title: Transcriptional profiling reveals differential changes in the expression of oxytocin and CARTpt  mRNAs in the nucleus accumbens and dorsal striatum of rats

status: Public on Sep 26 2017

city: Baltimore

first: Jean Lud

last: Cadet

state: MD

address: 251 Bayview Blvd, Suite 200

department: Molecular Neuropsychiatry Research Branch

country: USA

institute: NIDA, IRP

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

overall_design: Refer to individual Series


title: Inferring gene regulatory networks that control maintenance and identity of the Arabidopsis root stem cells

status: Public on Sep 18 2017

city: Raleigh

first: Maria

middle: Angels

last: de Luis Balaguer

state: NC

address: 2115 Gardner Hall, Box 7612

department: Plant and Microbial Biology

institute: North Carolina State University

summary:
We isolated QC and xylem cells by sorting GFP+ cells marked with pWOX5::GFP and pTMO5::GFP respectively.
We obtained cell-type specific transcriptional profiles of QC and xylem cells.

overall_design: Seedlings were grown for 5 days. WOX5::GFP and pTMO5::GFP sorted fluorecent cells were harvested for RNA extraction.

first: Barbara

last: Muller

first: Rosangela

last: Sozzani


title: Phenotypic plasticity of temperature induced Daphnia gene expression; experiment 1

city: Birmingham

first: John

middle: Kenneth

last: Colbourne

state: West Midlands

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

summary:
This study measured the differential expression of genes from a single clonal Daphnia pulex isolate obtained from an eutrophic flooded opencast mine near Gräfenhain (Saxony, Germany) and has been kept in the laboratory since 2002. The daphniids (50 adult animals per batch) were raised in 3-L glass beakers under a 16 h:8 h L:D photoperiod. Three-quarter of the culture medium (M4) was renewed once a week, and the animals were equally fed ad libitum with algae (Desmodesmus subspicatus; SAG 53.80, Göttingen, Germany). Long-term-acclimated animals were kept at three different temperatures (i.e., 10 ± 0.5°C, 20 ± 0.3°C, and 24 ± 0.3°C) under normoxia (Po2 ≥ 20 kPa) for at least twelve weeks. Time-resolved experiments (acute heat stress) were carried out with long-term 20°C acclimated animals, which were exposed for three different time intervals (2, 4, and 8 h) to either 30 ± 0.2°C (test conditions) or 20 ± 0.3°C (control conditions). For this, 50 animals each were rapidly transferred with a sieve (mesh size: 1.2 mm) from 20°C-medium to a set of beakers containing 30°C-medium. As control, 50 animals each were transferred from 20°C-medium to another set of beakers with 20°C-medium. Only adult female animals with a body length of 2−2.5 mm (between the base of the apical spine and the anterior part of the head) and carrying parthenogenetic eggs and embryos were used for experiments. Animals were not fed during short-term exposures. During experiments, all animals were in good physical condition. After thermal acclimation or heat exposure, animals were transferred into 1.5-ml microcentrifuge tubes and shock-frozen in liquid nitrogen after removing adhering water with a tissue paper. Samples were short-term stored at -80°C. For all experimental conditions, four independent replicates (50 animals each) were analyzed.
This GEO record is for the contrasts between animals conditioned to 10 degrees Celsius (condition 1) versus 20 degrees Celsius (condition 2), 10 degrees Celsius (condition 1) versus 24 degrees Celsius (condition 3), and 20 degrees Celsius (condition 2) versus 24 degrees Celsius (condition 3)

overall_design: We compared the gene expression patterns for condition 1 versus condition 2,  condition 1 versus condition 3, and  condition 2 versus condition 3 using four biological replicates for each condition, including balanced dye-swaps. All probes including random probes were quantile-normalized across chips, subarrays, samples and replicates.

first: Doerthe

last: Becker

middle: K

first: Jacqueline

last: Lopez

first: Jeong-Hyeon

last: Choi


title: Transcriptional profiling reveals differential changes in the expression of oxytocin and CARTpt  mRNAs in the nucleus accumbens and dorsal striatum of rats (striatum)

summary: Methamphetamine addiction is mimicked in rats that self-administer the drug and accelerate their intake when given long access to it. Self-administration (SA) models do not include adverse consequences that are necessary to reach a diagnosis of addiction in humans. Here, we studied transcriptional consequences of methamphetamine SA and repeated foot-shocks in rat brain.

overall_design: Six rats from each of the 3 groups including control, shock resistant, and shock sensitive and three rats from each of 2 groups including saline yoked to shock resistant and saline yoked to shock sensitive were selected based on RNA quality and integrity for RNA extraction and hybridization on Affymetrix microarrays.

first: Jean

middle: L

first: Irina

middle: N

last: Krasnova

first: Donna

last: Walther

first: Subramaniam

last: Jayanthi

first: Bruce

last: Ladenheim

first: Michael

middle: T

last: McCoy

first: Christie

last: Brannock


title: Phenotypic plasticity of temperature induced Daphnia gene expression


title: Effect of vaccine administration routes on responses to a Bordetella pertussis outer membrane vesicle vaccine - lymph nodes

status: Public on Sep 21 2017

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

summary:
Pulmonary immunization with an outer membrane vesicle pertussis vaccine led to improved protection and induction of a completely distinct immune response compared to subcutaneous administration.
These adaptive responses were linked to early local and systemic signatures on the transcriptome level.

overall_design: 48 samples, including replicates and controls, analyzed on Affymetrix genechips

first: René

last: Raeven

first: Jolanda

last: Brummelman


title: Phenotypic plasticity of temperature induced Daphnia gene expression; experiment 2

summary:
This study measured the differential expression of genes from a single clonal Daphnia pulex isolate obtained from an eutrophic flooded opencast mine near Gräfenhain (Saxony, Germany) and has been kept in the laboratory since 2002. The daphniids (50 adult animals per batch) were raised in 3-L glass beakers under a 16 h:8 h L:D photoperiod. Three-quarter of the culture medium (M4) was renewed once a week, and the animals were equally fed ad libitum with algae (Desmodesmus subspicatus; SAG 53.80, Göttingen, Germany). Long-term-acclimated animals were kept at three different temperatures (i.e., 10 ± 0.5°C, 20 ± 0.3°C, and 24 ± 0.3°C) under normoxia (Po2 ≥ 20 kPa) for at least twelve weeks. Time-resolved experiments (acute heat stress) were carried out with long-term 20°C acclimated animals, which were exposed for three different time intervals (2, 4, and 8 h) to either 30 ± 0.2°C (test conditions) or 20 ± 0.3°C (control conditions). For this, 50 animals each were rapidly transferred with a sieve (mesh size: 1.2 mm) from 20°C-medium to a set of beakers containing 30°C-medium. As control, 50 animals each were transferred from 20°C-medium to another set of beakers with 20°C-medium. Only adult female animals with a body length of 2−2.5 mm (between the base of the apical spine and the anterior part of the head) and carrying parthenogenetic eggs and embryos were used for experiments. Animals were not fed during short-term exposures. During experiments, all animals were in good physical condition. After thermal acclimation or heat exposure, animals were transferred into 1.5-ml microcentrifuge tubes and shock-frozen in liquid nitrogen after removing adhering water with a tissue paper. Samples were short-term stored at -80°C. For all experimental conditions, four independent replicates (50 animals each) were analyzed.
This GEO record is for the acute heat stress temperature contrasts between animals conditioned to 20 degrees Celsius (condition 1) versus heat shock to 30 degrees Celsius (condition 2) exposed for 2 hours (treatment 1), 4 hours (treatment 2), and 8 hours (treatment 3).

overall_design: We compared the gene expression patterns for condition 1 versus condition 2 for each treatment 1,  treatment 2 and treatment 3 using four biological replicates for each treatment, including balanced dye-swaps. All probes including random probes were quantile-normalized across chips, subarrays, samples and replicates.


title: Identification of FOXJ1 effectors during ciliogenesis in the fetal respiratory epithelium and embryonic left-right organizer of the mouse - IMCD3 screen

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

country: Germany

institute: Medical School Hannover

summary: Formation of motile cilia in vertebrate embryos is essential for proper development and tissue function. Key regulators of motile ciliogenesis are the transcription factors FOXJ1 and NOTO, which are conserved throughout vertebrates. Downstream target genes of FOXJ1 have been identified in a variety of species, organs and cultured cell lines; in murine embryonic and foetal tissues, however, FOXJ1 and NOTO effectors have not been comprehensively analysed and our knowledge of the downstream genetic programme driving motile ciliogenesis in the mammalian lung and ventral node is fragmentary. We compared genome-wide expression profiles of undifferentiated E14.5 vs. abundantly ciliated E18.5 micro-dissected airway epithelia as well as Foxj1+ vs. Foxj1-deficient foetal (E16.5) lungs of the mouse using microarray hybridisation. 326 genes deregulated in both screens are candidates for FOXJ1-dependent, ciliogenesis-associated factors at the endogenous onset of motile ciliogenesis in the lung, including 123 genes that have not been linked to ciliogenesis before; 46% of these novel factors lack known homologues outside mammals. Microarray screening of Noto+ vs. Noto null early headfold embryos (E7.75) identified 59 of the lung candidates as NOTO/FOXJ1-dependent factors in the embryonic left-right organiser that carries a different subtype of motile cilia. For several uncharacterised factors from this small overlap – including 1700012B09Rik, 1700026L06Rik and Fam183b – we provide extended experimental evidence for a ciliary function.

overall_design: Microarray experiments were conducted in dual-colour mode using amplified, fluorescently-labelled material from unstarved vs. starved cultured IMCD3 cells. Experiments were performed twice as true biological replicates (4 samples). Each pair (unstarved vs. starved) was used for dual-colour based co-hybridisation, including a technical dye-swap replicate, resulting in four dual-colour microarray hybridisations in total. In order to enable inspection of intensity values, dual-colour results were integrated into a single-color GEO matrix.

last: Stauber

first: Marina

last: Weidemann

first: Katharina

last: Lobschat

first: Leonie

last: Alten

first: Michaela

last: Mai

first: Anja

last: Beckers

last: Kracht

first: Achim

last: Gossler


title: Generation of intestinal progenitor cells from mouse fibroblasts

status: Public on Sep 22 2017

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Division of Organogenesis and Regeneration

country: Japan

institute: Medical Institute of Bioreguration, Kyushu University

summary: We show direct conversion of mouse fibroblasts to cells that closely resemble intestinal stem cells (ISCs), through the state of fetal-type progenitor cells, called FIPCs. The induced ISCs (iISCs) exhibit self-renewal capacity and intestinal multi-lineage differentiation potential. Upon transplantation, iFIPCs and iISCs reconstitute colonic and intestinal epithelia, respectively.

overall_design: We conducted comparative global gene expression analyses among MEFs, iHep cells, iISC-derived budding organoids, Crypt-derived budding organoids, iFIPC-derived spherical organoids and budding organoids, and FI-derived spherical organoids and budding organoids.

