo-p-dioxin Exposed Amputated Adult Zebrafish Heart Ventricles

status: Public on Nov 29 2011

city: Madison

first: Peter

middle: Jacobs

last: Hofsteen

state: WI

address: 777 Highland Ave

department: Pharmacy

institute: University of Wisconsin - Madison

summary:
The purpose of this experiment is to understand which transcripts are differentially expressed following exposure to TCDD.
We used microarrays to understand global changes in gene signal intensity

overall_design: Adult zebrafish (danio rerio) were injected (i.p) to vehicle control or TCDD (70 ng/g) one day prior to heart ventricle amputation.  A subset of fish were exposed but the hearts were not amputated.  Amputated hearts were collected at 6 hours post amputation and 7 days post amputation and processed for microarray analysis

first: Min-Sik

last: Kim


title: A zebrafish transgenic model of Ewing's Sarcoma reveals conserved mediators of EWS-FLI1 tumorigenesis


title: Microarray profile of p62P392L-regulated gene expression in RANKL and M-CSF stimulated normal human bone marrow derived non-adherent cells

status: Public on Oct 01 2011

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

summary:
Paget’s disease of bone (PDB) is a chronic focal skeletal disorder that affects 2-3% of the population over the age of 60. PDB is inherited as an autosomal dominant trait with genetic heterogeneity.  SQSTM1/p62 UBA domain mutation (p62P392L) is widely identified in PDB and has been shown to increase osteoclastogenesis. Further, environmental factors such as paramyxovirus are implicated in PDB and MVNP has been shown to induce Pagetic phenotype in osteoclasts. However, the molecular mechanisms underlying p62P392L and MVNP stimulation of osteoclast differentiation in PDB are unclear. We therefore determined p62P392L regulated gene expression profiling during osteoclast differentiation.
We identified 9.7% genes were upregulated (> 4-fold) in p62P392L transduced cells.  P62P392L mutant increased Integrin β3 (185 fold), integrin β5 (26 fold), IL-1α (11 fold), IL-6R (8 fold), CXCL-2 (7.5 fold), CXCL-3 (5 fold) compared to p62WT transduced cells. Furthermore, bone marrow mononuclear cells derived from patients with PDB showed high levels of SIRPβ1 mRNA expression compared to normal subjects.  Thus, p62P392L mutant regulated gene expression profiling during osteoclast differentiation provides new insights into molecular mechanisms and therapeutic targets to control elevated osteoclast activity in PDB.

overall_design: Total RNA isolated from normal human bone marrow mononuclear cells transduced with p62EV, p62WT, p62P392L retroviral expression vectors and stimulated with M-CSF and RANKL for 48 h were subjected to Agilent microarray (~26,000 genes) analysis. One replicate per treatment was hybridized.

first: Kumaran

last: Sundaram

first: Srinivasan

last: Shanmugarajan

first: Sakamuri

last: Reddy


title: Study of Mid-Blastula Transition of zebrafish embryos

status: Public on Oct 13 2011

first: Hui

last: Yu

address: No.100, Rd. Qinzhou

institute: Shanghai Center for Bioinformation Technology

summary:
Sox31 is a member of the zebrafish SoxB1 subfamily, and its expression can be detected both pre- and post-MBT. To distinguish the function of its maternal and zygotic transcripts, a splice blocking morpholino (Sb MO) was designed to interfere with the processing of new, zygotically synthesised mRNAs without interfering with mRNAs of maternal origin. Developmental arrest was observed in Sb MO which could not bypass MBT.
Mid-Blastula Transition (MBT) functions as a time window for zygotic genome activation and maternal mRNA degradation. To uncover whether the “zygotic up” and “maternal down” event during MBT is retarded in Sb morphants, we performed microarray experiment at the end of MBT (about 4.3 hours post fertilication/4.3 hpf) to compare mRNAs from Sb morphants and control embryos.

overall_design: In one experiment, three flocks of zebrafish eggs were injected with the Sox19b morpholino immediately after fertilization, while another three control populations were injected with placebo. At 4.3 hpf, these six flocks of embryos were sent for gene expression profiling with six Affymetrix Zebrafish Genome Arrays. In another experiment, we compared two wildtype embryo samples at 4h (post-MBT) against two wildtype samples at 2.5 h (pre-MBT).

first: Shengnan

last: Hu


title: The human Ewing's Sarcoma oncoprotein EWS-FLI1 causes developmental defects in zebrafish embryos

summary:
The  fusion oncoprotein EWS-FLI1 arises from a t(11;22)(q24;q12) chromosomal translocation and causes Ewing's Sarcoma, a malignant bone tumor.  The mechanism whereby EWS-FLI1 transforms cells is unknown.  We made germline transgenic zebrafish expressing human EWS-FLI1 under the control of the heat shock promoter.  Induction of EWS-FLI1 expression causes multiple defects in embryonic development.
We compared gene expression in control and transgenic EWS-FLI1 zebrafish.  The results identify a conserved set of EWS-FLI1-regulated genes, and provide insight into the pathogenesis of Ewing's Sarcoma tumors.

overall_design: We performed heat shock and isolated total RNA for microarray studies comparing wildtype AB strain zebrafish with transgenic zebrafish expressing human EWS-FLI1 [Tg(HSP:EWS-FLI1)].  RNA was biotin-lableled and hybridized to zebrafish-specific Affymetrix arrays.


title: Microarray profiling reveals broad and differential effects of RBM3 on miRNA expression.

