title: Gene Expression In Drosophila Hearts Harboring Ion Channel Mutations

status: Public on Apr 01 2017

city: Claremont

first: Alexander

last: Zambon

state: CA

address: 517 Watson Drive

department: Biopharmaceutical Sciences

institute: Keck Graduate Institute

summary:
Age-dependent electrical and morphological remodeling of the Drosophila heart caused by hERG/seizure mutations
Sei and KCNQ mutants were compared to their control lines, Canton S-CS and KCNQ370

overall_design: 30, 3-week old hearts were isolated and RNA was extracted and prepared for arrays

first: Karen

last: Ocorr


title: Gene expression analysis of PiZ mouse livers

status: Public on Mar 23 2017

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

summary: Transgenic PiZ mice have been genetically engineered to express ATZ and have been a valuable experimental model for studing liver disease associated with AAT deficiency. ATZ accumulates in these mice within the ER of hepatocytes in a nearly identical manner to livers of affected patients. To investigate the pathogenesis of liver damage induced by ATZ, we performed gene expression analysis in livers of 6-week-old PiZ mice and strain-, age-, and gender-matched wild-type mouse controls. All samples were processed on Affymetrix Mouse 430A 2.0 arrays using GeneChip 3’-IVT Plus and Hybridization Wash and Stain kits by means of Affymetrix’s standard protocols. The analysis indicated that most genes upregulated in PiZ livers were associated with response to unfolded proteins, ER nuclear signaling pathway, and response to protein stimulus.

overall_design: Gene expression analysis of 6 week-old wild-type (WT) and PiZ mouse livers

first: Nunzia

last: Pastore

first: Nicola

last: Brunetti-Pierri


title: Microarray analysis of gene expression in the livers of C57BL/6J mice fed a choline- and folate-deficient diet

city: Jefferson

first: Volodymyr

last: Tryndyak

address: 3900 NCTR Rd

department: Division of Biochemical Toxicology

country: USA

institute: US-FDA National Center for Toxicological Research

summary: Non-alcoholic steatohepatitis (NASH) is becoming one of the leading causes of hepatocellular carcinoma (HCC), replacing viral HBV-, HCV-, and alcohol-related chronic liver diseases as major etiological risk of factors for HCC. The goal of the present study was to investigate transcriptomic alterations in the livers of male C57BL/6J mice fed a choline- and folate-deficient (CFD) diet. Feeding mice a CFD diet for 12 weeks caused NASH-like liver injury exhibiting uniform morphological features of human NASH. High-throughput whole-genome transcriptomic analysis showed that 1750 genes were differentially expressed (344 down-regulated and 1396 up-regulated) in the livers of mice fed a CFD diet as compared to control mice. The functional pathway analysis revealed that these differentially-expressed genes were associated with diverse cellular processes, including cellular growth and differentiation, cell-to-cell signaling and interaction, lipid metabolism, inflammation, fibrosis, molecular transport, and drug metabolism. These findings demonstrate that deregulation of global gene expression is the prominent fundamental feature of NASH in mice induced by a CFD diet.

overall_design: Male C57BL/6J inbred mice were maintained on either control or CFD diets for 12 weeks. Gene expression profiles in the livers from control mice and mice fed a CFD-diet were investigated.

first: Tao

last: Han

first: Levan

last: Muskhelishvili

first: James

middle: C

last: Fuscoe

first: Sharon

middle: A

last: Ross

first: Frederick

last: Beland

first: Igor

middle: P

last: Pogribny


title: Gene expression profiles in Drosophila phagocytes after incubation with apototic cell fragments

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

country: Japan

institute: Hirosaki University

summary: The phagocytic elimination of cells undergoing apoptosis is an evolutionarily conserved innate immune mechanism for eliminating unnecessary cells. Previous studies showed an increase in the level of engulfment receptors in phagocytes after the phagocytosis of apoptotic cells, which leads to the enhancement of their phagocytic activity. However, precise mechanisms underlying this phenomenon require further clarification. We found that the pre-incubation of a Drosophila phagocyte cell line with the fragments of apoptotic cells enhanced the subsequent phagocytosis of apoptotic cells, accompanied by an augmented expression of the engulfment receptors Draper and integrin αPS3. The DNA-binding activity of the transcription repressor Tailless was transiently raised in those phagocytes, depending on two partially overlapping signal-transduction pathways for the induction of phagocytosis as well as the occurrence of engulfment. The RNAi knockdown of tailless in phagocytes abrogated the enhancement of both phagocytosis and engulfment receptor expression. Furthermore, the hemocyte-specific RNAi of tailless reduced apoptotic cell clearance in Drosophila embryos. Taken together, we propose the following mechanism for the activation of Drosophila phagocytes after an encounter with apoptotic cells: two partially overlapping signaltransduction pathways for phagocytosis are initiated; transcription repressor Tailless is activated; expression of engulfment receptors is stimulated; and phagocytic activity is enhanced. This phenomenon most likely ensures the phagocytic elimination of apoptotic cells that stimulated phagocytes find thereafter and is thus considered as a mechanism to prime phagocytes in innate immunity.

overall_design: S2 cells, a cell line established from Drosophila embryos, were maintained at 25 °C in Schneider's Drosophila medium (Life Technologies Japan, Tokyo, Japan) containing 10% heat-inactivated FBS, 100 units/ml penicillin, and 100 μg/ml streptomycin. To prepare apoptotic cell fragments, S2 cells were incubated in the presence of cycloheximide (1.5 μg/ml) for 24 h to induce apoptosis. The cells were then centrifuged at 300 × g for 3 min at room temperature, and the resulting supernatants were collected. They were re-centrifuged at 1500 × g for 3 min at 4 °C, and the supernatants were further centrifuged at 3500 × g for 3 min at 4 °C. The resulting precipitates were recovered, suspended with Schneider's Drosophila medium with 1% heat-inactivated FBS, microscopically determined for the number of membranous particles using a hemocytometer, and used as the fragments of apoptotic S2 cells. Semi-confluent S2 cells maintained in Schneider's Drosophila medium with 1% heat-inactivated FBS were supplemented with the apoptotic cell fragments, at a responder/effector ratio of 1 : 25.  The mixtures, together with phagocyte cultures with no fragments added as a negative control, were incubated at 25 °C for 1h, and cells were detached from culture containers by the treatment with 0.25% (w/v) trypsin and 0.02% (w/v) EDTA. The recovered cells were collected by centrifugation at 300 × g for 3 min at room temperature, washed twice with PBS, and used as phagocytes stimulated by apoptotic cell fragments, or an untreated control, in the preparation of RNA for a microarray analysis.

first: Saori

last: Nonaka

first: Yuki

last: Ando

first: Takuto

last: Kanetani

first: Chiharu

last: Hoshi

first: Firzan

last: Nainu

first: Kaz

last: Nagaosa

first: Akiko

last: Shiratsuchi

first: Yoshinobu

last: Nakanishi


title: Intestinal SIRT1 in the regulation of intestinal tissue homeostasis

status: Public on May 30 2017

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: The goal of this project is to investigate the role of SIRT1, the most conserved mammalian NAD+-dependent protein deacetylase, in the regulation of intestinal tissue integrity. Using a mouse model with specific deletion of SIRT1 in intestinal epithelium (SIRT1 iKO mice), we recently discovered that deletion of intestinal SIRT1 in mice age-dependently elicits NF-κB signaling and other stress response pathways, activates intestinal secretory cells, enhances spontaneous inflammation, and alters commensal gut microbial composition. To understand the molecular mechanisms underlying these age-dependent phenotypes, we examined the transcriptomes of young (6-8 week old) and aged (24-month old) ilea and aged colons from Flox controls and SIRT1 iKO mice by microarray analysis.

overall_design: Total RNA were extracted from ileum and colon tissues of 3-4 young and aged Flox controls and SIRT1 iKO mice, and gene expression profiles were analyzed using Agilent Whole Mouse Genome 4x44 multiplex format oligo arrays (014868) (Agilent Technologies, Santa Clara, CA), following the Agilent 1-color microarray-based gene expression analysis protocol.

first: Xiaoling

last: Li

first: Mallikarjuna

middle: R

last: Metukuri


title: Drosophila CNS OXPHOS inhibition microarray

status: Public on Mar 21 2017

city: London

first: Joseph

middle: M.

last: Bateman

state: (Click to Select US State)

address: Guy's campus

country: United Kingdom

institute: King's College London

summary:
Mitochondrial dysfunction causes biophysical, metabolic and signalling changes that alter homeostasis and reprogram cells. We used a Drosophila model in which individual subunits of 4 OXPHOS complexes are knocked-down in neurons in the larval CNS.
We used microarray analysis to investigate gene expression changes caused by knock down of OXPHOS subunits of complexes I, III, IV and V in neurons.

overall_design: RNA was purified from the late third instar larval CNS from control larvae (nSyb-Gal4/w), or larvae expressing RNAi transgenes targeting ND-75 (complex I, RNAi line #33910), UQCR-14 (complex III, RNAi line #109542), COX5B (complex IV, RNAi line #105769) and ATPsynCf6 (complex V, RNAi line #107826) in neurons using nSyb-Gal4.  Three replicates are included for the each condition.

middle: M

first: Olivia

middle: F

last: Duncan


title: The phosphorylation status of T522 modulates tissue-specific functions of SIRT1 in energy metabolism in mice

status: Public on Feb 22 2017

summary: The goal of this project is to understand how the phosphorylation status of T522 at SIRT1,  the most conserved mammalian NAD+-dependent protein deacetylase, regulates its activity and function in vivo. We have previously reported that SIRT1 can be phosphorylated and activated by two anti-apoptotic members of the dual specificity tyrosine phosphorylation-regulated kinase (DYRK), DYRK1A and DYRK3, in response to acute environmental stresses. However, whether this modification is involved in regulation of SIRT1 activity remains elusive. To assess the physiological impacts of the phosphorylation of T522 on SIRT1, we generated SIRT1 T522 phosphorylation mimic (T522E mutation, or TEKI) and dephosphorylation mimic (T522A mutation, or TAKI) knock-in mouse models. Our current findings indicated that TAKI mice but not TEKI mice displayed impaired hepatic fatty acid oxidation and developed hepatic steatosis after high-fat diet feeding. To understand the molecular mechanisms underlying this phenotype, we examined the hepatic transcriptomes of SIRT1 WT, TAKI and TEKI mice after 5-month high-fat diet feeding by microarray analysis.

overall_design: 5 WT, 5 TAKI, and 3 TEKI mice were fed with a western-style high-fat diet for 5 months. Their hepatic total RNA was isolated using the Qiagen RNeasy mini-kit, and gene expression profiles were analyzed using Agilent Whole Mouse Genome 4x44 multiplex format oligo arrays (014868) (Agilent Technologies, Santa Clara, CA), following the Agilent 1-color microarray-based gene expression analysis protocol.