first: Shizuka

last: Miura


title: Expression data from Chronic Unpredict Mild Stress-induced depression in GK rats‘ liver

status: Public on Sep 25 2017

city: Changsha

first: Hongyan

last: Wei

state: Hunan

address: No. 61 Jiefang West Road, Changsha, Hunan, China

department: Pharmacy

country: China

institute: Hunan Provincial People’s Hospital

summary:
To explored the mechanism of pharmacokinetic perturbation in chronic unpredicted mild stress (CUMS) resulting depression, CUMS-induced depression animal model with spontaneous diabetic GK rats were established.
The expression profile in GK rats' livers were screened using Affymetrix Rat 230 2.0 Array.

overall_design: Male GK rats emergenced of diabetes symptom, then were randomly divided into two groups: control group and CUMS group. Rats were sacrificed after 8 weeks' CUMS resulting in depression. Rat’s livers were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Boyu

last: Tan

first: Feng

last: Xu


title: Cystatin C modulates the release of inflammatory cytokines in Lipopolysaccharide-activated monocytes

city: Maaloev

first: Thomas

middle: Bovbjerg

last: Rasmussen

address: Novo Nordisk Park

country: Denmark

institute: Novo Nordisk A/S

summary: Cystation modulates expression of inflammatory cytkines in LPS activated monocytes

overall_design: Gene expression in monocytes treated LPS+Cystatin C is compared to monocytes treated with LPS only. The dataset also includes a number of control treatments.

first: Susanne

last: Gren

first: Sabina

last: Janciauskiene

first: Danny

last: Jonigk

first: Peter

middle: H

last: Kvist

middle: B

first: Jens

middle: G

last: Gerwien

first: Katarina

last: Håkansson

first: Olof

last: Grip


title: Effect of vaccine administration routes on responses to a Bordetella pertussis outer membrane vesicle vaccine

first: Jeroen

last: Pennings


title: Transcription analysis of the responses of porcine heart to Erysipelothrix rhusiopathiae

status: Public on Sep 15 2017

city: wuhan

first: kang

last: chao

state: hubei

address: shizhishan

department: College of Veterinary Medicine

institute: huazhong Agricultural university

summary: Erysipelothrix rhusiopathiae is generally regarded as an opportunistic pathogen that causes erysipelas in swine and other diseases in several mammalian and avian species.This study aimed to perform a whole-genomic analysis of the transcriptional responses of a pig heart to virulent and avirulent strains and PBS by using Affymetrix Porcine Gene 1.0 ST Microarray to elucidate the immune responses of hosts to E. rhusiopathiae.

overall_design: A total of 9 healthy pigs were randomly allocated to 3 groups with 3 pigs each: two groups of piglets were challenged intradermally with virulent and avirulent strains , respectively, and the remaining piglets were used as controls. Challenged by an identical volume of PBS.

first: Chao

last: Kang

first: Weifeng

last: Zhu

first: Qiang

last: Zhang

first: Xiaomei

last: Sun

first: Chengzhi

last: Cai

first: Meilin

last: Jin


title: Identification of FOXJ1 effectors during ciliogenesis in the fetal respiratory epithelium and embryonic left-right organizer of the mouse - Lung subscreen B

first: Oliver

last: Dittrich-Breiholz

overall_design: The Microarray experiment was conducted in dual-colour mode using amplified, fluorescently labelled material from Foxj1+ vs. Foxj1-deficient E16.5 lung samples for co-hybridisation on one microarray. In order to enable inspection of intensity values, dual-colour results were integrated into a single-color GEO matrix.

first: Michael

last: Stauber

first: Marina

last: Weidemann

first: Katharina

last: Lobschat

first: Leonie

last: Alten

first: Michaela

last: Mai

first: Anja

last: Beckers

last: Kracht

first: Achim

last: Gossler


title: MicroRNAs expression different in Serum between Trauma-induced  osteonecrosis  of  the  femoral  head (TIONFH) and healing patients

status: Public on Sep 14 2017

city: Luoyang

first: zhang

last: ying

state: Henan

address: No. 82, South Qiming Road

institute: Medical Center of Hip, Luoyang Orthopedic-Traumatological Hospital (Orthopaedic Hospital  of Henan Province)

summary: We recently showed that microRNA different profile from Trauma-induced osteonecrosis of the femoral head (TIONFH) and healing patients.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Macacine alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
Herpesvirus saimiri (strain 11)
JC polyomavirus
Human immunodeficiency virus 1
Human betaherpesvirus 6B
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Ten patients in each group had been employed to observe. Serum collected and extract microRNA using reagent kit , then assayed by microassay chip

first: Ying

first: You-wen

last: Liu


title: Real-time quantitative PCR analysis of microRNAs in CML stem cells

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

summary: Lin-CD34+CD38+ and Lin-CD34-CD38- cells were isolated from 5 CML patients at diagnosis and 4 healthy donors.

overall_design: qPCR microRNA expression profiling

first: Simona

last: Salati

first: Valentina

last: Salvestrini

first: Chiara

last: Carretta

first: Sebastiano

last: Rontauroli

first: Roberta

last: Zini

last: Rossi

first: Samantha

last: Ruberti

first: Elisa

last: Bianchi

first: Antonio

last: Curti

first: Roberto

middle: M

last: Lemoli


title: Gene expression profiles of human Mesenchymal Stromal Cells (MSC) from JAK2+ myeloproliferative neoplasms (MPN)

city: Salamanca

first: Beatriz

middle: Roson

last: Burgo

address: Campus Miguel de Unamuno

department: Cancer Research Centre

country: Spain

institute: Consejo Superior de Investigaciones Científicas & Universidad de Salamanca

summary: In this study we analyzed the behavior of bone marrow MSC (BM-MSC) from MPN patients with the mutation in JAK2V617F. We initially characterized the biological function and gene expression profile changes in BM-MSC from MPN patients when compared to BM-MSC of healthy donors (HD). Then, we established co-cultures between MSC cell lines (HTERT and HS5) and the UKE-1 MPN cell line, and performed RT-PCR to study if the leukemic cells were able to modify the genes related to hematopoietic support.

overall_design: To obtain a global view of the differences between healthy donors (HD) and MPN cells, we extracted the genetic profiles of BM-MSC from 8 JAK2V617F patients: 4 Polycythemia Vera (PV), and 4 Essential Thrombocythemia (ET). 10 healthy donors (HD) and 6 Chronic Myeloid Leukemia (CML) patients were also included. After assessment of RNA integrity (Agilent 2100 Bioanalyzer, Agilent), samples were hybridized in the platform Gene Chip Gene 1.0 ST array system (Affymetrix, Santa Clara, CA), following manufacturer’s instructions.

first: Teresa

last: Ramos

first: Luis

middle: I

last: Sánchez-Abarca

last: Rosón-Burgo

first: Alba

last: Redondo

first: Ana

last: Rico

first: Silvia

last: Preciado

first: Rebeca

last: Ortega

first: Concepción

last: Rodríguez

first: Sandra

last: Muntión

first: Ángel

last: Hernández-Hernández

first: Javier

last: De Las Rivas

first: José

middle: R

last: Porras

first: Consuelo

last: del Cañizo

first: Fermín

last: Sánchez-Guijo


title: Transcriptional profiling reveals differential changes in the respective expression of oxytocin and CART mRNA levels in the nucleus accumbens and dorsal striatum of compulsive methamphetamine taking rats (nucleus accumbens)

first: Jean Lud

last: Cadet

first: Jean

first: Irina

last: Krasnova

first: Donna

last: Walther

first: Subramaniam

last: Jayanthi

first: Bruce

last: Ladenheim

first: Michael

last: McCoy

first: Christie

last: Brannock


title: Non-replicative persistence of M. tuberculosis under iron starvation

city: Newark

first: G

middle: Marcela

last: Rodriguez

state: NJ

address: 225 Warren St

department: Public Health Research Institute

institute: Rutgers University

summary: Iron restriction is a growth limiting condition encountered by M. tuberculosis in the host. In this study we examined the survival and physiology of iron depleted M. tuberculosis. We found that iron depleted M. tuberculosis survive for long time with little or no replication and is able to resume normal growth  when iron becomes available. To understand the mechanism used by M. tuberculosis to survive under iron starvation we examine the transcriptional profile of iron-starving in comparison to that of iron-sufficient M. tuberculosis.

overall_design: M. tuberculosis was depleted of exogenous iron and pressed to use stored iron(Fe) at which point cells stop growing but remained viable for long time. Total RNA of iron depletion adapted Mtb (IDAM) at 1 day,  1 week and 2 weeks  after cells have entered growth arrest was extracted and transcripts compared  to those of cells subjected to Fe-depletion but then supplemented with Fe 24hr before RNA extraction. These cells are referred to as iron sufficient mycobacterium (ISM)

first: Krishna

last: Kurkothi


title: Transcript and metabolite profiling indicate rapid regulation of the deacclimation process in cold acclimated Arabidopsis thaliana

city: Aalborg East

first: Majken

last: Pagter

address: Fredrik Bajers Vej 7H

department: Chemistry and Bioscience

institute: Aalborg University

summary:
During low temperature exposure, temperate plant species increase their freezing tolerance in a process termed cold acclimation. During deacclimation in response to warm temperatures cold acclimated plants lose freezing tolerance and resume growth and development. While considerable effort has been directed toward understanding the molecular and metabolic basis of cold acclimation, much less information is available about the regulation of deacclimation. Here, we report metabolic (GC-MS) and transcriptional (microarrays, qRT-PCR) responses underlying deacclimation during the first 24 h after a shift of cold acclimated Arabidopsis thaliana (Columbia-0) plants to warm temperature. The data revealed a faster response of the transcriptome than of the metabolome and provided evidence for tightly regulated temporal responses at both levels. Metabolically deacclimation is associated with decreasing contents of sugars, amino acids and glycolytic and TCA cycle intermediates, indicating an increased need for carbon sources and respiratory energy production associated with growth resumption under warm temperature conditions. Deacclimation also involves extensive down-regulation of protein synthesis and changes in the metabolism of lipids and cell wall components. Altered hormonal regulation appears particularly important during deacclimation, with changes in the expression of genes related to auxin, gibberellin, brassinosteroid, jasmonate and ethylene metabolisms. Several transcription factor families controlling fundamental aspects of plant development are significantly regulated during deacclimation, emphasizing that loss of freezing tolerance and growth resumption are interrelated processes that are transcriptionally highly interrelated. Expression patterns of some clock oscillator components during deacclimation resembled those under warm conditions, indicating at least partial re-activation of the circadian clock. This study provide the first comprehensive analysis of the regulation of deacclimation in cold acclimated plants. The data indicate cascades of rapidly regulated genes and metabolites that underly the developmental switch resulting in reduced freezing tolerance and the resumption of growth. They constitute a reference dataset of genes, metabolites and pathways that are crucial during the first rapid phase of deacclimation and will be useful for the further analysis of this important but under-researched plant process.
We used whole genome microarrays to monitor changes in gene expression in the Arabidopsis thaliana accession Columbia-0 during the first 24 h after a shift of cold acclimated plants to warm temperature.

