title: Deregulated gene profiles of zebrafish larvae exposed to environmentally relevant concentrations of synthetic glucocorticoid

first: Siew Hong

last: Lam

address: #02-01, T-Lab Building, 5A Engineering Drive 1

institute: National University of Singapore

summary: To investigate the effects of glucocorticoids on the gene expression profiles in zebrafish, we performed a microarray-based transcriptomic study using larvae exposed to three representative glucocoriticoids at environmentally relevant high and low concentrations. Transcriptiomic profiel of developing zebrafish larvae exposed to dexamethasone, prednisolone or triamcinolone at 50 pM to 50 nM from 3 hours post-fertilisation to 5 days post-fertilisation were analyzed using G2519F Agilent Zebrafish Whole Genome Oligo Microarray Ver3.0, 4x44K.

overall_design: Embryos aged 3 h post-fertilisation were exposed to 5 nM or 50 nM of glucocorticoid (dexamethasone, prednisolone or triamcinolone) in 0.05% (v/v) DMSO while the control group was exposed to 0.05% (v/v) DMSO only. At 5 days of exposure, larvae were collected for transcriptomic study. Four biological replicates from control group and five biological replicates from treated groups were analyzed using microarry.

first: Siew

first: Qiyu

last: Chen


title: MicroRNA expression in CD34+-EC aggregates

status: Public on Jul 07 2017

city: Philadelphia

first: Sezin

last: Aday

state: Pennsylvania

address: 210 South 33rd Street, Skirkanich Hall

country: USA

institute: University of Pennsylvania

summary: To understand the the effect of microparticles conjugated with vascular endothelial growth factor (VEGF) on human endothelial cells derived from human umbilical cord blood (UCB) CD34+ hematopoietic stem cells, we have employed microRNA microarray profiling. The microparticles used in this study were purchased from Invitrogen (Dynal magnetic microparticles coated with streptavidin, 4.5 micron in size) and modified in our lab. Cell suspensions were mixed with blank microparticles (without VEGF), soluble VEGF or VEGF-conjugated microparticles and seeded as hanging drops to prepare endothelial cell aggregates. Cell aggregates without any treatments were used as control. After 2 h or 8 h, the cell aggregates were collected and miRNA expression profiles were detected.

overall_design: The microRNA expression in CD34+-EC aggregates was evaluated after incubation with blank microparticles, VEGF-conjugated microparticles, soluble VEGF or without treatment for 2 h (for all experimental groups) and 8 h (for soluble VEGF and VEGF-conjugated microparticle groups). Three independent experiments were performed at each time.


title: Ectodini cichlid brain comparison of mating type

status: Public on Mar 28 2017

city: Portland

first: Suzy

last: Renn

state: OR

address: 3203 SE Woodstock Blvd

department: Biology

institute: Reed College

summary: Throughout the animal kingdom, we know many examples of mating system evolution that exemplify adaptive responses to changes in the environment, yet our understanding of the accompanying neural and molecular mechanisms that give rise to such behavioral changes remains understudied. In the present study we aimed to define the molecular basis of interspecific variation in social organization in Ectodini cichlids from Lake Tanganyika. We selected four closely related species that represent two independent evolutions of monogamy: the polygynous Xenotilapia ochrogenys, the monogamous Xenotilapia flavipinnis, the polygynous Microdontochromis tenuidentata and the monogamous Asprotilapia leptura. Using a single cichlid microarray platform, we conducted a total of 28 direct comparisons for neural gene expression level among males and 26 among females of four species that represent 2 independent evolutions of monogamy. Our results indicate the gene expression profiles display remarkable plasticity across different time scales because we find differences associated with sex, mating system, and lineage.

sample_organism:
Xenotilapia tenuidentata
Xenotilapia ochrogenys
Xenotilapia flavipinnis
Xenotilapia leptura

overall_design: We used a nested loop design with dye-swap to emphasize within-lineage comparison between species of different mating strategies. This data series represents males and females only and includes, for each sex, 9 arrays comparing inidividuals from 2 differeent species with different mating types (monogomous and polygamous)within the xenotilaipa lineage and 9 arrays comparing individuals from two different species of different mating types (polygamovus vs. monogomous) in the non-xenotilapia-lineage. There are 8 hybridizations that compare between the two lineages 4 of which are within-mating strategy and 4 of which are between mating strategy. Features have been filtered for sequence conservation across species under study.

middle: C

first: Hans

middle: A

last: Hofmann


title: Evaluation of DNA-binding preferences of non-metazoan C2H2 zinc finger proteins by PBM

status: Public on Jul 10 2017

city: Montreal

first: Hamed

middle: S

last: Najafabadi

state: QC

address: 740 Dr. Penfield Avenue, Room 7202

department: Human Genetics

country: Canada

institute: McGill University

summary: The largest and most diverse class of eukaryotic transcription factors contain Cys2-His2 zinc fingers (C2H2-ZFs). Here, we have explored the diversity of sequence preferences of C2H2-ZF proteins in non-metazoan organisms using PBM experiments.

sample_organism:
Physcomitrium patens
Arabidopsis thaliana
Schizosaccharomyces pombe
Histoplasma capsulatum
Neurospora crassa
Puccinia graminis
Schizophyllum commune
Toxoplasma gondii
Dictyostelium discoideum
Batrachochytrium dendrobatidis
Rhizopus delemar

overall_design: Protein binding microarray (PBM) experiments were performed for a set of 43 full-length non-metazoan C2H2-ZF proteins. Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to two double-stranded 44K Agilent microarrays, each containing a different DeBruijn sequence design, in order to determine their sequence preferences. Details of the PBM protocol are described in Berger et al., Nature Biotechnology 2006.

first: Matthew

middle: T

last: Weirauch

first: Ally

last: Yang

first: Mihai

last: Albu

first: Timothy

middle: R

last: Hughes


title: GATA4-dependent organ-specific endothelial differentiation controls liver development and embryonic hematopoiesis (1 of 3)

status: Public on Mar 09 2017

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: Microvascular endothelial cells (EC) are increasingly recognized as organ-specific gatekeepers of their microenvironment. Microvascular EC instruct neighboring cells in their organ-specific vascular niches by angiocrine factors that comprise secreted growth factors/angiokines, but also extracellular matrix molecules and transmembrane proteins. The molecular regulators, however, that drive organ-specific microvascular transcriptional programs and thereby regulate angiodiversity, are largely elusive. Opposite to continuous barrier-forming EC, liver sinusoids are a prime model of discontinuous, permeable micro-vessels. Here, we show that transcription factor GATA4 controls liver sinusoidal endothelial (LSEC) specification and function. LSEC-restricted deletion of GATA4 caused transformation of discontinuous liver sinusoids into continuous capillaries. Capillarization was characterized by ectopic basement membrane deposition and formation of an abundantly VE-Cadherin expressing continuous endothelium. Correspondingly, ectopic expression of GATA4 in cultured continuous EC mediated downregulation of continuous EC transcripts and upregulation of LSEC genes. Regarding angiocrine functions, the switch from discontinuous LSEC to continuous EC during embryogenesis caused liver hypoplasia, fibrosis, and impaired colonization by hematopoietic progenitor cells resulting in anemia and embryonic lethality. Thus, GATA4 acts as master regulator of hepatic microvascular specification and acquisition of organ-specific vascular competence indispensable for liver development. The data also establish an essential role of the hepatic microvasculature for embryonic hematopoiesis.