title: Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans [IlluminaPsychArray]

status: Public on Mar 19 2017

city: St. Augustine

first: Rajini

last: Haraksingh

address: The University of the West Indies

department: Life Sciences

country: Trinidad and Tobago

institute: The University of the West Indies

summary: Background High-resolution microarray technology is routinely used in basic research and clinical practice to efficiently detect copy number variants (CNVs) across the entire human genome. A new generation of arrays combining high probe densities with optimized designs will comprise essential tools for genome analysis in the coming years. We systematically compared the genome-wide CNV detection power of all 17 available array designs from the Affymetrix, Agilent, and Illumina platforms by hybridizing the well-characterized genome of 1000 Genomes Project subject NA12878 to all arrays, and performing data analysis using both manufacturer-recommended and platform-independent software. We benchmarked the resulting CNV call sets from each array using a gold standard set of CNVs for this genome derived from 1000 Genomes Project whole genome sequencing data. Results The arrays tested comprise both SNP and aCGH platforms with varying designs and contain between ~0.5 to ~4.6 million probes.  Across the arrays CNV detection varied widely in number of CNV calls (4 - 489), CNV size range (~40 bp to ~8 Mbp), and percentage of non-validated CNVs (0 - 86 %). We discovered strikingly strong effects of specific array design principles on performance. For example, some SNP array designs with the largest numbers of probes and extensive exonic coverage produced a considerable number of CNV calls that could not be validated, compared to designs with probe numbers that are sometimes an order of magnitude smaller. This effect was only partially ameliorated using different analysis software and optimizing data analysis parameters. Conclusions High-resolution microarrays will continue to be used as reliable, cost- and time-efficient tools for CNV analysis. However, different applications tolerate different limitations in CNV detection. Our study quantified how these arrays differ in total number and size range of detected CNVs as well as sensitivity, and determined how each array balances these attributes. This analysis will inform appropriate array selection for future CNV studies, and allow better assessment of the CNV-analytical power of both published and ongoing array-based genomics studies. Furthermore, our findings emphasize the importance of concurrent use of multiple analysis algorithms and independent experimental validation in array-based CNV detection studies.

overall_design: We systematically compared the genome-wide CNV detection power of all 17 available array designs from the Affymetrix, Agilent, and Illumina platforms by hybridizing the well-characterized genome of 1000 Genomes Project subject NA12878 to all arrays in two technical replicates, and performing data analysis using both manufacturer-recommended and platform-independent software. We benchmarked the resulting CNV call sets from each array using a gold standard set of CNVs for this genome derived from 1000 Genomes Project whole genome sequencing data.


title: Expression data from wildtype and beta-catenin activated cultured fetal mouse kidneys.

status: Public on Feb 20 2017

city: New York

first: Emily

last: Hsu

state: NY

address: 1130 St. Nicholas Ave.

department: ICG

institute: Columbia University

summary: Oncogenic stabilizing mutations in the beta-catenin gene CTNNB1 are common in one class of human Wilms tumors. To model these tumors, we crossed mice carrying an inducible Cre recombinase (Rosa26-CreERT2) with a conditional gain-of-function beta-catenin allele (Ctnnb1Ex3flox). We obtained kidneys at embryonic day 13.5 and placed them in organ culture with tamoxifen. Multiple small tumors formed in the Ctnnb1∆Ex3 kidneys while the control kidneys developed normally. Immunostaining for Sall1, a marker of condensing metanephric mesenchyme, indicated that the tumors arise from this tissue compartment, analogous to the origin of human Wilms tumors. Expression profiling identified a set of induced genes overlapping with those up-regulated in human Wilms tumors with CTNNB1 mutations, including genes encoding feedback inhibitors of Wnt/beta-catenin signaling, the epithelial-mesenchymal transition (EMT) inducers, and the transcription factor E2-2 (ITF2/TCF4). A conditional deletion of E2-2 showed that this gene is important for growth of the nephroblastomas, in part via promoting an epithelial to mesenchymal transition downstream of beta-catenin. Given these cross-species validations, and genetic proof of the oncogenic function of a key downstream target gene, we expect that this rapid and efficient organ culture model will be useful for further studies to dissect and inhibit oncogenic Wnt/beta-catenin signaling.

overall_design: The expression of six wildtype cultured fetal mouse kidneys was compared with six beta-catenin activated cultured fetal mouse kidneys.

first: Iveta

last: Yotova

first: Benjamin

last: Tycko


title: Gene expression of fly testes with dMi-2, kumgang (CG5204) knock downs

status: Public on May 18 2017

city: Ithaca

first: Jongmin

middle: J

last: Kim

address: 930 Campus Road

department: Biomedical Sciences

institute: Cornell University

summary:
The effect of different loss of functions; kumgang (kmg or CG5204), dMi-2, and kmg and always early (aly) double on the gene expression in spermatocyte differentation was assessed by microarray.
TITLE: Blocking promiscuous activation at cryptic promoters directs cell type–specific gene expression    ABSTRACT: To selectively express cell type–specific transcripts during development, it is critical to maintain genes required for other lineages in a silent state. Here, we show in the Drosophila male germline stem cell lineage that a spermatocyte-specific zinc finger protein, Kumgang (Kmg), working with the chromatin remodeler dMi-2 prevents transcription of genes normally expressed only in somatic lineages. By blocking transcription from normally cryptic promoters, Kmg restricts activation by Aly, a component of the testis-meiotic arrest complex, to transcripts for male germ cell differentiation. Our results suggest that as new regions of the genome become open for transcription during terminal differentiation, blocking the action of a promiscuous activator on cryptic promoters is a critical mechanism for specifying precise gene activation.

overall_design:
RNA was obtained from whole testes of flies with following mutations: 1) UAS-RNAi-kmg (VDRC# 107395); TM6b (kmg_Ctrl1/2.CEL), 2) UAS-RNAi-kmg (VDRC# 107395); bam-gal4, UAS-dicer2 (kmg_KD1/2.CEL), 3) UAS-RNAi-kmg(VDRC# 107395); bam-gal4, aly[2]/aly[5p] (kmg_KD_aly1/2.CEL), 4) UAS-RNAi-dMi-2 (VDRC# 107204); TM6b (dMi2_Ctrl1/2.CEL), 5) UAS-RNAi-dMi-2 (VDRC# 107204); bam-gal4, UAS-dicer2 (dMi2_KD1/2.CEL). Each genotype had two biological replicates. All experiments were done in 30C.

RNA was obtained from whole testes of flies. Genotypes of flies and treatment applied to those lines are like the following: 1) w; ;bam[1]/bam[delta86] (no heat shock, 1 sample), 2) w; ;bam[1]/bam[delta86] (24 hours after 30 minutes pulse heat shock, 1 sample), 3) hs-Bam;;bam[1]/bam[delta86] (no heat shock, 2 samples), 4) hs-Bam;;bam[1]/bam[delta86] (24 hours after 30 minutes pulse heat shock, 2 samples). Flies were raised in 25C.

first: Margaret

middle: T

last: Fuller


title: Apoptosis, Toll-like, RIG-I-like and NOD-like receptors are pathways jointly induced by diverse respiratory bacterial and viral pathogens

status: Public on Mar 01 2017

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

summary: Lower respiratory tract infections are among the top five leading causes of human death. Fighting these infections is therefore a world health priority. Searching for induced alterations in host gene expression shared by several relevant respiratory pathogens represent an alternative to identifying new targets for wide-range host-oriented therapeutics. With this aim, alveolar macrophages were independently infected with three unrelated bacterial (Streptococcus pneumoniae, Klebsiella pneumoniae and Staphylococcus aureus) and two dissimilar viral (respiratory syncytial virus and influenza A virus) respiratory pathogens which are nevertheless highly relevant for human health. Cells were also activated with bacterial lipopolysaccharide (LPS) as a prototypical pathogen-associated molecular pattern. Patterns of differentially expressed cellular genes shared by the indicated pathogens were searched by microarray analysis. Most of the commonly up-regulated genes were related to the innate immune response and/or apoptosis, with Toll-like, RIG-I-like and NOD-like receptors among the top ten signaling pathways with over-expressed genes. These results identify new potential broad-spectrum targets to fight the important human infections caused by the bacteria and viruses studied here.

overall_design: Differential gene expression analysis by Agilent microarrays. Three or more biological replicates per sample. Single-channel hybridizations (label: Cy3) to Agilent Whole Mouse Genome microarray (G4122F, Agilent Technologies, Palo Alto, CA), representing about 44,000 human genes, transcripts and controls. In all cases, comparisons are infected vs. not infected.

first: Isidoro

last: Martínez

first: Isabel

last: Cuesta

first: Jorge

last: de la Barrera

first: Vicente

last: Ausina

first: Cristina

last: Casals

first: Alba

last: de Lorenzo

first: Ernesto

last: García

first: Belén

last: García-Fojeda

first: Junkal

last: Garmendia

first: Mar

last: González

first: Alicia

last: Lacoma

first: Margarita

last: Menéndez

first: David

last: Moranta

first: Amelia

last: Nieto

last: Ortín

last: Pérez-González

last: Prat

first: Elisa

last: Ramos-Sevillano

first: Verónica

last: Regueiro

first: Ariel

last: Rodríguez-Frandsen

first: Dolores

last: Solís

first: José

last: Yuste

last: Bengoechea

last: Melero


title: Gene expression in neonatal NKT cells and lymphoma samples from mice with high E protein levels [Microarray Expression]

status: Public on Apr 20 2017

city: Durham

first: Yuan

last: Zhuang

address: 207 Research Drive

department: Immunology

institute: Duke University

type:
Expression profiling by array
Third-party reanalysis

summary: Inhibitor of DNA binding proteins (ID), including Id1-4, are transcriptional regulators involved in promoting cell proliferation and survival in various cell types. Although upregulation of Id proteins have been widely reported to be associated with a broad spectrum of tumors, recent studies have identified that Id3 also plays a tumor suppressor role in the development of Burkitt’s lymphoma in humans and Hepatosplenic T cell lymphomas in mice. However, there is a lack of evidence to suggest the tumor suppressor roles for other Id genes, particularly Id2, which is highly expressed in many T lymphocytes. In this study we report that Id2 plays a tumor suppressive role in collaboration with Id3 in developing T cells in mice. We found that there was rapid lymphoma development in Id2f/fId3f/fLckCre mice caused by unchecked neonatal expansion of invariant Natural Killer T (iNKT) cells and a unique subset of innate-like, CD1d-independent T cells. These tumors also gave rise to lymphomas in Rag-deficient mice, reaffirming the inherent tumorigenic potential of these cells. Microarray analysis revealed a significantly modified program in expanding iNKT cells that ultimately contributed to tumorigenesis. We found chromosome instability and significant upregulation of several different signaling pathways, including pathways for multiple chemokines, cytokines and their receptors, in these tumors. While Id proteins are being considered as potential therapeutic targets in some cancer models, our results highlight the possibility of aggravated tumorigenesis upon suppression of Id2 and Id3.

