title: Gene expression profiling in response to radiation treatment in breast cancer [patient samples]

city: Durham

first: Wei

last: Chen

state: NC

address: 101 Science Drive

department: Center for Genomic and Computational Biology

institute: Duke University

summary: Introduction: Breast radiotherapy is currently “one size fits all” regardless of breast cancer subtype (eg. luminal, basal). However, recent clinical data suggests that radiation response may vary significantly among subtypes.  Therefore, current practice leads to over- or under-treatment of women whose tumors are more or less radiation responsive.  We hypothesized that this clinical variability may be due, in part, to differences in cellular radiation response. Methods: We exposed 16 biologically-diverse breast tumor cell lines to 0 or 5GY radiation. Microarray analysis was performed on RNA harvested from those cell lines.  Samples were run in triplicate. Following quality assessment, differential gene expression analysis was performed using a two-way multiplicative linear mixed-effects model.  A candidate radiation response biomarkers with  biologically plausible role in radiation response, were identified and confirmed at the RNA and protein level with qPCR and Western blotting assays.  Induction in human breast tumors was confirmed in 32 patients with paired pre- and post-radiation tumor samples using IHC and microarray analysis.  Quantification of  protein was performed in a blinded manner and included positive and negative controls.

overall_design: The objective of our study was to identify genomic determinants of radiation sensitivity using clinical samples as well as breast tumor cell lines. In order to identify differences in the radiation response gene expression profiles of specific breast cancer subtypes, we exposed 16 biologically-diverse breast tumor cell lines to 0 or 5GY radiation. Microarray analysis was performed on RNA harvested from those cell lines.  Samples were run in triplicate. Following quality assessment, differential gene expression analysis was performed using a two-way multiplicative linear mixed-effects model.  Candidate radiation response biomarker with a biologically plausible role in radiation response, were identified and confirmed at the RNA and protein level with qPCR and Western blotting assays.  Induction of the genes of interest were further evaluated and confirmed in human breast tumors in 32 breast cancer patients with paired pre- and post-radiation tumor samples using IHC and microarray analysis assays.

first: Janet

last: Horton

first: Mark

last: Dewhirst

first: Joseph

last: Geradts

first: Diane

middle: R

last: Fels

first: Yingchun

last: Zhou

first: Chenting

last: Lee

first: Sharareh

last: Siamakpour-Reihani

first: Kathleen

last: Ashcraft

first: Jeff

last: Groth

first: Hsiu-Ni

last: Kung

first: Ashley

last: Chi


title: Identification of on/off switch genes in the zebrafish and rainbow trout anterior intestine transcriptome according to nutritional status

status: Public on Jan 01 2018

city: Talence

first: Patrick

middle: J.

last: BABIN

address: Avenue des facultés

department: UFR Biologie

country: France

institute: Université Bordeaux

summary: Comparison of transcriptome data in fed and fasted conditions of zebrafish (Danio rerio) and rainbow trout (Oncorhynchus mykiss) anterior intestine using the serial analysis of gene expression (SAGE) method was done in a strategy to identify key regulated genes at the transcript level and to allow the identification of activated/deactivated pathways after feeding.

sample_organism:
Danio rerio
Oncorhynchus mykiss

platform_organism:
Danio rerio
Oncorhynchus mykiss

overall_design: For the fasted group of zebrafish, total RNAs from the anterior intestines of a pool of 6 animals were used to generate the SAGE library (14bp TAGs, including the 4-bp anchor enzyme site) using the I-SAGE kit (Invitrogen, Cergy Pointoise, France). For the fed group of zebrafish (pool of 6 animals), and the fed and fasted trout (pool of 8 animals each), total RNAs extracted from the anterior intestine were used to generate long-SAGE libraries (20pb TAGs, including the 4-bp anchor enzyme site) using the I-SAGE Long kit (Invitrogen, Cergy Pointoise, France).

first: Anja

last: Knoll-Gellida

first: Michèle

last: André

last: Babin


title: The IKK complex requires Morgana to drive NF-kB dependent breast cancer metastatisation

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

country: Italy

institute: Fondo Edo Tempia

summary: Identification of Morgana associated gene expression by comparing morgana knockdown (MDA-sh1/2) and control (MDA-1/2) MDA-MB-231 cells.

overall_design: Two condition experiments, morgana knockdown MDA-MB-231 cells vs control cells. Biological replicates:  2 control, 2 sh-morgana infected, independently grown and harvested.

first: Federica

last: Fusella

first: Laura

last: Seclì

first: Elena

last: Busso

first: Anna

last: Krepelova

first: Enrico

last: Moiso

first: Stefania

last: Rocca

last: Annaratone

first: Maurizia

last: Mello-Grand

first: Paola

last: Ostano

first: Salvatore

last: Oliviero

first: Giovanna

last: Chiorino

first: Lorenzo

last: Silengo

first: Fiorella

last: Altruda

first: Alessandro

last: Morotti

first: Isabella

last: Castellano

first: Paolo

last: Provero

first: Guido

last: Tarone

first: Mara

last: Brancaccio


title: Possible molecular mechanisms by which an essential oil blend from star anise, rosemary, thyme, and oregano and saponins increase the performance and ileal protein digestibility of growing broilers [Jejunum]

status: Public on Dec 31 2017

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf

summary: Individual male broilers (Cobb500; n=16) were allotted to 4 experimental diets containing either no phytogenic feed additives, an essential oil blend, saponin extract or a combination of both phytogenic preparations. Jejunum samples were used  for transcriptome profiling.

overall_design: per dietary group 4 chickens were collected for expression profiling

first: Henry

last: Reyer

first: Andreas

last: Müller


title: Trophoblast epithelial-mesenchymal transition (EMT) in abnormally invasive placenta (AIP)

city: Maplewood

first: Nick

last: Illsley

state: NJ

address: Richmond Ave

country: USA

institute: Placental Research Group LLC

summary: Comparison of genes associated with the EMT between cytotrophoblast cells (CTB) and extravillous trophoblast cells (EVT) from normal third trimester placenta and abnormally invasive placenta (AIP)

overall_design: EMT-associated genes compared between (a) CTB and EVT from normal thrd trimester placenta (b) EVT from normal third trimester placenta and EVT from placenta previa (c) EVT from placenta previa and AIP (d) CTB from placenta previa and AIP

first: Nicholas

middle: P


title: Possible molecular mechanisms by which an essential oil blend from star anise, rosemary, thyme, and oregano and saponins increase the performance and ileal protein digestibility of growing broilers

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

overall_design: Refer to individual Series


title: Systematic analysis of ESCRT mutants reveals an essential function for the MVB pathway in amino acid recycling.

city: Innsbruck

first: Daniel

last: Bindreither

state: Tirol

address: Innrain 82

department: Division of Molecular Pathophysiology

country: Austria

institute: Medical University Innsbruck

summary:
The ESCRT machinery drives the multivesicular body (MVB) pathway in eukaryotic cells and thus is required for the degradation of ubiquitinated membrane proteins in lysosomes. To systematically characterize how cells respond to loss of ESCRT function, we used quantitative proteomics and gene expression profiling in yeast. We find that ESCRT mutants display severe defects in amino acid homeostasis, resulting in lower levels of free intracellular amino acids. This deficit renders the growth of ESCRT mutants highly sensitive to nutrient limitation. Further proteomic analysis revealed that the MVB pathway essentially contributes to proteome remodeling under nutrient limitation. The rapid decline of protein synthesis upon starvation no longer enables ESCRT mutants to complete their cell cycle and properly enter a quiescent state, which strongly affects their long-term survival. Thus, the MVB pathway functions to selectively down-regulate integral membrane proteins and, together with autophagy and proteasomal degradation, considerably contributes to amino acid recycling.
We used microarrays to identify gene expression changes between delta VPS4 knock out and wild type Saccharomyces cerevisiae strains

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Total RNA of midlog phase yeast cells was isolated via RNeasy Kit

first: Martin

first: Oliver

last: Schmidt

first: Mihaela

last: Angelova

first: Marietta

last: Brunner

last: Faserl

first: Johannes

last: Rainer

first: Leo

last: Kremser

first: Thaddäus

last: Pfaffenwimmer

first: Claudine

last: Kraft

first: Zlatko

last: Trajanoski

first: Herbert

last: Lindner

first: David

last: Teis


title: Transcriptomic analysis of basidiocarp development in Ustilago maydis (DC) Dcd

city: Irapuato

first: Claudia

middle: Geraldine

last: Leon-Ramirez

state: Guanajuato

address: Km. 9.6 Lib. Nte Carretera Irapuato-León

department: Ingeniería Genética

country: Mexico

institute: Cinvestav Unidad Irapuato

summary:
Study of gene regulation basidiocarps development in Ustilago maydis using  transcriptomic analysis.
In 2012, Cabrera-Ponce et al. established conditions allowing a completely different developmental program in U. maydis when grown on solid medium containing Dicamba (synthetic auxin) in dual cultures with maize embryogenic calli.

overall_design: High density-one color arrays from Nimblegen were used according to a design from Scott Gold from University of Georgia. The design has five different oligonucleotides of 60 bp in lenght in duplicate, representing each one of the 6883 gene of the U. maydis genome.

middle: G

last: León-Ramírez

first: José

middle: L

last: Cabrera-Ponce

first: Domingo

last: Martínez-Soto

middle: A

last: Sánchez-Arreguín

first: Elva

middle: T

last: Aréchiga Carbajal

last: Ruiz-Herrera


title: Transcriptome analysis using customized AZ microarray on tomato Flower Abscission zone of transgeneic line TAPG::antisense KD gene

city: Bet-Dagan

first: Srivignesh

last: Sundaresan

state: Israel

address: P.O.Box 6, Bet- Dagan

department: Post Harvest Technology

country: Israel

institute: Agricultural Research Organisation, The volcani center, Israel

summary: To extend our previous knowledge from our gene expression studies on Flower pedicel Abscission zone using Affymetrix microarray chip we have employed whole transcriptome analysis by NGS as a discovery platform to identify and add the transcripts to pre-existing database. We designed the Customized AZ Microarray chip with the transcripts obtained from NGS (includes novel transcripts), pre existing Agilent probes, and some additional transcripts from previous databases. We developed transgenic lines by antisense silencing the genes, which are expressed in the AZ to study the functional role in abscission process. In the current stuty we silenced KD gene by antisense technology under abscisson promoter (TAPG::antsisense KD). The flower pedicel AZ tissue tissue was sampled at six time points (0, 4, 8, 12, 16 and 20 h), following flower removal, and analyzed for their gene expression profiles using the customized AZ microarray.

first: Shimon

last: Meir

first: Sonia

last: Philosoph-Hadas


title: Torn supraspinatus muscle vs. intact subscapularis muscle in rotator cuff tears patients

city: Tsukuba

first: Taro

last: Takemura

state: Ibaraki

address: 1-2-1 Sengen

department: Nanotechnology Innovation Station

country: Japan

institute: National Institute for Materials Science

summary: Rotator cuff tear is a common disease in elderly patients. The satellite cell has central role of muscle regeneration, however, there are few reports about human muscle. The purpose of this study was to compare features of human myogenic and adipogenic precursors in both torn supraspinatus (SSP) and intact subscapularis (SSC). Comprehensive gene expression patterns were compared between SSP and SSC muscles by microarray analisys.