overall_design: Plants from Arabidopsis thaliana accession Columbia-0 were cold acclimated at 4°C for three days. Plants were then deacclimation at 20°C for 24 h. Rosettes of non-acclimated and cold acclimated plants and plants deacclimated for 2 h, 4 h, 6 h, 12 h and 24 h were collected for RNA extraction and hybridization on Affymetrix Arabidopsis Gene 1.0 ST arrays in order to explore temporal transcriptome changes during deacclimation. For each sample total RNA was isolated from a pool of rosettes of 10 plants. The experiment was performed in three idenpendent biological replicates.

first: Jessica

last: Alpers

first: Alexander

last: Erban

first: Joachim

last: Kopka

first: Ellen

last: Zuther

first: Dirk

last: Hincha


title: Identification of FOXJ1 effectors during ciliogenesis in the fetal respiratory epithelium and embryonic left-right organizer of the mouse - Lung subscreen A

first: Oliver

last: Dittrich-Breiholz

overall_design: The Microarray experiment was conducted in dual-colour mode using amplified, fluorescently labelled material from E14.5 and E18.5 micro-dissected airway epithelial samples for co-hybridisation on one microarray. In order to enable inspection of intensity values, dual-colour results were integrated into a single-color GEO matrix.

last: Stauber

first: Marina

last: Weidemann

first: Katharina

last: Lobschat

first: Leonie

last: Alten

first: Michaela

last: Mai

first: Anja

last: Beckers

last: Kracht

first: Achim

last: Gossler


title: Investigating global transcript dynamics in mitotically arrested budding yeast cells

city: Durham

first: Steven

last: Haase

department: Biology

institute: Duke University

summary: Transcript dynamics in mitotic exit mutants in the S. cerevisiae BF264-15D strain background. We examined the extent to which periodic cell-cycle transcription persisted in cells arrested in anaphase with intermediate level of B-cyclins.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design:
Early G1 cells were obtained by α-factor arrest at 25°C and then released at 37°C for time-series microarray.

This study includes new samples and re-analyzed samples from GSE8799, GSE32974 and GSE49650.

first: Chun-Yi

last: Cho


title: Global effect of H2A.Z hypervariant knockdown on basal expression of neuronal genes

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Variant histone H2A.Z is an essential and conserved regulator of eukaryotic gene transcription. However, the exact role of this histone in the process remains perplexing. In vertebrates, H2A.Z has two hypervariants – H2A.Z.1 and H2A.Z.2 – that have almost identical amino-acid sequences excepting three residues. Due to such similarity, functional specificity of these hypervariants in neurobiological processes, if any, remain largely unknown. In this study with dissociated mature cortical neurons, we asked if H2A.Z hypervariants have functional specificity in regulating basal and activity-induced gene transcription. Hypervariant-specific RNAi and microarray analyses revealed that H2A.Z.1 and H2A.Z.2 regulate basal expression of largely non-overlapping gene-sets, including genes that code for several synaptic proteins. In response to neuronal activity, depletion of H2A.Z hypervariants impairs transcription of our model gene Arc differentially. As part of the +1 nucleosome, H2A.Z.2, not H2A.Z.1, is necessary for rapid immediate-early transcription by facilitating RNA Pol II promoter proximal pausing. In contrast, H2A.Z.1 plays complicated and perhaps indirect roles that affect Arc transcription kinetics context-dependently. Context-dependent roles of H2A.Z hypervariants are also evident amongst several other immediate early genes where their regulatory roles vary from gene to gene under different conditions. Together, our data suggest that H2A.Z hypervariants have context-specific roles that complement each other to mediate activity-induced neuronal gene transcription.

overall_design: Seven-day-old rat dissociated cortical neurons were treated with lentiviruses expressing shRNA against H2A.Z.1 or H2A.Z.2 mRNA (versus scrambled shRNA as control) for seven days and gene expression was tested by microarray.

first: Ramendra

last: Saha

first: Serena

last: Dudek


title: Identification of FOXJ1 effectors during ciliogenesis in the fetal respiratory epithelium and embryonic left-right organizer of the mouse

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

overall_design: Refer to individual Series


title: SAGA Is a General Cofactor for RNA Polymerase II Transcription

city: Illkirch

first: Didier

last: Devys

address: 1 rue Laurent Fries / BP 10142

country: France

institute: Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)

summary:
The SAGA co-activator has been implicated in the regulation of a smal subset of genes in budding yeast in transcriptomic analyses performed in steady-state levels of RNA.
We used microarrays to analyse newly-synthesized RNA in several mutants for the SAGA complex to disclose and readdress the impact of this complex in RNA Polymerase II transcription.

overall_design: Newly-transcribed RNA in wild-type and mutant strains lacking diverse SAGA subunits were labeled using 4-thiouracil. Mutants were chosen according to its impact on SAGA activity in order to have a diverse representativity of the whole complex and its distinct funtions.

first: Tiago

last: Baptista

first: Sebastian

last: Grünberg

first: Nadège

last: Minoungou

first: Maria

middle: J

last: Koster

first: Marc

last: Timmers

last: Hahn

first: Laszlo

last: Tora


title: Identification of miRNAs in sheep heart

city: Singapore

first: Lee Lee

last: Wong

address: 14 Medical Drive, 08-01

department: Medicine

country: Singapore

institute: National University of Singapore

summary: MicroRNA profiling of myocardium of ovine comparing normal (Control), paced-induced heart failure (HF) and heart failure recovery (HF-R) after discontinuation of pacing.

overall_design: Three-condition experiment: Control vs HF vs HF-R. Biological replicates: 2 control, 4 HF and 3 HF-R. One replicate per array.

first: L

first: A

last: Richards

first: P

last: Wang


title: Strategies towards improved feed efficiency in pigs comprise molecular shifts in hepatic lipid and carbohydrate metabolism

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

institute: FBN Dummerstorf

summary: Individual pigs [(Large White × Landrace) x Hylean Maxgro] divergent in residual feed intake were sampled for hepatic transcriptome profiling at day 140.

overall_design: per RFI group 6 pigs were collected for expression profiling

first: Eduard

last: Murani

first: Henry

last: Reyer


title: The microRNA profile in neosquamous oesophageal mucosa following ablation of Barrett's oesophagus

city: Bedford Park

first: Damian

middle: James

last: Hussey

address: Flinders Drive

country: Australia

institute: Flinders University

summary:
mucosal biopsies were taken from patients at pre and post-argon plasma coagulation (APC) ablation of Barrett's oesophagus, and from healthy controls. Total RNA was extracted using Trizol. miRNA was reversed transcribed using a TaqMan® microRNA Reverse Transcription Kit (Life technologies, #4366596). miRNA profiling was performed with a high throughput TaqMan® OpenArray® Human microRNA panel  (Life technologies, #4461104). The panel consisted of probes for 754 human miRNAs that are based on miRNA sequences derived from Sanger miRBase v14.
Endoscopic surveillance remains the mainstay of cancer prevention in individuals with Barrett’s oesophagus, and definitive management by surgery or endoscopy is reserved for high grade dysplasia or cancer. There are several endoscopic treatments that are widely used for Barrett’s oesophagus, including argon plasma coagulation (APC). The normality of the regenerated neosquamous epithelium after ablation has been called into question. In the current study we profiled global microRNA expression in oesophageal mucosa before and after ablation of Barrett’s oesophagus using Argon plasma coagulation. Our aim was to  investigate differences in microRNA expression between neosquamous and normal squamous tissues.

overall_design: Openarray high throughput real time PCR of microRNAs -- 10 patients without oesophageal disease, 17 patients with Barrett's oesophagus who underwent APC ablation of their Barrett's mucosa and 16 of these contributed a datapoint to neosquamous mucosa PCRs

first: Loveena

last: Sreedharan

first: George

last: Mayne

first: David

last: Watson

first: Timothy

last: Bright

first: Reginald

middle: V

last: Lord

first: Alfiya

last: Ansar

first: Tingting

first: Jakob

last: Kist

middle: S

last: Astill


title: Identification of FOXJ1 effectors during ciliogenesis in the fetal respiratory epithelium and embryonic left-right organizer of the mouse - Noto screen

first: Oliver

last: Dittrich-Breiholz

summary: Formation of motile cilia in vertebrate embryos is essential for proper development and tissue function. Key regulators of motile ciliogenesis are the transcription factors FOXJ1 and NOTO, which are conserved throughout vertebrates. Downstream target genes of FOXJ1 have been identified in a variety of species, organs and cultured cell lines; in murine embryonic and foetal tissues, however, FOXJ1 and NOTO effectors have not been comprehensively analysed and our knowledge of the downstream genetic programme driving motile ciliogenesis in the mammalian lung and ventral node is fragmentary. We compared genome-wide expression profiles of undifferentiated E14.5 vs. abundantly ciliated E18.5 micro-dissected airway epithelia as well as Foxj1+ vs. Foxj1-deficient foetal (E16.5) lungs of the mouse using microarray hybridisation. 326 genes deregulated in both screens are candidates for FOXJ1-dependent, ciliogenesis-associated factors at the endogenous onset of motile ciliogenesis in the lung, including 123 genes that have not been linked to ciliogenesis before; 46% of these novel factors lack known homologues outside mammals. Microarray screening of Noto+ vs. Noto null early headfold embryos (E7.75) identified 59 of the lung candidates as NOTO/FOXJ1-dependent factors in the embryonic left-right organiser that carries a different subtype of motile cilia. For several uncharacterised factors from this small overlap – including 1700012B09Rik, 1700026L06Rik and Fam183b – we provide extended experimental evidence for a ciliary function.

overall_design: Microarray experiments were conducted in dual-colour mode using amplified, fluorescently labelled material from wildtype and mutant samples for co-hybridisation on one microarray. A second microarray hybridisation was performed as technical replicate with inverted dye allocation (dye-swap). In order to enable inspection of intensity values, dual-colour results were integrated into a single-color GEO matrix.

first: Michael

last: Stauber

first: Marina

last: Weidemann

first: Katharina

last: Lobschat

first: Leonie

last: Alten

first: Michaela

last: Mai

first: Anja

last: Beckers

last: Kracht

first: Achim

last: Gossler


title: Effect of vaccine administration routes on responses to a Bordetella pertussis outer membrane vesicle vaccine - lung

city: Bilthoven

first: Jeroen

last: Pennings

institute: Natl. Inst. Public Health & Environment

summary:
Pulmonary immunization with an outer membrane vesicle pertussis vaccine led to improved protection and induction of a completely distinct immune response compared to subcutaneous administration.
These adaptive responses were linked to early local and systemic signatures on the transcriptome level.

overall_design: 23 arrays, including replicates and controls, analyzed on Affymetrix genechips

first: René

last: Raeven

first: Jolanda

last: Brummelman


title: Transcription profiling of blood, dentate gyrus and anterior cingulate cortex in mice exposed Unpredicatble Chronic Mild Stress and treated with fluoxetine

city: MARSEILLE CEDEX 09

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

institute: TAGC INSERM U1090


title: LY294002 induced gene expression changes in Hodgkin lymphoma cell line KMH2.

status: Public on Sep 11 2017

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

institute: Durham University

summary: In this study, we investigated the effect of LY294002 on gene expression in Hodgkin lymphoma cell line KMH2 cells.

overall_design: In experimental design, gene expression was going to be compared between LY294002-treated and DMSO-treated KMH2 cells in triplicates. However, one microarray had high background and therefore was excluded from further analysis.