overall_design: Pre-malignant iNKT (TCRβ+CD1dTet+) cells were sorted from three 20 day old L-DKO mice. Lymphoma cells (T cells that are CD1dTet+ or CD1dTet-) were sorted from tissues of 18-37 week old L-DKO mice. Total RNA was extracted, and mRNA profiling was done using GeneChip Mouse Genome 430A 2.0 arrays (GPL8321, Affymetrix)

first: Jia

last: Li

first: Sumedha

last: Roy

first: Young-Mi

last: Kim

first: Shibo

first: Baojun

last: Zhang

first: Cassandra

last: Love

first: Anupama

last: Reddy

first: Deepthi

last: Rajagopalan

first: Anna

last: Diehl

first: Sandeep

last: Dave


title: Gene expression profiling of FDCPmix sub-fractions

status: Public on Feb 10 2017

first: Dapeng

last: Wang

address: Gower Street

department: Stem Cell Laboratory

institute: UCL Cancer Institute

summary: The mouse bone marrow cell line FDCPmix was fractionated on the basis of surface detection of c-Kit, Sca-1, and Gr1 antigens. Four compartments were profiled Gr1+ cells (myeloid-committed compartment = MCP); kit-Gr1- cells (erythroid-committed compartment = ECP); kit+Gr1- cells (self-renewing cells = SR) further sub-divided as the lowest and highest 20% of Sca-1 expression (SR Sca1-lo and SR Sca1-hi, respectively). Bulk (unfractionated) FDCPmix cells were included as controls.

overall_design: Bulk cultures or their respective fractions were sorted for RNA extraction and processed for microarray hybridisation as biological replicates: 2 for bulk; 3 for the remaining samples.

first: Cristina

last: Pina


title: Wilms Tumor in Beckwith-Wiedemann Syndrome and Loss of Methylation at Imprinting Centre 2 [HumanOmni2.5M]

city: Toronto

first: Jack

last: Brzezinski

state: ON

address: 555 University Avenue

country: Canada

institute: University of Toronto

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Beckwith-Wiedemann syndrome (BWS) is an overgrowth syndrome caused by a variety of molecular changes on chromosome 11p15.5. Children with BWS have a significant risk of developing Wilms tumours with the degree of risk being dependent on the underlying molecular mechanism. In particular, only a relatively small number of children with loss of methylation at the centromeric imprinting centre (IC2) were reported to have developed Wilms tumour. Discontinuation of tumour surveillance for children with BWS and loss of methylation at IC2 has been proposed in several recent publications. We report here three children with BWS reported to have loss of methylation at IC2 on clinical testing who developed Wilms tumour or precursor lesions.  Using multiple molecular approaches and multiple tissues, we reclassified one of these cases to paternal uniparental disomy for chromosome 11p15.5. These cases highlight the current challenges in definitively assigning tumour risk based on molecular classification in BWS. The confirmed cases of loss of methylation at IC2 also suggest that the risk of Wilms tumour in this population is not low as previously thought. Therefore, we recommend that for now, all children with a clinical diagnosis of BWS be screened for Wilms tumour by abdominal ultrasonography until the age of 8 regardless of the molecular classification.

overall_design: 2 blood samples (Case 1 and Case 2) are genotyped on the Illumina HumanOmni2.5M SNP array (GPL20641). 3 blood samples (Case 1, Case 2, and Case 3) have methylation measured on the Illumina HumanMethylation450 Bead Chip array (GPL13534). 21 Control blood samples were analyzed on the HumanMethylation BeadChip Array, there were no controls used for the HumanOmni2.5M SNP array. Pyrosequencing and MS-MLPA in cases and controls were done as described in the associated publication. There are no replications in this submission.

first: Brzezinski

last: Jack

first: Shuman

last: Cheryl

first: Choufani

last: Sanaa

first: Ray

last: Peter

first: Stavropolous

last: Dmitri

first: Basran

last: Raveen

first: Steele

last: Leslie

first: Parkinson

last: Nicole

first: Grant

last: Ronald

first: Thorner

last: Paul

first: Lorenzo

last: Armando

first: Weksberg

last: Rosanna


title: Differentiation related tumorigenic potential and transcriptional profile of the fusion reprogrammed mouse cancer cell lines

city: Shanghai

first: Lei

last: Zhang

address: Yueyang Road

country: China

institute: SIBS

summary: Rebuild tumorgenicity during differentiation of fusion reprogrammed Hepa1-6 cells.

overall_design: Hepa1-6 was successfully reprogrammed by fusion with ES cells. After differentiation of hybrids in vitro for 7 and 14 days, gene expression was analysed and compared to Hepa1-6 and ES cells.

first: Jiayi

last: Yao


title: Gene expression analysis for OpAP2-3 lines in Nicotiana tabaccum cv Xanthi

status: Public on Feb 12 2017

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Expression analysis of AP2/ERF overexpression in Tobacco

overall_design: Organism : Nicotiana tabaccum, Agilent's Tobacco Gene Expression  4x44k Array (AMADID: 021113).

first: Sonal

last: Mishra

first: Rakesh

middle: K

last: Shukla


title: O-GlcNAcase is an epigenetic regulator of nutrient-responsive Drosophila Oogenesis

status: Public on Jan 09 2017

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: Nutrient-responsive oogenesis in Drosophila is a complex and dynamic process regulated, in part, by members of the Pc and Trx complexes. The recent finding that O-GlcNAc Transferase (ogt/sxc) is essential for Pc repression raises the question of whether this nutrient-sensing pathway plays a role in regulating oogenesis. OGT transfers O-GlcNAc to key transcriptional regulators in response to graded levels of the nutrient-derived precursor UDP-GlcNAc; O-GlcNAcase (OGA) catalyzes the removal of O-GlcNAc. Here we produced a null allele of oga (oga1) in Drosophila to examine its in vivo function. We found that oga mutant flies were viable, but that females displayed greatly reduced fecundity. The ovaries from the female OGA knockout exhibited a starvation-like phenotype, even under well-fed conditions. Germline stem cell division was slowed in the germarium of OGA knockout fly ovarioles. Ovaries from the oga1 mutants displayed significantly decreased H3K4 monomethylation in germline stem cells. The Trithorax family members Trx and Ash1 and Compass member Set1 histone methyltransferases are O-GlcNAc modified in oga1 mutant ovaries. Our results suggest that the loss of OGA disrupts oogenesis at least in part by interfering with H3K4 monomethylation in germ cells in the ovary. The findings also suggest that O-GlcNAc cycling is an essential part of the nutrient-responsive epigenetic machinery regulating Drosophila oogenesis in response to a changing nutrient supply.

overall_design: Three replications for Drosophila genotype WT, and mutant OGA and SXC.

first: Ilhan

last: Akan

first: Katryn

last: Harwood

first: Dona

last: Love

first: John

last: Hanover


title: Gene expression profiling of mouse uterine decidua isolated on morning of day 8 of pregnancy

status: Public on Feb 09 2017

city: Urbana

first: Juanmahel

last: Davila

state: Illinois

address: 2001 S. Lincoln Avenue

department: Comparative Biosciences

institute: University of Illinois

summary:
Placenta development involves complex molecular and cellular interactions between the maternal endometrium and the developing embryo, however, it is not clear what are the precise mechanisms regulating this maternal-fetal crosstalk. Using genetic and cell biological approaches, we have demonstrated that Ras-related C3 botulinum toxin substrate 1 (Rac1), a maternal factor expressed in decidual cells and is markedly elevated in mouse decidua on days 7 and 8 of gestation, regulates the secretory pathways that mediate stromal-endothelial and stromal-trophoblast crosstalk within a narrow temporal window during placenta development.
Our study revealed that ablation of Rac1 did not affect the formation of the decidua but led to fetal loss in mid gestation accompanied by extensive hemorrhage. To gain insights into the molecular pathways affected by the loss of Rac1, we performed gene expression profiling which revealed that RAC1 signaling regulates the expression of genes involved in angiogenesis and vesicle trafficking. Consequently, the Rac1-null decidual cells exhibited impaired secretory functions that led to poor vascularization of the uterus and abnormal trophoblast expansion and placentation.

overall_design: Mouse uterine decidual masses were isolated from control and conditional knockout mice on the morning of day 8 of pregnancy. The decidual masses, from 3 animals/genotype, were pooled and total RNA was isolated and then hybridized to high density affymetrix microarrays according to the Affymetrix protocol (Mouse Genome 430A 2.0 Array)

first: Indrani

last: Bagchi

first: Milan


title: Distinct gene expression patterns of highly and poorly malignant melanocytic tumors from genetically engineered mouse models of mice carrying specific inactivating mutations in Ink4A or ARF respectively

status: Public on Feb 01 2017

first: Prasun

middle: J.

address: 37 Convent Drive

department: United States Department of Health and Human Services

institute: National Cancer Institute, National Institutes of Health

summary: Cutaneous malignant melanoma is among the most deadly human cancers, broadly resistant to most clinical therapies. A majority of patients with BRAFV600E melanomas respond well to inhibitors such as vemurafenib, but all ultimately relapse. Moreover, there are no viable treatment options available for other non-BRAF melanoma subtypes in the clinic. A key to improving treatment options lies in a better understanding of mechanisms underlying melanoma progression, which are complex and heterogeneous. In this study we perform gene expression profilling of highly and poorly malignant melanocytic tumors from genetically engineered mouse models to discover important drivers of cancer progression.

overall_design: Briefly, RNA (three biological replicates) was isolated using TRIzol reagent, according to the manufacturer's instructions (Invitrogen), and quantified fluorimetrically using an Agilent Bioanalyser (Agilent Technologies).vBiotinylated cRNA were prepared according to the standard Affymetrix protocol. Affymetrix GeneChip Mouse Genome 430 2.0 Array was scanned using Affymetrix standard scan protocol.


title: Electroconvulsive seizure-induced expression change in the dentate gyrus of the hippocampus in mice as an index of the neuronal responsiveness in vivo.

status: Public on Jan 21 2017

city: Tokyo

first: Eri

last: Segi-Nishida

state: Tokyo

address: Niijuku 6-3-1

institute: Tokyo University of Science

summary: The dentate gyrus (DG) of the hippocampus is one of major targets for antidepressant treatments. Using electroconvulsive stimulation (ECS), a model of highly effective and fast-acting antidepressant therapy, here we show that neural stimulation via ECS induces rapid and lasting dematuration of granule neurons in DG. A single time of stimulation transiently reduced mature marker expression and mature synaptic functions. Repetitive stimulation converted this transient dematuration into a stable form lasting more than 1 month.  We compared the activity-dependent neuronal responsiveness in the DG between a single ECS and repeated ECS.

overall_design: The dentate gyrus was dissected 1h  after a single sham, a single ECS or 11 times of ECS,  or 48h after 10 times of ECS ( n= 3, each group).  Total RNA was extracted by using an RNeasy micro kit (Qiagen) and the samples of the same groups were put together. From each group, 100 ng of total RNA was mixed and amplified with 3?IVT Express kit (Affymetrix, Inc., Santa Clara, CA, USA). All samples were hybridized to the GeneChip mouse genome 430A 2.0 array (Affymetrix, Inc.), and the microarray suite 5.0 of the Affymetrix gene chip operating software was used for the analysis of the GeneChip data.

first: Yuki

last: Imoto

first: Katsunori

last: Kobayashi


title: A Molecular Roadmap for Induced Multi-lineage Trans-differentiation of Fibroblasts by Chemical Combinations [gene expression]

status: Public on Jan 17 2017

city: Hangzhou

first: Guoji

last: Guo

state: Zhejiang

address: Yuhangtang Road 866

department: School of Medicine

institute: Zhejiang University

summary:
Recent advances highlight the power of small molecules for promoting cellular reprogramming. Yet, the full potential of such chemicals in cell fate manipulation and the underlying mechanisms needs further characterization. Through functional screening assays, we found that mouse embryonic fibroblast can be induced to trans-differentiate into a wide range of somatic lineages simultaneously by treatment with a combination of four chemicals. Genomic analysis of the process indicates activation of multi-lineage modules and relaxation of epigenetic silencing programs. In addition, we identify Sox2 as an important regulator within the induced network. Single cell analysis uncovers a priming state that enables transition from fibroblast cells to diverse somatic lineages. Finally, we demonstrate that modification of the culture system enables directional trans-differentiation towards cardiac, neuronal or adipocytic lineages. Our study describes a cell fate control system that may be harnessed for regenerative medicine.
We used microarrays to detect the global gene expression patterns underlying induced multi-lineage trans-differentiation

overall_design: Time course microarray analysis for two chemical combinations treatment (6TCF or SGCF) on MEF at Day 0, Day 5 and Day 10

first: Daosheng

last: Huang

first: Xiaoping

last: Han


title: Gene expression profile of diploid and tetraploid mouse primary hepatocyte

city: Boston

first: Shang-Yi

last: Chiu

state: MA

address: 44 Binney St.