overall_design: Two-condition experiment, torn supraspinatus muscle vs. intact subscapularis muscle. Two patients. 2 replicates (dye-swap) for each patient.

first: Masashi

last: Koide


title: Simultaneous Genome-Wide Gene Expression and Transcript Isoform Profiling in P. falciaprum using Exon Arrays

city: Notre Dame

first: Michael

last: Ferdig

state: IN

address: 100 Galvin Life Science Building

department: Biological Science

institute: University of Notre Dame


title: Possible molecular mechanisms by which an essential oil blend from star anise, rosemary, thyme, and oregano and saponins increase the performance and ileal protein digestibility of growing broilers [Liver]

first: Klaus

last: Wimmers

summary: Individual male broilers (Cobb500; n=16) were allotted to 4 experimental diets containing either no phytogenic feed additives, an essential oil blend, saponin extract or a combination of both phytogenic preparations. Liver samples were used  for transcriptome profiling.

first: Henry

last: Reyer

first: Andreas

last: Müller


title: Evidence for an evolutionary hourglass pattern in herbivore-induced transcriptomic responses

city: Jena

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

summary: Kenetics of herbivore induced responses in Nicotiana attenuata leaves

overall_design: Gene expression in leaves of Nicotiana attenuata wild type plants were measured at different time points (0.5 h, 1 h, 2 h, 5 h, 6 h, 11 h, 13 h) after elicitation with oral secretions (OS) of Manduca sexta larvae. Three independent experiments were performed for  control plants and plants treated with OS.

first: Shuqing

last: Xu


title: MicroRNA microarray identifies a miRNA signature to predict chemotherapy response in breast cancers

city: Jinan

first: Peng

last: Gao

address: Wen Hua Xi Road 44

country: China

institute: Shandong University

summary: To identify miRNAs involved in drug resistance of human breast cancer, a miRNA microarray was performed on 10 cases of drug resistant tissues and 10 cases of drug sensitive tissues. There were 29 differentially expressed miRNAs between drug resistant and drug sensitive tissues, including  22 significantly up-regulated and 7 down-regulated RNAs in drug resistant tissues compared to drug sensitive tissues. A signature of five miRNAs, including miR-23a-3p, miR-200c-3p, miR-214-3p, miR-638, and miR-451a was established.  A risk score from the miRNA signature was calculated and  patients were classified into high-risk and low-risk groups. Compared with the patients with low-risk scores, the patients with high risk scores showed resistant response to chemotherapy in the training, internal testing and independent sets.

overall_design: Group 1: Examination of miRNAs in drug resistant tissues (10 cases), including C22, C28, C29, C100, C142, C149, C151, C153, C173, and C178. Group 2: Examination of miRNAs in drug sensitive tissues (10 cases), including H8, H15, H19, H20, H31, H32, H80, H131, H135 and H170.


title: Transcriptomic analysis of three Sorghum bicolor landraces following progressive water stress and re-watering

city: Pretoria

first: Dave

middle: Kenneth

last: Berger

state: Gauteng

address: Lynnwood Road

department: Plant and Soil Science

country: South Africa

institute: University of Pretoria

summary:
Background: Sorghum bicolor is a remarkably drought tolerant cereal crop. Its natural biodiversity that enables this tolerance has developed in sub-Saharan Africa. The sequencing of the sorghum genome in 2009 has expedited research of this crop which has also been proposed as a model C4 cereal crop for genomics. In this study, the genetic response mechanisms involved in sorghums’ tolerance to progressive water deficit and moderate re-watering were investigated in three previously uncharacterized South African landraces (designated: LR5, LR6 and LR35) using cDNA microarrays comprising 35 899 transcript probes.
Results: Across the three landraces, significant differential expression of 1 797 genes, including 264 genes with currently unknown functions, were altered in response to progressive water stress and re-watering. The modulated sorghum genes had homology to proteins involved in growth, regulation, and protection. Gene ontology analysis identified significant enrichment of 26 genes involved in the ‘response to abiotic stimulus’ GO category in LR6 during severe stress. The expression of USP responded to progressive water stress and moderate re-watering in LR6 and LR35. Moreover, our results indicate a putative role for β-alanine betaine biosynthesis in drought tolerance of sorghum.
Conclusions: This study identified the drought responsive gene complement of three previously uncharacterized South African sorghum landraces. Each landrace is a distinct genotype and similar responses to water deficit and re-watering were not expected. Functional characterizations of some of the differentially expressed genes found in this study may be used as possible targets for marker-assisted breeding or transgenic initiatives for sorghum and, other closely related crop species.

overall_design: 3 Sorghum landraces, 3 stress conditions per landrace, 3 biological replicates per stress condition, 3 controls per landrace

first: Natricia

last: Devnarain

first: Bridget

last: Crampton

first: Nicky

last: Olivier

first: John

middle: V

last: Becker

first: Maretha

middle: M

last: O’Kennedy


title: Simultaneous Genome-Wide Gene Expression and Transcript Isoform Profiling in P. falciaprum using Exon Arrays [Agilent]

summary:
Investigation of whole genome expression profiles during four time points during the intraerythrocytic lifecycle of the malaria parasite Plasmodium falciparum for transcript isoforms using Exon Arrays.
The samples used in this study are further described in Turnbull et. al., Simultaneous Genome-Wide Gene Expression and Transcript Isoform Profiling in the Human Malaria Parasite (in review)

overall_design: Using the Agilent 60K platform exon array to measure whole genome expression profiles at four timepoints: 12 hours (2 biological replicates), 24 hours (2 biological), 36 hours (2 biological replicates), and 48 hours (2 biological replicates) post invasion, and the detection of transcript isoforms between 12 hours and 36 hours post invasion.

first: Lindsey

middle: B

last: Turnbull


title: Expression data for human acute myeloid leukemia KG1a cells and KG1a LKB1 gene knock down cells

city: Shenyang

first: Huihan

last: Wang

address: No. 36 Sanhao Street

institute: China Medical University

summary: To explore the function and signaling pathway of LKB1 gene in maintaining the characteristics of  leukemic stem cells, we use shRNA to knock down(KD) the expression of LKB1 gene at the human acute myeloid leukemia KG1a cells which is CD34+CD38- and shows some of the characteristics of  leukemic stem cells. Gene expression profile was used to analysis the difference gene expression in LKB1-KD KG1a cells and negative control (NC) KG1a cells.

overall_design: LKB1 gene knock down (KD) human acute myeloid leukemia KG1a cells (LKB1-KD KG1a) and negative control (NC) (LKB1-NC) KG1a cells were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the difference expression gene in order to explore the signaling pathway and mechanism of LKB1 gene in maintaining the characteristics of leukemic stem cells.

first: Xiaobin

first: Chenghai

last: Zhao

first: Zhuogang

last: Liu


title: Analysis of small RNA by microarray in the cell cycle

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

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

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

summary: Dicer plays a key role in RNA silencing. By processing pre-miRNAs and dsRNAs, Dicer generates miRNAs and siRNAs that act as post-transcriptional regulators of gene expression. Dicer is also implicated in heterochromatin formation and toxic RNA degradation.  Here we report that Dicer is controlled in cell cycle. The Dicer protein level drastically rises at late G1 phase and falls at early S phase.  Interestingly, the protein stability of Dicer is decreased specifically at early S phase. MG132, an inhibitor of proteasome, increases Dicer protein level, suggesting that the stability of Dicer is controlled via ubiquitination-dependent proteasome pathway.

overall_design: Examination of small RNA regulation in the cell cycle

first: Jung

middle: H

last: Lee

first: Kwontae

last: You

first: V

middle: N

last: Kim


title: Comparative Gene Expression in the female mouse brain during different reproductive life stages

status: Public on Dec 30 2017

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: The present study aims at understanding differential gene-expression patterns in the female mouse brain tissues at different stages of reproductive life cycle   Methods: Total RNA from brain tissues of 3, 12 and 40 week old female mice was subjected to cDNA and labelled cRNA synthesis and hybridized on 4X44k array. For the same samples, transcriptome sequencing was done followed by qPCR validation of the common genes. Data was analyzed using Gene spring GX 11.5 with MM10 reference along with GSEA and STRING analysis. We primarily focused on understanding gene expression changes in female mice brain which occur during various reproductive life stages viz. 3, 12, 40 weeks which is akin to adolescent, mature and pre-menopausal states.The genes involved in metabolic activity, neurological activity, inflammation and signalling along with genes involved in reproductive regulation show differential expression. The changes observed provide physiological insights in changes in the female brain associated with development, fertility and progressing age.

overall_design: Agilent two-color experiment, Organism: Mouse, Agilent Whole Genome Mouse 4x44K (AMADID: 026655). Single channel based analysis was performed,.

first: Deepti

last: Saini

first: Ishangi

last: Agarwal

first: Sudha

last: Rao

first: Raja

middle: C

last: Mugasimangalam

first: Mohamed

last: Aiyaz

first: P

last: Sriram

first: K

last: Venkatesh


title: PRMT5 mediated H4R3sme2 confers cell differentiation in Pediatric Acute B-Lymphoblastic Leukemia

status: Public on Dec 23 2017

city: Beijing

first: Mei

last: Mei

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: To gain insight into the molecular mechanisms involved in the regulation of PRMT5 in human leukemic cells, microarray analysis was performed in NALM6 cell. Upon PRMT5 knockdown, 40 genes were highly expressed and 18 genes were downregulated (cut off fold induction > 0.8 or < -0.8, P<0.05). Potential target genes of PRMT5 were screened in B-ALL cells by microarray, and identified  in B-ALL cells by quantitative real-time PCR (qRT-PCR) and chromatin immunoprecipitation.

overall_design: To identify genes that are regulated by PRMT5 in B-ALL cells, we performed microarray analysis in NALM6 cells with PRMT5 knockdown (sh-PRMT5) by sh-RNA transiently transfected, and sh-Luc was used as control.  n = 3 for each condition.

first: RuiDong

last: Zhang

first: Zhongwei

last: Zhou

first: Zhengzhou

last: Ying

first: Han

first: Huyong

last: Zheng

first: Shilai

last: Bao


title: Cardamonin attenuate colon tumorigenesis by inhibiting cell proliferation and inflammation

city: Thycaud

first: Dr. Harikumar

middle: K

last: B

state: Kerala

address: Poojappura

department: Cancer Research Program

institute: Rajiv Gandhi centre for Biotechnology

summary:
The effect of Cardamonin was checked on Azoxymethane (AOM) induced colon cancer in C57Bl/6 mice.
C57Bl/6 were given single weekly injection of AOM (10mg/kg B.wt) for six weeks. Cardamonin treatment (10mg/Kg B.wt, p.o) was started simulatenously for one group. For the second group it was started after 16 of first AOM injection. The study was terminated at 30 weeks. The RNA was ioslated uisng mirVANA kit from each samples followed miRNA analysis uisng affymetrix gene chip miRNA array 4.0

overall_design: 14 samples were analysed. The differential expression of miRNAs between groups were analysed.