first: Amanda

last: Dutton

first: Katerina

last: Vrzalikova

first: Paul

last: Murray


title: BATF3siRNA induced gene expression changes in Hodgkin lymphoma cell line L428.

summary: In this study, we investigated the effect of BATF3 silecing on gene expression in Hodgkin lymphoma cell line L428.

overall_design: L428 cells were treated with BATF3siRNA (Silencer® Select s195280 BATF3 siRNA, Catalog number: 4392420) and control siRNA (Silencer® Select Negative Control No. 1 siRNA, ThermoFisher Scientific, Catalog number: 4390843) in triplicates and their gene expresson profiles were obtained using Affymetrix PrimeView human gene expression array.


title: Chinese lung SCC adjacent normal sample exon-level expression

status: Public on Sep 08 2017

city: Shanghai

first: Hongbin

last: Ji

address: YueYang Rd

institute: SIBCB

overall_design: In order to search for novel gene fusions which may play important roles in lung SCC initiation and progression, we performed Exon array on lung SCC and adjacent normal samples.

first: Fei

last: Li

first: Zhaoyuan

last: Fang


title: Transcription profiling of blood in mice exposed Unpredicatble Chronic Mild Stress and treated with fluoxetine

summary:
Groups of 8 adult BALB/c male mice were either untreated or exposed for 9 weeks to unpredicatble chronic mild stress (UCMS), or exposed for 7 weeks to UCMS and  treated for the last 5 weeks with fluoxetine (Flx) diluted in drinking water, or untreated for 2 weeks and received Flx for 5 weeks.
Total RNAs from whole blood (WB) were profiled after hybridization with Agilent SurePrint G3 Mouse GE 8x60K Microarray v1 to identify transcriptional biomarkers of major depression.

overall_design: Total RNAs were extracted from 32 samples including: (8 control, 8 UCMS, 8 UCMS+Flx, 8 Flx) for whole blood.

first: Mylène

last: Hervé

first: Aurélie

first: Nicolas

last: Fernandez-Nunez

first: Anne-Marie

last: Le Guisquet

first: Samuel

last: Leman

first: Catherine

last: Belzung

first: E

last: Ibrahim


title: Plasma-derived exosome characterization reveals a distinct microRNA signature in long duration Type 1 diabetes

status: Public on Sep 06 2017

city: Miami

first: Marta

last: Garcia-Contreras

state: FL

address: 1450 NW 10 th Ave

department: Diabetes Research Insitute

institute: University of Miami

summary: Type 1 diabetes mellitus (T1DM) results from an autoimmune attack against the insulin-producing ß cells which leads to chronic hyperglycemia. Exosomes are lipid vesicles derived from cellular multivesicular bodies that are enriched in specific miRNAs, potentially providing a disease-specific diagnostic signature. To assess the value of exosome miRNAs as biomarkers for T1DM, miRNA expression in plasma-derived exosomes was measured. Nanoparticle tracking analysis and transmission electron microscopy confirmed the presence of plasma-derived exosomes (EXOs) isolated by differential centrifugation. Total RNA extracted from plasma-derived EXOs of 12 T1DM and 12 control subjects was hybridized onto Nanostring human v2 miRNA microarray array and expression data were analyzed on nSolver analysis software. We found 7 different miRNAs (1 up-regulated and 6 down-regulated), that were differentially expressed in T1DM. The selected candidate miRNAs were validated by qRT-PCR analysis of cohorts of 24 T1DM and 24 control subjects.  Most of the deregulated miRNAs are involved in progression of T1DM. These findings highlight the potential of EXOs miRNA profiling in the diagnosis as well as new insights into the molecular mechanisms involved in T1DM.

overall_design: In the study presented here, a consecutively operated, well-defined cohort of 12 Type 1 diabetes cases,  followed up more than 25 years, and 12 age matched controls, was used to acquire expression profiles of a total of 800 unique miRNAs, leading to the successful identification of a miRNA profiling on exosomes


title: To evaluate the change in gene expression profile of Sertoli cells after busulphan treatment

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: In order to evaluate whether chemoablative busulphan treatment alters the expression profile of Sertoli cells in testis, adult male Swiss mice were treated intraperitoneally with 25mg/Kg body weight of busulphan. 1 month post busulphan treatment, the isolated Sertoli cells were evaluated for gene expression profile and compared to expression profile of Sertoli cells from age matched normal adult Swiss mice.

overall_design: Gene expression of isolated Sertoli cells 1 month after busulphan treatment from adult male Swiss mice

first: Sandhya

last: Anand

first: Deepa

last: Bhartiya

first: Kalpana

last: Sriraman

first: Alpna

last: Mallick


title: Genome-wide characterization of CREB-dependent transcriptional programs in astrocytes

city: Bellaterra

first: Luis

last: Pardo

state: Barcelona

address: Campus UAB Edificio M

institute: Universitat Autónoma de Barcelona

summary: Transcriptome profiling of astrocyte cultures treated with forskolin (FSK), noradrenaline (NE) or infected with adenovirus carrying a constitutively active form of CREB (VP16-CREB) vs. untreated or infected with null virus. Goal is to characterize the transcriptional programs elicited by CREB activation in astrocytes.

overall_design: Five group experiment. Two independent experiments for the treated (loop design) and the infected samples (direct comparison). Each group was balanced with respect to the use of Cy3 and Cy5 in the samples. Number of replicates: FSK: 3; NE:3; Ctrl:3; VP16: 3; Null: 3.

last: Valor

first: Abel

last: Eraso

first: Ángel

last: Barco

first: Roser

last: Masgrau

first: Elena

last: Galea


title: Transcription profiling of dentate gyrus and anterior cingulate cortex in mice exposed Unpredicatble Chronic Mild Stress and treated with fluoxetine

first: Aurelie

last: Bergon

summary:
Groups of 8 adult BALB/c male mice were either untreated or exposed for 9 weeks to unpredicatble chronic mild stress (UCMS), or exposed for 7 weeks to UCMS and  treated for the last 5 weeks with fluoxetine (Flx) diluted in drinking water, or untreated for 2 weeks and received Flx for 5 weeks.
Total RNAs from dentate gyrus (DG) and anterior cingulate cortex (ACC) were profiled after hybridization with Agilent SurePrint G3 Mouse GE 8x60K Microarray v1 to identify transcriptional biomarkers of major depression.

overall_design: Total RNAs were extracted from 64 samples including: (8 control, 8 UCMS, 8 UCMS+Flx, 8 Flx) for  DG, ACC tissues.

first: Mylène

last: Hervé

first: Aurélie

last: Fernandez-Nunez


title: Global gene expression analysis of NMN-induced disease resistance in  Arabidopsis thaliana.

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

institute: Kanazawa University

summary: We performed transcriptome analysis using an Agilent Arabidopsis ver.3 44k Microarray (Palo Alto, CA, USA) to profile effect of NMN treatment in uninoculated leaves and inoculated leaves with F. graminearum.

overall_design: Four condition experiments. NMN-treated vs water-treated leaves. Inoculated leaves with F. graminearum after pretreatment of NMN vs Inoculated leaves after pretreatment of water. Two biological replicates.


title: Transcriptomic changes of Campylobacter jejuni subsp. jejuni strain 81-176 in water

status: Public on Sep 01 2017

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

summary:
Campylobacter jejuni is the leading cause of campylobacteriosis in the developed world. Although most cases are caused by consumption of contaminated meat, a significant proportion is caused by consumption of contaminated water. Some C. jejuni isolates are better than others at surviving in water, which suggests that these strains are better adapted to transmission by water than others.
The aim of this study is to investigate this phenomenon further. CFU counts and viability assays showed that strain 81116 survives better than strain 81-176 in a defined freshwater medium at 4°C. Comparative transcriptomic profiling using microarray revealed that these strains respond differently to water. This series presents the transcriptome of strain 81-176 in water.

sample_organism: Campylobacter jejuni subsp. jejuni 81-176

overall_design: Campylobacter jejuni was first cultured on TSA-Blood plate at 42 °C for 2 days. C. jejuni was suspended in 100 ml of Fraquil or Brucella broth at an OD600 of 1 in triplicates and washed three times with either Fraquil or Brucella broth. The suspensions were then incubated at 4°C for 4h. RNA was extractedl, labelled, and hybridized on microarrays, with labeled gDNA as reference channel.

first: Hana

last: Trigui

first: Kristen

last: Lee

first: Alexandre

last: Thibodeau

first: Simon

last: Lévesque

first: Philippe

last: Fravalo

first: Ann

last: Letellier

middle: P


title: Identification and functional characterization of genes positively affecting lamina inclination and grain size in rice

status: Public on Sep 05 2017

city: Tainan

first: Seonghoe

last: Jang

state: Tainan

address: No.59, Siraya Blvd. Xinshi Dist.

country: Taiwan

institute: Academia Sinica

overall_design: Refer to individual Series


title: Global transcriptomic analysis of the response of Corynebacterium glutamicum to ferulic acid

city: Yangling

first: Can

last: Chen

address: No.3 Taicheng Road

institute: Northwest A&F University

summary: Corynebacterium glutamicum can survive by using ferulic acid as the sole carbon source. In this study, we assessed the response of C.glutamicum to ferulic acid stress by means of a global transcriptional response analysis. The transcriptional data showed that several genes involved in degradation of ferulic acid were affected. Moreover, several genes related to the stress response; protein protection or degradation and DNA repair; replication, transcription and translation; and the cell envelope were differentially expressed. Deletion of the katA or sigE gene in C. glutamicum resulted in a decrease in cell viability under ferulic acid stress. These insights will facilitate further engineering of model industrial strains, with enhanced tolerance to ferulic acid to enable easy production of biofuels from lignocellulose.

overall_design: Samples were collected during the mid-logarithmic growth phase in minimal medium with added glucose (control sample: 100 mM) or ferulic acid as the sole carbon source (3 mM), respectively.

first: C

first: J

last: Pan

first: X

last: Yang

first: H

last: Xiao

first: Y

last: Zhang

first: M

last: Si

last: Shen


title: Segregation of naturally occurring mitochondrial DNA variants in a mini-pig model

city: Clayton

first: Justin

last: StJohn

state: Victoria

address: 27-31 Wright Street

department: Centre for Genetic Diseases

institute: Hudson Institute of Medical Research

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

summary: We have generated a mini-pig model to study the transmission of naturally occuring mitochondrial DNA variants. To determine the chromosomal genotype of the model's founders, we have used the Illumina PorcineSNP60 v2 BeadChip.

overall_design: DNA extracted from 15 mini-pig samples was run on an Illumina PorcineSNP60 v2 BeadChip, containing 61,565 SNPs, delivering uniform genome-wide coverage with an average probe spacing of 43.4 Kb. Image processing and SNP calling were performed using the genotyping module of GenomeStudio software (GenCall cutoff for failed genotypes of 0.15,  = software versions 1.9.4 and 2011.1, respectively).