status: Public on Nov 10 2011

city: La Jolla

first: Julie

last: Pilotte

state: CA

address: 10550 North Torrey Pines Rd, Sbr-14

department: Neurobiology

institute: The Scripps Research Institute

summary: MicroRNAs (miRNAs) are a family of short, noncoding RNAs that regulate translation of mRNAs by mechanisms involving the binding of complementary sequences.  The influence of miRNAs on the proteome and cellular events is extensive as they regulate an estimated 60% of the transcriptome and play key roles in differentiation, plasticity, circadian rhythm, immunity, and disease. The post-transcriptional biogenesis of most miRNAs involves a sequential cleavage process mediated by RNase III family enzymes.  Primary transcripts (pri-miRNAs) are first cleaved by Drosha in the nucleus to yield ~70nt hairpin precursors (pre-miRNAs).  These intermediates are transported to the cytoplasm where ~22mer dsRNAs are excised by Dicer.  Typically, one strand of the dsRNAs is inserted as a mature miRNA into the RNA-induced silencing complex (RISC), which contains members of the Argonaute (Ago) protein family that contribute to translational regulation.  Recent studies indicate that some RNA-binding proteins (RNA-BPs) can regulate discrete processing steps, differentially blocking or promoting the formation of specific miRNAs to control cellular proliferation and differentiation.  Elegant examples of this mechanism include the attenuation of let-7 biogenesis in embryonic stem cells by the pluripotency factor LIN28, and the selective enhancement of miR-18a biogenesis from a polycistronic transcript by hnRNPA1.

overall_design: Mature miRNA expression profiles in B104 cells were measured after siRNA-mediated knockdown of RBM3 in the B104 neuronal cell line. Mock treated B104 cells were used as a control. Experiments were replicated in duplicates.

first: J

first: E

last: Dupont-Versteegden

first: P

middle: W

last: Vanderklish


title: MicroRNA-mediated gene regulation plays a minor role in the transcriptomic plasticity of cold-acclimated Zebrafish brain tissue

status: Public on Oct 29 2011

city: beijing

first: zhonghua

last: dai

state: beijing

address: no.3 nan-yi-tiao

institute: chinese academy of sciences

summary: Growing evidence shows that miRNAs play essential roles in cell development by regulating the growth and differentiation of cell lineages. However, the potential roles of miRNA-mediated regulation in the environmental adaptation of organisms are largely unknown. To examine this potential regulatory capability, we systematically identified and compared the miRNAs of zebrafish brains under normal and cold-acclimated conditions using Solexa sequencing. We then predicted the potential target protein genes of the miRNAs and compared their gene expression profile patterns derived from microarray analyses. We defined a set of 25 differentially expressed miRNAs between the cold-acclimatized and normal zebrafish and predicted their functions based on the GO annotation of their targets. We also compared the expression of mRNAs and found that genes related to mRNA processing and response to stress were overrepresented among the up-regulated genes of the cold-stress condition. We analyzed the potential regulatory roles of these miRNAs on gene transcription patterns under low-temperature conditions using several statistical models and a novel, network-based approach. Our results indicate that these miRNAs, either individually or together and either directly or indirectly mediated by transcription factors (TFs), contribute a minor amount to the change in gene expression patterns under low-temperature conditions.

overall_design:
Adult zebrafish (Danio rerio) were raised under the normal laboratory breeding temperature (28C) or subjected subjected to cold (10C) stress. After 10 days of cold adaption, the brains of the zebrafish were dissected, and total RNAs were extracted from these brains. Expressional profiles of miRNAs and mRNAs were detected through high-throughput Solexa sequencing and microarray respectively.
This submission represents transcriptome component of study

first: Ruolin

last: Yang

first: Zhonghua

last: Dai

first: Sue

last: Chen

first: Liangbiao


title: Expression analysis of transgenic embryos carrying the mitf-BRAFV600E allele in the presence or absence of p53 function

status: Public on Mar 30 2011

city: New York

first: Richard

middle: Mark

last: White

state: NY

address: 1275 York Avenue MB 424

department: Cancer Biology & Genetics

institute: Memorial Sloan Kettering Cancer Center

summary:
Investigation of expression differences between melanomas harvested from MiniCoopR-GFP versus MiniCoopR-SETDB1 transgenic zebrafish
The embryos described in this study are further analyzed in a manuscript submitted for publication by White, et al.

overall_design: A 12 chip study comparing gene expression levels in 80hpf animals either WT (Tu), mitf-BRAFV600E, p53-/-, or mitf-BRAFV600E;p53-/- (double)


title: Serous ovarian benign tumor and type II carcinoma data set for expression and paracrine signaling investigation

status: Public on May 11 2011

city: Charlotte

first: Timothy

middle: L

last: Tickle

address: 9201 University City Blvd

department: Bioinformatics and Genomics

institute: University of North Carolina at Charlotte

summary:
A data set of normal epithelium, serous ovarian surface epithelial-stromal tumors (benign and type II malignancies), stroma distal to tumor, and stroma adjacent to tumor (50 samples total). Additional cel files are included which represent replicate sampling from patients, and cel files that failed quality control but may be bioinformatically interesting. Additional replicate or failed cel files were not included in the final analysis (and so these samples were not included in the matrix).
Background: Ovarian cancer is the most lethal gynecologic cancer in the United States. If caught in early stages, patient survival rate can reach 94%, when diagnosed at late stages survival rates drop to 28%. Correct diagnosis depends on the presence of definite symptoms: while ~90% of diagnosed ovarian cancers have symptoms, they tend to be unfocused and subacute. A definitive and early molecular signature of disease is thus desired. To further progress towards this goal, we present an Affymetrix™ human exon array data set measuring ovarian tumor expression, assembled using best practices. Method: Samples were collected from patients with benign and malignant (type II) serous ovarian surface epithelial-stromal tumors. Normal epithelium, tumor, stroma adjacent to tumor, and distal stroma were selected based on histopathology, and isolated using laser capture microdissection. Nugen products were used to perform random-primed mRNA amplification procedures (for full transcript capture) before hybridization to Affymetrix exon chips. Tumor expression and paracrine signaling was assessed using GC-RMA and a two-way Model I ANOVA. Single enrichment ontological analysis and gene network construction were performed to guide inferences about biological context. Results: In total, across 50 microarrays, ~270 million measurements were obtained. Based on comparisons to known ovarian cancer properties as established in molecular genetics literature, the initial analysis presented emphasizes data quality. Major trends between sample classes included: apical surface and tight junction activity, mitotic activity, benign tumor suppression, epithelial-mesenchymal transitioning, tumor oncogene activity, and paracrine signaling. A list of differentially expressed transcripts has been produced to enable rapid comparisons with published biomarker lists, but it is expected that detailed alternative transcript analysis will refine these predictions. Conclusions: A data set of 50 arrays, from carefully dissected serous ovarian surface epithelial-stromal tumors, has been produced, from which high quality measurements were obtained. While relatively small in number, this represents an important addition to the community pool of ovarian tumor samples, and the chosen platform enables bridging between 3' expression and exome sequencing data sets. This represents a significant contribution to the ovarian cancer genetics community.