first: S

last: James

first: J

middle: S

last: Aparna

first: A

last: Paul

first: B

last: Manendra

first: M

last: Sabira

first: R

last: Girijadevi

first: Kuzhuvelil

last: Harikumar


title: A High Parasite Density Environment Induces Transcriptional Changes and Cell Death in Plasmodium falciparum Blood Stages

city: Parkville

first: Karen

last: Day

state: VIC

address: Building 155, University of Melbourne

department: Faculty of Science

country: Australia

institute: University of Melbourne

summary:
Transient regulation of Plasmodium numbers below the density that induces fever has been observed in chronic malaria infections in humans and this species transcending control cannot be explained by immunity alone. Using an in vitro system we have observed density dependent regulation of malaria parasitemia as a mechanism to possibly explain these in vivo observations.
P. falciparum blood stages from a high but not low-density environment exhibited what appeared to be programmed changes during the late trophozoite and schizont stages of the intraerythrocytic cycle.

platform_organism:
Plasmodium falciparum
Anopheles gambiae

overall_design: No. Conditions: 3 (Experimental: HD and LD; Reference: U); Incubation Time: 2hrs; Biological Replicates Per Condition: 3

first: Evelyn

last: Chou

first: Sabia

middle: Z

last: Abidi

first: Marian

last: Teye

first: Aleksandra

last: Leliwa-Sytek

first: Thomas

last: Rask

first: Simon

last: Cobbold

first: Gerry

middle: Q

last: Tonkin-Hill

first: Krishanthi

last: Subramaniam

first: Anna

middle: E

last: Sexton

first: Darren

middle: J

last: Creek

first: Johanna

last: Daily

first: Michael

middle: F

last: Duffy


title: The Gene Expression Study (GEP) was based on a 6 MCL cell line models.

city: Aviano

first: Riccardo

last: Bomben

address: Via Franco Gallini 2

department: D-RT

institute: CRO Aviano

summary: The aggressive clinical behavior of mantle cell lymphoma (MCL) is attributed to specific genetic and molecular mechanisms involved in its pathogenesis, mainly the t(11;14)(q13;q32) traslocation and cyclin D1 (CCND1) overexpression. Nevertheless, evidence of a certain degree of heterogeneity has been disclosed by gene expression profile (GEP) and (immuno)genetic/immunohistochemistry studies. AIM: To use a GEP approach in MCL cell line models.

overall_design: GEP experiments were performed in 6 MCL cell line models, with Agilent platform. Bioinformatics analyses were performed by Gene Springs

first: Tiziana

last: D'Agaro

first: Valter

last: Gattei


title: Functional subnetwork modules and hub gene discovery using RNA-Seq (wild type Fusarium verticillioides and the FSR1 mutant)

status: Public on Dec 21 2017

city: College Station

first: Man

last: Kim

state: TX

address: 202N  LF Peterson, Texas A&M Univ., Plant Pathology & Microbiology

department: Plant Pathology & Microbiology

institute: Texas A&M University

type: Expression profiling by high throughput sequencing

summary: Using RNA-Seq datasets, we identified subnetwork modules (group of genes) and key functional (hub) genes associated with the fungal pathogenicity by developing a computational pipeline with network-based comparative analusis approach

sample_organism:
Zea mays
Fusarium verticillioides

platform_organism:
Zea mays
Fusarium verticillioides

overall_design: Network-based comparative analysis between wild type Fusarium verticillioides and the FSR1 mutant

first: Won-Bo

last: Shim


title: miR-200c induction in BT549 TNBC cells

status: Public on Dec 20 2017

city: Aurora

first: Jessica

last: Christenson

state: CO

department: Pathology

institute: University of Colorado Anschutz Medical Campus

summary: We performed microarray analysis on BT549 cells that express miR-200c in a doxycycline (dox)-inducible manner from the miR-200c-TripZ system.

overall_design: Six samples. Two groups in biological triplicate. BT549-pTripZ-200c cells, plated in triplicate, were cultured in DOX for 48 hours. Control cells were left untreated.

last: Rogers

first: Lisa

middle: I

last: Greene

middle: L

first: Kathleen

last: O'Neill

last: Gordon

first: Travis

last: Nemkov

first: Angelo

last: D'Alessandro

first: Greg

last: Degala

first: Jimin

last: Shin

first: Aik-Chook

last: Tan

first: Jim

last: Lambert

last: Torkko

first: Jennifer

last: Richer


title: Transcriptomic Regulation Of Scion/Rootstock Harmony And Drought Response In The Roots Of Grapevine Rootstock

city: TOKAT

first: KUBILAY

last: YILDIRIM

address: TASLICIFTLIK

department: BIOENGINEERING

country: Turkey

institute: GAZIOSMANPASA UNIVERSITY

summary: Grafting is a well-established practice for grapevine to facilitate propagation of productive and tolerant cultivars against several stress factors. It is also considered to be a suitable method for studying molecular aspects of root-to-shoot and/or shoot-to-root signaling events. So far, controlling only effect of rootstock over scion was investigated and root-to-shoot transcriptomic alterations were fallowed on the scions or graft interfaces. The objective of this study was to investigate transcriptomic and physiological influence of scion on the rootstock under drought stress. Therefore, drought tolerant 110R rootstock were firstly grafted with sultana seedless and tested under drought stress with its non-grafted counterpart. The results of treatment indicated that grafted 110R performed the highest root elongation under drought. We carried out a microarray based transcriptome analysis on the roots of grafted and non-grafted 110R to explain this drought derived interaction through scion-to-rootstock. The highest expression increase under drought was recorded for sugar (SWEET) and nitrate or di/tri-peptide (NRT1/ PTR FAMILY) transporter proteins. Expression level of these genes was more highly increased in grafted 110R than its non-grafted counterpart. This situation indicated their potential role in drought tolerance and scion/rootstock harmony. Overexpression of these transporters attributed to increased amount of released nutrient and nitrogen source from abscised leaves of sultana seedless under drought. Remobilization of these rich sources was suggested to chance transcriptomic response of rootstocks and enabled much better growth in grafted 110R. Other transcripts annotated to cell wall modification enzymes (chitinases), osmoregulator proteins (dehydrins, proline-glycine rich proteins) and secondary metabolites (stilbene synthase) were also more highly induced in grafted 110R. This is the first report indicating transcriptomic influence of scion on the grapevine rootstocks and representing the genes responsible in scion/rootstock harmony and drought tolerance.

sample_organism: Vitis cinerea var. helleri x Vitis rupestris

overall_design: Total RNA used in the microarray experiment was isolated from the roots of two grafted and non-grafted 110R rootstock, which is known to be tolerant to drought stress, grown under well watered and drought treated conditions. RNA isolation was made according to Lithium chloride precipitation method described in Chang et al. (1993). These two isolated RNAs (biological replicates) for grafted and non-grafted plants loaded onto two Affymetrix Vitis Genome arrays (technical replicates). Totally, 8 GeneChips (2 rootstock/scion combination x 2 different water availability x 2 biological replicates) were used for transcriptional analysis.

first: Kubilay

last: Yildirim


title: Simultaneous Genome-Wide Gene Expression and Transcript Isoform Profiling in P. falciaprum using Exon Arrays [NimbleGen]

first: Michael

last: Ferdig

overall_design: Using the Nimblegen platform exon array to measure whole genome expression profiles at four timepoints: 12 hours (4 biological replicates), 24 hours (4 biological and 2 technical replicates), 36 hours (4 biological replicates), and 48 hours (4 biological replicates) post invasion, and the detection of transcript isoforms between 12 hours and 36 hours post invasion.

middle: T

first: Lindsey

last: Turnbull


title: Single-cell transcriptome analysis of avian neural crest migration reveals signatures of invasion and molecular transitions [scRNA-seq]

status: Public on Dec 19 2017

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

summary: Neural crest cells migrate throughout the embryo, but how cells move in a directed and collective manner has remained unclear. Here, we perform the first single-cell transcriptome analysis of cranial neural crest cell migration at three progressive stages in chick and identify and establish hierarchical relationships between cell position and time-specific transcriptional signatures. We determine a novel transcriptional signature of the most invasive neural crest Trailblazer cells that is consistent during migration and enriched for approximately 900 genes. Knockdown of several Trailblazer genes shows significant but modest changes to total distance migrated. However, in vivo expression analysis by RNAscope and immunohistochemistry reveals some salt and pepper patterns that include strong individual Trailblazer gene expression in cells within other subregions of the migratory stream. These data provide new insights into the molecular diversity and dynamics within a neural crest cell migratory stream that underlie complex directed and collective cell behaviors.

overall_design: 501 single cells analyzed from various parts of the migrating neural crest during various timepoints in development. 96 cells from HH11 Trailblazers, 50 cells from HH13 Trailblazers, 50 cells from HH13 Leaders, 60 cells from HH13 Trailers, 50 each from HH15 Trailblazers, Leaders, and Trailers. For definitions, see the extract protocol. Neural crest from a neural tube placed in culture were also analyzed.

first: Jason

middle: A

last: Morrison

first: Rebecca

last: McLennan

first: Lauren

last: Wolfe

first: Samuel

last: Meier

first: Mary

last: McKinney

last: Teddy

first: Laura

last: Holmes

first: Craig

last: Semerad

first: Andrew

last: Box

first: Hua

last: Li

first: Kathryn

last: Hall

first: Anoja

middle: G

last: Perera

first: Paul

last: Kulesa


title: Gene expression analysis following 24h siRNA-mediated knockdown of transforming growth factor β receptor III (TGFBR3) in human pulmonary arterial endothelial cells (hPAEC).

status: Public on Dec 16 2017

city: Bad Nauheim

first: Rory

last: Morty

address: Parkstr. 1

department: W.G. Kerckhoff-Institut

institute: MPI für Herz- und Lungenforschung

summary: We explored the impact of transforming growth factor β receptor III (TGFBR3) knockdown on the gene expression in the human pulmonary arterial endothelial cells (hPASMC).

overall_design: Human pulmonary arterial endothelial cells (hPAEC) in P2 were plated in 6-well plates, and transfected with 200nM siRNA to transforming growth factor β receptor III (TGFBR3) (Santa Cruz Biotechnology) or Scrambled control (Ambion). Total RNA was extracted at 24h timepoint with peqGOLD TOTAL RNA Kit (VWR).

first: Gero

last: Niess


title: Snail-dependent epithelial splicing regulatory protein 1 (ESRP1) silencing drives malignant transformation of human pulmonary epithelial cells [miRNA]

city: Los Angeles

first: Linh

middle: My

last: Tran

state: California

department: Medicine - Pulmonary & Critical Care

institute: University of Los Angeles

summary: The significance of epithelial-to-mesenchymal transition (EMT)-inducing transcription factors in the onset of non-small cell lung cancer has not been resolved.  Here, we report increased Snail expression in pulmonary premalignant lesions relative to histologically normal-appearing pulmonary epithelium.  Utilizing immortalized human pulmonary epithelial cells and isogenic derivatives, we document Snail-dependent anchorage-independent growth of the epithelial cells in vitro, as well as transformation, primary tumor growth, and metastatic behavior in vivo.  Epithelial splicing regulatory protein 1 (ESRP1) tumor suppressor silencing was a requirement for Snail-driven transformation in vivo, and we identified ESRP1 loss in Snail-expressing pulmonary premalignant lesions in situ.  Snail drives these and other carcinogenic signaling programs in an ALDH+CD44+CD24- pulmonary stem cell subset in which ESRP1 and stemness-repressing micro-RNAs are inhibited.