overall_design: Fetal livers of E11.5 embryos from Stab2-Cre;Gata4fl/fl and control mice were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Cyrill

last: Géraud

first: Philipp-Sebastian

last: Koch

first: Johanna

last: Zierow


title: Expression data of tongue mucosa from normal mice and mice treated by the 4-NQO

status: Public on Dec 06 2016

city: Lyon

first: PIERRE

last: SAINTIGNY

address: 28 Rue Laennec

country: France

institute: Centre Léon Bérard

summary:
A better understanding of molecular changes during oral tumorigenesis may help defining new personalized prevention strategies. In order to test this hypothesis, we analyzed whole-genome expression changes in a murine model of oral carcinogenesis, induced by an oral carcinogen (4-NQO)
We generated genome-wide expression profiles of microdissected cells from murine tongue at each step of oral tumorigenesis: normal mucosa, hyperplasia, dysplasia and tumor.

overall_design: 4-NQO was administered in half of them in their drinking water at the dose of 100 ug/mL for 8 weeks. Four mice treated with 4-NQO and four control mice were sacrificed every four weeks. Immediately following death, tongues were excised, longitudinally bisected, each half of the tongue was frozen on dry ice, embedded in OCT and stored at -80°C. By week 24, experiment was completed. Sections of mouse tongues allowed to identify histologic changes associated with oral tumorigenesis including normal mucosa in untreated mice tongue, and hyperplasia, dysplasia, and tumor in 4-NQO treated mice tongue. Biological replicates of normal mucosa, hyperplasia, dysplasia and tumor from 3 different mice were selected for microdissection and RNA extraction.

first: Pierre

last: Saintigny

first: Jean-Philippe

last: Foy


title: GATA4-dependent organ-specific endothelial differentiation controls liver development and embryonic hematopoiesis

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Ovarian Cancer and platin resistance: Different methylation in isogenic pairs of sensitive and resistant cell lines

status: Public on Jun 15 2017

city: Jena

first: Norman

last: Häfner

address: Bachstrasse 18

department: Gynecology

institute: Jena University Hospital

type: Methylation profiling by genome tiling array

summary: Identification of differently methylated regions of CpG islands in 3 pairs of EOC cell lines. Parental and cisplatin resistant cultures from A2780, SKOV3 and HeyA8 were compared for their genome wide methylation pattern.

overall_design: Comparative hybridisation of enriched, methylated DNA from parental and resistant cells.

first: Daniel

last: Steinbach

first: Matthias

last: Dürst

first: Ingo

middle: B

last: Runnebaum


title: microRNA counts from HepG2 (ENCSR257DJT)

status: Public on Oct 14 2016

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
Nanostring miRNA Array on human HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: microRNA counts from endothelial cell of umbilical vein (ENCSR223FVU)

summary:
Nanostring miRNA Array on human HUVEC

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: microRNA counts from K562 (ENCSR000AJL)

summary:
Irvine Nanostring K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Trancriptomic profiling of liver tumors in rats after chronical phenobarbital treatment

status: Public on Jul 12 2017

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

summary: Here we investigate the difference in global gene expression in different tumor types found in the liver of rats after NNM-initiation/PB-promotion of tumor growth. We aim to identify tumor characteristic expression in nodules, focii, adenomas and carcinomas.

overall_design: 4 weeks old male Wistar rats received a tumor initiation dose of 250 mg/kg NNM followed by daily administration of 50 mg/kg/day Phenobarbital (PB) for 17 months. We profiled mRNA expression in liver tumor tissues (carcinomas, adenomas, nodules, foci) to assess the differences between different tumor types. Surrounding liver tissue was used as control.

first: Teresa

last: Riegler

first: Michael

last: Römer

first: Bettina

last: Graup-Grasl


title: Trancriptomic profiling of hepatocytes and mesenchymal cells of rats treated with nongenotoxic carcinogens for up to 2 weeks

summary: Conventional notion regards the action of non-genotoxic carcinogens (NGC) an autonomous process largely confined to parenchymal cells. Here we aim to elucidate the role of the hepatic mesenchyme for the action of two prototypical NGC, phenobarbital (PB), an anti-epileptic drug, and cyproterone acetate (CPA) a gestagen used in contraceptive pills.

overall_design: 8 weeks old male and female Wistar rats received either 50 mg/kg/day Phenobarbital (PB) or 100 mg/kg/day Cyproterone acetate (CPA) for up to 14 days. We profiled mRNA expression in hepatocytes and mesenchymal cells to assess the different effects of PB and CPA on different liver tissues. Time-matched control animals received vehicle (Corn oil for CPA or Water for PB).


title: microRNA counts from HCT116 (ENCSR165GUQ)

summary:
Nanostring miRNA Array on human HCT116

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: microRNA counts from MCF-7 (ENCSR201IBH)

summary:
Nanostring miRNA Array on human MCF-7

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: microRNA counts from GM12878 (ENCSR000AJK)

summary:
Irvine Nanostring GM12878

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Influence of Anti-VEGFA and dexamathasone treatments on the early phase of cornea angiogenesis

status: Public on Feb 28 2017

city: Linkoping

first: Neil

last: Lagali

address: sandbacksgatan 7

department: Ophthalmology

country: Sweden

institute: linkoping University

summary:
Inflammation is a key component of pathological angiogenesis. Here we monitor gene expression profiles of the pre-sprouting phase of corneal angiogenesis in the rat model, as influenced by topically applied treatments.
We used GeneChip Rat Genome 230 2.0 Array to monitor gene expression profies of several genes in the different treatment groups

overall_design: Animals were sutured as a stimuli for neovascularisation, and treatments (anti-VEGFA, goat IgG and dexamethasone) given topically to module the early response. Eyedrops were given four times per day, for two days.