overall_design: A total of 50 human ovary samples were used in analysis: 23 tissue samples laser capture microdissected from an ovary with a benign serous tumor (specifically 4 normal epithelium samples, 5 tumor samples, 6 stroma samples adjacent to the tumor, and 8 stroma samples distal of the tumor), and 27 tissue samples laser capture microdissected from an ovary with a malignant serous tumor (specifically 5 normal epithelium samples, 8 tumor samples, 7 stroma samples adjacent to the tumor, and 7 stroma samples distal of the tumor). Additional cel files were provided which, although were used in the quality control of the data set, were not used in the final experimental analysis. 8 replicates are included as cel files (1 from each cohort previously listed). 14 cel files were also included which failed quality control. Although the replicate and failed cel files were not used in the final analysis, they may still be interesting in other research.

first: Zahra

last: Baharani-Mostafavi

first: Jennifer

last: Weller

first: Kevin

last: Thompson

first: Christine

last: Richardson

first: Jayanthi

middle: S

last: Lea

first: Robert

last: Higgins

first: James

middle: B

last: Hall

first: David

last: Tait

first: M

last: Mostafavi


title: Musashi 2 is a regulator of the hematopoietic stem cell compartment identified by a retroviral insertion screen and knockout mice

status: Public on May 21 2011

city: Barcelona

first: Eric

middle: M.

last: Kallin

address: C/ Dr. Aiguader, 88

department: Differentiation and Cancer

institute: Center for Genomic Regulation

summary: We have used a retroviral integration screen to search for novel genes that regulate hematopoietic stem cell (HSC) function. One of the genes that conferred HSC dominance when overexpressed due to an adjacent retroviral insertion was Musashi 2 (Msi2), an RNA binding protein that can act as a translational inhibitor. A gene trap mouse model that inactivates the gene shows that Msi2 is more highly expressed in long term (LT) and short term (ST) HSCs as well as in lymphoid myeloid primed progenitors (LMPPs), but much less in intermediate progenitors and mature cells. Mice lacking Msi2 are fully viable up to more than a year but exhibit severe defects in primitive precursors, most significantly a reduction in the number of ST-HSCs and LMPPs and a decrease of leukocyte numbers, effects that are exacerbated with age. Cell cycle and gene expression analyses suggest that the main hematopoietic defect in Msi2 defective mice consists in a decreased proliferation capacity of ST-HSCs and LMPPs. In addition, HSCs lacking Msi2 are severely impaired in competitive repopulation experiments, being overgrown by wild type cells even when mutant cells were provided in excess. Our data indicate that Msi2 maintains the stem cell compartment mainly by regulating the proliferation of primitive progenitors downstream of LT-HSCs.

overall_design: RNA from 2 different cell populations (LSK cells and KIT+ cells) were analyzed for both wildtype and Msi2-/- null samples. Two technical replicates were analyzed for the KIT+ samples and three technical replicates were analyzed for the LSK samples.

first: Luisa

last: de Andrés-Aguayo

first: Florencio

last: Varas

middle: M

first: José

last: Infante

first: Wolfgang

last: Wurst

first: Thomas

last: Floss

last: Graf


title: Lack of hepatic response of microRNA in mice following chronic benzo(a)pyrene exposure (miRNA)

status: Public on Oct 19 2011

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

country: Canada

institute: Health Canada

summary:
Benzo[a]pyrene (BaP) is a very extensively studied prototypical polycyclic aromatic hydrocarbons (PAHs). Previous work in our laboratory showed no changes of microRNA (miRNA) expression in liver following a 3 days exposure to BaP, suggesting a lack of miRNA transcriptional responses to aryl hydrocarbon receptor agonists and/or DNA damage.  Here, we studied 25-week old male MutaTM Mouse exposed to 25, 50, and 75 mg/kg/day BaP by oral gavage for 28 consecutive days.  MAANOVA identified 110 differentially expressed genes (adjusted p < 0.05) with fold change greater than 1.5. The genes most affected included those involved in xenobiotic metabolism, phase II metabolizing enzymes, as well as the downstream targets of p53. Pathway specific RT-PCR was used to confirm the p53 response. A single significant increase in miRNA expression was identified (mir-34a and validated using the Qiagen miScript PCR system). This miRNA is known to be transcriptionally activated by p53. Ingestion of BaP leads to widespread changes in gene expression in mouse liver, with enrichment of genes involved in cell cycle arrest, DNA damage response, and apoptosis via the p53 pathway. In contrast, miRNA expression was relatively unaffected. Only miR-34a was significantly up-regulated, and may therefore play a critical role in the post-transcriptional regulation of p53 and/or its downstream targets.

Keywords: Agilent mouse 8 x 15K miRNA microarray system with miRNA complete labeling and hyb kit were used to assess miRNA expression in response to 25, 50, and 75 mg/kg BaP treatment

overall_design: RNA samples from 3 control and 5 mice per treatment group (24mg/kg, 50mg/kg, and 75mg/kg) containing 100 ng were labelled using Agilent?s miRNA complete labelling and Hyb Kit (Agilent Tech, Mississauga, ON, Canada).

first: Amal

middle: I

last: Malik

last: Lemieux

first: Paul

last: White

first: Carole

last: Yauk


title: Expression analysis of 24hpf zebrafish embryos treated with Leflunomide 6.5uM

first: Richard

summary: Identification of genes differentially regulated after treatment of zebrafish embryos from 50% epiboly to 24hpf with 6.5uM leflunomide

overall_design: A six chip study comparing expression levels of zebrafish embryos treated with leflunomide 6.5uM


title: Integrated cell-to-cell signaling networks regulate vertebrate axis formation and left-right asymmetry

status: Public on Feb 01 2011

city: Kansas City

first: Olivier

last: Pourquie

state: MO

address: 1000 E. 50th Street

institute: Stowers Institute for Medical Research

summary: Target genes of four signaling pathways (Notch, Fgf, Retinoic Acid [RA] and Wnt) are identified in the posterior presomitic mesoderm of 12 somite stage zebrafish embryos.