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

overall_design: Two distinct HBEC cell lines were transduced with a retroviral vector containing human SNAI1 (Snail) cDNA or the empty vector.  Their micro RNAs were profiled to determine the impact of ectopic Snail expression on the isogenic epithelial background of the HBECs.

first: Tonya

last: Walser

first: Zhe

last: Jing

middle: M

first: Ying

last: Lin

first: Natalie

last: Yakobian

first: Gerald

last: Wang

first: Kostyantyn

last: Krysan

first: Li

middle: X

last: Zhu

first: Sherven

last: Sharma

first: Mi-Heon

last: Lee

first: John

last: Belperio

first: Aik

last: Ooi

first: Brigitte

last: Gomperts

first: Jerry

middle: W

last: Shay

first: Jill

last: Larsen

middle: D

last: Minna

first: Long-Sheng

last: Hong

first: Michael

last: Fishbein

first: Steven

last: Dubinett


title: Identification of foliar fingerprints in response to arbuscular mycorrhizal fungus in Nicotiana attenuata

first: Klaus

last: Gase

summary: Identification of induced genes in leaf

overall_design: Early and late time points after infection, leaves were collected from empty vector and irCCaMK plants

first: Ming

first: Julia

last: Wilde

first: Karin

last: Groten

first: Ian

last: Baldwin


title: Gene expressions of mice hepatocellular adenoma, which correlated with low-dose-rate gamma ray radiation dependent inflammatory response

city: Rokkasho

first: Takashi

last: Sugihara

state: Aomori

address: 2-121 Hacchazawa

department: Radiobiology

institute: Institute for Environmental Sciences

summary: The gene expression changes of hepatocellular adenoma from Low-dose rate (20 mGy/d) irradiated female B6C3F1 mice.

overall_design: (a) non-irradiated mice without HCA (Control) (b) LDR-irradiated mice without HCA (c) LDR-irradiated mice with HCA (HCA, c1: normal sections, c2: adenoma section)


title: Induction of DNA methylation changes in primary human hepatocytes by valproic acid

status: Public on Dec 15 2017

city: Maastricht

first: Simone

last: van Breda

state: Limburg

address: Universiteitssingel 50

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

type: Methylation profiling by genome tiling array

summary: Valproic acid (VPA) is a very potent anti-cancer and neuro-protective drug. However, exposure to VPA may cause accumulation of lipids in the liver which could result in the development of steatosis. As VPA is a fatty acid analogue, most of the performed studies focus on inhibition of the mitochondrial b-oxidation pathway as the possible mode of action. However, investigations exploring the contribution of other processes in particular by using whole genome studies in a relevant human liver model are limited. Furthermore, the contribution of gene expression regulation by DNA methylation changes and/or miRNA changes is hardly known. Therefore, in the present study, we investigated the effect of repetitive VPA exposure on primary human hepatocytes (PHH) on whole genome gene expression-, DNA methylation-, and miRNA changes, using microarrays and integrated data analyses. PHH were exposed to a non-cytotoxic dose of 15 mM VPA for 5 days daily thereby inducing accumulation of lipids. Part of the PHH was left untreated for an additional 3 days in order to study the persistence of changes. VPA modulated the expression of a number of nuclear receptors and their target genes, leading to disturbed fatty acid metabolism and - uptake, ultimately leading to accumulation of triglycerides in the liver which is the key event leading to steatosis. Part of the gene expression changes was epigenetically regulated. Furthermore, after terminating the treatment, the expression and DNA methylation changes of several genes remained persistent, indicating a permanent change in the PHH, causing steatosis development to continue and/or making the PHH more sensitive for steatosis development during a subsequent exposure.

overall_design: Primary human hepatocytes were exposed to 15 mM of VPA in a 24 hour repeat-dose testing regime. Medium was changed daily thereby providing a new dose of VPA to the PHH each day. A bi-phasic treatment regime was applied, combining a 5-day VPA exposure with a subsequent 3-days washout period during which the PHH were exposed to medium only. 1% Ethanol was used as solvent control.


title: Induction of miRNA changes in primary human hepatocytes by valproic acid


title: Expression analysis of Wild-type, lncGata6 deficient and Ehf deficient ISCs

status: Public on Dec 13 2017

first: Pingping

last: Zhu

state: Beijing

address: Datun Road 15#

institute: Institute of Biophysics, Chinese Academy of Sciences

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

summary: Investigation of differentially expressed genes in lncGata6 deficient and Ehf deficient ISCs

overall_design: mRNA and lncRNA expression profiling of GFP+ intestinal stem cells (ISCs), GFP- non-ISCs, LncGata6mut ISCs and Ehf-/- ISCs.  Intestinal crypts from Lgr5GFP-CreERT2 mice were isolated for ISCs enrichment by FACS. Total RNA from each samples was quantified using the NanoDrop ND-1000. The sample preparation and microarray were performed in accordance with the Affymetrix ClariomTM D mouse array analysis protocol (previously known as GeneChip™ Mouse Transcriptome Array 1.0)

first: JiaYi

last: Wu

first: Zusen

last: Fan


title: Study of gene expression alteration in male androgenetic alopecia: evidence of predominant molecular signaling pathways

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

institute: Miltenyi Biotec GmbH

summary: Background: The male androgenetic alopecia (AGA) is the most common form of hair loss in men and is hereditary in more than 80% of cases and characterized by a distinct pattern of progressive hair loss starting from the frontal area and the vertex of the scalp. Although several genetic risk loci have been identified, relevant genes for AGA remain to be identified.   Objectives: Herein, molecular biomarkers associated with premature AGA were identified through gene expression analysis using cDNA generated from scalp skin vertex biopsies of hairless/bold men with premature AGA and healthy volunteers.   Results: This monocentric study reveals that genes encoding mast cell granule enzymes, inflammatory and immunoglobulin-associated immune mediators were significantly over-expressed in AGA. In contrast, under-expressed genes appear to be associated with the Wnt/β-catenin and BMP/TGF-β signaling pathways. Although the involvement of these pathways in hair follicle regeneration is well-described, functional interpretation of the transcriptomic data highlights different events that account for their inhibition. In particular, one of these events depends on the dysregulated expression of proopiomelanocortin (POMC), as confirmed by RT-qPCR and immunohistochemistry. In addition, a lower expression of CYP27B1 in AGA patients supports that alteration of vitamin D metabolism contributes to hair loss.   Conclusion: Altogether, this study provides evidence for distinct molecular events contributing to alopecia that might be targeted for new therapeutic approaches.

overall_design: monocentric study of scalp punch biopsy from AGA patients and healthy donors

first: L

last: Michel

first: P

last: Reygagne

last: Benech

first: F

last: Jean-Louis

first: S

last: Scalvino

last: Ly Ka So

first: Z

last: Hamidou

last: Bianovici

first: J

last: Pouch

first: B

last: Ducos

first: M

last: Bonnet

first: A

last: Bensussan

last: Patatian

first: E

last: Lati

last: Wdzieczak-Bakala

middle: C

last: Choulot

last: Loing

last: Hocquaux


title: GA responses in the ap1-15 mutant

city: Freising-Weihenstephan

first: Claus

last: Schwechheimer

address: WZW - Lehrstuhl Systembiologie der Pflanzen, Am Hochanger 4

institute: Claus Schwechheimer

summary:
We have used Agilent whole genome arrays (v4) to compare the gene expression changes between 17 days-old Arabidopsis wild type seedlings and ap1-15
Three independent biological samples were prepared for each genotype.

overall_design: Three replicate measurements of three biological samples were prepared for each genotype.

first: René

last: Richter

first: Carina

last: Klermund née Behringer


title: Immune response induced by an HSV-1 mutant strain: a discrepancy analysis of immune system gene profile in comparison with a wild type virus strain

status: Public on Dec 25 2017

city: Kunming

first: Xiaolong

last: Zhang

address: 935 jiaoling Road

institute: Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: We previously generated an HSV-1 mutant strain, M3, which contained partial deletions in ul7, ul41 and LAT and produced an attenuated phenotype in mice. In the present study, we performed a comparative analysis to characterize the immune responses induced by M3 versus wild type HSV-1 in a mouse model. Infection with wild type HSV-1 triggered an inflammatory-dominated response and the suppression of adaptive immunity and was accompanied by severe pathological damage. In contrast, infection with M3 induced a systematic immune response involving the full activation of both innate and adaptive immunity and was accompanied by no obvious pathological changes.

overall_design: The mRNA expression profile in splenocytes of HSV-1 mutant strain M3 infected (3×10^4 PFU) and HSV-1 wild type strain Mckrae infected (3×10^4 PFU) BALB/c mice were measured at day 7 post-infection, and uninfected mice were used as control. The mRNA expression profile in splenocytes of HSV-1 mutant strain M3 infected (3×10^4 PFU) mice were also measured at day 30 and day 60 post-infection. Three independent experiments were performed at each time using different mice for each experiment.

first: Qihan

last: Li


title: Transcriptional profiling of putative  ABC Transporter gene orf19.4531 knockout in Candida albicans

city: New Delhi

first: Nitesh

middle: Kumar

last: Khandelwal

state: Delhi

address: Near Munirka

department: School of Life Sciences

institute: Jawaharlal Nehru University

summary: Since, ABC transporters do perform various physiological roles.To get better insight about possible involvement of putative ABC transporter orf19.4531 in different functions transcriptional profiling have been peformed and compared between WT(SC5314) Candida albicans cells vs  putative orf19.4531 knockout cells after 6hrs growth of culture.The assay as peformed in biological duplicate sample.