first: Anthony

last: Mukwaya

first: Pierfrancesco

last: Mirabelli

first: Maria

last: Xeroudaki

first: Beatrice

last: Peebo

first: Anton

last: Lennikov


title: microRNA counts from fibroblast of arm (ENCSR138ZXT)

summary:
Nanostring miRNA Array on human fibroblast of arm

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Improvement of isopropanol tolerance of Escherichia coli using adaptive laboratory evolution and omics technologies

status: Public on Jun 21 2017

city: Suita

first: Chiara

last: Furusawa

state: Osaka

address: Furuedai

country: Japan

institute: RIKEN Quantitative Biology Center

summary: To understand the mechanism of isopropanol tolerance of Escherichia coli for improvement of isopropanol production, we performed genome re-sequencing and transcriptome analysis of isopropanol tolerant E. coli strains obtained from parallel adaptive laboratory evolution under IPA stress.

overall_design: To examine the contribution of the gene expression changes to the isopropanol tolerance, transcriptome of the parent strain (duplicated) and 6 tolerant strains were analyzed.

first: Takaaki

last: Horinouchi

first: Kumi

last: Tanabe

first: Chikara


title: HDAC4 gene therapy

status: Public on Jul 27 2016

first: Carsten

last: Sticht

summary: C57BL/6N animals received at the age of 6 weeks either adeno associated virus from serotype 9 (AAV9) leading to cardiac overexpression of luciferase (Luc, as control) or amino acids 1-201 of histone deacetyase 4 (HDAC4-NT) under the control of the cardiac myocyte-specific CMV-enhanced short (260bp) myosin light chain promoter (CMVenh/MLC260). Transaortic constriction (TAC) and sham operation was conducted 6 weeks later in 12 week old mice to induce pathological pressure overload. Organs were harvested 4 weeks after TAC at the age of 16 weeks and total RNA was used for microarray analysis. Three groups were compared: 1) sham-operated mice that were pretreated with AAV9 (CMVenh/MLC260)-Luc, 2) TAC-operated mice that were pretreated with AAV9 (CMVenh/MLC260)-Luc, 3) TAC-operated mice that were pre-treated with AAV9 (CMVenh/MLC260)-HDAC4-NT.

overall_design: 3 male animals per group at an age of 8 weeks were included in the microarray analysis, treated with adenoassociated virus (AAV) containing a coding sequence for Luziferase or Histone Deacetylase 4 (HDAC4, aminoacids 1-201) under the control of the MLC-promoter. Both groups were then exposed to transaortic constriction. As a control to HDCA4 served AAV treatment with overepression of luziferase and sham-op as a control to TAC-surgery.

first: Johannes

last: Backs

first: Lorenz

middle: H

last: Lehmann


title: Expression data from primary myoblasts with active Beta-catenin

status: Public on Apr 15 2016

first: Fabien

last: Le Grand

address: 8 avenue Rockefeller

department: Melis

institute: Institut Neuromyogene

summary:
Regeneration of the adult skeletal muscle tissue relies on a population of muscle stem cells called satellite cells. During tissue repair, satellite cells exhibit active canonical Wnt/beta-catenin signaling.
To identify genes that become transcribed following activation of the Wnt/β-Catenin pathway in satellite cells, we performed microarray analysis of primary myoblasts expressing an active form of beta-catenin

overall_design: Primary myoblasts were prepared from the limb muscles of Pax7-CreERT2*Beta-cetenin-Exon3-loxP/+ mice. Conditional activation of the beta-catenin gene was validated by genotyping PCR and Western Blotting. RNA was extracted from three independent cultures for each conditions.

first: Anja

last: Rudolf


title: Circadian mRNA expression in skeletal muscle of young and aged mice

status: Public on Mar 31 2016

city: Berlin

first: Paul

middle: Florian

last: Thaben

state: Berlin

address: Philippstr. 13, Haus 4

department: Institute for Theoretical Biology

institute: Charite Universitätsmedizin Berlin

summary:
Aging animals undergo a variety of changes in molecular processes. Among these, the cellular circadian clock has been shown to change as animals age.  Moreover, there is evidence that also core circadian clock proteins could influence the ageing behavior of vertebrates.
To investigate the interplay between aging and the circadian clock, we studied circadian mRNA expression in skeletal muscles from young (8 weeks) and aged (80 weeks) mice. In order to detect differences in circadian patterns, we used microarray-based transcriptome-wide time series of mRNA expression, containing 16 independent measurements for both young and aged animals. Each individual time point consists of total RNA from hind limb skeletal muscles from 3 different animals.

overall_design: Young and aged mice where entrained to 12 hr/12 hr light-dark conditions. From these mice, hind limb skeletal muscles were extracted at different times of day, in order to measure circadian mRNA expression patterns.

middle: F

first: Pål

middle: O

last: Westermark


title: microRNA counts from H1-hESC (ENCSR408BER)

status: Public on May 26 2016

first: ENCODE

last: DCC

summary:
Nanostring miRNA Array on human H1-hESC

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: LPS stimulation of Mouse (RAW 264.7) macrophages

status: Public on Feb 25 2016

city: Hannover

first: Aravind

last: Tallam

state: Lower Saxony

address: Feodor-Lynen str. 7

department: BIOM

institute: TWINCORE

summary: Immunoresponsive gene 1 (IRG1) is one of the highest induced genes in macrophages under pro-inflammatory conditions and its function has been recently described: it codes for immune-responsive gene 1 protein/cis-aconitic acid decarboxylase (IRG1/CAD), an enzyme catalyzing the production of itaconic acid from cis-aconitic acid, a tricarboxylic acid (TCA) cycle intermediate. Itaconic acid possesses specific antimicrobial properties inhibiting isocitrate lyase, the first enzyme of the glyoxylate shunt, an anaplerotic pathway that bypasses the TCA cycle and enables bacteria to survive on limited carbon conditions. To elucidate the mechanisms underlying itaconic acid production through IRG1 induction in macrophages, we examined the transcriptional regulation of IRG1. Using a combination of literature information, transcription factor prediction models and genome-wide expression arrays, we inferred the regulatory network of IRG1 in mouse and human macrophages.

overall_design: 3 unstimulated (Control) and 3 LPS-stimulated RAW 264.7 macrophages

first: Alessandro

last: Michelucci


title: The study of inflammatory responses in mammalian macrophages with LPS stimulation

status: Public on Feb 24 2016

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


title: Identification of genes involved in cold shock response in rainbow trout (Oncorhynchus mykiss)

status: Public on Dec 02 2015

city: Dummerstorf

first: Alexander

last: Rebl

address: Wilhelm-Stahl-Allee 2

department: Institute of Genome Biology

institute: Research Institute for Farm Animal Biology

summary: A rapid decline in temperature poses a major challenge for poikilothermic fish. The gene expression of rainbow trout Oncorhynchus mykiss having undergone such a cold shock (0 °C) and a control (5 °C) were compared in a microarray-based study.

overall_design: Fish were either incubated in water of ambient temperature (5°C) or cooled water (0°C) for 30 minutes and tissues extracted.