overall_design: Tissue samples from were dissected from wild-type (AB), transgenic or drug treated embryos, RNA is amplified and hybridized to arrays

first: Ertugrul

last: Ozbudak


title: Expression analysis of zebrafish melanoma and skin from the mitf-BRAFV600E;p53-/- line

summary:
Investigation of expression differences between skin and melanomas from a transgenic BRAFV600E zebrafish model of melanoma
The embryos described in this study are further analyzed in a manuscript submitted for publication by White, et al.

overall_design: A 15 chip study using RNA extracted from either WT zebrafish skin, mitf-BRAFV600E;p53-/- skin or mitf-BRAFV600E;p53-/- melanoma


title: Lack of de novo phosphatidylinositol synthesis leads to endoplasmic reticulum stress and hepatic steatosis in cdipt-deficient zebrafish

status: Public on May 09 2011

city: Pittsburgh

first: Carsten

last: Stuckenholz

state: PA

address: 3501 Fifth Avenue, Room 5065.5B

department: Department of Medicine, Division of Hematology and Oncology

institute: University of Pittsburgh

summary: cdipt is an essential gene in the synthesis of phosphatidylinositol (PtdIns) in the zebrafish, Danio rerio. The zebrafish mutant cdipt^hi559Tg (ZL782) carries a retroviral insertion which inactivates cdipt. Homozygous mutants exhibit hepatocellular endoplasmic reticulum (ER) stress and non-alcoholic fatty liver disease (NAFLD) pathologies at 5 days post fertilization (dpf). This study reveals a novel link between PtdIns, ER stress, and steatosis.

overall_design: We compared whole animal gene expression profiles of hi559 mutant larvae with phenotypically wild type larvae from a heterozygote incross in triplicate.

first: Prakash

last: Thakur

first: Nathan

last: Bahary


title: Expression data comparing wild-type and spt mutant zebrafish tissues at two developmental time points.

status: Public on Aug 18 2010

city: Fort Collins

first: Rachel

middle: Lockridge

last: Mueller

state: CO

address: 1878 Campus Delivery

institute: Colorado State University

summary: Mesoderm differentiation in zebrafish relies on a complex interaction between transcription factors and signaling pathways. Tbx16 is a t-box transcription factor involved in this interaction. Here, we examine downstream targets of tbx16 in the intermediate mesoderm at the 4/5-somite stage and tail mesoderm at the 21-somite stage by comparing wild-type tissues with tissues from the tbx16 mutant, spadetail (spt).

overall_design: We isolated meodermal tissues at two developmental time points (4/5-somite and 21-somite) from both wild-type and spt mutant tissues using dissection and FACS. We compared patterns of gene expression between the mutant and wild-type using Affymetrix zebrafish arrays. We also used GSEA to look for globally disrupted signaling pathways in the mutant at both developmental time points.

first: Cheng

last: Huang

first: Robert

middle: K

last: Ho


title: DNA methylation profiling of somatic tissues from normal and trisomic fetuses

status: Public on May 06 2011

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

institute: University of British Columbia

summary: The DNA methylation profiles in normal and abnormal fetal development were investigated using Illumina GoldenGate Methylation Cancer Panel I. DNA methylation status of 1505 CpG dinucleotides located in the regulatory regions of 807 genes was measured in 5 somatic tissues (brain, kidney, lung, muscle and skin) from second-trimester elective terminations of eight normal, five trisomy 21 and four trisomy 18 fetuses.

overall_design: Bisulfite-converted DNA from 60 samples were hybridized to the Illumina GoldenGate Methylation Cancer Panel I array.

first: Ryan

last: Yuen

middle: P

first: Michael

last: Kobor


title: Foxl1-Cre-marked Adult Hepatic Progenitors Have Clonogenic and Bi-Lineage Differentiation Potential - Differentiated vs Primary

status: Public on May 01 2011

city: Philadelphia

first: Jonathan

last: Schug

state: Pennsylvania

address: 12-156 Smilow Ctr Trans Research

department: School of Medicine

institute: University of Pennsylvania

summary: The winged helix transcription factor Foxl1 is a marker for progenitor cells and their descendants in the mouse liver in vivo. Here, we purify progenitor cells from Foxl1-Cre; RosaYFP mice and evaluate their proliferative and differentiation potential in vitro. Treatment of Foxl1-Cre; RosaYFP mice with 3,5-diethoxycarbonyl-1,4-dihydrocollidine diet led to an increase of the percentage of YFP-labeled Foxl1+ cells. Clonogenic assays demonstrated that up to 3.6% of Foxl1+ cells had proliferative potential. Foxl1+ cells differentiated into cholangiocytes and into hepatocytes in vitro, depending on the culture condition employed. Microarray analyses indicated that Foxl1+ cells express stem cell markers such as Prom1 as well as differentiation markers such as Ck19 and Hnf4a. Thus, the Foxl1-Cre; RosaYFP model allows for easy isolation of adult hepatic progenitor cells that can be expanded and differentiated in culture.

overall_design: In vitro Differentiated cells were compared to Primary cells

first: Soona

last: Shin

first: Gabriel

last: Walton

first: Reina

last: Aoki

first: Karrie

last: Brondell

first: Alan

last: Fox

first: Olga

last: Smirnova

first: Craig

last: Dorrell

first: Laura

last: Erker

last: Chu

first: Rebecca

last: Wells

first: Markus

last: Grompe

first: Linda

middle: E

last: Greenbaum

first: Klaus

middle: H

last: Kaestner


title: microRNA expression in LKS hematopoietic progenitors vs. total bone marrow

status: Public on Jul 09 2010

city: Pasadena

first: Aadel

last: Chaudhuri

address: 1200 E California Blvd

institute: Caltech

summary: Agilent chip was used to measure microRNA expression in the Lin- cKit+ Sca1+ bone marrow compartment and in total bone marrow.

overall_design: RNA was isolated by miRNeasy (Qiagen) from 1) Lin-cKit+Sca1+ cells, isolated from bone marrow using MACS column purification followed by fluorescent cell sorting, and 2) total Bone Marrow. Agilent microRNA microarray was run on these two samples.