overall_design: Agilent one-color experiment,Organism: Candida albicans  ,Custom Agilent Candida albicans 8x15k Microarray Gene expression  (AMADID: 026377) designed by Genotypic Technology Private Limited  , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

middle: K

first: Rajendra

last: Prasad


title: Progression risk of gland-forming gastric neoplasms assessed by DNA copy-number profiling

status: Public on Dec 27 2017

city: Otsu

first: Hiroyuki

last: Sugihara

state: Shiga

address: Seta, Tsukinowa-cho

institute: Shiga University of Medical Science

type: Genome variation profiling by genome tiling array

summary: We tried progression risk prediction of individual gland-forming gastric cancers using genomic DNA copy number profile as a genetic lineage marker. The unsupervised clustering of DNA copy-number profiles of 107 gastric cancer samples, using large-sized (≥ 6 probes) genes, were divided into the loss-rich (A) and gain-rich (B) clusters. The T1/T2-4 ratio was significantly higher in cluster B and in cluster A (P < 0.0007). Small cancers (≤ 2 cm in diameter) were more frequent in cluster B than in cluster A. These 2 clusters were not linked to the frequency of metastasis but to the liability to progression from early to advanced stage; the cluster A may more readily become advanced than cluster B. Our approach suggested that the genetic lineages of early and advanced gland-forming gastric cancers are largely different; the eradication of small cluster B tumors (≤ 2 cm) by the present ESD indication may be valid, but not be effective for reduction of large, aggressive cluster A tumors.

overall_design: We used formalin-fixed paraffin embedded tissues from 55 gland-forming invasive gastric cancers with or without LN metastasis. Genomic DNAs extracted from 107 samples that were taken from mucosal, invasive and lymph node parts of tumors were used for array CGH analysis and subsequent hierarchical clustering analysis and penetrance plots

first: Tu

last: Duong


title: Hepatic gene expression profiles of db/db mice with non-alcoholic fatty liver

city: Guangzhou

first: Yangzhi

last: Xu

address: No.250, Changgang East Road

department: Gastroenterology

institute: The Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhou

summary: Nonalcoholic fatty liver disease (NAFLD) is a common disorder in obese people and is becoming the leading cause of hepatocellular carcinoma (HCC). Recently, lncRNAs have been proven to play remarkable roles in numerous biological processes and human diseases, including NAFLD. However, the function of lncRNA in NAFLD pathogenesis remains largely unknown. The aim of this study was to explore the lncRNA expression profile in NAFLD mice and to identify novel lncRNAs involved in the pathogenesis of NAFLD. We performed microarray analysis to compare the expression profiles of lncRNAs and mRNAs in the liver of diabetic db/db mice with NAFLD and normal mice.

overall_design: Three female C57BLKS/J db/db mice and three female C57BLKS/J mice  were used as the NAFLD and control groups, respectively. All the mice were fed with normal chow. At the age of 8 weeks,  mice were sacrificed and liver was harvested for further studies.

first: Hui

last: Yang

first: Xingtian

last: Chen


title: Expression Profiles of Long Noncoding RNAs and mRNAs in Post-Cardiac Arrest Rat Brains

city: GUANGZHOU

first: rong

last: liu

address: YANJIANGXILU NO.151

institute: GUANGZHOU MEDICAL UNIVERSITY

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

summary: To investigate lncRNA and mRNA expression profiles in post-cardiac arrest (CA) brains, an external transthoracic electrical current was applied for eight minutes to induce CA (the CA group). Four rats received sham-operations and served as the blank control (BC) group. Upon return of spontaneous circulation (ROSC), lncRNA and mRNA expression in the rat cerebral cortex was assayed with high-throughput Agilent lncRNA and mRNA microarrays. Thirty-seven lncRNAs were upregulated and 21 lncRNAs were downregulated in the CA group, and 258 mRNA transcripts were differentially expressed with 177 mRNAs upregulated and 81 mRNAs downregulated in the CA group.

first: Rong

last: Liu

first: Xiaoxing

last: Liao

first: Xin

first: Hongyan

last: Wei

first: Qing

last: Liang

first: Zuopeng

first: Meixian

last: Yin

first: Xiaoyun

last: Zeng

first: Zijing

first: Chunlin

last: Hu


title: Single-cell transcriptome analysis of avian neural crest migration reveals signatures of invasion and molecular transitions [bulk RNA-seq]

first: Madelaine

last: Gogol

overall_design: 12 bulk RNA-seq samples in total; 3 biological replicates of 4 different conditions

first: Jason

last: Morrison

first: Rebecca

last: McLennan

first: Lauren

last: Wolfe

first: Samuel

last: Meier

first: Mary

last: McKinney

first: Jessica

last: Teddy

first: Laura

last: Holmes

first: Craig

last: Semerad

first: Andrew

last: Box

first: Hua

first: Kathryn

last: Hall

first: Anoja

last: Perera

first: Paul

last: Kulesa


title: Gene expression profiling of HepG2 cells treated with extracts of hawk tea vs. DMSO-treated control group

status: Public on Dec 10 2017

city: Beijing

first: Juan

last: Feng

address: No.30, Shuangqing Road, Haidian District

department: School of Medicine

institute: Tsinghua University

summary: Hawk tea (Litsea coreana var. lanuginose) is a traditional Chinese tea, widely cultivated and consumed in southwestern China. It has been widely used to treat gastrosis, hepatitis, and inflammatory diseases for hundreds of years. Modern pharmacological studies demonstrate that hawk tea has protective effects against liver fibrosis, hypercholesterolemia, hyperglycemia, and inflammatory diseases . However, the molecular mechanism of hawk tea against hypercholesterolemia remains unclear. The aims of this study were to investigate the mechanisms of hawk tea extract (HTE) to lower cholesterol. Therefore, we performed genome-wide transcriptional analysis of hawk tea extracts treated HepG2 cells.

overall_design: Analysis used DMSO-treated RNA as control samples for comparison to the experimental samples treated with hawk tea extracts. Indirect comparisons were made across multiple arrays with raw data pulled from different channels for data analysis and comparison to the control data.

first: Long

last: Zhao

first: Lan

last: Xie

middle: Y

last: An


title: Hepatic Gene Expression Profiles of Growing versus Finished Beef Steers

status: Public on Dec 11 2017

city: Lexington

first: James

last: Matthews

state: KY

address: 207 W.P. Garrigus Buidling

department: Animal and Food Sciences

institute: University of Kentucky

summary:
Growing and finishing phases are two important animal production stages, which differ fundamentally in compositional growth. However, the physiological mechanisms altered concomitantly with the shift in whole-body compositional gain as cattle fatten (growing vs. finished steers), are poorly understood.
Microarray analysis using the Bovine Gene 1.0 ST Array was conducted to determine shifts in hepatic genomic expression profiles of growing vs. finishing beef steers. The specific overall hypothesis tested was that genes involved in amino acid, carbohydrate and lipid metabolism, antioxidant capacity and immune responses were differentially expressed in growing vs. finishing steers.

overall_design: Sixteen weaned Angus steers (BW = 209 ± 29.4 kg) were randomly assigned (n = 8) to develop through growing (final BW = 301 kg) or finished (final BW = 576 kg) growth phases and individually fed enough of a cotton seed hull-based diet to achieve a constant ADG (1.5 kg/d). Steers had ad libitum access to fresh water and an industry standard vitamin-mineral supplement. Liver samples were collected for RNA extraction and microarray analysis.

first: Jing

last: Huang

first: Phillip

last: Bridges


title: Idiopathic oligozoospermic patients vs. Normozoospermic fertile controls

city: Ribeirão Preto

first: Juliana

middle: Dourado

last: Grzesiuk

state: São Paulo

address: Avenida Bandeirantes, 3900

department: Genetics

country: Brazil

institute: USP

summary: Characterization of Y-chromosome CNVs in the AZF regions that may be involved with oligozoospermia through Array-CGH.

overall_design: Eighteen patients with at least two spermograms showing sperm density lower than 15 million/ml,  normal hormone levels, no chromosomal abnormalities detected by karyotyping method or microdeletions of the Y-chromosome detected by multiplex PCR technique. Four patients had moderate oligozoospermia (5-15million/ml), seven had severe oligozoospermia (1-5million/ml) and seven had extreme oligozoospermia (<1million/ml  ). The control group included six proven fertile men (with at least two children, the youngest being at most two years old) with normal karyotype, and no chromosome Y-microdeletions.

last: Dourado Grzesiuk

first: Carlos

last: Henrique Paiva Grangeiro

first: Flávia

last: Gaona Oliveira-Gennaro

first: Thiago

last: Vidotto

first: Amanda

last: Freire Assis

first: Lucia

last: Martelli


title: Gene expression data of alveolar macrophages derived from Standardbred racehorses before and during training period

status: Public on Dec 12 2017

city: Edinburgh

first: Anna

middle: Eleonora

last: Karagianni

address: Easter Bush Campus

country: United Kingdom

institute: The Royal (Dick) School of Veterinary Studies and The Roslin Institute

summary:
Mild to moderate equine asthma is prevalent in young racehorses, particularly early in their training period. Although the precise aetiopathogenesis remains undetermined, it is possible that the susceptibility of this population might partly reflect an exercise-associated immune derangement at the level of the airway.
We performed a genome-wide basal gene expression scan on alveolar macrophages (AMs) isolated from Standardbred racehorses prior to and after commencement of competition race training with a view to identifying any exercise-associated gene expression modulation consistent with functional alterations which might reflect training-associated immunological derangement.

overall_design: Microarray technology was used to analyse the basal gene expression profiles of bronchoalveolar fluid-derived AMs, harvested from six systemically healthy Standardbred racehorses prior to (T0) and following (T1) entry into training. The samples were collected from the animals at least one week after the entry into training (up to 7 weeks).

middle: E

first: Kim

last: Summers

first: Anne

last: Couroucé

first: Marianne

last: Depecker

first: Bruce

last: McGorum

first: David

last: Hume

first: Scott

middle: R

last: Pirie


title: Liver gene expression profiles of catalase knockout mice fed normal and high fat diet

status: Public on Dec 18 2017

city: Gwangju

first: Joo Young

last: Huh

address: 77 Yongbong-ro

department: College of Pharmacy

institute: Chonnam National University

summary: Nonalcoholic fatty liver disease (NAFLD) is the most common type of chronic liver disease. NAFLD is associated with obesity, type 2 diabetes, dyslipidemia, and cardiovascular diseases, and characterized by excessive accumulation of triglycerides in the form of lipid droplets. Liver injury in NAFLD through inflammation and oxidative stress ultimately leads to development of nonalcoholic steatohepatitis and liver cancer. Recently it has been reported that catalase, a major peroxisomal antioxidant, plays a protective role in high-fat diet-induced liver injury. In this study, we further investigated the role of catalase in development of liver disease using transcriptome analysis. Catalase knockout and wild type mice were fed either normal chow or high-fat diet and the gene expression profiles in the liver were compared.

overall_design: Total RNA was isolated from livers of wild type or catalase knockout mice fed either normal or high-fat diet for 11 weeks using Trizol method. Agilent’s Mouse Oligo Microarray (44K) was used to examined the gene expression profile. Data was extracted using GeneSpring GX 7.3 (Agilent Technology, USA) and differential expressed genes were compared between groups.