first: Andreas

last: Borchel

first: Marieke

last: Verleih

first: Tom

last: Goldammer


title: CricRNA expression profiling  in human gastric cancer

status: Public on Feb 20 2016

city: Haikou

first: Yousheng

last: Huang

state: Hainan

address: The 3rd Xueyuan Road

department: Department of pathology

country: China

institute: Hainan Medical university

summary: Using the highly sensitive cricRNA array, we screened 13617 circRNAs abundant in the human gastric cancer and Adjacent normal gastric mucosa  tissues, and the function of differentially expressed circRANs were analyzed by bioinformatics. The enrichment results indicated that these circRNAs perhaps participated in the occurrence and development process of gastric cancer.

overall_design:
In this study, three cases of  gastric cancer were used to acquire the circRNA expression profiling, and qPCR was employed to confirm the results of circRNA chip. The function of the differentially expressed circRAN were analyzed by bioinformatic methods.Finally,compared with the adjacent mormal moucosa tissues，the expression of  16 cirRNAs  were up regulated,and 84 cicRANS were down regulated in gastric cancer..qPCR results showed an expression pattern consistent with that of the chip analysis,of those ,three circRNAs exhibited significant differently expression, hsa_circ_0061274 up regulated expression(3.5fold,p<0.01)，hsa_circ_0000026(-2.1fold,p<0.01) and hsa_circ_0005927 (-2.7fold,p<0.01) down regulated expression .
The expression profiles of circRAN were compared between garstic cancer and its adjacent normal tissues

first: You

last: Xie


title: Global Gene Expression of Methicillin-resistant Staphylococcus aureus USA300 During Human and Mouse Infection

status: Public on Oct 16 2015

city: South San Francisco

first: Mark

last: McCreary

state: California

address: 1 DNA Way, MS 93

department: Bioinformatics

institute: Genentech

summary: Little is known about the expression of methicillin-resistant Staphylococcus aureus (MRSA) genes during infection conditions. Here, we described the transcriptome of the clinical MRSA strain USA300 derived from human cutaneous abscesses, and compared it with USA300 bacteria derived from infected kidneys in a mouse model. Remarkable similarity between the transcriptomes allowed us to identify genes encoding multiple proteases and toxins, and iron- and peptide-transporter molecules, which are upregulated in both infections and are likely important for establishment of infection. We also showed that disruption of the global transcriptional regulators agr and sae prevents in vivo upregulation of many toxins and proteases, protecting mice from lethal infection dose, and hinting at the role of these transcriptional regulators in the pathology of MRSA infection.

platform_organism: Staphylococcus aureus subsp. aureus USA300_FPR3757

overall_design: Staphylococcous aureus USA300 were derived from C57Bl/6 mice Mouse kidney abscesses and from human patient cutaneous abscesses. Control wild-type Staphylococcus aureus USA300 samples were taken from 4 hours' culture in TSB. The Mouse, Human, and Control cRNA were Cy5 labeled. A pool of RNA isolated from USA300 bacteria, from various in vitro culture conditions [early log phase (2 h), mid log phase (4 h), post exponential phase (8 h), and stationary phase (20 h) in TSB; mixed at equal ratios] to ensure broad gene expression, was used as reference RNA and was Cy3 labeled.

first: Shailesh

middle: V

last: Date

first: Zora

last: Modrusan

first: Michael

last: Lawrence

first: J

last: Morisaki

first: Karen

last: Toy

first: Ishita

middle: M

last: Shah

first: Janice

last: Kim

first: Summer

last: Park

first: Min

last: Xu

first: Li

last: Basuino

first: Liana

last: Chan

first: Deborah

last: Zeitschel

first: Henry

last: Chambers

first: Man-Wah

last: Tan

first: Eric

middle: J

last: Brown

first: Binh

last: Diep

first: Wouter

middle: L

last: Hazenbos


title: Expression data from post-natal rat Achilles tendons

status: Public on Jul 10 2015

city: Hangzhou

first: Jialin

last: Chen

address: Yuhangtang Road

institute: Zhejiang University

summary: We have compared the gene expression profile of post-natal 1 day and 7 day rat Achilles tendons.

overall_design: Post-natal 1 day and 7 day rat Achilles tendons were collected. Each sample contains at least two individuals. Total RNA was extracted and fragmented biotin-tagged cRNA was hybridized to Rat Genome 230 2.0 Array.


title: Expression data from gonads of Meioc+/+ and Meioc-/-mice

status: Public on Nov 19 2015

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

summary:
Meiosis is a specialized division that is specifically engaged in germ cells. This program is finely and dichotomically regulated: germ cells enter meiosis at fetal life in ovaries (13.5 dpc) and only at post-natal life in testes (8 dpp).
We used microarrays to determine the gene expression modifications in Meioc mutant gonads displaying early meiotic defects.

overall_design: 14.5 dpc ovaries and 8 dpp testes from Meioc+/+ and Meioc-/- mice (NMRI) were dissected and processed for RNA extraction and hybridization on Affymetrix microarrays. Two pools were analysed for each genotype and each sex. We sought to constitutes pairs (A and B) of wild type and knock-out pools from embryos and pups that were homogenous for developmental stages and from matched littermates. 10 ovaries from 5 embryos composed each pool for females and 4 testes from 4 pups composed each pool for males.

first: E

last: Abby

first: G

last: Livera


title: Intermittent Hypoxia Alters Gene Expression in Peripheral Blood Mononuclear Cells (PBMC) of Healthy Volunteers

status: Public on Jul 27 2015

city: Baltimore

first: Dmitry

middle: N

last: Grigoryev

state: MD

address: 620 W. Lexington St.

department: Alumni

institute: UMB

summary: Intermittent hypoxia (IH) of obstructive sleep apnea (OSA) has been implicated in cardiovascular morbidity and mortality1. Although underlying mechanisms of the cardiovascular risk in OSA are not well defined, experiments in cell culture and animal models suggest that IH up-regulates pro-inflammatory genes that can promote atherosclerosis and insulin resistance. We hypothesized that short-term IH (5 h) will induce pro-inflammatory genes in healthy volunteers

overall_design:
We performed a cross-over study of healthy volunteers (n = 8) who were exposed to IH or control conditions in a randomized fashion for 5 hours while awake as previously described4. IH was induced by inspiration of the hypoxic (95% N2 and 5% O2) gas until the oxyhemoglobin saturation dropped to 85% followed by reoxygenation to the baseline, resulting in ~25 hypoxic events/h. In control exposures hypoxic gas was substituted with air. Whole blood was collected before and after the exposures.
Total RNA was isolated from PBMCs using the Trizol Reagent method (Invitrogen, Carlsbad, California 92008, cat. no. 15596-026) with subsequent RNEasy clean up (Qiagen, Valencia, CA 913555, cat. no. 74104). 0.5 µg of total RNA from each sample were labeled using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX 78744-1832, cat. no. IL1791). mRNA was converted into double-stranded cDNA using an oligo-dT primer containing the T7 RNA polymerase promoter. Single stranded RNA (cRNA) was from double-stranded cDNA in an in vitro transcription reaction. cRNA was labeled by incorporating biotin-16-UTP. 0.85 ugs of biotin-labeled cRNA was hybridized (16 hours) to Illumina’s Sentrix HumanRef-8 Expression BeadChips (Illumina, San Diego, CA 92121-1975, cat.no. 11201828). The hybridized biotinylated cRNA was detected with streptavidin-Cy3 and quantified with Illumina’s BeadStation 500GX Genetic Analysis Systems scanners.