first: Gael

middle: L

last: Cagnone

first: Te-Sha

last: Tsai

first: Kanokwan

last: Srirattana

first: Fernando

last: Rossello

first: David

last: Powell

first: Ian

middle: A

last: Trounce

first: Gary

last: Rohrer

first: Lynsey

last: Cree

middle: C


title: Microarray using WT (Dongjin rice) and OsBUL1KO Lamina joint samples

first: Seonghoe

last: Jang

summary: We compared transcripts using microarray hybridization between lamina joint samples of WT and OsBUL1 KO.

overall_design: We used 22k probed rice microarray from Phalanx Biotech.

first: Hsing-Yi

last: Li

first: Lynda

last: Kuo


title: Microarray using WT (TNG67) and pOsBUL1:OsBDG1 Lamina joint samples (TNG67 vs. #13 vs. #20)

summary: We compared transcripts using microarray hybridization between lamina joint samples of WT and pOsBUL1:OsBDG1 plants.


title: The whole transcriptome expression profiling comparison between the ovarian cancer spheroids and monolayer cells

status: Public on Aug 31 2017

city: Boston

first: Shu-Wing

last: Ng

state: MA

address: 221 Longwood Avenue

department: Department of Obstetrics, Gynecology and Reproductive Biology

institute: Brigham and Women’s Hospital; Harvard Medical School

summary:
To discover the core gene expression features of ovarian cancer spheroids
The compared the whole transcript expression profiling between 5 pairs of spheroids and monolayer cancer cells, including the RMG1, MCAS and Ov432 plus two cases of serous ovarian cancer ascites cells.

overall_design: The 3 paired good spheroid formed ovarian cancer cells (MCAS, RMG1 and OV432) and two pairs of serous ovarian cancer ascites (RB-223 and RB-407) were used to discover the ovarian cancer spheroid feature signature. The RNA was extracted from well cultured spheroid (4days cultured) and monolayer cells (4 days cultured) using TRIzol reagent, and whole transcriptome gene expression  profiling were performed using an Affymetrix Human Gene 1.1 ST microarray platform.

first: Shubai

last: Liu


title: Microarray using WT (Dongjin rice) and OsBUL1KO Panicle samples

summary: We compared transcripts using microarray hybridization between panicle samples of WT and OsBUL1 KO.


title: Oncogenic Ras regulated long non-coding RNA Orilnc1 in human cancer

city: Philadelphia

first: Lin

last: Zhang

state: Pennsylvania

address: 421 Curie Blvd

institute: University of Pennsylvania

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

summary: Ras and its downstream cascades transmit cellular signals, resulting in increased transcription of a large  number of genes involved in cell growth and division. Research on long non-coding transcripts regulated  by the Ras signaling cascade is still in its infancy. Long non-coding RNAs (lncRNAs) are operationally  defined as transcripts that are larger than 200 nt that do not appear to have protein-coding potential. Using  a custom-designed lncRNA microarray, we identified a novel lncRNA (oncogenic Ras-induced lncRNA 1,  Orilnc1) whose expression is significantly induced by activation of Ras. Further molecular studies  demonstrated that the expression of Orilnc1 is regulated by the Ras-Raf-MEK-ERK signaling cascade via  the transcriptional factor AP1. Importantly, Orilnc1 is highly expressed in BRAF mutant cancers such as  BRAF-driven melanoma. Inhibition of Orilnc1 expression by small RNA interference (siRNA)  significantly blocked tumor cell proliferation and growth in vitro and in vivo. Finally, we observed that  blocking Orilnc1 reduced expression levels of cell cycle related genes such as Cyclin E1 and induced G1/S  arrest in tumor cells. Taken together, Orilnc1 may function as a novel non-protein mediator to respond the  Ras/Raf activation and could serve as a potential therapeutic target for RAS or BRAF-driven cancers such  as melanoma.

overall_design: KRASG12D- expressing or control lentiviruses were used to infect IMR90 cells, and total  RNAs were harvested from cells at different time points (0, 4, 7, and 10 days for KRas cells and 0, 7, and  10 days for control cells).


title: Gene expression profiles of tumor epithelium and tumor-associated stroma of HER2+ breast tumors, plus normal epithelium and stroma from HER2+ and HER2- breast tumors

city: Montreal

first: Morag

last: Park

state: Quebec

address: 1160 Ave. des Pins O.

department: Goodman Cancer Research Centre

summary: Breast cancer is a heterogeneous disease. This heterogeneity can be observed at multiple levels, including gene expression, chromosomal aberrations, and disease pathology. A clear understanding of these differences is important since they impact upon treatment efficacy and clinical outcome. Many studies have shown that the tumor microenvironment also plays a critical role in cancer initiation and progression. Although genomic technologies have been used to gain a better understanding of the impact of gene expression heterogeneity on breast cancer outcome by identifying gene expression signatures associated with clinical outcome, histopathological breast cancer subtypes, and a variety of cancer-related pathways and processes, relatively little is known about the spectrum of heterogeneity in the tumor microenvironment.

overall_design: 107 samples isolated by laser capture microdissection; in total, 40 samples of tumor epithelium, 39 samples of tumor stroma, 14 samples of normal epithelium and 14 samples of normal stroma; 2 samples possess biological replicates; each subjected to gene expression profiling in a common reference design using Agilent whole human genome oligonucleotide arrays.


title: Development of a new low density stress response microarray STREM

status: Public on Aug 17 2017

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

summary:
Development of a new low density stress response microarray to evaluate biological effects of contaminants in Mytilus sp: laboratory validation.
Background: Despite the increasing use of mussels in environmental monitoring, their genome and gene functions remain weakly explored. Recently several cDNA microarrays were proposed in Mytilussp, however partial putatively identified transcripts are provided rendering very difficult the generation of robust transcriptional responses in term of pathwaysidentification. In this study we developed a new medium density oligonucleotide microarray with 476 probes covering the same number of well identified genes representing 16 Biological processes at cellular and tissue levels among the most important in mussel’s response to stress (Lysosomal activity, DNA Metabolism, Translation, Mitochondrial activity, Carbohydrate metabolism, Heat choc response, Oxydatif stress, Proteolysis, Phase I and II detoxification, Metal resistance, Endocrine disruptors,  Endocytosis,  Macrophage, Pumps, Cytoskeleton, Adhesion to substrate). Our new platform STREM (STress Response Microarray in Mytilussp) consists of eight sub-arrays with 3 repetitions for each target in each sub-array.   To assess the potential use of the new array, we tested the effect of three Benzo[a]pyren (B[a]P) concentrations, a relevant environmental contaminants in two mussel’s tissues; gills and digestive gland.  Our data provided clues about the higher sensitivity of the new array. Moreover transcriptional data were confirmed using Q-RT-PCR and the possible implication in biological role by conventional biomarkers of stress (oxidative stress biomarkers) as well as immune-histochemical analysis (Tubulin).

platform_organism:
Mytilus californianus
Mytilus edulis
Mytilus galloprovincialis
Magallana gigas

overall_design: Digestive gland and gills tissue from individual animals in different experimental conditions were analyzed in a complete loop design. Dual color competitive hybridizations (Control vs BaP 5µg/L vs 50µg/L and 100 µg/L ). Single individuals. Four biological replicates. two replicates per array.

first: PACCHIONI

last: Beniamina

first: MILLINO

last: Caterina

first: BANNI

last: Mohamed

first: OLIVERI

first: VIARENGO

last: Aldo


title: Proteomic Comparison of Acute Myocardial Infarction and Stress Cardiomyopathy in Women

status: Public on Aug 03 2017

city: Worcester

first: Dr Yvonne

last: Edwards

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

summary: Background:  Stress cardiomyopathy (SCM) is a unique form of LV dysfunction that more often occurs in women.  Patients with SCM have a higher Troponin I/B-type natriuretic peptide ratio than AMI, but little is known about other circulating proteins.  The goals of this study were to compare plasma proteins in SCM and AMI to learn about the pathophysiology of SCM and also to identify putative biomarkers of SCM.  Methods: Blood was drawn in normal controls (n=6), women with AMI (n=12) or women with acute SCM (n=15).  Two-week follow up samples were available in AMI (n=4) and SCM patients (n=11).  Relative concentrations of 1310 serum proteins were measured in each of the 48 samples using the SOMAscan aptamer based assay.  Women with AMI tended to be younger (57.87 ± 16.0 vs. 65.08 ± 9.11 years, p=0.12) and had a higher peak troponin I (AMI 32.03 ± 29.46 vs. SCM 2.68 ± 2.6 ng/mL, p=0.02).  No differentially expressed proteins were detected (absolute log2 fold change>1; q<0.05) between AMI and SCM in the acute or recovery phase.  In the normal vs. AMI comparison there was differential expression of 35 proteins.  In the normal vs. SCM comparison there were 45 proteins with differential expression.  Pathway analysis demonstrated activation of complement, coagulation, and inflammation in both AMI and SCM.  Conclusions:  The acute phase of SCM is characterized by a severe inflammatory response similar to AMI.  Despite recovery of LV function in SCM at two weeks, differences in circulating proteins remain in comparison to normal controls.

overall_design: 48 serum samples total measured. Non fasting venous blood, collected in SST tubes, within 24 hours of hospital admission. Normal controls (n=6), Acute myocardial infarction (AMI) (n=12), acute stress cardiomyopathy (SCM)(n=15), Follow up AMI (n=4), Follow up SCM (n=11)

first: Timothy

last: Fitzgibbons


title: Chinese lung SCC exon-level expression

first: Hongbin

last: Ji

summary: Chinese lung squamous cell carcinomas exon-level expression

overall_design: In order to search for novel gene fusions which may play important roles in lung squamous cell carcinomas initiation and progression, we performed Exon array in lung squamous cell carcinomas samples.

first: Fei

first: Zhaoyuan

last: Fang


title: Transcriptomic response of the yeast Saccharomyces cerevisiae EC1118® during wine alcoholic fermentation under unusual nutrient starvations.

status: Public on Jul 30 2017

city: Montpellier

first: Bruno

last: Blondin

address: 2 place Pierre Viala

institute: INRA

summary: In order to asses yeast EC1118® strain expression changes during wine alcoholic fermentation triggered by various nutrient starvations, this experiment describes the gene expression under  micronutrient starvations that lead to yeast cell death (oleic acid starvation, ergosterol starvation, pantothenic acid starvation and nicotinic starvation) or allow the maintenance of yeast viability (nitrogen starvation).

overall_design: For each fermentation condition (low nitrogen, low nitrogen/low ergosterol, high nitrogen/low oleic acid, high nitrogen/low ergosterol, high nitrogen/low pantothenic acid, high nitrogen/low nicotinic acid), three independent fermentations were carried out in parallel . Sampling was performed at 4 time-points of the fermentation (20 106 cells/mL, 12 g of CO2 produced, 40 g of CO2 produced and 75 g of CO2 produced) for each biological repetition of each fermentation condition, giving a total of 72 samples. The condition low nitrogen serves as reference as this condition is known to lead to set up of the environmental stress response.

first: Camille

last: Duc

first: Isabelle

last: Sanchez

first: Martine

last: Pradal

first: Catherine

last: Tesnière


title: MicroRNA-31 promotes adverse cardiac remodeling and dysfunction in ischemic heart disease.

first: Eliana

last: Martinez

address: 1501 N.W. 10th Avenue. BRB 803

institute: University of Miami Miller School of Medicine

summary:
RATIONALE:

Myocardial infarction (MI) triggers a dynamic microRNA response with the potential of yielding therapeutic targets.