first: Hunjoo

last: Ha

first: Joo

first: Lingjuan

last: Piao

first: Inah

last: Hwang


title: Extent and Patterns of MGMT Promoter Methylation in Glioblastoma- and Respective Glioblastoma-Derived Spheres

city: Lausanne

first: Pierre

last: Bady

address: Quartier UNIL-Sorge

department: Swiss Institute of Bioinformatics

country: Switzerland

institute: CHUV / BCF / SIB

summary: Quantitative methylation-specific tests suggest that not all cells in a glioblastoma with detectable promoter methylation of the O6-methylguanine DNA methyltransferase (MGMT) gene carry a methylated MGMT allele. This observation may indicate cell subpopulations with distinct MGMT status, raising the question of the clinically relevant cutoff of MGMT methylation therapy. Epigenetic silencing of the MGMT gene by promoter methylation blunts repair of O6-methyl guanine and has been shown to be a predictive factor for benefit from alkylating agent therapy in glioblastoma. Samples of glioblastoma and respective glioblastoma-derived spheres (GS), cultured under stem cell conditions, were analyzed for the degree and pattern of MGMT promoter methylation by methylation-specific clone sequencing, MGMT gene dosage, chromatin status, and respective effects on MGMT expression and MGMT activity.

overall_design: Copy number  information for 4 GBM derived Sphere lines and 2 adherent GBM derived cell line.

first: Davide

last: Sciuscio

first: Pierr

first: Danielle

last: Martinet

first: Monika

last: Hegi


title: miRNA profiling of primate cervicovaginal lavage and extracellular vesicles reveals miR-186 as a potential retroviral restriction factor in macrophages

status: Public on Dec 09 2017

city: Baltimore

first: Kenneth

last: Witwer

state: MD

address: 733 N Broadway, BRB Rm 820

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

summary: The goal of this study was to examine microRNA profiles of primate cervicovaginal lavage (CVL) during the menstrual cycle and simian immunodeficiency virus (SIV) infection, and to determine if CVL-associated miRNAs might influence replication of retroviruses.

overall_design: CVL was collected for five weeks from two uninfected and four SIV-infected macaques. EVs were enriched by stepped ultracentrifugation and characterized by population-level and single vesicle analyses. miRNA profiles were assessed with a medium-throughput stem-loop/hydrolysis probe qPCR platform and validated by targeted qPCR assays.

first: K

first: Z

last: Zhao


title: Induction of gene expression changes in primary human hepatocytes by valproic acid

first: Simone

last: van Breda


title: Expression data of CFC1 overexpressed neuroblastoma cell line, NGP

status: Public on Dec 01 2017

city: Kitaadachi-gun Ina town

first: Takehiko

last: Kamijo

state: Saitama

address: 780, Komuro

institute: Saitama Cancer Center

summary: We performed a microarray analysis on CFC1-expressing NGP cells. Expression data in CFC1- and mock-NGP cells were generated and compared. Differentially expressed genes (DEGs) were functionally annotated by a pathway analysis and Gene Set Enrichment Analysis (GSEA). Both analyses showed that genes involved in “differentiation”, “oncogene-induced senescence”, “stem cell proliferation” and “Activin signaling” pathways were significantly enriched in DEGs. “TGFbeta pathway” and “Nodal pathway” were also enriched in the GeneSpring GX pathway analysis, but were not significant in the GSEA analysis. This result suggests that the pathways involved in cell stemness and Activin signaling were enhanced by the expression of CFC1 in NB cells accompanied by transcriptional changes in their related gene members.

overall_design: Neuroblastoma cell line NGP were induced CFC1 using lenti-viral system. Microarray analysis on CFC1-expressing NGP cells was performed to assess its effects on transcriptional profiles. Expression data in CFC1- and mock-NGP cells were generated and compared. Differentially expressed genes were functionally annotated by a pathway analysis and Gene Set Enrichment Analysis (GSEA).

first: Koji

last: Chikaraishi


title: Gene expression profiling of LRRC26-depleted HCC70 cells

status: Public on Nov 30 2017

city: Tokushima

first: Yosuke

last: Matsushita

address: 3-18-15 Kuramoto

department: Institute for Genome Research

institute: Tokushima University

summary: To serach gene expression change under knockdown of LRRC26, Leucin Rich Repeat Containing 26 in human triple negative breast cancer cells HCC70, we performed genome-wide DNA microarray analysis and compared the expression levels of control-siRNA treated cells and LRRC26-siRNA treates cells at 48 to 72 h after siRNA transfection

overall_design: HCC70 cells were transfected with 10 nM of siRNA for EGFP(control) and LRRC26. After 48 hr and 72 h, cells were harvested and RNA was purified for microarray analysis.

first: Yoshimasa

last: Miyagawa

first: Toyomasa

last: Katagiri


title: Arraystar circRNA array data for foam cells formation in phorbol 12-myristate 13-acetate-induced macrophages model

city: WenZhou

first: Bozhi

last: Ye

state: ZheJiang

address: 2 Fuxue Road

department: Department of Cardiology

institute: the First Affiliated Hospital of WenZhou Medical University

summary: The phagocytosis of oxidized low-density lipoprotein (oxLDL) by monocyte-derived macrophages and the subsequent differentiation of  macrophages into foam cells are the key steps in atherogenesis. Our study provides a potential new therapeutic strategy to alleviate oxLDL accumulation and foam cell formation.

overall_design: The THP-1 were pretreated with 100 nM PMA for 48 h, stimulated with oxLDL (50 mg/ml) for 24h and then collected for detection.The cells in control group were only treated with PMA for 48h. Three independent experiments were performed at each group.

first: Zhouqing

last: Huang


title: The effect of Bcl6 on liver sex difference

status: Public on Nov 29 2017

city: Isehara

first: Akihide

last: Kamiya

state: Kanagawa

address: 143 Shimokasuya

institute: Tokai University

summary: To confirm the effect of Bcl6 on the liver sex difference, we performed the gene expression analysis in male and female wild type mice and male and female liver specific Bcl-6 deficient mice.

overall_design: Male and female wild type mice and  male and female liver specific Bcl-6 deficient mice were dissected. RNA extraction was performed from livers for the microarray analysis.

first: Hiromi

last: Chikada


title: Expression data from NP366-374/Db and PA224-233/Db CD103 positive and negative T-cells

city: Boston

first: Kevin

last: Bi

state: MA

address: 450 Brookline Ave.

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary:
To investigate the role of TCR-pMHC interaction in regulating lung tissue-resident CD8 T cell differentiation, polyclonal responses were compared against NP366-374/Db and PA224-233/Db, two immunodominant epitopes that arise during influenza A infection.
To characterize the molecular programs associated with the lung tissue-resident CD8 T cell subpopulations, we measured by microarray the global gene transcriptional profile of NP366-374/Db CD103+ and NP366-374/Db CD103-, PA224-233/Db CD103+, PA224-233/Db CD103- lung resident T cells.

overall_design: For each microarray dataset, lung tissue-resident CD8 T cells from 9 female B6 mice were sorted and pooled. Previously, influenza A/PR8/8/34 (H1N1)-infected mice were re-challenged with influenza A/HK/X31 (H3N2) virus 35 days after primary infection. Five days post re-challenge, lungs were harvested after in vivo CD8alpha staining was performed. After cell suspension from the collagen-digested lungs was prepared, non-CD8 T cells were removed using mouse CD8+ T Cell Isolation Kit (Miltenyi Biotec, Inc.). The untouched CD8 T cell-enriched fraction was stained with H-2Db Influenza NP366-374 Tetramer, H-2Db Influenza PA224-233 Tetramer, followed by additional staining with anti-CD8beta and anti-CD103 Abs. Then 4-way sorting was performed using a FACsAria IIu (BD Biosciences) to obtain NP366-374/Db CD103+, NP366-374/Db CD103-, PA224-233/Db CD103+ and PA224-233/Db CD103- CD8 T cells.

first: Bi

last: Kevin

first: Yoshikawa

last: Akihiro


title: Colorectal cancer susceptibility loci as predictive markers of rectal cancer prognosis after surgery

status: Public on Nov 28 2017

city: Bethesda

first: Yue

last: Hu

address: 50 South Drive, Bldg. 50, Rm. 1408

department: Genetic

institute: NCI

summary: To understand the molecular mechanism of rectal cancer and develop markers for disease prognostication, we generated and explored a dataset from 243 rectal cancer patients by gene expression microarray analysis of cancer samples and matched controls, and SNP-arrays of germline DNA.  We found that two of the loci most strongly linked with colorectal cancer (CRC) risk, 8q24 (upstream of MYC) and 18q21 (in the intron of SMAD7), as well as 20q13 (in the intron of LAMA5), are tightly associated with the prognosis of rectal cancer patients.  For SNPs on 18q21 (rs12953717 and rs4464148) and 20q13 (rs4925386), alleles that correlate with higher risk for the development of CRC are associated with shorter disease free survival (DFS).  However, for rs6983267 on 8q24, the low risk allele is associated with a higher risk for recurrence and metastasis after surgery, and importantly, is strongly correlated with the resistance of CRC cell lines to chemoradiotherapy (CRT).  We also found that although MYC expression is dramatically increased in cancer, patients with higher levels of MYC have a better prognosis.  The expression of SMAD7 is weakly correlated with DFS.  Notably, the presence of the 8q24 and 18q21 SNP alleles is not correlated with expression levels of MYC and SMAD7.  rs4464148, and probably rs6983267 and rs4925386, are linked with overall survival time of patients.  In conclusion, we show that several CRC risk SNPs detect subpopulations of rectal cancer patients with poor prognosis, and that rs6983267 probably affects prognosis through interfering with the resistance of cancer cells to CRT.

overall_design: Dataset of expression microarray of cancer samples and matched mucosa control, as well as SNP arrays of DNA extracted from peripheral blood lymphocytes from 230 rectal cancer patients was generated and analyzed together with patient's clinical data and long-term follow-up.


title: Dysregulated mRNA and miRNA expression networks in Helicobater pylori infected gastric epithelial cell line, AGS (mRNA)

city: Kolkata

first: Manikuntala

last: Kundu

state: West Bengal

address: 93/1, Acharya Prafulla Chandra Road

institute: Bose Institute

summary: We performed genome-wide mRNA and miRNA expression analysis in gastric epithelial cell line AGS infected with Helicobacter pylori at 100 Multiplicity of Infection (MOI), comparing the expression profile of infected cells with uninfected cells. Differentially expressed mRNAs and miRNAs wered identified, which showed a 1.5 fold change in expression in infected cells compared to uninfected cells. We performed in silico analysis of miRNA-mRNA target interactions among the inversely correlated differentially expressed miRNAs and mRNAs, and performed functional enrichment analysis of the target genes, to identify important cellular pathways that reflect the patho-biology of H. pylori infected cells. Among the important miRNA-mRNA target pairs, PHLPP1, reported to be associated with poor prognosis in cancer, was predicted to be a putative target of miR-29b-1-5p. Therefore, we focused on the miR-29b-1-5p/PHLPP1 miRNA/target pair for detailed investigation into their role in H. pylori-mediated signalling in gastric epithelial cells. This study demonstrates that an integrated analysis of global mRNA and miRNA expression patterns, combined with miRNA-mRNA target prediction and functional analysis of miRNA target genes can yield an understanding of the critical pathways regulating the behaviour of gastric epithelial cells challenged with H. pylori.