first: Vsevolod

middle: Y

last: Polotsky


title: caArray_kuppe-00390: Broad: Lesional gene expression profiling in cutaneous T-cell lymphoma reveals natural clusters associated with disease outcome

status: Public on Jun 27 2015

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

summary: Cutaneous T-cell lymphoma (CTCL) is defined by infiltration of activated and malignant T cells in the skin. The clinical manifestations and prognosis in CTCL are highly variable. In this study, we hypothesized that gene expression analysis in lesional skin biopsies can improve understanding of the disease and its management. Based on 63 skin samples, we performed consensus clustering, revealing 3 patient clusters. Of these, 2 clusters tended to differentiate limited CTCL (stages IA and IB) from more extensive CTCL (stages IB and III). Stage IB patients appeared in both clusters, but those in the limited CTCL cluster were more responsive to treatment than those in the more extensive CTCL cluster. The third cluster was enriched in lymphocyte activation genes and was associated with a high proportion of tumor (stage IIB) lesions. Survival analysis revealed significant differences in event-free survival between clusters, with poorest survival seen in the activated lymphocyte cluster. Using supervised analysis, we further characterized genes significantly associated with lower-stage/treatment-responsive CTCL versus higher-stage/treatment-resistant CTCL. We conclude that transcriptional profiling of CTCL skin lesions reveals clinically relevant signatures, correlating with differences in survival and response to treatment. Additional prospective long-term studies to validate and refine these findings appear warranted.

overall_design:
kuppe-00390
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: U133AAofAv2
Organism: Homo sapiens (ncbitax)
Tissue Sites: Skin
Material Types: total RNA, synthetic_RNA, organism_part, whole_organism
Disease States: Cutaneous T-cell lymphoma


title: transcription of ectopic lignification-Identification of genes differentiallty expressed in mur1 basal stems

status: Public on Dec 01 2015

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary: ra15-04_elim1 - transcription of ectopic lignification - What are genes involved in lignin modifications in mur1 stems? - RNA extractions have been performed on mur1 and WT stems of 13 cm. Three biological repeats were used for the transcriptomic analysis.

overall_design: 3 dye-swap - genotype comparaison

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Richard

last: Sibout

first: Marie-Laure

last: Martin-Magniette


title: MicroRNA (miRNA) expression profile in quadriceps of wild-type (WT) and NF90-NF45 double transgenic (dbTg) mice.

status: Public on Sep 03 2014

city: Nankoku

first: Shuji

last: Sakamoto

state: Kochi

address: Oko-cho, Kohasu

department: Science Research Center

institute: Kochi University

summary: To investigate regulation of miRNA biogenesis by NF90-NF45 complex, we performed comprehensive analysis of miRNA expression in quandriceps of WT and NF90-NF45 dbTg mice.

overall_design: Comparison of miRNA expression profile in quandriceps between WT and NF90-NF45 dbTg mice.


title: CaM Kinase II mediates maladaptive post-infarct remodeling but not acute myocardial ischemia/reperfusion injury

status: Public on Sep 08 2014

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

institute: University Heidelberg

summary: Calcium/calmodulin-dependent protein kinase II (CaMKII) was suggested to mediate ischemic myocardial injury and adverse cardiac remodeling. However, the specific functions of the CaMKII isoforms and splice variants in ischemia/reperfusion (I/R) injury have not been investigated yet. Thus, we studied the roles of the CaMKII isoforms and splice variants in I/R by the use of various CaMKII mutant mice. CaMKIIδC was up-regulated already one day after I/R injury but surprisingly, acute I/R injury was neither affected in CaMKIIδ-deficient mice, CaMKIIδ-deficient mice in which the splice variants CaMKIIδB and C were re-expressed nor in conditional CaMKIIδ/γ double-knockout mice (DKO). In contrast, 5 weeks after I/R, DKO mice were protected against extensive scar formation and cardiac dysfunction. Leukocyte infiltration was not altered one day but five days after I/R, explaining the late effects of CaMKII deletion on post-I/R remodeling. Other than reported before, we demonstrate that CaMKII is not critically involved in the immediate mechanisms that regulate acute I/R injury but in the process of post-infarct remodeling.

overall_design: We analysed 6 groups in total: 3 groups from wild-type control animals and 3 groups from CaMKII delta/gamma double-KO mice. Sham operated animals served as controls in both wild-type and KO animal groups. 2 different time points in ischia/reperfusion operated animals were investigated: 1 day and 5 days post-surgery.

first: Martin

last: Weinreuter

first: Michael

last: Kreusser

first: Jan

last: Beckendorf

first: Friederike

last: Schreiter

first: Florian

last: Leuschner

first: Lorenz

last: Lehmann

first: Kai

middle: P

last: Hofmann

first: Nathalie

last: Diemert

first: Julia

last: Rostosky

first: Hans

last: Volz

first: Andreas

last: Jungmann

first: Alexander

last: Nickel

first: Norbert

last: Kretz

first: Christoph

last: Maack

middle: D

last: Schneider

first: Hermann

last: Gröne

first: Oliver

last: Müller

first: Hugo

last: Katus

last: Olson

first: Johannes

last: Backs


title: The impact of a drug transporter ABCG2 haplotype in molecular response of chronic myelogenous leukemia patients is modulated by imatinib dose

status: Public on Jun 30 2014

city: Paris

first: Marc

last: Delord

address: Hopital Saint-Louis, 1 avenue Claude Vellefaux

department: Recherche clinique

institute: Centre hospitalier de Versailles

summary: We analysed the impact of single nucleotide polymorphisms (SNPs) in drug transporter genes on the molecular response to imatinib, using 857 SNPs covering 94 drug transporter genes on 355 chronic phase chronic myeloid leukemia (CP-CML) patients.