OBJECTIVE:

We aimed to identify novel aberrantly expressed cardiac microRNAs post-MI with potential roles in adverse remodeling in a rat model, and to provide post-ischemic therapeutic inhibition of a candidate pathological microRNA in vivo.

METHODS AND RESULTS:

Following microRNA array profiling in rat hearts 2 and 14days post-MI, we identified a time-dependent up-regulation of miR-31 compared to sham-operated rats. A progressive increase of miR-31 (up to 91.4±11.3 fold) was detected in the infarcted myocardium by quantitative real-time PCR. Following target prediction analysis, reporter gene assays confirmed that miR-31 targets the 3´UTR of cardiac troponin-T (Tnnt2), E2F transcription factor 6 (E2f6), mineralocorticoid receptor (Nr3c2) and metalloproteinase inhibitor 4 (Timp4) mRNAs. In vitro, hypoxia and oxidative stress up-regulated miR-31 and suppressed target genes in cardiac cell cultures, whereas LNA-based oligonucleotide inhibition of miR-31 (miR-31i) reversed its repressive effect on target mRNAs. Therapeutic post-ischemic administration of miR-31i in rats silenced cardiac miR-31 and enhanced expression of target genes, while preserving cardiac structure and function at 2 and 4weeks post-MI. Left ventricular ejection fraction (EF) improved by 10% (from day 2 to 30 post-MI) in miR-31i-treated rats, whereas controls receiving scrambled LNA inhibitor or placebo incurred a 17% deterioration in EF. miR-31i decreased end-diastolic pressure and infarct size; attenuated interstitial fibrosis in the remote myocardium and enhanced cardiac output.

CONCLUSION:

miR-31 induction after MI is deleterious to cardiac function while its therapeutic inhibition in vivo ameliorates cardiac dysfunction and prevents the development of post-ischemic adverse remodeling.

overall_design: In the study presented, 345 miRNAs were profiled in two samples- sham and MI at Day 2 and 656 miRNAs at Day 14. Each samples were pooled from 3 rats from the same groups.

first: Shera

last: Lilyanna

first: Peipei

last: Wang

first: Leah

last: Vardy

first: Xiaofei

last: Jiang

first: Arunmozhiarasi

last: Armugam

first: Kandiah

last: Jeyaseelan

first: Arthur

last: Richards


title: Expression profile in Plk1(+/-) aortas

status: Public on Jul 01 2017

city: Madrid

first: Marcos

last: Malumbres

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

institute: Centro Nacional de Investigaciones Oncológicas (CNIO)

summary: Transcriptional profiling of mouse aortas comparing control wild-type animals with aortas from three different Plk1(+/-) mice. Goal was to determine the effects of Plk1 haploinsufficiency in aorta expression profiles.

overall_design: Two-condition experiment, Plk1(+/+) vs. Plk1(+/-) aortas. Biological replicates: Pool of three Plk1(+/+) samples, 3 individual Plk1(+/-) samples.

first: Guillermo

last: de Carcer


title: High resolution profiling of gene expression during probenazole (PBZ) treatment in Arabidopsis

status: Public on Sep 02 2017

city: shanghai

first: Benke

last: Kuai

state: shanghai

department: Insititute of plant biology

institute: fudan university

summary:
Leaf senescence is a developmentally programmed event, which is also regulated by several phytohormones such as SA. SA has been shown to regulate the expression of many genes during leaf senescence, the fact that the mutants defective in SA biosynthesis and signaling have negligible senescence-related phenotypes makes it difficult to evaluate the exact role of SA in regulating leaf senescence. We have previously shown that probenazole (PBZ) is able to induce endogenous SA biosynthesis when applied by root drenching. We also detected an accelerated leaf yellowing phenotype about two weeks after PBZ treatment. Analysis of PBZ response genes identifies several MAPKs genes may be involved in SA induced senescence signaling pathway.
We used microarrays to detail the global programme of gene expression underlying probenazole (PBZ) treatment in Arabidopsis and identified distinct classes of MAPKs genes during this process.

overall_design: We used 5 week old Arabidopsis to conduct 0.5 mM probenazole (PBZ) root drenching to induce endogenous SA biosynthesis. The 5th through the 8th true leaves were chosen for physiological and molecular analyses because they exhibited the most significant leaf yellowing phenotypes. We used two biological replicates for each time points: before PBZ treatment (PBZ_T0-1, PBZ_T0-2) and after 72h PBZ treatment (PBZ_T72-1, PBZ_T72-2), respectively.

first: Jianjian

last: Zhang

first: Jiong

last: Gao

first: Zheng

last: Zhu

first: Jinxiao

last: Yang

first: Jin

last: Yu

first: Xiaoyan

first: Xiaolei

first: Yi

last: Song

first: Xin

last: Zhou

first: Guodong

last: Ren


title: Transcriptomic changes of Campylobacter jejuni in water

first: Sebastien

last: Faucher

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

sample_organism: Campylobacter jejuni subsp. jejuni 81116

platform_organism: Campylobacter jejuni subsp. jejuni 81-176


title: MicroRNA-497~195 cluster regulates angiogenesis during coupling with osteogenesis via maintaining endothelial Notch and HIF-1α activity

status: Public on Jun 30 2017

city: Changsha

first: Xianghang

last: Luo

address: 87# Xiangya Road

institute: Endocrinology Research Center, The Xiangya Hospital of Central South University

summary: Recently a specific vessel subtype in bone, strongly positive for CD31 and endomucin (CD31hiEmcnhi), is identified as coupling angiogenesis and osteogenesis. To figure out underlying mechanism of type H vessels generation, we isolated CD31hiEmcnhi and CD31loEmcnlo endothelial cells from one months old mice and perfermed microarrays to detail the microRNA expression. we identified that the miR-497~195 cluster was strongly expressed in CD31hiEmcnhi endothelial cells.

overall_design: CD31hiEmcnhi and CD31loEmcnlo endothelial cells (type H and type L ECs) isolated from one months old mice were cultured with endothelial cell growth medium for RNA extraction and hybridization on Agilent Mouse miRNA Microarray.

first: Mi

first: Changjun

last: Li

first: Xi

last: Sun

first: Manli

last: Tu

first: Hui

last: Peng

first: Qiong

last: Lu

first: Mei

last: Wan

first: Xu

last: Cao


title: Using Domestic and Free-Ranging Arctic Canid Models for Environmental Molecular Toxicology Research

status: Public on Jul 18 2017

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: 11 Arctic fox samples were analyzed to see if blood cells contained polychlorinated biphenyls (PCBs) and/or mercury.

first: Theodor

middle: K

last: Bammler

first: Richard

last: Beyer


title: Exposure of Campylobacter jejuni to Sub-inhibitory Concentrations of Pinocembrin Affects the Bacterial Virulence Potential

city: Ljubljana

first: Jasna

last: Kovac

address: Jamnikarjeva 101

department: Department of Food Science and Technology

country: Slovenia

institute: University of Ljubljana, Biotechnical Faculty

summary: Objectives: The aim of the study was to investigate the Campylobacter jejuni response to subinhibitory concentrations of natural antimicrobial compound pinocembrin

sample_organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

overall_design:
Influence of pinocembrin on gene expression in C. jejuni NCTC 11168 was determined by expressional analysis and qRT-PCR. Exponential phase culture was adjusted to OD600=0.2 in MHB using spectrophotometer (Smart Spec, Bio-Rad, Hercules, CA, USA). Five ml of culture was treated with 16 mg/l pinocembrin dissolved in DMSO. Only DMSO (0.048 %) was added to untreated samples. Cultures were treated for 2 h, incubated microaerobically shaking (160 rpm) at 42°C. Experiments were carried out in 4 biological replicates. RNA Protect Bacteria reagent (Qiagen, Maryland, USA) was added to the culture and total RNA was isolated using RNeasy mini kit (Qiagen) and treated with Ambion® Turbo DNA-freeTM kit (Invitrogen, USA).
Microarrays with 4751 probes targeting 1756 genes specific for Campylobacter jejuni subsp. jejuni NCTC 11168 (Mycroarray, Biodiscovery-LLC, MI, USA) were used for gene expression analysis. The cDNA was synthesized with random hexamers, SuperScriptTM III Reverse Transcriptase and amynoallyl dUTP (all supplied by Invitrogen, USA) and labeled with monofunctional NHS-ester dye Amersham C3 or Cy5 (GE Healthcare, Buckinghamshire, UK). Concentration of cDNA and labeling efficiency was determined spectrophotometrically with NanoDrop 1000. Four biological replicates were hybridized to four microarrays according to manufacturer’s protocol, incubated for 24 hours at 42⁰C and scanned at 550 nn for Cy3 and 650 nm for Cy5 with General Scanning ScanArray 5000 (PerkinElmer, Boston, USA). Flourescence intensities were converted to digital signal with ImaGene software (BioDiscovery, EI Segundo, USA).

last: Kovač

first: Zuowei

last: Wu

first: Anja

last: Klančnik

first: Franz

last: Bucar

first: Zhang

last: Qijing

first: Sonja

last: Smole Možina


title: The whole transcriptome expression profiling comparison between the CtBP1 knockdown, CtBP2 knockdown and scramble control in ovarian cancer SKOV3 cells

first: Shu-Wing

last: Ng

summary:
To discover the core gene expression features of CtBP1, CtBP2 differently regulated in ovarian cancer SKOV3 cells.
The compared the whole transcript expression profiling between CtBP1 knockdown, CtBP2 knockdown and scramble control in ovarian cancer skov3 cells.

overall_design: The 2  scramble control clones, 3 CtBP1 knockdown clones and 2 CtBP2 knockdown  clones from ovarian cancer SKOV3 cells  were used to discover the key feature genes that CtBP1/CtBP2 differential regulated . The RNA was extracted from well cultured  cells  using TRIzol reagent, and whole transcriptome gene expression  profiling were performed using an Affymetrix Human Gene 1.1 ST microarray platform.

first: Shubai

last: Liu


title: Transcriptome Profiling in Mycobacterium leprae. Implications for Type 2 Reactions (ENL) in Leprosy

city: Vellore

first: Sundeep

middle: Chaitanya

last: Vedithi

state: Tamil Nadu

address: Karigiri

department: Molecular Biology

institute: Schieffelin Institute of Health Research and Leprosy Center

type: Expression profiling by genome tiling array

summary:
Background: Reactions in Leprosy are immune exacerbations that cause debilitating consequences like nerve damage and permanent deformities. Prediction of these reactional states using appropriate biomarkers would enable early treatment interventions to prevent nerve function impairment. The current study investigated whole transcriptomic expression profiles of Mycobacterium leprae (M. leprae) that differentiate leprosy cases in type 2 (Erythema Nodosum Leprosum) reactions with those without reactions in host skin tissue derived RNA.