overall_design: AGS cells (human gastric epithelial cell line) were infected with H. pylori 26695 at 100 MOI for 4 h.Total RNAs were isolated from both AGS cells infected with H. pylori (2 samples) and uninfected AGS cells (2 samples).Total RNA for each sample was sent to Genotypic for further processing.

first: Zhumur

last: Ghosh


title: Microarray data from ferulate/coniferaldehyde 5-hydroxylase F5H Arabidopsis mutant lines

city: Denton

first: Lina

last: Gallego-Giraldo

state: Texas

address: 1155 Union Circle #311428

department: Biology

institute: University of north Texas, Biodiscovery Institute

summary:
Transcriptomic analysis was performed on the main inflorescence stems of wild-type and lignin-modified lines growing under the same conditions. Study transcriptomic changes in arabidopsis stem manipulated in F5H. Loss of function fah-1 mutant and F5H overexpression (F5H-OE)
We used microarrays to detail the global determine changes of gene expression in loss of function fah-1 mutant and F5H overexpression (F5H-OE)  up and down-regulated genes were identified.

overall_design: One and a half month old plants were harvested, stems from 5 different plants were pooled as one biological replicate, and three biological replicates were included for analysis. Stem material was frozen immediately in liquid nitrogen and stored at -80 ºC prior to RNA extraction.

first: Rick

last: Dixon


title: Morphological and transcriptomic effects of endocrine modulators on the gonadal differentiation of chicken embryos: the case of tributyltin (TBT)

city: Frankfurt am Main

first: GenXPro

last: GenXPro

address: Altenhöferallee 3

institute: GenXPro GmbH

summary:
Chicken eggs (Gallus gallus domesticus) were incubated, after 24 h of incubation either non-injected (control, C), or injected with the solvent sesame oil (Oleum Sesame Raffinatum, solvent control, SC), and the substances Tributyltin (TBT, 10pg TBT-SN/g egg) or 17alpha-Methyltestosteron (MT, 30 pg/g egg).
Animals were decapitated on breeding day 19, 2 days before anticipated hatching. Right and left gonads of female and male chicken were accurately separated from adhesing tissues, stored in RNA lysis buffer (Promega) at -80°C until until RNA isolation with the SV Total RNA Isolation System Kit according to manual 048 (Promega).
Sequencing was performed on Illumina’s Genome Analyzer IIx, and subsequent base calling was carried out by Illumina’s GAPipeline.
Our study represents the first detailed analysis of whole chicken gonad transcriptomes, with biologic replicates, generated by SuperSAGE technology.

overall_design: SuperSAGE analysis of substance-induced whole-gemome expression in 19-days-bred chicken gonads

first: Jessica

last: Scheider

first: Fabian

last: Afonso-Grunz


title: Endogenous hippocampal leptin in mediating strong potentiation by Astaxanthin supplementation for mild exercise-enhanced neurogenesis and memory functions

status: Public on Nov 25 2017

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

summary: Although exercise and dietary interventions on cognitive function have been investigated, synergistic interactions remain unclear.  As tested on hippocampus-dependent functions, mild exercise (ME) or astaxanthin (AX), a naturally-occurring antioxidant and cognitive enhancer, each boost the hippocampus-related memory and neurogenesis. Here we show that leptin (LEP) is required for the synergistic enhancement of hippocampal function by a combination of ME and AX. In C57BL/6J mice, ME or AX alone enhanced spatial memory and neurogenesis, but the enhancement was greater with their combination. DNA microarray analysis showed that the up-regulation of the Lep gene by ME alone was further elevated when combined with AX. The combined interventions synergistically increased hippocampal LEP protein, which was positively correlated with memory enhancement. In LEP-deficient mice, the combined interventions did not enhance memory compared to ME alone, leading us to suggest that the brain-derived LEP has an essential role for the synergistic effect on hippocampal functions.

overall_design: Male C57BL/6J mice (11-weeks-old) were obtained from SLC (Shizuoka, Japan). Based on the ventilatory threshold (VT), we determined the intensity of treadmill running for the WT mice. Their running speed at VT value was found to be 12.29 m/min and 8.66 m/min for the WT  mice. AX diets were made by mixing the MF powder with either AX or a placebo powder (AstaREAL-20F based on 2% content of AX derived from Haematococcus pluvialis; Fuji Chemical Industry, Japan) at concentrations of 0.5% (wt:wt). For DNA microarray and sqRT-PCR, the total RNA was extracted from finely powdered hippocampal tissue of WT mice (n=8/group- SED, ME, AX, and AX+ME) using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol. DNA microarray was performed using A SurePrint G3 Mouse GE 8X60K Microarray Kit (Agilent Technologies). All samples were labeled with eitehr Cy3 (4 samples) or Cy5 (4 samples). The 1 chip conatined all the 8 samples.

first: Jang

middle: S

last: Yook

first: Randeep

last: Rakwal

first: Junko

last: Shibato

first: Bruce

last: McEwen

first: Hideaki

last: Soya


title: Metabolic flexibility of a prospective bioremediator: Desulfitobacterium hafniense Y51 challenged in chemostats

status: Public on Nov 21 2017

city: Wageningen

first: Ye

last: Tian

address: Stippeneng 4

department: AFSG

institute: Wageningen University

summary: The physiology of D. hafniense strain Y51 under close to natural conditions were examined: D. hafniense Y51 was subjected to a variety of limiting conditions (carbon or electron acceptor) or ammonium deprivation, in chemostat. Its physiology was assessed by transcriptomic and proteomic analyses and compared to that in batch culture. Electron donor/acceptor-limited growth conditions cause a switch to alternative metabolic pathways allowing the organism with a capacity to survive in polluted environments and with a readiness to use alternative electron acceptors such as PCE; (ii) nitrogen limitation induces nitrogen fixation implying a robustness vis-a-vis ammonia shortage; (iii) limiting conditions trigger a general stress response that should enable the organism to cope with even more environmental constraints.

overall_design: A custom-designed based on the complete genome sequences of D. hafniense DCB-2 and Y51 (NCBI Genbank accession numbers NC_007907 and NC_011830, respectively). The array contains 21905 distinct 45 to-60 oligonucleotides designed with PICKY (Chou et al., 2004; Chou et al., 2009), including two or three probes per target transcript, as well as sense and antisense probes targeting intergenic regions that were larger than 60 oligonucleotides. In total, 11652 probes targeting genes and intergenic regions shared by both genomes. Probes were printed in duplicate on the Agilent 8 x 60 K custom gene expression microarray platform, containing in addition 1319 Agilent control probes.

first: Maria

last: Suarez


title: Wnt ligands 3a and 5a regulate proliferation and migration in human fetal liver progenitor cells

status: Public on Nov 13 2017

city: Stockholm

first: David

last: Brodin

address: Hälsovägen 7-9

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

summary: Since human fetal liver progenitor cells (hFLPC) can differentiate into multiple liver cell types in vitro and in vivo, hFLPC may be a suitable source for cell therapy and regeneration strategies. Imperative for effective clinical applications of hFLPC is the enhanced knowledge of growth factors that mediate and improve migration and proliferation. The canonical wingless/int-1 (Wnt) signal transduction pathway is known to play a key role in proliferation and migration of stem cells. So, we investigated a role for Wnt3a and Wnt5a ligands in regulating the proliferation and migration of hFLPC. We used alamarBlue assay and transwell migration assay and examined proliferation and migration of hFLPC to Wnt3a and Wnt5a. In addition, the target genes of Wnt signal transduction pathway was identified using microarray analysis and validated by quantitative real-time polymerase chain reaction (qPCR).  We found that Wnt3a or Wnt5a independently significantly increased migration and proliferation in a dose-dependent manner which was significantly inhibited by Wnt inhibitors Wnt-C59 or KN-62. Addition of Wnt3a to hFLPC resulted in increased mRNA expression of the known Wnt target genes Axin-2, DKK2, while Wnt5a increased CXCR7, all of which are closely associated with an enhanced proliferation capacity of stem cells.  Thus, we report that Wnt3a and Wnt5a may play an important role in the proliferation and migration of hFLPC by possibly regulating key target genes-involved in these processes. Incorporating recombinant human Wnt3a and Wnt5a in regenerative strategies using liver stem/progenitor cells might improve the process of liver regeneration.

overall_design: Examination of Wnt ligands 3a and 5a induced gene expression changes in SV40LT-HFL cells and human fetal liver  progenitor cells. In total 18 samples were analyzed in two different cell lines treated with control, Wnt3a or Wnt5a. Each group contained three replicates.

first: Zhiwen

last: Liu

first: Vijay

last: Kuma

first: Bo

last: Xu

first: Suchitra

last: Sumitran-Holgersson


title: Propofol alters the mRNA profile in the developing mouse hippocampus

status: Public on Nov 14 2017

city: Milwaukee

first: Xiaowen

last: Bai

state: WI

address: 8701 Watertown Plank Road

department: Anesthesiology

institute: Medical College of Wisconsin

summary: Propofol has been found to be toxic to developing neurons.  The goal of the current study was to nominate novel genes predicted to underly the neurotoxicity, and use these candidates for future functional pathway assessment

overall_design: 7 day old mice received an intraperitoneal injection of 50mg/kg propofol or 50mg/kg intralipid vehicle control, with a total exposure of 3h.  This was followed by a 3h washout.  Mice were sacrificed, hippocampal tissues were collected, and RNA was extracted prior to profiling.

first: Congshan

last: Jiang

first: Sarah

last: Logan

first: Yasheng

last: Yan

first: Thiago

last: Arzua

first: Peizhong

last: Ma

first: Shemin

last: Lu

first: Zeljko

middle: J

last: Bosnjak


title: Gene expression analysis of murine pluripotent stem cells treated with myxothiazol for 12 h

city: Dresden

first: Natalia

last: Pashkovskaia

address: Zellescher Weg 20B

country: Germany

institute: Technische Universität Dresden

summary: ROS are frequently associated with deleterious effects caused by oxidative stress. Despite the harmful effects of non-specific oxidation, ROS also function as signal transduction molecules that regulate various biological processes, including stem cell proliferation and differentiation. Here we show that elevated ROS level by myxothiazol exposure makes murine P19 pluripotent stem cells more potent to differentiate in trophoblast cells, but not in neurons.

overall_design: For gene expression analysis samples were extracted from P19 cells grown under normal conditions (4 independent samples) or treated with 5 nM myxothiazol for 12 h (3 independent samples).