overall_design:
Samples were analyzed with respect to sex, imatinib daily dose, SOKAL score and the levels of molecular responses.
The 'characteristics: molecular response' values represent the ratio BCR-ABL/ABL*100, which is determined by RT-QPCR (real time quantitative PCR). It is the percentage of the number of copies of BCR-ABL transcript on the number of ABL transcript copies.

first: Philippe

last: Rousselot

first: Jean

last: Cayuela

first: François

last: Sigaux

first: Joëlle

last: Guilhot

first: Claude

last: Preudhomme

first: Heriberto

last: Bruzzoni-Giovanelli

first: Fabien

last: Calvo

first: Emmanuelle

last: Génin

first: Daniela

last: Geromin

first: Emmanuel

last: Raffoux

first: Pascale

last: Loiseau


title: Cyanidiales Transcriptomics in Acidic Geothermal Environments

status: Public on Mar 31 2014

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

summary: Ultra-violet (UV) and high-intensity visible (VIS) radiation are environmental stressors known to harm photosynthetic organisms through the generation of reactive intermediates that damage photosynthetic machinery. This study shows the potential of using a thermoacidophilic red alga of the order Cyanidiales to model in situ algal gene expression dynamics as a function of UV exposure and seasonal shifts in UV-VIS intensity. These algae exhibit a dynamic seasonal biomass fluctuation referred to as 'mat decline' where viability drastically decreases as seasonal UV-VIS irradiance intensity increases. In Yellowstone National Park (YNP), temporal experiments coupling UV irradiance manipulations (filtering) with whole-community transcription profiling revealed significant cyanidial gene expression changes occurring as a result of exposure to UV, and that patterns of response adjust across low and high irradiance time periods. Separate analyses examined genes responding to either increasing seasonal UV or VIS intensity, or by the combined effects of both irradiance wavelengths (UV and VIS). Results not only corroborated known physiological changes to solar irradiance, but also suggested the strategies employed to deal with excess VIS and UV intensity may be highly integrated. Finally, a suite of comparative analyses determined the relative utility of environmental transcriptomics technologies in studying ecologically-relevant expression patterns. Results suggest in situ expression profiles will improve understanding of how photosynthetic organisms are responding to environmental stressors as they are observed in nature.

overall_design: 16 samples with 3 biological replicates each.

first: Dana

last: Skorupa

first: Timothy

last: McDermott

first: Richard

middle: W

last: Castenholz

first: Scott

last: Miller

first: Aurélien

last: Mazurie

first: Frank

last: Rosenzweig


title: Array CGH of cutaneous neurofibromas (cNFs) from NF1 patients

status: Public on May 28 2014

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

institute: Kinjo Gakuin University

type: Genome variation profiling by genome tiling array

summary: Somatic copy number changes in cNFs samples in NF1 patients

overall_design: 9 cNFs and matched DNA samples were hybridised to the SurePrint G3 human 400k CGH microarray

first: Akiko

last: Asai

first: Sivasundaram

last: Karnan


title: Genome-wide analysis of HL60 cells after 24h pulse of 10nM vincristine

status: Public on Aug 15 2013

city: San Francisco

first: Angela

last: Oliveira Pisco

address: 499 Illinois St

department: Data Science

institute: Chan Zuckerberg Biohub

summary: Analysis of HL60 response to low-dose vincristine at gene expression level. The hypothesis tested in the present study was that population heterogeneity has functional consequences in drug response. Since the presence of discrete efflux^High and efflux^Low subpopulations may reflect transitions between distinct stable cellular states (attractor states), we measured the transcriptomes when the cell population exhibited a stable bimodal distribution. We also measured the transcriptomes for 17 days after washing the drug (samples 5 - 9).

overall_design: Total RNA obtained from HL60 cells untreated (sample 3), treated for 24h (sample 4) and sorted after 24h treatment for Calcein AM efflux low (sample 1) and high (sample 2). Sample 5 corresponds to total RNA of untreated cells, sample 6 to total RNA after 24h treatment with 10nM vincristine and samples 7 to 9 to total RNA after washing the drug.

last: Pisco

first: Amy

last: Brock

first: Joseph

last: Zhou

first: Andreas

last: Moor

first: Mitra

last: Mojtahedi

first: Dean

last: Jackson

first: Sui

last: Huang


title: Comparative functional genomics of adaptation to muscular disuse in hibernating mammals (Arctic ground squirrels)

status: Public on Oct 16 2014

city: ShangHai

first: Haifang

last: Wang

address: NO 320, Yueyang Road

department: functional genomics group

institute: PICB

summary: Hibernation is energy saving adaptation involving suppression of activity to survive in highly seasonal environments. Immobility and disuse generate muscle loss in most mammalian species. In contrast to other mammals, bears and ground squirrels demonstrate limited muscle atrophy over the physical inactivity of winter hibernation. This suggests that hibernating mammals have adaptive mechanisms to prevent disuse muscle atrophy. To identify common transcriptional program underlying molecular mechanisms preventing muscle loss, we conducted a large-scale gene expression screening in hind limb muscles comparing hibernating and summer active black bears and arctic ground squirrels by the use of custom 9,600 probe cDNA microarrays. The molecular pathway analysis showed an elevated proportion of overexpressed genes involved in all stages of protein biosynthesis and ribosome biogenesis in muscle of both species during hibernation that implies induction of translation at different hibernation states. The induction of protein biosynthesis likely contributes to attenuation of disuse muscle atrophy through prolonged periods of immobility and starvation. This adaptive mechanism allows hibernating mammals to maintain full musculoskeletal function and preserve mobility during and immediately after hibernation, thus promoting survival. The lack of directional changes in genes of protein catabolic pathways does not support the importance of metabolic suppression for preserving muscle mass during winter.  Coordinated reduction of multiply genes involved in oxidation reduction and glucose metabolism detected in both species is consistent with metabolic suppression and lower energy demand in skeletal muscle during inactivity of hibernation.

overall_design: Arctic ground squirrels sampled during winter hibernation were compared with the animals sampled during summer. Muscle was hybridized on a custom 9,600 probes nylon membrane microarray platform. Ten in late torpor, four in early arousal, then in late arousal were studied in experiments.