Methods: Post clinical examination, excisional skin biopsy specimens were collected from skin lesions of subjects with and without type 2 reaction. Total RNA was extracted following the Trizol protocol and bacterial RNA was enriched in the samples.  A 2 x 400K gene expression array (whole genome tiling array) was designed with the probes having 60-mer oligonucleotides tiling every 10bp of the genome sequence of M. leprae (NC_011896.1). The array comprised 420288 features which include probes and Agilent controls. The quality of RNA was estimated using BioAnalyzer (Agilent Technologies) followed by labelling, reverse transcription, amplification and hybridization to the arrays. The hybridized slides were scanned on a G2600D scanner (Agilent Technologies). The data thus acquired is analysed using GeneSpring GX Version 12.1 software. Data was normalized and fold difference in expression was noted from 359,922 probes which include sense and antisense orientations of 179,961 probes. The differentially expressing M. leprae genomic regions between type 2 reactions and non reactional cases were noted.

Results: Considering a statistical cut-off value of 0.6 for fold difference in expression between the test and the control samples, a set of 107 genes indicated statistically significant up-regulation with volcano plot p-values less than 0.05. Functional characterization revealed higher-expression of genes encoding transmembrane proteins (12), regulatory proteins (9), fatty acid biosynthesis (6), amino acid metabolism (13), nucleic acid metabolism (7), DNA replication and repair (7), Secretory proteins (2) Krebs Cycle (1), Glycolysis (1), Drug Efflux Protein (1),Stress Response Protein (1), Energy Metabolism (2), Pantothenate biosynthesis (1), Metalloproteins (3), Hydrolases (1) and Hypothetical Proteins (40). Additionally there are 157 genes that are down regulated in cases with reaction.

Conclusion: Differential expression of genes in the human skin biopsy specimens among leprosy cases with type 2 reaction in contrast to those without reaction suggests the role of pathogen associated gene expression triggers with the aetiology of these reactions. As most of the transmembrane and cell wall proteins possess epitope and surface exposed domains, higher expression levels of genes encoding these proteins may have a possible role in enhancing host immune responses characteristic of type 2 reactions in leprosy.

first: V

last: Chaitanya

first: M

last: Das

first: A

last: Geluk

first: I

last: Horo

first: L

last: Rajan

last: Ebenezer

first: Bipin

last: Chand


title: Transcriptional profiles of stomach organoids from human embryonic stem cells.

city: Tsukuba city

first: Takaaki

last: Noguchi

state: Ibaraki prefecture

department: Life and environmental sciences

institute: The University of Tsukuba

summary: Gastric ulcer, which affect many of patients and is deeply related with gastric cancer, is caused by chronic gastric acid stimulation. Stomach fundus, the main body of stomach, is a major source of gastric acid and peptidase for food digestion. Recapturing the main body of stomach requires mainly 3 functionally differentiated cells; parietal (oxyntic) cells, chief (zymogenic) cells, and surface mucous foveolar (pit) cells. We have previously shown the induction of stomach tissue with functional secreting activities by directed differentiation of mouse embryonic stem cells (ES cells) to stomach primordium with both gut epithelium and splanchnic mesoderm. However, generating human stomach with fundus and such functions has been elucidated and a long-desired goal. Here, we describe the method for establishing human embryonic stem cell-derived stomach organoids with fundus gland structure. Along with mouse stomach development and de novo stomach generation from mouse ES cells in vitro, we observed gut-like structure formation from human embryonic stem cells by induction of both endoderm and mesoderm. These human embryonic gut could differentiate into stomach primordium by growth factor stimulation as well as stomach development, and form stomach tissue in three-dimensional organoid culture. Furthermore, these stomach organoids contain fundus-like gland with parietal cells and chief cells, some of secreting activities, and is transcriptionally close to human stomach. Human functional stomach derived from embryonic stem cells represent powerful tools for analying human stomach development, and gastric ulcer related disease including gastric tumorgenesis.

overall_design: We generated arrays from stomach organoids derived from human embryonic stem cells.


title: Mature Arabidopsis leaves: RAP2.6L overexpressing vs wild-type (Ws)

city: York

first: Katherine

last: Denby

address: Department of Biology

institute: University of York

summary: Transcriptional profiling of Arabidopsis thaliana, comparing control wild-type (ecotype Wassilewskija, Ws) leaves with leaves from transgenic plants overexpressing the transcription factor RAP2.6L under control of the cauliflower mosaic virus 35S promoter (RAP2.6L-OX; this line was originally described in Krishnaswamy et al (2010)).

overall_design: Leaf samples for the 35S:RAP2.6L line and the Ws control were harvested from 28 day old plants. Three individual leaves (Leaf 7) from separate plants were harvested from both Ws and 35S:RAP2.6L genotypes. Total RNA from the three biological replicates of Ws and 35S:RAP2.6L samples were pooled separately. Expression was compared between Ws vs. 35S:RAP2.6L using six technical replicates including dye-swaps.

first: Johanna

last: Rhodes


title: Global gene expression profiles of induced lung progenitor (iLung) cells

city: Tsukuba

first: Naoto

last: Ninomiya

state: Ibaraki

address: 1-1-1 Higashi

department: Biotechnology Research Institute for Drug Discovery

institute: National Institute of Advanced Industrial Science and Technology

summary: We generated mouse embryonic and adult fibroblasts into lung progenitor-like cells by defined transcription factors. To evaluate characteristic of iLung cell, we compared the global gene expression profiles of iLung cells with those of mouse embryonic fibroblasts (MEFs), mouse dermal fibroblasts (MDFs), adult trachea, lung, esophagus, thyroid and E11.5 embryonic lung cells using microarrays.

overall_design: MEFs were prepared from E13.5 mouse dorsal skin and limb skin. For MDFs preparation, skin tissue behind the ear of 12 week old mice was used. iLung cells were generated by retroviral transduction of transcription factors. In addition we also extracted total RNA form the trachea, lung, esophagus, and thyroid tissues isolated from 8 week old mice.

first: N

first: T

last: Sekine

last: Kurisaki


title: PIWI-interacting RNAs as novel regulators of pancreatic beta-cell function [p10, adult samples]

status: Public on Jun 29 2017

city: Lausanne

first: Imene

last: Henaoui

state: Vaud

address: Rue du Bugnon 9

country: Switzerland

institute: Unil-DNF

summary: There is mounting evidence indicating that piRNAs are also present in somatic cells where they may accomplish additional regulatory tasks. The aim of this study was to identify the piRNAs expressed in pancreatic islets and to determine whether they are involved in the control of beta-cell activities. piRNA profiling of rat pancreatic islets was performed by microarray. We detected about 18’000 piRNAs in rat pancreatic islets, many of which were differentially expressed throughout islet postnatal development.

overall_design: Total RNA from two P10 pups islets were pooled while islets from adult rats were extracted individually. 3 Adult rat islets samples and 3 p10 rats islets samples were labeled using a RNA ligase method and were hybridized onto the piRNA Array in Agilent’s SureHyb Hybridization Chambers. The arrays were scanned by the Agilent Scanner G2505C.

first: Cécile

last: Jacovetti

first: Imène

first: Romano

last: Regazzi


title: PIWI-interacting RNAs as novel regulators of pancreatic beta-cell function [GK, wistar samples]

summary: There is mounting evidence indicating that piRNAs are also present in somatic cells where they may accomplish additional regulatory tasks. The aim of this study was to identify the piRNAs expressed in pancreatic islets and to determine whether they are involved in the control of beta-cell activities. piRNA profiling of rat pancreatic islets was performed by microarray. We detected about 18’000 piRNAs in rat pancreatic islets, many of which were differentially expressed throughout islet of Goto-Kakizaki rats, a well-established model of Type 2 diabetes.

overall_design: Total RNA from adult rats pancreatic islets were extracted individually. 3 wistar rat islets samples and 3 Goto-Kakizaki rats islets samples were labeled using a RNA ligase method and were hybridized onto the piRNA Array in Agilent’s SureHyb Hybridization Chambers. The arrays were scanned by the Agilent Scanner G2505C.


title: A Conserved Mitochondrial Surveillance Pathway Is Required for Defense against Pseudomonas aeruginosa

status: Public on Jun 20 2017

city: Houston

first: Natalia

last: Kirienko

state: TX

address: 6100 Main St. MS140

department: BioSciences

country: USA

institute: Rice University

summary: In the arms race of bacterial pathogenesis, bacteria produce an array of toxins and virulence factors that disrupt host processes while hosts respond with immune countermeasures. One key virulence mediator of the ubiquitous, opportunistic, extracellular pathogen Pseudomonas aeruginosa is the iron-binding siderophore pyoverdin (PMID:10722571;PMID: 8550201). The mechanisms used by pyoverdin to acquire iron from the host remain incompletely elucidated. Here we demonstrate that mitochondria represent an important target for iron acquisition and that exposure to this toxin results in loss of mitochondrial membrane potential, altered mitochondrial dynamics, and mitophagy in both Caenorhabditis elegans and mammalian cells. We also show that animal mitophagy protects the consequences of siderophore activity, conferring resistance to pyoverdin-mediated host killing. In C. elegans, the conserved autophagic genes bec-1/BECN1 and lgg-1/LC3, and the mitophagic regulator pink-1/PINK1 are required for iron chelator-elicited mitochondrial turnover and provide protection against iron sequestration by P. aeruginosa, likely by ameliorating the mitochondrial damage. While autophagic mechanisms have been implicated in the destruction of intracellular bacteria via a process called “xenophagy” (PMID: 24005326), our findings represent the first report of resistance to an extracellular pathogen being conferred by authentic autophagic activity that targets host organelles.

overall_design: There are 21 samples total that comprise three biological replicates of glp-4(bn2) animals exposed to E.coli OP50 on solid NGM agar, E. coli OP50 on solid SK agar, E. coli OP50 in liquid LK media, P. aeruginosa PA14 on solid SK agar, P. aeruginosa PA14 in liquid LK media, DMSO + E.coli in liquid S Basal media, and 1 mM 1,10-phenanthroline + E.coli in liquid S Basal media  for 8 hours at 25°C. Each biological replicate consists of glp-4 C. elegans animals in the young adult developmental stage.


title: Circular RNAs in Rat Models of Cardiovascular and Renal diseases

status: Public on Jul 27 2017

city: Toledo

first: Bina

last: Joe

state: Ohio

address: Block Health Science Bldg, 3000 Arlington Ave

department: Department of Physiology and Pharmacology

institute: University of Toledo, College of Medicine and Life Sciences

summary: The objective of this study was to profile circular RNAs (circRNAs) in rat genetic models of cardiovascular and renal disease. Renal profiles were obtained from the Dahl Salt-Sensitive rat (S), the Dahl Salt-Resistant rat (R), the Spontaneously Hypertensive Rat (SHR) and the Wistar Kyoto rat (WKY).

overall_design: At 57 days of age,  kidneys were collected from male Dahl salt-sensitive rats (S), Dahl salt-resistant rats (R), spontaneously hypertensive rats (SHR) and Wistar Kyoto rats (WKY) (n = 3 rats  per group) and snap frozen. RNA isolated was used for microarray studies conducted by ArrayStar Inc. (Rockville, MD, USA).