last: O'Connell

middle: A


title: prdm1a mutant vs. wild type

status: Public on Mar 29 2011

city: Aurora

first: KRISTIN

last: ARTINGER

address: 12801 East 17th St

department: Craniofacial Biology

institute: University of Colorado Denver

summary: The PR domain containing 1a, with ZNF domain factor, gene prdm1a plays an integral role in the development of a number of different cell types during vertebrate embryogenesis, including neural crest cells, Rohon-Beard (RB) sensory neurons and the cranial neural crest-derived craniofacial skeletal elements.  To better understand how Prdm1a regulates the development of various cell types in zebrafish, we performed a microarray analysis comparing wild type and prdm1a mutant embryos and identified a number of genes with altered expression in the absence of prdm1a. Rescue analysis determined that two of these, sox10 and islet1, lie downstream of Prdm1a in the development of neural crest cells and Rohon-Beard neurons, respectively.  In addition, we identified a number of other novel downstream targets of Prdm1a that may be important for the development of diverse tissues during zebrafish embryogenesis.

overall_design: RNA was isolated from whole zebrafish embryos at 25hpf, three replicates each for wildtype and prdm1a mutant embryos.

first: Eugenia

last: Olesnicky

last: Hernandez-Lagunas

first: Kristin

last: Artinger


title: Comparison of expression data between control and Ovo1 morphant zebrafish embryos

status: Public on Apr 28 2010

city: Irvine

first: Sarah

last: Piloto

address: 4462 Natural Sciences II, Dept. Dev. and Cell Biology

department: Developmental and Cell Biology

institute: University of California, Irvine

summary:
A fundamental issue in cell biology is how migratory cell behaviors are controlled by dynamically regulated cell adhesion.
Vertebrate neural crest (NC) cells rapidly alter cadherin expression and localization at the cell surface during migration. Secreted Wnts induce some of these changes in NC adhesion and also promote specification of NC-derived pigment cells. Here, we show that the zebrafish transcription factor Ovo1 is a Wnt target gene that controls migration of pigment precursors by regulating the intracellular movements of N-cadherin (Ncad). Ovo1 genetically interacts with Ncad and its depletion causes Ncad to accumulate inside cells. Ovo1-deficient embryos strongly upregulate factors involved in intracellular trafficking, including several rab GTPases, known to modulate cellular localization of cadherins. Surprisingly, NC cells express high levels of many of these rab genes in the early embryo, chemical inhibitors of Rab functions rescue NC development in Ovo1-deficient embryos and overexpression of a Rab-interacting protein leads to similar defects in NC migration. These results suggest that Ovo proteins link Wnt signaling to intracellular trafficking pathways that localize Ncad in NC cells and allow them to migrate. Similar processes probably occur in other cell types in which Wnt signaling promotes migration.

overall_design:
Total RNA from control and Ovo1 morphant, sox10(7.2):gfp transgenic
embryos was isolated using Trizol reagent (Gibco/BRL) from 12 hpf embryos, when morphants first show NC defects. Experiments were performed in triplicate. RNA samples were processed as per manufacturer’s instructions (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetric, Inc., Santa Clara, CA, USA).

first: Thomas

middle: F

last: Schilling


title: Expression data from zebrafish depleted of Esco2

status: Public on Mar 01 2011

city: Dunedin

first: Julia

last: Horsfield

address: Cnr Hanover and Great King Streets

department: Pathology Department

country: New Zealand

institute: University of Otago

summary:
Our study in zebrafish is the first to use an animal model to understand the biology of the developmental disorder Roberts Syndrome (RBS). RBS is caused by mutations in the ESCO2 gene.
We have used morpholinos (MO) to knock down esco2 in zebrafish to better understand the pathology of this rare human syndrome. Our zebrafish model nicely phenocopies the developmental defects observed in RBS.

overall_design: RNA from esco2 morphants and control (injected with buffer only) zebrafish embryos collected at 24 hours post-fertilization (h.p.f.) and 48 h.p.f. was hybridized to Affymetrix microarrays (Gene Chip zebrafish genome arrays cat. no. 900488).  Four pools of 50 embryos for each genotype and time point were used as the RNA source, and RNA from each pool was hybridized independently such that the experiment had four biological replicates. Note that the chip for the 2nd replicate of the control embryos at 48 h.p.f. was faulty and the data is therefore not included.

first: M

last: Mönnich

first: L

last: McNoe

first: C

middle: G

last: Print

first: J


title: Detection of the up-regulated and down-regulated genes in stac mutant of zebrafish by cDNA microarray

status: Public on Jun 24 2010

city: Beijing

first: Xinyi

last: Zhao

address: Haidian District, Tsinghuayuan, No.1

department: Department of Biological Sciences and Biotechnology

institute: Tsinghua University

summary: We performed a zebrafish forward genetic screen by Tol2 mediated gene-trap approach and uncovered one mutant stac (The number of the transgenic line: B55) that showed severe cell-death distributed in the various brain and trunk in the homozygote embryos. Analysis of stac homozygous embryos demonstrates typical apoptosis. So it is necessary to analyze whether the apoptosis and cell cycle regulated signaling transductions are changed in the mutant, in order to provide valuable clues to some other species. And the up-regulated and down-regulated genes in the mutant compared to the WT were examined by zebrafish cDNA microarray.

overall_design: Total RNA was isolated from wild-type and mutant embryos in 24hpf and 30hpf and their quality was checked by the company with LAB-ON-A –CHIP system. The reverse transcription and Biotin-labeling has been done with the RNA as template. The hybridization and elution was performed with Affymetrix GeneChip® Zebrafish Genome Array. Both the control group (wild-type) and the experimental group (mutant) have two repeats.

first: Long

first: Tian

last: Tian

first: Yu

last: Zhang

first: Jingyuan

last: Tong

first: Xiaofeng

last: Zheng

first: Anming

last: Meng


title: Aberrant expression of microRNAs is associated to the progression of liver fibrosis

status: Public on Jan 12 2011

city: Tokyo

first: Nobuyoshi

last: Kosaka

address: 5-1-1, Tsukiji, Chuo-ku

department: Section for Studies on Metastasis

institute: National Cancer Center Research Institute

summary: Establish the miRNA expression profile between advanced liver fibrosis and liver without fibrosis in mice

overall_design: Administrate CCL4 or olive oil in mouse twice a week first 4 weeks per peritoneum and then administrated once a week next four weeks. Mice were sacrificed on 4, 6, and 8 weeks.

first: Yoshiki

last: Murakami

first: Katsuyuki

last: Hayashi

first: Masami

last: Tanaka


title: Cross-platform correlation analysis of global microRNA expression technologies

status: Public on Oct 18 2010

first: Andrew

last: Williams

summary:
Two reference pools comprised of different miRNA content were hybridized to four different miRNA microarray platforms (Agilent, LC Sciences, Exiqon and a homemade chip (generated from an Inviteogen Ncode probeset))
This dataset includes the reference samples on the Agilent miRNA array.