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary:
Genetically unstable tetraploid cells can promote tumorigenesis. Recent estimates suggest that ~37% of human tumors have undergone a genome-doubling event during their development. This potentially oncogenic effect of tetraploidy is countered by a p53-dependent barrier to proliferation. However, the cellular defects and corresponding signaling pathways that trigger growth suppression in tetraploid cells are not known. Here we combine genome-scale RNAi screening and in vitro evolution approaches to demonstrate that cytokinesis failure activates the Hippo tumor suppressor pathway in cultured cells as well as in naturally occurring tetraploid cells in vivo. Induction of the Hippo pathway is triggered in part by extra centrosomes, which alter small G-protein signaling and activate LATS2 kinase; LATS2 in turn stabilizes p53 and inhibits the transcriptional regulators YAP and TAZ. These findings define an important tumor suppression mechanism. Furthermore, our experiments uncover adaptations that allow nascent tumor cells to bypass this inhibitory regulation.
Hepatocytes of newborn mice are initially diploid, but become progressively tetraploid with age.  To study the mechanism of cell cycle arrest in naturally occurred tetraploidy, we used microarrays to detail the overall gene expression profile of diploid and tetraploid primary hepatocytes and identified YAP target genes up-regulated in diploid cells.

overall_design: Primary hepatocytes from 3-week-old, wild type C57BL/6 mice were isolated for FACS sorting.  Samples are prepared in 3 biological replicates.

first: Shang

middle: Y


title: Gene expression signature of differentiated human and mouse muscle cells

status: Public on Dec 31 2016

city: Cambridge

first: Zuzana

last: Keckesova

address: 9 Cambridge Center

institute: Whitehead Institute

summary: Transcription profiling was used to identify differentially expressed factors in differentiated and un-differentiated human and mouse muscle cells

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Human and mouse muscle progenitor cells were differentiated in vitro for 8 and 5 days respectively. The RNA was then extracted and used for gene expression microarray on Agilent 4x44K platform. There were two to three biological replicates for each sample.

first: Robert

last: Weinberg


title: Expression data from intestinal mucosa of Zucker rats

status: Public on Dec 25 2016

city: Granada

first: Julio

middle: Ramon

last: Plaza Diaz

state: Granada

address: Avda. del Conocimiento s/n

department: Biochemistry and Molecular Biology II

institute: University of Granada

summary:
Obesity is a chronic, complex and multifactorial disease that has reached pandemia levels and is becoming a serious health problem. Intestinal microbiota is considered a main factor that affects body weight and fat mass, which points toward a critical role in the development of obesity. In this sense, probiotic bacteria might modulate the intestinal microbiota and the mucosal-associated lymphoid tissue. The aim of this study was to investigate the effects of L. paracasei, L. rhamnosus and B. breve feeding on the intestinal mucosa gene expression in a genetic animal model of obesity.
We used microarrays to investigate the global gene expression on intestinal mucosa after the treatment with probiotic strains.

overall_design: Forty-eight Zucker-Leprfa/fa and 16 Zucker-lean+/fa male rats weighing 168-180 g were used. After 5 days of adaptation, 8 Zucker-lean+/fa (lean reference) and 8 Zucker-Leprfa/fa rats (obese reference) were euthanized as a reference. The remaining 40 Zucker-Leprfa/fa rats were then randomly assigned to receive 10^10 CFUs of one of the three probiotic strains (probiotic strains groups), or a placebo (obese placebo) by oral administration each day for 30 days. An additional group of 8 Zucker-lean+/fa rats (control placebo) received placebo. Samples of intestinal mucosa were taken and RNA isolated to carry out a differential gene expression study.  with an Affymetrix microarray (Rat Gene 1.1 ST Array Plate).

last: Plaza-Diaz

first: Candido

last: Robles Sanchez


title: Gene expression data from murine CAR T cells

status: Public on Jan 05 2017

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: Compare the gene expression profile among Mouse m19delta.GFP and m1928z.GFP T cells and examine the differential upregulation of Bim, Bid, FasL and Apaf1 in m1928z T cells.

overall_design: GFP+ mouse CAR T cells were sorted by FACS from ABM-->BM12 recipient splenocytes 14 days after HSCT for RNA extraction and hybridization for Affymetrix microarrays.

first: Arnab

last: Ghosh

first: Marcel

last: van den Brink


title: 3T3-L1: GDE5 Knockdown

city: Higashi-Hiroshima

first: Yanaka

last: Noriyuki

address: Kagamiyama 1-4-4

department: Graduate School of Biosphere Science

institute: Hiroshima University

summary: Transcriptional profiling of mouse 3T3-L1 adipocytes. The objective of this study is to explore gene expression profiles of 3T3-L1 adipocytes in response to GDE5 siRNA transfection.

overall_design: 3T3-L1: GDE5 Knockdown

first: Noriyuki

last: Yanaka


title: Expression data from mice after knockout or overexpression of Tcfeb in muscle

status: Public on Dec 23 2016

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem

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

overall_design: Refer to individual Series


title: Gene expression data from DSS-treated crypts, normal colon crypts and tumor crypts

status: Public on Jan 01 2017

summary:
Comparative gene expression profiling between DSS-treated crypts and normal colon crypts
Comparative gene expression profiling between normal colon crypts and tumor crypts

overall_design: Colonic crypts were isolated from pooled distal colons derived from two Lgr5-lacZ male mice at day 2 after initiation of DSS treatment or two untreated controls, or from 12-pooled adenomas derived from two Lgr5-lacz male mice treated with AOM/DSS. Two independent biologic replicates were performed

first: Guoqiang

last: Hua

first: Richard

last: Kolesnick

first: Yongchun


title: Expression data from Tcfeb KO mice specifically in muscle

summary:
In order to identify the effects of the absence of Tcfeb on the muscle transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the KO mice as compared with wt mice
Transcriptome analysis of the Tcfeb KO mice specifically in muscle

overall_design: For the analysis on the Tcfeb KO mice, total RNA was extracted from the muscle of three mice; RNA extracted from the muscle of three wt muscles was used as control.


title: Expression data from injected mice overexpressing Tcfeb specifically in muscle

summary:
In order to identify the effects of Tcfeb overexpression on the muscle transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the mice injected with an AAV vector expressing Tcfeb as compared with mice injected with an AAV vector expressing GFP as control.
Transcriptome analysis of the injected mice overexpressing Tcfeb specifically in muscle.

overall_design: For the analysis on the injected mice with an AAV vector expressing Tcfeb, total RNA was extracted from the muscle of three mice; RNA extracted from the muscle of mice  injected with an AAV vector expressing GFP was used as control.


title: SIRT1 dosage-dependent effects on cell proliferation and metabolism

status: Public on Dec 20 2016

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

institute: NIEHS

summary: The goal of this project is to understand the dosage-dependent effects of SIRT1,  the most conserved mammalian NAD+-dependent protein deacetylase, on cell proliferation and metabolism.   Our recent studies indicate that SIRT1 has a dosage-dependent effect on cell metabolism and proliferation. Heterozygous deletion of SIRT1 enhance glycolysis and glutaminolysis, thereby promoting cell proliferation and stress resistance. Yet homozygous deletion of SIRT1 triggers cellular apoptotic pathways, leading to increased cell death. To understand the molecular mechanisms underlying this dose-dependent effect, we examined the transcriptomes of SIRT1 WT, Het, and KO MEFs cultured in complete DMEM medium by microarray analysis.

overall_design: 4 groups of female WT, SIRT1 Het, and SIRT1 KO MEFs were cultured in complete medium and harvested in the log-growth phase.Total RNA was isolated using the Qiagen RNeasy mini-kit, and gene expression profiles were analyzed using Agilent Whole Mouse Genome 4x44 multiplex format oligo arrays (014868) (Agilent Technologies, Santa Clara, CA), following the Agilent 1-color microarray-based gene expression analysis protocol.

first: Xiaoling

last: Li


title: Glycosylation of the HA protein of H5N1 virus increases its virulence in mice by exacerbating the host immune response

status: Public on Dec 22 2016

city: Harbin

first: Dongming

state: HeilongJiang

address: 678 Haping Road

institute: Harbin Veterinary Research Institute

summary: The highly pathogenic avian influenza (HPAI) H5N1 viruses continue to circulate in nature and threaten public health. Although several viral determinants and host factors that influence the virulence of HPAI H5N1 viruses in mammals have been identified, the detailed molecular mechanism remains poorly defined and requires further clarification. In our previous studies, we characterized two naturally isolated HPAI H5N1 viruses that had similar viral genomes but differed substantially in their lethality in mice. Here, we explored the molecular determinants and potential mechanism for this difference in virulence. By using reverse genetics, we found that a single amino acid at position 158 of the hemagglutinin (HA) protein substantially affected the systemic replication and pathogenicity of these H5N1 influenza viruses in mice. We further found that the G158N mutation introduced an N-linked glycosylation at sites 158–160 of the HA protein and that this N-linked glycosylation enhanced viral productivity in infected mammalian cells and induced stronger host immune and inflammatory responses to viral infection. These findings further our understanding of the determinants of pathogenicity of H5N1 viruses in mammals.

overall_design: For all gene expression analyses, groups of three mice were inoculated with PBS or 106 EID50 of CK/1180 or CK/1180-1214HA. Total RNA was extracted from lung tissues on day 3 p.i. by using a QIAGEN RNeasy kit. The microarray assay was performed by using a Low RNA Input Linear Amplification Kit (Agilent Technologies, Santa Clara, CA) and Agilent’s Whole Mouse Genome Microarray Kit, 4×44 K (G4122F)

first: Libin

last: Liang

first: Hualan

last: Chen


title: Transcriptome profiling of CycG1-/- and CycG2-/- knockout deficient mouse embryonic fibroblasts

status: Public on Dec 19 2016

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: To examine if lack of CycG1 or CycG2 causes genome-wide alterations of gene expression, we performed DNA microarray analysis on G1KO and G2KO MEFs at their logarithmic growth phase.