first: Xi

last: Cheng


title: Array-CGH for cell lines derived from paired primary and metastatic tumor

status: Public on Jul 21 2017

city: Singapore

first: Shumei

last: Chia

state: Singapore

institute: Genome Institute of Singapore

type: Genome variation profiling by genome tiling array

summary:
Characterization of DNA copy number changes in cell line derived from patient using DNA microarray-based comparative genomic hybridization method.
Our study identified genomic alterations between primary and metastatic tumor within a single individual

overall_design: Two samples: HN137 metastatic cell line and HN137 primary cell line. One replicate per sample. Reference sample: HN137 blood


summary: Comparison of copy number variations and gene expression profiles of cell lines obtained from the primary and lymph node metastatic tumors from a single patient.

overall_design: Gene expression analysis of patient (HN137) primary and metastatic tumor derived cell lines. Total RNA obtained from HN137-Pri and HN137-Met cell lines for microarray analysis.

first: Chia

last: Shumei


title: Characterization of two Acinetobacter baumannii rifampin-spontaneous mutants lacking twitching motility

status: Public on Jun 12 2017

city: Barcelona

first: Jesús

last: Aranda

address: Facultat de Biociències, Plaza Cívica, s/n

department: Departament de Genètica i Microbiologia

institute: Universitat Autònoma de Barcelona

summary: Transcriptional profiling of A. baumannii ATCC 17978 comparing two spontaneous rpoB mutants (Rif5 and Rif 8) with the wild-type parental strain

overall_design: Three strain comparison. Two and four biological replicates.

last: Aranda Rodríguez

first: Jordi

last: Barbé García


title: Genome-wide location of Candida albicans transcription factor Skn7p

city: Paris

first: Sadri

last: ZNAIDI

address: 25 rue du Docteur Roux

department: Mycology Department

institute: Institut Pasteur

type: Genome binding/occupancy profiling by genome tiling array

summary: Skn7 is a conserved fungal heat shock factor-type transcriptional regulator. It participates in maintaining cell wall integrity and regulates the osmotic/oxidative stress response (OSR) in S. cerevisiae, where it is part of a two-component signal transduction system. Here, we comprehensively address the function of Skn7 in the human fungal pathogen Candida albicans. We provide evidence reinforcing functional divergence, with loss of the cell wall/osmotic stress-protective roles and acquisition of the ability to regulate morphogenesis on solid medium. Mapping of the Skn7 transcriptional circuitry, through combination of genome-wide expression and location technologies, pointed to a dual regulatory role encompassing OSR and filamentous growth. Genetic interaction analyses revealed close functional interactions between Skn7 and master regulators of morphogenesis, including Efg1, Cph1 and Ume6. Intracellular biochemical assays revealed that Skn7 is crucial for limiting the accumulation of reactive oxygen species (ROS) during filamentous growth on solid medium. Interestingly, functional domain mapping using site-directed mutagenesis allowed decoupling of Skn7 function in morphogenesis from protection against intracellular ROS. Our work identifies Skn7 as an integral part of the transcriptional circuitry controlling C. albicans filamentous growth and illuminates how C. albicans relies on an evolutionarily-conserved regulator to protect itself from intracellular ROS during morphological development.

overall_design: A total of 2 samples are included, corresponding to 2 biological replicates : samples SKN7_ChIP_Upper array and SKN7_ChIP_Lower array.

last: Znaidi


title: Effect of odor inhalation of rats with restraint stress on their hypothalamic gene expression profiles

status: Public on Jun 16 2017

city: Kawasaki

first: Kazushi

last: Yoshida

state: Kanagawa

address: 29-7 Kariyado, Nakahara-ku

institute: T. Hasegawa Co., Ltd.

summary:
To uncover molecular mechanisms underlying reduction of responses to restraint stress by racemic (R,S)-linalool inhalation,  gene expression profiling at the hypothalamus of restraint stressed rats exposed to racemic (R,S)-linalool was carried out.
Inhaled (R,S)-linalool returned the expression of 560 stress-induced probe sets to a normal status. These genes were associated with synaptic transmission via neurotransmitters including anxiolytic neuropeptides such as oxytocin and neuropeptide Y, and also included a number of major histocompatibility complex (MHC) class I necessary for neural development and plasticity. These results reveal some of the molecular mechanisms for odor inhalation under stress condition at the hypothalamus.

overall_design:
Male Wistar rats aged 7 weeks were housed in a room maintained on a light/dark cycle with lights turned on at 8:00 a.m. and off at 8:00 p.m. They were allowed to get free access to food and water. After acclimatization to the environment and to investigators for one week, 18 rats were divided into three groups (n = 6 each): group C, control; group S, exposure to stress only; and group SO, exposure to both stress and odor. Rats in groups S and SO were placed in steel-wire mesh cages for restraint treatment for 2 h (10:00 - 12:00); they were able to breathe freely but unable to turn around. Twenty microliters of (R,S)-linalool was evaporated and allowed to spread throughout a 40 L box in which the rats (group SO) with the tubes were placed. After the exposure, all the 18 rats were immediately sacrificed by decapitation and then the brains were dissected to isolate the hypothalamic blocks. To look at the brain from the ventral side, two coronal cuts were placed at the apex of the optic chiasm and at the rostral margin of the mammillary bodies using a razor blade. This slab was then placed flat, and two cuts were placed on either side of the optic chiasm. The last cut was placed just above the third ventricle. The block was then put in ice-cold RNAlater.

Please note that the data was normalized in two groups; [1] the control and group S samples; [2] the group S and group SO samples, respectively.

last: Yamamoto

first: Satoshi

last: Fujiwara

first: Asuka

last: Kamei

first: Keiko

last: Abe

first: Akio

last: Nakamura


title: Genome-wide expression profiling of Candida albicans transcription factor Skn7p

overall_design: Two-condition experiments: Reverse-transcribed RNA from Anhydrotetracycline (ATc)-untreated (Cy3-labeled) and ATc-treated (Cy5-labeled) C. albicans strains carrying i) a SKN7 allele placed under the control of the tetracycline derivative-inducible promoter (Samples 1-8) or ii) the empty vector control (samples 9-16) and grown during 0, 2 and 4h in liquid rich (Yeast Peptone Dextrose) medium at 30ºC. Samples 1-2 and 9-10: time point 0 h (2 replicates), samples 3-5 and 11-13: time point 2 h (3 replicates) and samples 6-8 and 14-16: time point 4h (3 replicates).


title: The histone acetyltransferase Mst2 prevents epigenetic silencing via specific acetylation of the ubiquitin ligase Brl1 [microarray data]

status: Public on Jun 22 2017

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

summary: Faithful propagation of distinct chromatin states is crucial to maintain cellular identity. Whereas mechanisms that sustain repressed states have been intensely studied, regulatory circuits that protect active chromatin from inactivating signals are not well understood. Here we report the discovery of a self-reinforcing feedback loop that preserves the transcription-competent state of RNA polymerase II transcribed genes. We found that the chromatin reader Pdp3 recruits the histone acetyltransferase Mst2 to H3K36me3 marked chromatin. Thereby, Mst2 binds to all transcriptionally active regions genome-wide. Besides histone H3K14, Mst2 specifically acetylates Brl1, a component of the histone H2B ubiquitin ligase complex (HULC). Brl1 acetylation results in increased histone H2B ubiquitination, which together with H3K14ac positively feeds back on transcription and prevents assembly of ectopic heterochromatin. Our work uncovers a molecular pathway that secures epigenome integrity and highlights the importance of opposing feedback loops for the partitioning of chromatin into transcriptionally active and inactive states.

overall_design: The study comprises 18 datasets from cells expressing a Dam fusion construct at low levels: 5 control Dam-only strains, 4 Dam-Mst2 in wild type cells, 5 Dam-Mst2 in pdp3D cells, 2 Dam-Mst2 in set2D cells, 2 Dam-Mst2 in set1D cells

first: Valentin

last: Flury

first: Paula

last: Georgescu

first: Vytautas

last: Iesmantavicius

first: Yukiko

last: Shimada

first: Tahsin

last: Kuzdere

first: Sigurd

last: Braun

first: Marc

last: Bühler


title: PIWI-interacting RNAs as novel regulators of pancreatic beta-cell function

first: Imene

last: Henaoui

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

overall_design: Refer to individual Series


title: Real-time quantitative PCR analysis of primary human dermal fibroblasts: young, old and treated with GC4419

status: Public on Jul 08 2017

city: Iowa City

first: Kranti

last: Mapuskar

state: Iowa

address: 500 Newton Road

department: Radiation Oncology

institute: University of Iowa


title: Effect of persistent exposure to Porphyromonas gingivalis on human immortalized oral epithelial cells

status: Public on Jun 01 2017

city: Shenyang

first: Fengxue

last: Geng

state: Liaoning

address: Nanjing North St. 117, Heping District

department: Periodontics

institute: China Medical University

summary:
Recent epidemiological studies revealed a significant association between oral squamous cell carcinoma (OSCC) and Porphyromonas gingivalis, a major pathogen of periodontal disease. As a keystone pathogen, P. gingivalis is known not only to damage local periodontal tissue, but also to evade from the host immune system and eventually affect systemic health. However, its role in OSCC has yet to be well studied. To explore the underlying effect of chronic P. gingivalis infection on OSCC and to identify relevant biomarkers as promising targets for therapy and prevention, we established a novel model by exposing human immortalized oral epithelial cells (HIOECs) to P. gingivalis at a low MOI for 5 to 23 weeks. The P. gingivalis-infected HIOECs were monitored in tumor biological alteration. Bioinformatics analyses were performed on HIOECs infected for 15 weeks, and some selected data were validated by q-PCR and (or) Western blot on cells infected for 15 and 23 weeks. Accordingly, we found that persistent exposure to P. gingivalis induced tumor biological properties on HIOECs. Tumor-related genes such as NNMT, FLI1, GAS6, lncRNA CCAT1, PDCD1LG2 and CD274 were aberrantly expressed in response to long-term exposure of P. gingivalis. In addition, some clinical biomarkers and novel proteins were presented. In conclusion, chronic P. gingivalis infection may be a potential risk factor of OSCC. The key regulators and biomarkers might be used in monitoring OSCC with chronic periodontal infection.
We applied lncRNA Microarray (Affymetrix) which could simultaneously detect coding and non-coding genes to explore the differences of cell gene expression after long-term exposure to P. gingivalis.

overall_design: Total RNAs of cells without infection and cells infected with P. gingivalis for 15 weeks were extracted and hybridized on Affymetrix microarrays.

first: Yaping

last: Pan


title: Transcriptomal analysis of mouse healthy skin sample and of DMBA/TPA-induced skin Tumor

status: Public on Jun 07 2017

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: In this analysis we plan to identify the genes that are differentially expressed  during the development of skin carcinoma (SCC) subsquent to the chronic and topical application of  a carcinogene agent (DMBA) and a tumor promoter (TPA)

overall_design: Female FVB/N mice were topically treated with DMBA, then twice weekly for 6 weeks with (PMA). A second dose of DMBA was administered on the eighth week followed by the resumption of PMA treatment for 14 more weeks. Mice were monitored weekly for papillomas and tumors. Healthy skins (acetone treated), and tumors were harvested throughout the protocol, and biopsies were frozen for RNA extraction

first: G

last: Ponzio

first: N

last: Nottet

first: B

last: Mari

first: K

first: P

last: Barbry

first: R

last: Rezzonico