Keywords: miRNA

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Two reference pools were created from commercially available reference RNA (FirstChoice® mouse Total RNA including the small fraction (Catalogue # AM7800-AM7828, Ambion, Streetsville, ON)). Reference #1 contained equal parts of mouse testicle, ovary and 10-12 day embryo. Reference #2 contained liver, heart and lung. These references were hybridized to four different miRNA microarray platforms (two in two colour, two in one-colour, with 4 replicates each). Data from each platform were normalized by cyclic lowess and analysed by correlation analyses both within and between platforms.

first: Carole

last: Yauk


title: Sex- and gonad-biased gene expression in zebrafish

status: Public on Feb 20 2010

city: College Station

first: Clayton

last: Small

address: 3258 TAMU

department: Biology

institute: Texas A&M University

summary: A microarray study of sex- and gonad-biased gene expression was conducted to determine whether zebrafish demonstrate male-specific patterns consistent with those observed in other animals.  We identified a large number of genes (5899) demonstrating statistical differences in transcript abundance between male and female Danio rerio.  All sex-biases in gene expression were due to differences between testis and ovary, although differences between male and female body likely went undetected due to constraints imposed by study design and statistical criteria.  Male-enriched genes were more abundant than female-enriched genes, and the magnitude of expression bias for male-enriched genes was greater than that for female-enriched genes.  We also identified a large number of candidate reproductive genes based on elevated transcript abundance in testes and ovaries, relative to male body and female body, respectively.  Gene expression patterns in adult zebrafish from this study are consistent with the male-biased patterns typical of most animal taxa studied to date.  Recent zebrafish studies designed to address more specific questions have not reported the same findings, but major methodological and analytical differences across these studies could explain discrepancies.

overall_design:
Adult male and female zebrafish (3 each) were allowed to spawn, and were then separated for 5 days before gonad excision.  Total RNA was extracted from each individual's gonads, as well as the remainder of the body.  Each individual sample was hybridized to an Affymetrix Zebrafish Genome Array, for a total of 12 arrays (3 male body, 3 female body, 3 testis, 3 ovary).  Male-female comparisons as well as gonad-soma comparisons were performed.

Data were analyzed four different ways (GCOS, GC-RMA, dCHIP PM-only, and dCHIP PM-MM). Published results were based on a strict consensus across all 4 methods. A gene will be considered differentially expressed if the t-test corresponding to each of the 4 methods is significant (False Discovery Rate = 0.05).

first: Ginger

last: Carney

first: Qianxing

last: Mo

first: Marina

last: Vannucci

first: Adam

last: Jones


title: Transcription profile of zebrafish hand2 (hanS6 allele) mutant embryos at 19hpf

status: Public on Aug 03 2010

city: La Jolla

first: Zayra

middle: Viviana

last: Garavito-Aguilar

address: 9500 Gilman Drive #0347

department: Division of Biological Sciences

institute: University of California, San Diego

summary: Heart formation requires the fusion of bilateral cardiomyocyte populations as they move toward the embryonic midline.  The bHLH transcription factor Hand2 is essential for cardiac fusion; however, the effector genes that execute this function of Hand2 are unknown.  Here, we provide the first evidence for a downstream component of the Hand2 pathway that mediates cardiac morphogenesis.  Although hand2 is expressed in cardiomyocytes, mosaic analysis demonstrates that hand2 plays a non-autonomous role in regulating cardiomyocyte movement.  Gene expression profiles reveal heightened expression of fibronectin 1 (fn1) in hand2 mutant embryos.  Reciprocally, overexpression of hand2 leads to decreased Fibronectin levels.  Furthermore, reduction of fn1 function enables rescue of cardiac fusion in hand2 mutants: bilateral cardiomyocyte populations merge and exhibit improved tissue architecture, albeit without major changes in apicobasal polarity.  Together, our data provide a novel example of a tissue creating a favorable environment for its morphogenesis: the Hand2 pathway establishes an appropriate environment for cardiac fusion through negative modulation of Fn1 levels.

overall_design: Embryos from three independent hand2 mutant (hanS6 allele) heterozyogous crosses were collected.  Examination of Tg(myl7:egfp) expression allow sorting of hand2 mutant embryos from their wild-type siblings.

middle: V

first: Deborah

last: Yelon


title: Transcriptome analysis of zebrafish mononuclear myogenic cells (zMNCs) during myogenic differentiation

status: Public on Mar 30 2010

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary: Analysis of the transcriptome of zebrafish mononuclear myogenic cells (zMNCs) during myogenic differentiation. The main goal is to identify the similarities of zMNC myogenic differentiation with that of mammalian myoblast differentiation. Critical time points were used to identify a switch from the activity of cell proliferation genes to myogenic structural genes.

overall_design: 15-20 adult zebrafish dorsal skeletal muscles were isolated at each of 6 distinct time points (day 0, day 1, day 4, day 7, day 10, day 14) in replicates.

middle: T

first: Matthew

last: Alexander

first: Louis

last: Kunkel


title: Expression data from zebrafish embryos homozygous mutant for the cohesin subunit Rad21

status: Public on Oct 30 2009

first: Julia

last: Horsfield

summary:
Rad21 is a subunit of cohesin.  The main function of cohesin is to hold replicated chromosomes together until cells divide, but it also plays a role in gene expression.  To find out which genes might be regulated by cohesin, a study was conducted to look for global changes in gene expression in zebrafish embryos lacking cohesin component Rad21.
The zebrafish Rad21 mutant used for expression analysis was rad21nz171, an allele isolated in a forward genetic screen for regulators of runx1.