overall_design: Microarray analyses were performed as dye-swapped regarding among WT, G1KO and G2KO.


title: Role of cytochrome c in α-synuclein radical formation: implications of α-synuclein in neuronal death in Maneb and paraquat-induced model of Parkinson's disease

status: Public on Nov 29 2016

summary: Altogether results show that peroxidase activity of cytochrome c contributes to α-synuclein radical formation and oligomerization, and that α-synuclein through its co-localization with cytochrome c or on it's own, affects several biological pathways which contribute to increased neuronal death in  Maneb and paraquat (MP)-induced model of Parkinson's disease.

overall_design: Nigrostriatal tissue of Controls, Wild-Type MP co-exposed mice, and MP-coexposed α-synuclein Knock out mice, were analysed by Microarray with three replicates for each group.

first: Ashutosh

last: Kumar

first: Douglas

last: Ganini

first: Ronald

last: Mason


title: Microarray analysis of innate immune response induced by immunization with the adjuvant QS-21 in lymph node and muscle in mice.

status: Public on Dec 06 2016

city: Rixensart

first: Margherita

last: Coccia

address: Rue de l'Institut 89

country: Belgium

institute: GSK Vaccines

summary: The goal of this study was to identify the transcriptional mechanisms involved in the activation of the immune system by QS-21, a triterpene glycoside purified from the bark of Quillaja saponaria which has adjuvant activity in vivo. Saponins represent a promising class of vaccine adjuvant. Together with the TLR4-ligand MPL, QS-21 is  part of the Adjuvant System AS01, a key component of the Malaria and Zoster candidate vaccines that  display demonstrated clinical efficacy. However, the mechanism of action of QS-21 in this liposomal  formulation is poorly understood. Upon intra-muscular immunisation, we observed that QS-21 rapidly  accumulated in CD169+ resident macrophages of the draining lymph node where it elicited a local  innate immune response. Depletion of these cells abrogated QS-21-mediated innate cell recruitment  to the lymph node, dendritic cell (DC) phenotypic maturation as well as the adjuvant effect on T cell and  antibody responses to co-administered antigens. DCs rather than lymph node-resident macrophages  were directly involved in T cell priming by QS-21 as revealed by the decrease in antigen-specific T cell  response in Batf3−/− mice. Further analysis showed that the adjuvant effect of QS-21 depended on the  integration of Caspase-1 and MyD88 pathways, at least in part through the local release of HMGB1.  Taken together, this work unravels the key role of lymph node sentinel macrophage in controlling the  adjuvant effect of a molecule proven to improve vaccine response in humans

overall_design: C57BL/6 mice (6-8 weeks old) were immunized in both hind limbs, in the gastrocnemius (gcm) muscles and in a volume of 50 µl/muscle with QS-21 (100mg/ml) formulated in liposomes or PBS. Ileac lymph nodes were identified as draining in setup experiments. Each tissue sample consisted of a pool of tissues of 2 mice ( either dLN or muscle). Total RNA was isolated by homogenizing tissues in Tripure reagent (1 ml/100 mg tissue; Roche Applied Science) and then extracted with chloroform followed by RNeasy™ Minikit (Qiagen) according to the manufacturer’s protocol. A DNAse treatment was applied on the RNeasy column to avoid genomic DNA contamination. RNA was concentrated by ethanol precipitation, and quantified by RiboGreen™ (Life Technologies). 1 µg of each RNA sample was used for target preparation,using a one-cycle cDNA synthesis kit, and hybridized to GeneChip_ Whole Mouse Genome 430 2.0 arrays (Affymetrix). Data acquisition was performed using GeneChip Operating Software (Affimetrix). For each condition, 6 mice were treated. dLN from 2 mice were pooled for each hybridization. 3 replicate chips were analysed per condition. Muscle_QS-21_4hpost_2 and Muscle_PBS_2hpost_3 have been excluded since they did not pass QC.

first: Sophie

last: Detienne

first: Iain

last: Welsby

first: Catherine

last: Collignon

first: Sandrine

last: Wouters

first: Laurye

middle: V

last: Maele

first: Severine

last: Thomas

first: Maelle

last: Swertvaegher

first: Aurelie

last: Detavernier

first: Abdelatif

last: Elouahabi

first: Stanislas

last: Goriely

first: Arnaud

last: Didierlaurent


title: The role of Calment in Drosophila longevity and oxidative stress resistance

status: Public on Dec 05 2016

city: Leuven

first: Patrick

last: Callaerts

address: Herestraat 49, bus 602

department: Department of Human Genetics

institute: University of Leuven

summary: The aim of this study is to gain insights into how Calment/CG3036 affects lifespan and oxidative stress resistance in Drosophila females. Here we perform a microarray analysis in isogenized Calment1/4 females and CanS controls

overall_design: Microarrays were performed on RNA extracted from whole adult females of Calment1/4 (isogenized into a CS10 background) and CanS, with microarrays performed in triplicate for both genotypes.

first: Callaerts

last: Patrick

first: Clements

last: Jason


title: Transcriptome profiling of CycG1-/- knockout, CycG2-/- knockout, and CycG1-/-CycG2-/- double knockout deficient mouse embryonic fibroblasts

first: Daisuke

last: Okuzaki


title: A druggable TCF4- and BRD4-dependent transcriptional network sustains malignancy in blastic plasmacytoid dendritic cell neoplasm

status: Public on Nov 15 2016

first: Louis

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

summary: We combined loss-of-function RNA interference screening and a high-throughput drug toxicity screening to define novel therapeutic targets in blastic plasmacytoid dendritic cell neoplasm (BPDCN), an aggressive hematologic malignancy for which no curative therapy exists. The E-box transcription factor TCF4 emerged as the master transcriptional regulator of the BPDCN oncogenic program, a finding that can be exploited for the accurate molecular diagnosis of BPDCN. Genetic interference with the TCF4-dependent network induced a rewiring of BPDCN gene expression, resulting in apoptosis. Treatment of BPDCN lines with bromodomain and extra-terminal domain inhibitors (BETi's) down regulated TCF4 and its target gene network, inducing apoptosis both in vitro and retarding growth of BPDCN xenografts in vivo, supporting the clinical evaluation of BETi's in this lethal cancer.

overall_design: For shRNA gene expression profiling, Cal-1 and Gen2.2 cells were infected with either Ctrl or TCF4 shRNAs. Following puromycin selection, shRNA expression was induced for 24 hours and 48 hours in Cal-1 cells (n=4), and for 12 hours and 24 hours in Gen2.2 cells (n=4). For JQ1 gene expression profiling, Cal-1 (n=4) and Gen2.2 (n=4) cells were treated with either DMSO or 100 nM JQ1 for 1 hour, 3 hours, 8 hours and 24 hours.


title: Host miRNA molecular signatures in the brains of mice are associated with acute herpes simplex virus 1 encephalitis

status: Public on Nov 01 2016

city: Winnipeg

first: Stephanie

last: Booth

state: Manitoba

address: 1015 Arlington Street

department: Molecular PathoBiology

institute: Public Health Agency of Canada

summary: Transcriptional profiling of mouse brain regions (microdissection of cerebellum and hippocampus regions) comparing control, untreated brain tissue with HSV-1 infected brain tissue. Two viral tires, 10^3 and 10^6 plaque forming units of HSV-1 strain F, were intracerebrally inoculated into the brain of SJL/J strain of mice. The goal was to assess global transcriptional dynamics in HSV-1 infected mice, a model of herpes simplex encephalitis, as compared to controls (either PBS or Vero cell suspension). The microarray data identified fluctuations in gene expression where many of these genes were also potential targets of miRNA-200 and miR-183 family members which were themselves upregulated within the same brain samples.

overall_design: Eight experimental conditions were compared: 1) hippocampus 10^3 plaque forming units of HSV-1 infected brain samples were compared to PBS control;  2) hippocampus 10^3 plaque forming units of HSV-1 infected brain samples were compared to Vero controls; 3) hippocampus 10^6 plaque forming units of HSV-1 infected brain samples were compared to PBS; 4) hippocampus 10^6 plaque forming units of HSV-1 infected brain samples were compared to Vero controls; 5) cerebellum 10^3 plaque forming units of HSV-1 infected brain samples were compared to PBS control;  6) cerebellum 10^3 plaque forming units of HSV-1 infected brain samples were compared to Vero controls; 7) cerebellum 10^6 plaque forming units of HSV-1 infected brain samples were compared to PBS; 8) cerebellum 10^6 plaque forming units of HSV-1 infected brain samples were compared to Vero controls. Biological replicates: 2 cerebellum 10^3 HSV-1 infected brain samples; 2 hippocampus 103 HSV-1 infected brain samples; 2 cerebellum 10^6 HSV-1 infected brain samples; 2 hippocampus 106 HSV-1 infected brain samples; 1 Vero control sample, 1 PBS control sample.  Dye swaps were performed for all array samples except for sample 251486812045_6LHippocmapus_10^3_555.txt.

first: Anna

last: Majer

first: Kyle

last: Caligiuri

first: Kamilla

last: Gale

first: Yulian

last: Niu

first: Clark

middle: S

last: Phillipson

first: Timothy


title: Expression data from D.melanogaster guts with a constitutively active Imd in the presence or absence of a microbiome

status: Public on Nov 03 2016

city: Edmonton

first: Edan

last: Foley

state: Alberta

address: 116 Street and 86 Ave

department: Medical Microbiology and Immunology

institute: University of Alberta

summary:
Innate immune responses contributed to the containment of intestinal microbes.
We used microarrays to examine transcriptional profiles of imflamed guts raised in convential or germ-free conditions. We found that gut inflammation and the gut microbiome regulate the expression of several hundred host genes.

overall_design: Genotype control flies and flies with a constitutively active Imd were raised on regular food or food supplemented with antibiotics to obtain conventionally reared (CR) or germ-free (GF) flies. Guts were dissected for RNA extraction and RNA was hybridized to Affymetrix GeneChip®Drosophila Genome 2.0 arrays to study the effects of gut inflammation in a microbiome dependant or independant manner on the transcriptional profile in host's gut.

first: Kristina

last: Petkau


title: Real-time quantitative PCR analysis of shed microvesicles and exosomes released by human colorectal cancer LIM1863 cell lines

status: Public on Oct 12 2016

city: Melbourne

first: MAOSHAN

last: CHEN

state: Victoria

address: La Trobe University, Bundoora

department: Department of Biochemistry and Genetics

country: Australia

institute: La Trobe University

summary:
Secreted microRNAs (miRNAs) enclosed within extracellular vesicles (EVs) play a pivotal role in intercellular communication by regulating recipient cell gene expression and affecting target cell function. Here, we report the isolation of three distinct EV subtypes from the human colon carcinoma cell line LIM1863--shed microvesicles (sMVs) and two exosome populations (immunoaffinity isolated A33-exosomes and EpCAM-exosomes). Deep sequencing of miRNA libraries prepared from parental LIM1863 cells/derived EV subtype RNA yielded 254 miRNA identifications, of which 63 are selectively enriched in the EVs--miR-19a/b-3p, miR-378a/c/d, and miR-577 and members of the let-7 and miR-8 families being the most prominent. Let-7a-3p*, let-7f-1-3p*, miR-451a, miR-574-5p*, miR-4454 and miR-7641 are common to all EV subtypes, and 6 miRNAs (miR-320a/b/c/d, miR-221-3p, and miR-200c-3p) discern LIM1863 exosomes from sMVs; miR-98-5p was selectively represented only in sMVs. Notably, A33-Exos contained the largest number (32) of exclusively-enriched miRNAs; 14 of these miRNAs have not been reported in the context of CRC tissue/biofluid analyses and warrant further examination as potential diagnostic markers of CRC. Surprisingly, miRNA passenger strands (star miRNAs) for miR-3613-3p*, -362-3p*, -625-3p*, -6842-3p* were the dominant strand in A33-Exos, the converse to that observed in parental cells. This finding suggests miRNA biogenesis may be interlinked with endosomal/exosomal processing.