first: V

last: Fedorov

first: A

last: Goropashnaya

first: Wang

last: Haifang


title: mRNAs and miRNAs expression data from AOM/DSS, AOM, DSS and control mouse colon epithelial tissue at day100 when tumor formed in AOM/DSS bearing mice

status: Public on May 10 2013

city: Harbin

first: yanqiao

last: zhang

state: Heilongjiang

address: Haping Road # 150, Nangang District,Harbin, Heilongjiang Province, P. R. China

institute: Harbin Medical University Cancer Hospital

type:
Non-coding RNA profiling by array
Expression profiling by array

overall_design: Refer to individual Series


title: Microarray studies of pqqE disruption mutant vs wild type

status: Public on Aug 25 2009

city: Mumbai

first: Hari

middle: S

last: Misra

state: MS

address: 2-46 S, Moldular Laboratories, Central Avenue, Bhabha Atomic Research Centre

department: Molecular Biology Division

country: India

institute: Bhabha Atomic Research Centre

summary: This bacterial genome encodes pyrroloquinoline quinone (PQQ) synthase enzyme required for the synthesis of PQQ in bacteria. The gene pqqE encoding PQQ synthase was annotated in Deinococcus radiodurans R1 genome and synthesis of PQQ was shown in this bacterium. PQQ roles as an antioxidant and as an inducer of protein kinase in bacterial system was shown. The pqqE disuption mutant showed several folds decrease in gamma radiation tolerance of wild type cells and strong impairment of DSB repair. Homology search analysis of PQQ binding domains showed the presence of multiple PQQ binding domains in proteins encoded by five uncharacterized ORFs of this bacterial genome. Many of these proteins are having STK domain of proteins kinases. The effect of pqqE mutation on gene expression under normal and post irradiation conditions was monitored by transcriptome analysis of mutant and compared with wild type cells.

sample_organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

overall_design: All the genes subjected to microarray analysis are as described in the genome sequence of bacterium available at ftp://ftp.ncbi.nih.gov/genomes/bacteria/Deinococcus_radiodurans. Oligonucleotides designed to represent the respective predicted ORFs of Deinococcus radiodurans ((NC_001263, NC_001264, NC_000958, NC_000959) are synthesized and purified by hydrophobic column on HPLC. The oligonucleotides are deposited on to poly-L-Lysine slide in triplicate. Microarrays were scanned using Gene Pix 4000B and hybridization signals were quantified using GenePix Pro 5.1. Prior to channel normalization, microarray outputs were filtered to remove spots of poor signal quality by excluding those data points with a mean intensity by less that 2 standard deviation above background in both channels.    Normalization of data and its statistical analysis were carried out in the R computing environment using linear models for microarray data package (Limma). Using this tool, the global LOESS normalization was carried out for each microarray. The 3- replicate spots per gene in each array were used to maximize the robustness of differential expression measurements of each gene via the “lmFit” function within Limma. Two biological replicates were carried out for transcriptome analysis of pqqE mutant strain against wild type cells.

first: Y

last: Rajpurohit

first: L-Y

first: L-F

last: Yin

last: Hua

first: H


title: MicroRNA expression signatures for developing tongue primordia in mouse embryos

status: Public on Mar 11 2014

city: Tokyo

first: Yuuichi

last: Soeno

address: 1-9-20 Fujimi, Chiyoda-ku

department: Pathology

institute: The Nippon Dental University

summary: We aimed to understand the molecular basis of muscular development in tongue. We focused on the critical stages of tongue myogenesis, namely, E10.5 (settlement of myogenic progenitors in tongue primordium), E11.5 (initiation of myoblast differentiation with the development of lateral lingual swellings).

overall_design: We conducted miRNA microarray analysis of the tongue primordia at E10.5 and E11.5, during which myoblast differentiation was induced as a result of the activation of muscle regulatory gene expression. The medial part of the fused mandibular prominences that corresponds to a tongue primordium were collected from E10.5 and E11.5 mouse embryos. Forty embryos for each time-point were used to obtain a pool of total RNA.

first: Kazuya

last: FUJITA

last: SOENO

first: Yuji

last: TAYA

first: Takaaki

last: AOBA


title: Expression analysis of rumen epithelium of cattle during weaning

status: Public on Nov 01 2009

city: Beltsville

first: Erin

middle: E

last: Connor

address: 10300 Baltimore Avenue

department: Animal and Natural Resources Institute

institute: USDA-ARS, BARC

summary: Investigation of whole genome gene expression level changes in rumen epithelium of dairy cattle at different stages of rumen development and on different diets.

overall_design: An 18-chip study using total RNA recovered from three calves per developmental stage or diet including 3 wks of age fed milk replacer (milk) only, 6 wks of age fed milk, 8 wks of age (2 wks post weaning) fed milk + calf starter (grain),  8 wks of age (2 wks post weaning) fed milk + orchard grass hay (hay), 10 wks of age (4 wks post weaning) fed milk + grain, or 10 wks of age (4 wks post weaning) fed milk + hay.  Each chip measures the expression level of approximately 41,000 transcripts from cattle.

first: Ransom

last: Baldwin VI

first: Robert

last: Li


title: Microarray studies of dr2518 knockout mutant vs wild type

summary:
Bacterial cells lacking pyrroloquinoline quinone (PQQ) were sensitive to gamma radiation as compared to wild type cells. Deinococcus radiodurans genome encode for five putative PQQ binding STK domain-containing proteins. The comparison of gamma radiation response of all five-deletion mutants with wild type suggested that dr2518 mutant was hypersensitive to gamma radiation as compared to wild type and other mutants. DR2518 is an auto kinase. Hence, the effect of dr2518 mutation on cellular response of Deinococcus radiodurans R1, to DNA damage and subsequently to its genome functions under both normal and post irradiation growth condition was further examined. Transcriptome analysis of dr2518 mutant grown under normal conditions and post-irradiated cells was done and compared with wild type cells.
Mutant lacking dr2518 become extremely sensitive to gamma radiation and complete arrest in DSB repair. These cells were therefore checked for gene expression profile in native growth and gamma irradiated growth conditions

overall_design: All the genes subjected to microarray analysis are as described in the genome sequence of bacterium available at ftp://ftp.ncbi.nih.gov/genomes/bacteria/Deinococcus_radiodurans. Oligonucleotides designed to represent the respective predicted ORFs of Deinococcus radiodurans ((NC_001263, NC_001264, NC_000958, NC_000959) are synthesized and purified by hydrophobic column on HPLC. The oligonucleotides are deposited on to poly-L-Lysine slide in triplicate. Microarrays were scanned using Gene Pix 4000B and hybridization signals were quantified using GenePix Pro 5.1. Prior to channel normalization, microarray outputs were filtered to remove spots of poor signal quality by excluding those data points with a mean intensity by less that 2 standard deviation above background in both channels.    Normalization of data and its statistical analysis were carried out in the R computing environment using linear models for microarray data package (Limma). Using this tool, the global LOESS normalization was carried out for each microarray. The 3- replicate spots per gene in each array were used to maximize the robustness of differential expression measurements of each gene via the “lmFit” function within Limma. Two biological replicates were analysed for global gene expression profile in dr2518 mutant against wild type cells.

last: Wang


title: Microarray gene expression profiles of peripheral blood mononuclear cells in patients with advanced stage non-small cell lung cancer treated with first line combination chemotherapy

status: Public on Aug 01 2012

city: Kaohsiung

first: yungche

last: chen

address: 123, Ta-Pei Rd. Niao-Sung Dist.