overall_design: RNA from rad21nz171 mutant and wild type zebrafish embryos collected at 24 hours post-fertilization (h.p.f.) and 48 h.p.f. was hybridized to Affymetrix microarrays (Gene Chip zebrafish genome arrays cat. no. 900488).  Four pools of 50 embryos for each genotype and time point were used as the RNA source, and RNA from each pool was hybridized independently such that the experiment had four biological replicates.

first: J

first: C

last: Print

first: L

last: Wiilliams

first: P

middle: S

last: Crosier


title: Transcriptome analysis of the zebrafish pineal gland

status: Public on Oct 27 2009

city: Bethesda

first: Reiko

last: Toyama

state: MD

address: Bldg.6B, Room 420, 9000 Rockville Pike

department: NICHD

institute: NIH

summary:
The zebrafish pineal gland (epiphysis) is an autonomous clock organ. In addition to being a site of melatonin production, it contains photoreceptor cells and functions as a circadian clock pace maker, making zebrafish a useful model system to study the developmental control of expression of genes associated with melatonin synthesis and photodetection, and the circadian clock.  Here we have used DNA microarray technology to study the zebrafish pineal transcriptome.  Analysis of gene expression at five different developmental stages (three embryonic and two adult) has revealed a highly dynamic transcriptional profile, revealing many genes that are highly expressed in the pineal gland.  Statistical analysis of the data based on Gene Ontology (GO) annotation indicates that many transcription factors and cell cycle genes are highly expressed during embryonic stages, whereas genes dedicated to visual system signal transduction are preferentially expressed in the adult. Furthermore, several genes were identified that exhibit day/night differences in expression.  Our data provide a rich source of candidate genes for distinct functions at different stages of pineal gland development.

Keywords: time course

overall_design: Adults and embryos were kept under a 14-hr-light/10-hr-dark cycle. Pineal glands were isolated manually, guided by GFP fluorescence, from embryonic (3d, 5d, and 10d) and adult (3 month and 1-2 yr) transgenic zebrafish in which expression of the GFP gene is driven by the pineal-specific aanat2 promoter.  For comparison, brain tissue from which the pineal gland and eyes had been removed was also collected (referred to as “brain”). Altogether, we collected 20 types of samples: five time points (3d, 5d, 10d, 3 mo, and 1-2 yr), two organs (pineal gland and brain), and two sampling times (day and night).  For each type of sample, tissue was obtained and processed three to five times.  Total RNA was prepared from each sample using the RNeasy Lipid Tissue Mini Kit (Qiagen) and biotin-labeled cDNA was generated using the Ovation Biotin system kit (NeuGen).  The Affymetrix GeneChip® Zebrafish Genome Array was hybridized and processed using the standard Affymetrix protocol.

first: Igor

middle: B

last: Dawid


title: B1 sox (sox2/3/19a/19b) quadruple knockdown in the zebrafish embryo

status: Public on Dec 31 2009

city: Suita

first: Yusuke

last: Kamachi

state: Osaka

address: 1-3 Yamadaoka

department: Graduate School of Frontier Biosciences

institute: Osaka University

summary:
The B1 SOX transcription factors SOX1/2/3/19 have been implicated in various processes of early embryogenesis. However, their regulatory functions in stages from the blastula to early neurula remain largely unknown, primarily because loss-of-function studies have not been informative to date. In our present study, we systematically knocked down the B1 sox genes in zebrafish. Only the quadruple knockdown of the four B1 sox genes sox2/3/19a/19b, which are active in the early embryo, resulted in very severe developmental abnormalities, confirming that the B1 sox genes are functionally redundant. We characterized the sox2/3/19a/19b quadruple knockdown embryos in detail by examining the changes in gene expression through microarray analysis as well as in situ hybridization.
Importantly, these phenotypic analyses of the quadruple knockdown embryos reveled that the B1 SOX proteins regulate the following distinct processes: (1) early dorsoventral patterning by controlling bmp2b/7; (2) gastrulation movements via the regulation of pcdh18a/18b and non-canonical wnt genes; (3) neural differentiation by regulating the Hes-class bHLH gene her3 and the proneural-class bHLH genes neurog1 (positively) and ascl1a (negatively), and regional transcription factor genes, e.g. hesx1, zic1 and rx3; and (4) neural patterning by regulating signaling pathway genes, cyp26a1 in RA signaling, oep in Nodal signaling, shh, and mdkb. These findings indicate that the B1 SOX proteins control a wide range of developmental regulators in the early embryo and suggest that the B1 sox functions are central to coordinating cell fate specification with patterning and morphogenetic processes occurring in the early embryo.

overall_design: Microarray analysis was carried out to compare gene expression profiles at the 30% epiboly (30%E), 75% epiboly (75%E) and tailbud (TB) stages between wild-type embryos and the sox2/3/19a/19b quadruple knockdown embryos. RNAs from two independent samples were analyzed for each embryonic stage.

first: Yuich

last: Okuda


title: microRNA profiling of myocardial infarction on a PI3K setting in mouse models

status: Public on Mar 08 2010

city: Sydney

first: Ruby

middle: CY

last: Lin

state: NSW

address: 176 Hawkesbury Road, Westmead

country: Australia

institute: The Westmead Institute for Medical Research

summary:
Cardiac hypertrophy can lead to heart failure, and is induced either by physiological stimuli eg postnatal development, chronic exrcise training or pathological stimuli eg pressure or volume overload. This data set looks at microRNA profiles in mouse models to examine whether phosphoinositide 3-kinase (p110 alpha isoform) activity is critical for the maintenance of cardiac function and long term survival in a seeting of heart failure (myocardial infarction). The significance and expected outcome are to recognise genes involved in models of heart failure and attempt to examine underlying regulator pathways involved in possible cardica maintenance in the PI3K mouse model. The matching mRNA gene expression profile (GSE7487) is examined to look for mRNA and microRNA interactions.
miRNA expression correlates directly with cardiac function. PI3K regulon ameliorates cardiac stress.