This work was supported by National Health and Medical Research Council of Australia (NHMRC) program grant #487922.

overall_design: qRT-PCR miRNA expression profiling. Same amount of total RNA was used for LIM1863 cells and released extracellular vesicles (sMVs, A33-Exos and EpCAM-Exos).

first: Maoshan

last: Chen


title: Transient RNA-DNA Hybrids Are Required for Efficient Double-Strand Break Repair

status: Public on Oct 28 2016

city: Canberra

first: Tamas

last: Fischer

state: ACT

address: Building 131, Garran Rd

department: The John Curtin School of Medical Research

institute: The Australian National University

type: Expression profiling by genome tiling array

summary:
RNA-DNA hybrids are a major internal cause of DNA damage within cells, and their degradation by RNAse H enzymes is important for maintaining genomic stability.
Here, we identified an unexpected role for RNA-DNA hybrids and RNase H enzymes in DNA repair.
Using a site-specific DNA double-stranded break (DSB) system in Schizosaccharomyces pombe, we showed that RNA-DNA hybrids form as part of the homologous recombination (HR)-mediated DSB repair process and RNase H enzymes are essential for their degradation and efficient completion of DNA repair.
Deleting RNase H stabilizes RNA-DNA hybrids around DSB sites and strongly impairs recruitment of the ssDNA-binding RPA complex.
In contrast, overexpressing RNase H1 destabilizes these hybrids, leading to excessive strand resection and RPA recruitment, and to severe loss of repeat regions around DSBs.
Our study challenges the existing model of HR-mediated DSB repair, and reveals a surprising role for RNA-DNA hybrids in maintaining genomic stability.

overall_design: Microarrays were performed twice in biological replicates.

first: Corina

last: Ohle

first: Rafael

last: Tesorero

first: Géza

last: Schermann

first: Nikolay

last: Dobrev

first: Irmgard

last: Sinning

first: Tamás


title: Comparison of gene expression patterns between Lgr5 positive cells and CD24 hi cells in murin colon

status: Public on Oct 05 2016

city: Utrecht

first: Kay

last: Wiebrands

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Using Lgr5_EGFP-ires-CreERT2 allows us to sort colonic stem cells and CD24 positive cell are subpopulation of Goblet cells in colon

overall_design: In Lgr5_EGFP-ires-CreERT2 knockin mice, GFP is expressed under the control of Lgr5 promoter, we used PE-conjugated anti-CD24 antibody to sort subset of Goblet cells from colonic crypts

first: Toshiro

last: Sato

first: Nobuo

last: Sasaki

first: Hans

last: Clevers


title: PRRUB FACS cells microarray

status: Public on Oct 15 2016

city: new orleans

first: IHOR

last: YOSYPIV

state: Louisiana

address: 1430 tulane ave.

department: PEDIATRICS

institute: Tulane University

summary: This experiment aimed to uncover the genome-wide alternation in gene expression resulting from the removal of PRR from the population ureteric bud and collecting duct  and successive changes to the series of events in kidney development.

overall_design: Two Wild type pooled samples and two KO pulled samples are performed for the microarray to compare the gene changes.

first: Ihor

last: Yosypiv

first: Renfang

last: Song


title: Expression analysis of cerebellar granular cell layer isolated from PTEN conditional null mutants and controls

status: Public on Sep 30 2016

city: Munich

first: Moritz

last: Rossner

address: Nussbaumstr. 7

department: Psychiatry

country: Germany

summary:
A neuronal PI(3,4,5)P3-dependent program of oligodendrocyte precursor recruitment and myelination was identified in mice that conditionally lack PTEN in cerebellar granular cells (PTEN cKO)
Expression analysis was performed with RNA obtained selectively from cerebellar granular cell layer of PTEN conditional null mutants and controls

overall_design: The cerebellar granule cell layer was microdissected from brain sections to isolate total RNA which was amplified and used for expression analysis using micrarrays

first: Sandra

last: Goebbels

first: Georg

middle: L

last: Wieser

first: Sven

last: Wichert

first: Klaus-Armin

last: Nave


title: Polycomb Underlies Transcriptional Heterogeneity in Lineage Priming of Embryonic Stem Cells [gene expression]

status: Public on Oct 11 2016

city: Edinburgh

first: Rob

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

institute: The University of Edinburgh

summary: Quantitation of polyA mRNA levels in subpopulations of the HexVenus reporter (clone HV5.1) mouse ES cell line growing under self-renewing conditions. Subpopulations were identified and isolated based on the expression of the ES cell surface marker SSEA 1 and the expression of the venus protein. At approximately 70% confluence, cells were trypsinised, resuspended in FACs buffer (10%FCS in PBS) and incubated with a mouse monoclonal antibody to SSEA 1 (MC-480, Developmental Hybridoma Studies Bank, University of Iowa). Cells were then incubated with an Alexa-647 conjugated anti-mouse IgM antibody (Invitrogen) and subpopulations were fractionated by flow cytometry. The aim was to identify genes which are differentially expressed between FACS-sorted HV-S+ and HV+S+ primed mESC populations.

overall_design: mESCs carrying a fluorescently tagged Hhex-Venus (HV) reporter construct were FACS sorted into Ssea1+HV- and Ssea1+HV+ populations. RNA was isolated from these populations immediately following FACS sorting and hybridised to Agilent 44k expression arrays. This process was performed as two independent biological replicates.

first: Robert

first: Jurriaan

last: Hölzenspies

first: Wendy

last: Bickmore

first: Joshua

last: Brickman


title: Bisphenol A modulation of DNA repair

status: Public on Sep 26 2016

first: NIEHS

last: Microarray Core

state: NC

department: DIR

summary: To better understand gene expression changes that occur after BPA co-exposure with the oxidizing agent potassium bromate (KBrO3), we have employed whole genome microarray expression profiling to identify genes that are uniquely regulated by exposure to KBrO3, BPA, and co-exposure to both agents. Mouse embryonic fibroblasts deficient in the non-homologous end joining protein Ku70 were exposed to KBrO3, BPA, and both KBrO3 and BPA. Treated samples were isolated 4 and 24 hours after the initiation of DNA damage, along with control untreated samples. Gene expression changes were identified between the treated samples and the controls. From these comparisons, 755 unique gene changes were attributed only to the co-exposure condition at both time points, with only 86 of these genes overlapping between 4 and 24 h. The 24 h time point showed significant up-regulation of DNA repair genes that address oxidatively-induced DNA damage, including Ercc4, Ercc5, Ercc8, and Ogg1.

overall_design: Mouse embryonic fibroblasts deficient in the non-homologous end joining protein Ku70 were exposed as follows: KBrO3 only samples were exposed to 20 mM KBrO3 for 1 hour, then allowed to repair for an additional 3 or 23 hours; BPA only samples were exposed to 150 uM BPA for 4 or 24 hours; and co-exposed samples were exposed to 150 uM BPA for 1 h, then 20 mM KBrO3 and 150 uM BPA for 1 h, and finally, 150 uM BPA for an additional 3 or 23 hours. Treated samples were isolated 4 and 24 hours after the initiation of DNA damage, along with control untreated samples at the same time points. Three independent experiments were performed at each time (4 or 24 hours).

first: Natalie

last: Gassman

first: Samuel

middle: H

last: Wilson


title: Expression data from bam and setdb1 mutant ovaries

status: Public on Aug 31 2016

city: Rensselaer

first: Sridar

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary:
Germline stem cell self-renewal and differentiation are required for sustained production of gamates. GSC differentiation in drosophila requires expression of setdb1 by the somatic niche, however its function is not known.
We used microarray analysis to determine what genes does setdb1 regulate to affect differentiation.

overall_design: Less than 5 day old Drosophila ovaries were selected for RNA extraction and hybridization on Affymetrix microarrays. Ovaries were selected from bam and setdb1 mutants as both of them are developmentally arrested at the same stage.

first: Prashanth

last: Rangan


title: Expression data from mice overexpressing Tcfeb specifically in P14 kidney

status: Public on Aug 29 2016

first: Rossella

last: De Cegli

summary:
In order to identify the effects of Tcfeb overexpression on the kidney transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the double heterozygous KSP_CRE/KSP_Tcfeb 14 days old mice as compared to control KSP_CRE mice
Transcriptome analysis of 14 days old mice overexpressing Tcfeb specifically in kidney

overall_design: For the analysis on 14 days old mice overexpressing Tcfeb, total RNA was extracted from the kidney of three mice; RNA extracted from the kidney of three mice was used as control.


title: Expression data from wildtype and foxL1null Drosophila embryos

status: Public on Sep 10 2016

city: Baltimore

first: Caitlin

middle: D

last: Hanlon

state: MARYLAND

address: 725 N Wolfe St, Hunterian G10

department: Cell Biology

institute: JHMI

summary:
Determining how organs attain precise positioning within an organism is a crucial facet of developmental biology. The Fox family winged-helix transcription factors are known to play key roles in development of multiple organs. Drosophila FoxL1 (aka Fd64A) is dynamically expressed in embryos but its function is completely uncharacterized. FoxL1 is expressed in a single group of body wall - muscles in the 2nd and 3rd thoracic segments, in homologous abdominal muscles at earlier stages, and in the hindgut mesoderm from early through late embryogenesis. We show that FoxL1 expression in T2 and T3 is in VIS5, which is not a single muscle spanning the entire thorax, as previously published, but is, instead, three individual muscles, each spanning a single thoracic segment. We generate mutations in foxL1 and show that, surprisingly, none of the tissues that express FoxL1 are affected by its loss. Instead, loss of foxL1 results in defects in salivary gland positioning and morphology, as well as defects in the migration of hemocytes, germ cells and Malpighian tubules. We also show that FoxL1-dependent expression of secreted Sema2a in T3 VIS5 is required for normal salivary gland positioning. Altogether, these findings suggest that Drosophila FoxL1 functions like its mammalian counterpart in non-autonomously orchestrating the behaviors of surrounding tissues.
We performed a microrarray analysis comparing gene expression changes between wild-type and foxL1 null embryos (foxL1del/foxL1cr). Total RNA was collected from embryos from stages 11-15, which correspondes with expression of foxL1 in the embryo.