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

summary: We have extended our investigation to advanced-stage NSCLC by analyzing gene expression in peripheral blood mononuclear cells (PBMC) from patients with newly-diagnosed NSCLC and histopathology of either AC or SCC. Furthermore, to establish a direct link between gene expression and chemotherapy treatment, PBMC from  patients who have received 4 courses of combination chemotherapy with CDDP and GEM were obtained, and the effects of chemotherapy on global gene expression were evaluated using microarray analyses.

overall_design: We analyzed microarray gene expression profiles of peripheral blood mononuclear cells from 30 patients with newly-diagnosed advanced stage NSCLC, and 20 age, sex, and co-morbidity-matched healthy controls (HC). All the cancer patients received a maximum of six courses of chemotherapy with cisplatin and gemcitabine of a 28-day cycle as first line treatment.Furthermore, to establish a direct link between gene expression and chemotherapy treatment, PBMC from patients who have received 4 courses of combination chemotherapy with CDDP and GEM were obtained, and the effects of chemotherapy on global gene expression were evaluated using microarray analyses.

first: Yung-Che

last: Chen

first: Kuang-Den


title: High-throughput sequencing of small RNAs in Carica papaya

status: Public on Apr 30 2011

city: Udine

first: Emanuele

last: De Paoli

state: UDINE

address: via delle Scienze 206

department: Agricultural, Food, Environmental and Animal Sciences

country: Italy

institute: University of Udine

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different Carica papaya tissues (including leaves and flowers). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features, such as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.

overall_design: Small RNA libraries were derived from leaves, virus-infected leaves and female flowers of Carica papaya. Total RNA was isolated using the TriReagent (Molecular Research Center) and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Ray Ming and Qingyi Yu for providing the plant material, as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.

first: Monica

last: Accerbi

first: Pamela

last: Green

first: Blake

middle: C

last: Meyers


title: CGH Analysis of Murine Squamous Cell Carcinoma: Control vs. Tumors overexpressing Aurora Kinase A

status: Public on May 27 2010

city: Aurora

first: Enrique

last: Torchia

state: CO

department: Dermatology

institute: University of Denver

summary: Genomic alterationsin murine skin Squamous Cell Carcinoma(SCC) generated were analyzed from mice that expressed human Aurora Kinase A under control of Keratin 14 driven and RU486 inducible GLP65 activator protein.  Monogenic GLP65 (control) and bigenic GLP65; Aurora-A mice were treated with DMBA once and thrice per week with TPA and RU486 to generate SCCs.

overall_design: Two conditions experiment: 12 control and 11 Aurora-A tumors were analyzed.


title: Comparative functional genomics of adaptation to muscular disuse in hibernating mammals (black bears)

first: Haifang

overall_design: Black bears sampled during winter hibernation were compared with the animals sampled during summer. Muscle tissue were hybridized on a custom 12,800 cDNA probe nylon membrane microarray platform . Six hibernating and six summer active bears were studied in the experiment.

first: V

middle: B

last: Fedorov

first: A

last: Goropashnaya

first: Wang

last: Haifang


title: mRNAs and miRNAs expression data from AOM/DSS, AOM, DSS and control mouse colon epithelial tissue at day100 when tumor formed in AOM/DSS bearing mice --- miRNA microarray

first: yanqiao

last: zhang

summary: To find out which miRNAs are significantly differential expression and potentially  involved in the process of inflammation promoting carcinogenesis of colorectal cancer (CRC). We established a colitis-associated CRC (AOM/DSS, Azoxymethane/Dextran sulfate sodium salt) model, colitis (DSS) model and high dose carcinogen (AOM, about 5 times AOM amount given than AOM/DSS model) model. At day 100 when tumor formed in AOM/DSS bearing mice (colitis-associated CRC mice) but no tumor was found in AOM (high dose carcinogen) and DSS model, we employed miRNA microarray as a discovery platform to identify genes with the potential to involve in the progression of CRC promoted by inflammation.

overall_design: 5-7 weeks female BALB/c mice, (1) AOM/DSS group: AOM 12.5mg/kg i.p. at day 1, DSS drinking 5d/21dx3circles from day 5; (2) AOM group: AOM 10mg/kg i.p. 1/weekx6 from day 1; (3) DSS group: DSS drinking 5d/21dx3circles from day 5. The distal colon epithelial tissues were collected at day100 when tumor formed in AOM/DSS bearing mice. The miRNA microarray experiments were performed together.

first: Yanqiao

last: Zhang

first: Yuyan

last: Gao


title: Microarray studies of drb0090 mutant vs wild type

first: Hari

last: Misra

summary:
Deinococcus radiodurans exposed to higher doses of gamma radiation showed induced levels of DRB0091 polypeptide annotated as a putative response regulator in an operon expressing upstream to DRB0090, histidine kinase. Deletion of drB0090 generated,  showed decreased tolerance to DNA damage and impairment in DSB repair. Recombinant DR0090 protein showed phosphotransferase activity on its cognate response regulator, DRB0091. The drb0090 deletion mutant was checked for its role in regulation of gene expression in response to DNA damage in Deinococcus radiodurans R1. The gene expression profiling of this mutant was carried out by complete transcriptome analysis of these cells grown under normal as well as upon gamma-irradiated conditions and compared with wild type cells.
DRB0090 mutant showed extreme sensitivity to gamma radiation and was used for Gene expression profiling using microarray and compared with wild type data.

overall_design: All the genes subjected to microarray analysis are as described in the genome sequence of bacterium available at ftp://ftp.ncbi.nih.gov/genomes/bacteria/Deinococcus_radiodurans. Oligonucleotides designed to represent the respective predicted ORFs of Deinococcus radiodurans ((NC_001263, NC_001264, NC_000958, NC_000959) are synthesized and purified by hydrophobic column on HPLC. The oligonucleotides are deposited on to poly-L-Lysine slide in triplicate. Microarrays were scanned using Gene Pix 4000B and hybridization signals were quantified using GenePix Pro 5.1. Prior to channel normalization, microarray outputs were filtered to remove spots of poor signal quality by excluding those data points with a mean intensity by less that 2 standard deviation above background in both channels.    Normalization of data and its statistical analysis were carried out in the R computing environment using linear models for microarray data package (Limma). Using this tool, the global LOESS normalization was carried out for each microarray. The 3- replicate spots per gene in each array were used to maximize the robustness of differential expression measurements of each gene via the “lmFit” function within Limma. Two biological replicates were analysed for global gene expression profile in drb0090 mutant against wild type cells.

first: S

last: Desai

first: Y

last: Rajpurohit

first: L-Y

first: L-F

last: Yin

last: Hua

first: D

last: Deobagkar

first: H