Keywords: microRNA profiling, regulatory pathway discovery, genotype comparison

overall_design: Ntg (non-transgenics), dnPI3K (cardiac-specific transgenic model with reduced PI3K activity) and caPI3K (transgenic mice with increased PI3K activity) mice at 3-4 months of age were used. Mice were then subjected to myocardial infarction (occlusion of the left anterior descending aorta) and sham (open heart surgery) for 8 weeks. Left ventricles were harvested. The resulting 6 experimental models were profiled accordingly. The assignment of the mouse models is as follows: caPI3K Sham, Ntg Sham, dnPI3K Sham, caPI3K MI (myocardial infarction), Ntg MI and dnPI3K MI with n = 4 in each group.

first: Julie

middle: R

last: McMullen

middle: C


title: Gene expression timecourse in zebrafish whole eye in response to optic nerve crush

status: Public on Feb 01 2010

first: Amy

last: McCurley

address: 5 Cummington Street

institute: Boston University

summary:
It is well-established that neurons in the adult mammalian central nervous system are terminally differentiated and, if injured, will be unable to regenerate their connections. In contrast to mammals, zebrafish and other teleosts display a robust neuroregenerative response. Following optic nerve crush (ONX), retinal ganglion cells (RGC) regrow their axons to synapse with topographically correct targets in the optic tectum, such that vision is restored in ~21 days. What accounts for these differences between teleostean and mammalian responses to neural injury is not fully understood. A time course analysis of global gene expression patterns in the zebrafish eye after optic nerve crush can help to elucidate cellular and molecular mechanisms that contribute to a successful neuroregeneration.
We used microarrays to detail the global gene expression patterns underlying a successful regeneration or the optic nerve following injury.

overall_design: Microarray analysis was performed on total RNA extracted from whole eye following optic nerve crush (ONX) or sham surgery at defined intervals (4, 12, & 21 days).

first: Gloria

last: Callard


title: Zebrafish heart regeneration

status: Public on Feb 25 2010

city: Barcelona

first: Stephanie

last: Boue

address: Dr Aiguader 88

institute: CMRB

summary: Ischemic cardiopathy is the leading cause of death in the world, for which efficient regenerative therapy is not currently available. In mammals, after a myocardial infarction episode, the damaged myocardium is replaced by scar tissue featuring collagen deposition and tissue remodelling with negligible cardiomyocyte proliferation. Zebrafish, in contrast, display an extensive regenerative capacity as they are able to restore completely lost cardiac tissue after partial ventricular amputation. Due to the lack of genetic lineage tracing evidence, it is not yet clear if new cardiomyocytes arise from existing contractile cells or from an uncharacterised set of progenitors cells. Nonetheless, several genes and molecules have been shown to participate in this process, some of them being cardiomyocyte mitogens in vitro. Though questions as what are the early signals that drive the regenerative response and what is the relative role of each cardiac cell in this process still need to be answered, the zebrafish is emerging as a very valuable tool to understand heart regeneration and devise strategies that may be of potential value to treat human cardiac disease. Here, we performed a genome-wide transcriptome profile analysis focusing on the early time points of zebrafish heart regeneration and compared our results with those of previously published data. Our analyses confirmed the differential expression of several transcripts, and identified additional genes the expression of which is differentially regulated during zebrafish heart regeneration. We validated the microarray data by conventional and/or quantitative RT-PCR. For a subset of these genes, their expression pattern was analyzed by in situ hybridization and shown to be upregulated in the regenerating area of the heart. The specific role of these new transcripts during zebrafish heart regeneration was further investigated ex vivo using primary cultures of zebrafish cardiomyocytes and/or epicardial cells. Our results offer new insights into the biology of heart regeneration in the zebrafish and, together with future experiments in mammals, may be of potential interest for clinical applications.

overall_design: In order to study zebrafish heart regeneration, a time course experiment was realized where amputated heart regenerating were compared to control heart. Samples in triplicate were extracted at 1, 3, 5 and 7 days post-amputation.

first: Eduard

last: Sleep

first: Clara

last: Fernandez

first: Marina

last: Raya

first: Yvonne

last: Richaud

first: Angel

first: Juan-Carlos

last: Izpisua-Belmonte


title: Zebrafish response to microbiota

status: Public on Jan 01 2010

city: Chapel Hill

first: John

last: Rawls

state: NC

address: 111 Mason Farm Rd.

department: Department of Cell and Molecular Physiology

institute: University of North Carolina at Chapel Hill

summary: Vertebrates are colonized at birth by complex microbial communities (microbiota) that influence diverse aspects of host biology. We have used a functional genomics approach to identify zebrafish genes that are differentially expressed in response to the microbiota.  We assessed RNA expression profiles from zebrafish larvae at 6 days post-fertilization (dpf) that were either raised continuously in the absence of any microorganism (germ-free or GF), or raised GF through 3dpf then colonized with a normal zebrafish microbiota (conventionalized or CONVD).

overall_design: Total RNA was purified from pooled intact zebrafish larvae (28-80 larvae/pool, 3 biological replicate pools/condition) using Trizol reagent (Invitrogen) followed by DNase I digestion (DNA-Free, Ambion) according to manufacturers' protocols. Total RNA from each replicate pool (12ug RNA/replicate) was used as template for independent cDNA synthesis and in vitro transcription reactions (BioArray HighYield RNA Transcript Labeling Kit; Enzo Life Sciences) to generate biotinylated cRNA targets. cRNA targets (20ug/replicate) were fragmented using standard methods. Hybridization and scanning were performed using standard Affymetrix protocol. Raw expression values were normalized (Invariant set method) and modeled (PM-MM model), and present/absent calls were generated using dChip software (build date Dec.11, 2005).


title: Spatiotemporal Analysis of Transcriptome in the paraxial mesoderm of zebrafish embryos

status: Public on Feb 04 2010

city: Kansas City

first: Olivier

last: Pourquie

address: 1000 E. 50th Street

institute: Stowers Institute for Medical Research

summary: Differentially expressed genes along the paraxial mesoderm of 12 somite stage zebrafish embryos are identified

overall_design: Tissue samples from 6 different spatial positions were dissected from wild-type (AB) embryos, RNA is amplified and hybridized to arrays

first: Ertugrul

middle: M

last: Ozbudak