overall_design: Total RNA was isolated from stage 11-15 foxLCr/foxL1del embryos and from stage-matched Oregon R wild-type embryos. The Qiagen RNeasy kit was used for RNA cleanup. Standard Affymetrix protocols were used to label and amplify total RNA (100 ng per sample). Three independent biological RNA samples (WT_rep1-3; KO_rep1-3) of each genotype were hybridized to the Drosophila genome 2.0 Chip.

first: Deborah

last: Andrew


title: Expression data from mice overexpressing Tcfeb specifically in P0 kidney

address: Via Campi Flegrei 34

summary:
In order to identify the effects of Tcfeb overexpression on the kidney transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the double heterozygous KSP_CRE/KSP_Tcfeb mice as compared to control KSP_CRE mice
Transcriptome analysis of mice overexpressing Tcfeb specifically in kidney

overall_design: For the analysis on mice overexpressing Tcfeb, total RNA was extracted from the kidney of three mice; RNA extracted from the kidney of two mice was used as control.


title: Adaptation of a RAS pathway activation signature from FF to FFPE tissues in colorectal cancer (FFPE Affymetrix)

status: Public on Sep 20 2016

city: Spartanburg

first: Bernard

last: Omolo

state: SC

address: 800 University Way

department: Mathematics and Computer Science

institute: University of South Carolina - Upstate

summary:
Background: The KRAS gene is mutated in about 40% of colorectal cancer (CRC) cases, which has been clinically validated as a predictive mutational marker of intrinsic resistatnce to anti-EGFR inhibitor (EGFRi) therapy. Since nearly 60% of patients with a wild type KRAS fail to respond to EGFRi treatment, there is a need to develop more reliable molecular signatures to better predict response. Here we address the challenge of adapting a gene expression signature predictive of RAS pathway activation, created using fresh frozen (FF) tissues, for use with more widely available formalin fixed paraffin-embedded (FFPE) tissues.
Methods: In this study, we evaluated the translation of an 18-gene RAS pathway signature score from FF to FFPE in 54 CRC cases, using a head-to-head comparison of five technology platforms. FFPE-based technologies included the Affymetrix GeneChip (Affy), NanoString nCounter(NanoS), Illumina whole genome RNASeq (RNA-Acc), Illumina targeted RNASeq(t-RNA), and Illumina stranded Total RNA-rRNA-depletion (rRNA).
Results: Using Affy_FF as the gold standard, initial analysis of the 18-gene RAS scores on all 54 samples shows varying pairwise Spearman correlations, with (1) Affy_FFPE(r=0.233, p=0.090); (2) NanoS_FFPE(r=0.608, p<0.0001); (3) RNA-Acc_FFPE(r=0.175, p=0.21); (4) t-RNA_FFPE (r=-0.237, p=0.085); and (5) t-RNA (r=-0.012, p=0.93). These results suggest that only NanoString has successful FF to FFPE translation. The subsequent removal of identified problematic samples (n=15) and gene (n=2) further improves the correlations of Affy_FF with three of the five technologies: Affy_FFPE (r=0.672, p<0.0001); NanoS_FFPE (r=0.738, p<0.0001); and RNA-Acc_FFPE (r=0.483, p=0.002).
Conclusions: Of the five technology platforms tested, NanoString technology provides a more faithful translation of the RAS pathway gene expression signature from FF to FFPE than the Affymetrix GeneChip and multiple RNASeq technologies. Moreover, NanoString was the most forgiving technology in the analysis of samples with presumably poor RNA quality. Using this approach, the RAS signature score may now be reasonably applied to FFPE clinical samples.

overall_design: Fifty-four (54) FFPE evaluable tumor specimens were selected from a larger multi-center cohort of 468 well-characterized colorectal adenocarcinoma patients whose tissues were obtained between October 2006 and September 2010 at the University of South Florida. The sample cohort was composed of tumor samples that were available as matched fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) pairs.

first: Mingli

last: Yang

first: Fang

last: Lo

first: Michael

last: Schell

first: Sharon

last: Austin

first: Kellie

last: Howard

first: Anup

last: Madan

first: Timothy

last: Yeatman


title: Adaptation of a RAS pathway activation signature from FF to FFPE tissues in colorectal cancer (FF Affymetrix)

overall_design: Fifty-four (54) FF evaluable tumor specimens were selected from a larger multi-center cohort of 468 well-characterized colorectal adenocarcinoma patients whose tissues were obtained between October 2006 and September 2010 at the University of South Florida. The sample cohort was composed of tumor samples that were available as matched fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) pairs.


title: Expression data on salivary glands tissues of 3rd instar larvae from w[1118] wildtype and dTCTP mutants.

status: Public on Aug 16 2016

city: Daejeon

first: Kwang-wook

last: Choi

address: KAIST 291, Daehak-ro, Yuseong-gu

country: South Korea

institute: KAIST

summary:
Drosophila translationally controled tumor protein (dTCTP) is important to repair double stranded DNA breaks in cell nucleus. However, besides damaged DNA loci, dTCTP is also located in interbands region of polytene chromsomes of salivary gland tissues.
To address whether dTCTP is involved in transcriptional regulation process, we performed microarrays in salivary gland tissues from dTCTP mutants and w[1118] wildtype control.

overall_design: Salivary glands tissues were dissected and collected from 3rd instar larvae or each genotype for RNA extraction and hybridization on Affymetrix microarrays.

first: Sung-Tae

last: Hong


title: Transcriptional profiles of induced thyroid follicular like cells.

city: Tsukuba city

first: Takaaki

last: Noguchi

state: Ibaraki prefecture

department: Life and environmental sciences

institute: The University of Tsukuba

summary: Defined transcription factors can direct changes in programmed cell fate to give rise to various cell lineages, in contrast to the one-way street during development. Direct lineage conversions from fibroblasts occur in all the three germ layer derivatives- neurons, cardiomyocytes, and hepatocytes. However, direct reprogramming of thyroid lineages has not been accomplished yet. Previous studies demonstrated that exogenous Pax8 and Nkx2.1, which are indispensable for proper thyroid development, enable the pluripotent stem cell-derived definitive endoderm to differentiate into functional thyroid follicular cells. This raised the question whether a cocktail of thyroid development-related transcription factors can directly convert fibroblasts into thyroid follicular cells in vitro. In the current study, we found that induction of defined transcription factors is able to generate thyroid follicular cells from fibroblasts. Further, Pax8, Nkx2.1, Foxe1, Oct3/4, Sox2, Klf4, and c-Myc were sufficient to generate thyroglobulin (Tg)+/EpCAM+ colonies from mouse embryonic fibroblasts, and these colonies built three-dimensional (3D) follicular-like structures in matrigel-based 3D culture. These induced thyroid follicular-like cells, named iTF cells, were morphologically and transcriptionally similar to those of the adult thyroid. Finally, iTF cells were transplantable into the kidney capsule, and formed huge follicular structures in vivo as well. Our study therefore reveals that thyroid lineage can be directly derived from fibroblasts in a single step, and contributes to rapid translational research on human thyroid diseases such as hyperthyroidism.

overall_design: We generated arrays from Pax8, Nkx2.1, Foxe1, Hhex, Oct3/4, Sox2, Klf4, and c-Myc induced thyroid follicular-like cells derived from fibroblast cutures. In addition, we also generated arrays from primary thyroid follicular cell cultures as controls. All the datas were normalized to 75% tile shift..

first: Naoto

last: Ninomiya


title: Increased metastasis with loss of E2F2 in Myc-driven tumors

status: Public on Aug 08 2016

city: East Lansing

first: Eran

middle: Robert

last: Andrechek

state: MI

address: 567 Wilson Rd. Room 2120

department: Physiology

institute: Michigan State University

summary: In human breast cancer, mortality is associated with metastasis to distant sites. Therefore, it is critical to elucidate the biological mechanisms that underlie tumor progression and metastasis.  Using signaling pathway signatures we previously predicted a role for E2F transcription factors in Myc induced tumors.  To test this role we interbred MMTV-Myc transgenic mice with E2F knockouts.  Surprisingly, we observed that the loss of E2F2 sharply increased the percentage of lung metastasis in MMTV-Myc transgenic mice. Examining the gene expression profile from these tumors, we identified genetic components that were potentially involved in mediating metastasis.  These genes were filtered to uncover the genes involved in metastasis that also impacted distant metastasis free survival in human breast cancer.  In order to elucidate the mechanism by which E2F2 loss enhanced metastasis we generated knockdowns of E2F2 in MDA-MB-231 cells and observed increased migration in vitro and increased lung colonization in vivo.  We then examined genes that were differentially regulated between tumors from MMTV-Myc, MMTV-Myc E2F2-/-, and lung metastases samples and identified PTPRD. To test the role of PTPRD in E2F2-mediated breast cancer metastasis, we generated a knockdown of PTPRD in MDA-MB-231 cells. We noted that decreased levels of PTPRD resulted in decreased migration in vitro and decreased lung colonization in vivo. Taken together, these data indicate that E2F2 loss results in increased metastasis in breast cancer, potentially functioning through a PTPRD dependent mechanism.

overall_design: Lung metastases from MMTV-Myc tumors in a E2F2 knockout and E2F3 +/- backgrounds were analyzed for their gene expression profile


title: Characterization of 5-aminolevulinic acid effects on radiotherapy using mouse tumor model.

status: Public on Aug 14 2016

city: Tsukuba

first: Junko

last: Takahashi

state: Ibaraki

address: 1-1-1 Umezono

institute: National Institute of Advanced Industrial Science and Technology　(AIST)

summary: B16-BL6 mouse melanoma that had been maintained in C57BL/6J mice were used to evaluate the 5-aminolevulinic acid (ALA) effects on radiotherapy. Mice were divided into 4 groups after implantation of B16-BL6 cells; (1) control group; (2) ALA treatment; (3) Xray treatment; (4) ALA and Xray treatment.

overall_design: B16-BL6 mouse melanoma tumor gene expressions in 4 groups were measured after fractionated doses of radiation with local administration of 50mg/kg ALA prior to fractional irradiation.

first: Hitoshi

last: Iwahashi


title: Cohesin in AML

status: Public on Aug 09 2016

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

summary: Depletion of Rad21 in murine bone marrow leads to enhanced self-renewal in vitro

overall_design: Bone marrow was extracted from mice, infected with lentiviruses encoding shRNAs to Rad21, and cultured in methylcellulose with cytokines for one passage.

first: Kirthi

last: Pulakanti


title: Activation of Ftz-F1-responsive genes through Ftz/Ftz-F1 dependent enhancers

status: Public on Sep 27 2016

city: College Park

first: William

middle: R

last: Anderson

state: MD

address: 4112 Plant Sciences Building

department: Entomology

institute: University of Maryland

summary: The orphan nuclear receptor Ftz-F1 is expressed in all somatic nuclei in Drosophila embryos but mutations result in a pair-rule phenotype. Previously characterized Ftz-F1 target genes were co-regulated by Ftz, which is expressed in stripes, consistent with the pair-rule phenotype observed for ftz-f1 and ftz mutants. However, attempts to identify new target genes on the basis of Ftz-F1 and Ftz binding sites alone has met with only limited success. To discern the rules for Ftz-F1 target site selection in vivo and to identify additional target genes, a microarray analysis was performed comparing wildtype and ftz-f1 mutant embryos.

overall_design:
Drosophila embryos from a cross between w[118] males and FRT germ-line clone ftz-f1 females or FRT germ-line clone w[118] females were hand selected at 3 stages of development (5, 6 and 8) for RNA extraction and hybridization on Affymetrix microarrays.
---------------------------------
The authors state that "Affymetrix CEL files have been lost."

first: W

first: Leslie

last: Pick


title: Genetic Susceptibility to Diabetic Nephropathy is Related to Pro-inflammatory Pathways

status: Public on Aug 13 2016

city: SINGAPORE

first: SUJOY

last: GHOSH

address: 8 COLLEGE ROAD

department: Cardiovascular & Metabolic Diseases

country: Singapore

institute: DUKE-NUS Graduate Medical School

summary: Diabetic nephropathy (DN) is a leading cause of ESRD worldwide, but its molecular pathogenesis is not well-defined and there are no specific treatments.   In humans, there is a strong genetic component determining susceptibility to DN.  However, specific genes controlling DN susceptibility in humans have not been identified.  Here we describe a new mouse model, combining type 1 diabetes with activation of the  renin angiotensin system (RAS), which develops robust kidney disease with features resembling human DN:  heavy albuminuria, hypertension and glomerulosclerosis.   Additionally, there is a powerful effect of genetic background regulating susceptibility to nephropathy.  The 129 strain is susceptible to kidney disease, whereas the C57BL/6 strain is resistant.  To examine the molecular basis of this differential susceptibility, we analyzed the glomerular transcriptome of young mice with albuminuria but without detectable alterations in glomerular structure .  We find dramatic difference in regulation of immune and inflammatory pathways with up-regulation of pro-inflammatory pathways in the susceptible (129) strain and coordinate down-regulation in the resistant (C57BL/6) strain, compared to their respective baselines.  Many of these pathways were also up-regulated in a rat model and in humans with DN.  Our studies suggest that genes controlling inflammatory responses, triggered by hyperglycemia and hypertension, may be critical early determinants of susceptibility to DN.

overall_design: The analysis was carried out on 2 strains of mice (129/SvEv and C57BL/6), each involving 2 genotypes (wild-type and RenTg/Ins2Akita mutations). Four replicates were used for each strain-genotype (with the exception of 129/SvEv wild-type mice, which had 3 replicates).

first: Susan

last: Gurley

first: Sujoy

last: Ghosh

first: Thomas

last: Coffman


title: Transcriptome profiling of Lats2 deficient mouse embryonic fibroblasts

status: Public on Jul 26 2016

city: Suita

first: Daisuke

last: Okuzaki

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Chromatin modifying activities for construction of appropriate epigenetic landscapes by polycomb repressive complex 2 (PRC2) play an essential role in development and tumorigenesis. However, the spatiotemporal mechanisms by which PRC2 achieves diverse epigenomes for specific tissue or cellular contexts remain poorly understood. Here, we discovered that LATS2 knockout causes dysregulation of PRC2 and subsequent transcriptome changes for differentiation in both mouse and human cells. LATS2 depletion dependent dysregulation of PRC2 also effects H3K4me3 and forms negative feedback loop for maintenance of PRC2. Further analyses reveal that LATS2 on chromatin binds to EZH2 and LATS2 has ability to phosphorylate PRC2 in vitro. These LATS2 dependent H3K27me3 targets are highly induced during neurogenesis, and statistical analysis of glioblastoma multiforme reveals that LATS2-high cases show more dedifferentiated transcriptome and poor prognosis with silencing of H3K27me3 targets. These observations suggest that LATS2-mediated epigenome coordination is pivotal for development and disease, including cancer.

overall_design: The labeled cRNAs from three pairs of MEFs (Lats2-/- vs Lats2 +/+) from three independent litter were subjected to Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F in dye swap setup, resulting in eight individual microarrays including tehnical replicates.

first: Kosuke

last: Torigata


title: Transcriptome profiling of mouse embryonic fibroblasts upon contact inhibition

overall_design: The labeled cRNAs from MEFs in two different culture conditions (low density vs high density culture) were subjected to Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F in dye swap setup, resulting in two individual microarrays.


title: The truncated somatostatin receptor sst5TMD4 stimulates the angiogenic process and is associated with lymphatic metastasis and poor prognosis in breast cancer patients

status: Public on Aug 04 2016

city: Madrid

first: Gema

last: Moreno-Bueno

state: Madrid

address: Arturo Duperier

department: Biochemistry

institute: IIB

summary: The presence of the truncated somatostatin receptor sst5TMD4 is associated with poor prognosis in breast cancers and increases malignancy in breast cancer cell lines. The objective of this study was to examine the cellular and molecular mechanisms underlying this association in order to identify new molecular targets for diagnosis, prognosis or therapy of these tumors. Therefore, a gene expression array was implemented using sst5TMD4 stably-transfected MCF-7 cells and their respective controls (empty plasmid); which revealed the existence of a profound alteration in the expression of genes involved in several tumoral processes such as cell survival or angiogenesis. Further characterization of sst5TMD4-overexpressing MCF-7 cells demonstrated increased expression/production of key pro-angiogenic factors and enhanced capacity to form mammospheres. These data were confirmed in a xenograft model of in vivo tumoral growth, where inoculation of sst5TMD4 transfected MCF-7 cells induced tumors with higher levels of VEGF and elevated number of blood vessels. Finally, sst5TMD4 was found to be expressed in a subset of human breast cancer samples where it correlated with angiogenic markers (VEGF, Angiopoietin-1 and CD34), the presence of lymphatic metastasis and disease-free survival of the breast cancer patients. Altogether, these data demonstrate a key role of the truncated sst5TMD4 receptor in the control of the angiogenic process during breast cancer progression. Therefore, these results support the role of sst5TMD4 in tumor malignancy and metastatic potential in breast cancers and may help to identifying new lines of actions for future drug therapies for these tumors.

overall_design: Four independent passages from stably-transfected sst5TMD4-pCDNA3.1 and empty-pCDNA3.1 vector, used as control (mock), MFC7 cells were used.

first: Manuel

last: Gahete

first: David

last: Rincón-Fernández

first: Mario

last: Durán-Prado

first: Marta

last: Hergueta-Redondo

first: Alejandro

last: Ibánez-Costa

last: Rojo-Sebastián

first: Francisco

last: Gracia-Navarro

first: Michael

last: Culler

first: Oriol

last: Casanovas

first: Raúl

last: Luque

first: Justo

middle: P

last: Castaño


title: Expression data from adult Drosophila melanogaster males

status: Public on Aug 05 2016

city: Aarhus

first: Jesper

middle: Givskov

last: Soerensen

address: Ny Munkegade 114

department: Bioscience

country: Denmark

institute: Aarhus University

summary:
We used microarrays to investigate the transcriptome of 6 days old male flies exposed to either 15 or 25 C development at either constant or fluctuating temperatures. Further, we investigated gene expression at benign (20C) and high (35C) temperatures
With global climate change temperature means and variability are expected to increase. Thus, exposures to elevated temperatures are expected to become an increasing challenge for terrestrial ectotherm populations. While evolutionary adaptation seems to be constrained or proceed at an insufficient pace, many populations are expected to rely on phenotypic plasticity (thermal acclimation) for coping with the predicted changes. However, the effects of fluctuating temperature on the molecular mechanisms and the implications for heat tolerance are not well understood. To understand and predict consequences of climate change it is important to investigate how different components of the thermal environment, including fluctuating thermal conditions, contribute to changes in thermal acclimation. In this study we investigated the impact of mean and diurnal fluctuation of temperature on heat tolerance in Drosophila melanogaster and on the underlying molecular mechanisms in adult male flies. Flies from two constant and two ecologically relevant fluctuating temperature regimes were tested for their critical thermal maxima (CTmax) and associated global gene expression profiles at benign and thermally stressful conditions. Both temperature parameters contributed independently to the thermal acclimation, with regard to heat tolerance as well as the global gene expression profile. Although the independent transcriptional effects caused by fluctuations were relatively small, they are likely to be essential for our understanding of thermal adaptation. Thus, high temperature acclimation ability might not be measured correctly and might even be underestimated at constant temperatures. Our data suggests that the particular mechanisms affected by thermal fluctuations are related to phototransduction and environmental sensing. Thus genes and pathways involved in those processes are likely to be of major importance in a future warmer and more fluctuating climate.

overall_design: Eight experimental groups were analyzed in triplicate, in total 24 Affymetrix GeneChip Drosophila Genome 2.0 Arrays

middle: G

last: Sørensen

first: Mads

last: Schou

first: Torsten

middle: N

last: Kristensen

first: Volker

last: Loeschcke


title: Gene expressions in reaggregated thymus organ culture (RTOC) and 2D culture of thymic stromal cells

status: Public on Jul 12 2016

city: Bunkyo-ku

first: Ryo

last: Motosugi

state: Tokyo

address: 7-3-1 Hongo

department: Graduate School of Pharmaceutical Sciences

institute: The University of Tokyo

summary:
Comparison of gene expression profiles between RTOC and 2D culture of thymic stromal cells
Beta5t, which is a specific subunit of thymoproteasomes, is indispensable for maturation of CD8+ T cells. beta5t is expressed in thymus, and it is necessary for its expression to maintain 3D architecture of thymus. To search for the genes associated with its expression, we performed the microarray analysis, and compared expression levels of each gene between reaggregate thymus organ culture (RTOC) and 2D culture of thymic stromal cells.

overall_design: Two independent experiments were performed using fetal thymus from E14.5 and E15.5 mice.

first: Yasumasa

last: Nishito

first: Shigeo

last: Murata


title: Ascl2 acts as an R-spondin/Wnt responsive switch to control stemness in intestinal crypts

status: Public on Jul 15 2016

city: Utrecht

first: Jurian

last: Schuijers

state: Utrecht

address: Uppsalalaan 8

institute: Hubrecht Insitute

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Identification of the molecular targets of Orm1 in regenerating mouse liver

status: Public on Jul 01 2016

city: Yokohama

first: Xian-Yang

last: Qin

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

institute: RIKEN Center for Integrative Medical Sciences

summary: To identify the molecular targets of orosomucoid (Orm1) during liver regeneration, GeneChip analysis was performed at 48 h after partial hepatectomy (PH) in regenerating mouse liver treated with siControl or siOrm. A total of 180 differentially expressed genes in Orm1 konckdown mouse liver by comparing with siControl were identified with a fold change more than 2. Then, pathway analysis performed on the altered gene expression profiles using Ingenuity Pathways Analysis (IPA) program revealed that cell cycle, Toll-like receptor and TGF-beta receptor signaling pathways were under control of Orm1 in regenerating mouse livers.

overall_design: Three days post In vivo knockdown of Orm1 with its siRNA administered to mice using Invivofectamine 3.0 by a single injection, 40% PH was perfomred and gene expression prolifes of regenerating mouse livers at 48 h after PH was measued using Affymetrix GeneChip Mouse Genome 430A 2.0 Array.

first: Soichi

last: Kojima