first: Uta

last: Gey

first: Gerhard

last: Rödel


title: Rhinovirus infection of polarized human macrophages induces differential gene expression

status: Public on Nov 16 2017

city: Ann Arbor

first: Marc

last: Hershenson

state: MI

address: 1150 West Medical Center Drive

department: Pediatrics

country: USA

institute: University of Michigan

summary: Expression profiling of differentially polarized human macrophages in response to Rhniovirus A16 treatment

overall_design: This study was designed to compare total RNA between unpolarized, M1 polarized and M2 polarized human macrophages in response to Rhinovirus A16 treatment

first: Charu

last: Rajput

first: Megan

middle: P

last: Walsh

first: Breanna

middle: N

last: Eder

first: Ediri

last: Metitiri

first: Antonia

last: Popova

middle: B


title: Time-course hypoxia incubation (1% O2) of D283-Med medulloblastoma cells

city: Liverpool

first: Violaine

last: See

address: Crown Street

department: Biochemistry

institute: University of Liverpool

summary:
Elucidation of the impact of  hypoxia in D283-Med (medulloblastoma Homo sapiens, human, ATCC® HTB-185™) cells to depict molecular mechanisms, which could explain drug resistance when cells are exposed to long-term hypoxia (5 days).
Global gene expression study by microarray analysis to allow an efficient search for a range of genes. D283-MED cells were incubated for a varied hypoxic duration (0, 6, 64 and 96 hours in triplicate), cDNA samples were prepared and sent directly to NimbleGen.

overall_design: 3 independent replicate were analysed. For each set of experiment, 4 time-points were analysed: 0h (control), 6h, 64h and 96h. Gewne expression was compared to the control condition (left at 21% O2).

first: Yuen

last: Fan


title: Overexpression of CUL4B promotes gastric cancer metastasis through upregulation of HER2

city: Jinan

first: Han

last: Bo

address: #44, Wenhua Xi Rd

department: Department of Pathology

institute: Shandong University Medical School

summary:
Cullin 4B (CUL4B), a scaffold protein that assembles CRL4B ubiquitin ligase complexes, has been reported to be overexpressed in several types of solid tumors and contributes to epigenetic silencing of tumor suppressor. However, its clinical significance and the molecular mechanisms underlying its regulation in gastric cancer (GC) remain largely unknown. Here, we showed that CUL4B was elevated in GC tissues and its overexpression was positively correlated with poor prognosis and lymph node metastasis. CUL4B knockdown in GC cells decreased proliferation, mesenchymal transition and invasion in vitro, as well as tumor growth and metastasis in nude mice, and CUL4B overexpression induced the opposite results. Further studies showed that miR-101 could inhibit CUL4B expression by directly targeting its 3’-UTR and they were inversely correlated in clinical GC specimens. Notably, a positive relationship between CUL4B and HER2 was found in GC clinical specimens, GC cells and GC xenograft tumors. Through bioinformatics analysis of miRNA-seq data and target prediction, we nominated miR-125a as a direct target of CUL4B. ChIP assays demonstrated that CUL4B directly repressed miR-125a expression by physically binding to its promoter. In addition, we confirmed miR-125a is the target of HER2. Consequently, we demonstrated that CUL4B can up-regulate HER2 expression through repressing miR-125a. Most importantly, silencing of HER2 by Herceptin or siRNA partially reversed CUL4B-induced epithelial-to-mesenchymal transition (EMT), cell invasion and metastasis in vitro and in vivo. These findings define a CUL4B-miR-125a-HER2 regulatory mechanism shed light on CUL4B oncogenic mechanisms and reveals promising therapeutic targets for progressive GC.
CUL4B proteins are frequently upregulated in human cancer, yet little is known about the underlying molecular mechanisms of CUL4B induced gastric cancer(GC) carcigenesis.Here, we uncover  the critical role of CUL4B in gastric cancer  growth and metastasis through the regulation of HER2 expression.CUL4B contributes to GC invasion and metastasis by transcriptional repression of HER2 targeting miR-125a, which provide a new insight into how CUL4B regulates GC progression and metastasis.

overall_design: A two chip study using total RNA recovered from MKN45 gastric cancer cells transfected with negative control(NC) or siRNA silencing CUL4B (si4B) for 48hs. Each chip measures the expression 27,958  genes were collected from the authoritative data source including NCBI.

first: Bo

last: Han

first: Mei

last: Qi


title: Comparison of gene expression profilings between parental A549, OSK-A549-Colony and OSK-A549-SN

status: Public on Nov 09 2017

city: Kobe City

first: Michiyo

last: Koyanagi-Aoi

address: Chuo-ku, Kusunoki-cho 7-5-1

institute: Kobe University

summary: In the present study, we successfully generated lung cancer stem cell (CSC)-like cells by introducing a small set of transcription factors into a lung cancer cell line (OSK-A549-Colony). In addition to properties that are conventionally referred to as CSC properties, the lung induced CSCs exhibited the ability to form lung cancer-like tissues in vitro with vascular cells and mesenchymal stem cells, which showed structures and immunohistological patterns that were similar to human lung cancer tissues.

overall_design: We extracted total RNA from 3 lung cancer cell lines (parental A549), 3 induced lung cancer stem like cells (OSK-A549-Colony) and 3 differentiated non lung cancer stem like cells (OSK-A549-SN)  and hybridized them to Agilent gene expression microarrays.

first: H

last: Ogawa


title: Ezh2 loss is associated with functional defects and ectopic gene expression in mature neutrophils

status: Public on Nov 18 2017

city: La Jolla

first: RAFAEL

last: BEJAR

state: CA

address: 3855 Heatlh Sciences Dr

department: MOORES CANCER CENTER

institute: UNIVERSITY OF CALIFORNIA SAN DIEGO

summary:
Gene expression profiling of progenitor and neutrophil-derived HoxB8-ER cells (WT and Ezh2-/-) and neutrophil-derived HOXB8-ER treated with GSK343 and vehicle for 9 days.
Ezh2 loss might lead to effective cytopenias caused by dysfunctional mature cells. To test this hypothesis, we examined Ezh2-null murine myeloid cell lines capable of neutrophilic differentiation. Bone marrow cells from Ezh2-/- and controls were immortalized with a HoxB8-estrogen receptor fusion and could be differentiated into mature neutrophils by removing estrogen from the culture medium.Gene expression profiling showed upregulation of oxidative phosphorylation pathway genes and ectopic expression of Gata1 and its associated erythroid gene targets. Functional and gene expression differences observed in Ezh2-/- derived neutrophils could be replicated in controls by treatment with the Ezh2-specific inhibitor GSK343. In conclusion, we demonstrate that Ezh2 loss allows for differentiation of normal appearing, but dysfunctional mature neutrophils characterized by ectopic gene expression and elevated levels of reactive oxygen species. These defects could contribute to the inflammatory bone marrow microenvironment and clinical phenotypes observed in patients with MDS.

overall_design: We analyzed data from undifferentiated WT cells, neutrophil-derived WT cells, undifferentiated Ezh2-mutated cells, neutrophil-derived Ezh2-mutated cells, neutrophil-derived WT cells treated with 1uM GSK343 drug and neutrophil-derived WT cells treated with vehicle. All conditions were conducted in duplicates and 250ng was subjected to GeneChip Mouse Transcriptome Asay 1.0 Kit (Affymetrix). RNA was hybridized on the Affymetrix Hybridization Oven 320 followed by a scan of the hybridized probe arrays in a GeneChip Scanner 3000.

first: Albert

last: Perez-Ladaga

first: Armon

last: Azizi

first: Huafeng

last: Xie

first: Stuart

middle: H

last: Orkin

first: David

last: Sykes

first: Rafael

last: Bejar


title: Expression analysis of wild-type Streptococcus pneumoniae PN4595-T23 and TprA2 deletion mutant

status: Public on Nov 10 2017

city: Pittsburgh

first: Anagha

last: Kadam

state: Pennsylvania

address: 4400 Fifth Avenue, Mellon Institute, Room 217

department: Biological Sciences

institute: Carnegie Mellon University

summary: Investigation of differentially regulated gene in deletion of TprA2 compared to the wild-type. TprA2 is a transcriptional regulator. Its characterization is described in Kadam et al 2017 Promiscuous signaling by a regulatory system unique to the pandemic PMEN1 pneumococcal lineage. PLoS Pathog. 2017 May; 13(5): e1006339.

overall_design: A three chip study using RNA isolated from three separate wild-type cultures of Streptococcus pneumoniae PN4595-T23 and three separate cultures of TprA2 mutant strain. Cultures were harvested at mid-log phase and used for RNA isolation and cDNA preparation and hybridized onto SpSGH array with custon designed probes. The SpSGH array covers the pneumococcal pangenome and a total of 1,930 genes were relevant for PN4595-T23. The design and validation of SpSGH array is described in Kadam et al 2015 Streptococcus pneumoniae Supragenome Hybridization Arrays for Profiling of Genetic Content and Gene Expression. Curr Protoc Microbiol. 2015; 36: 9D.4.1–9D.4.20.

first: Kadam

last: Anagha

first: Hiller

last: N. Luisa


title: MicroRNA expression data obtained from skin samples of female pattern hair loss patients, healthy females and males

status: Public on Nov 11 2017

city: Krasnoyarsk

first: Anna

last: Komina

address: Partizana Zheleznyaka

department: Pathological physiology

country: Russia

institute: Krasnoyarsk State Medical University

summary:
Female pattern hair loss  is a disease with genetic predisposition but precise mechanisms of its development remains unclear.
The goal of the study was to determine microRNAsexpression pattern specific for the FPHL.

overall_design: 3 alopecia skin samples, 5 skin biopsy samples from the head of healthy women and 5 skin biopsy samples from the back of men were used for microRNA profiling

first: Nadezhda

last: Palkina

first: Mariya

last: Aksenenko

first: Tatiana

last: Ruksha


title: Transcriptomic responses of Arabidopsis wild-type and amp1 seedlings after hyperphyllin treatment [AraGene-1_1-st array]

status: Public on Nov 08 2017

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

institute: University of Nottingham

summary: ALTERED MERISTEM PROGRAM1 (AMP1) is a member of the M28 family of carboxypeptidases with a pivotal role in plant development and stress adaptation. Its most prominent mutant defect is a unique hypertrophic shoot phenotype combining a strongly increased organ formation rate with enhanced meristem size and the formation of ectopic meristem poles. However, so far the role of AMP1 in shoot development could not be assigned to a specific molecular pathway nor is its biochemical function resolved. We used a chemical genetic approach to identify the drug hyperphyllin (HP), which specifically mimics the shoot defects of amp1, including plastochron reduction and enlargement and multiplication of the shoot meristem. To further assess whether hyperphyllin acts in an AMP1-dependent manner we compared the transcriptonal responses of hyperphyllin-treated wild-type and amp1 mutant seedlings.

overall_design: Wild-type  and amp1-13 seedlings were germinated and grown for 10 d in liquid medium in the presence of either DMSO (solvent) or 30 µM hyperphyllin. For each treatment three biological replicates were used for RNA extraction and subsequent hybridization on Affymetrix microarrays.

first: Olena

last: Poretska

first: Marcos

last: Castellanos

first: Tobias

last: Sieberer


title: Nuclear and cellular expression data from the whole 16-cell stage Arabidopsis thaliana embryo and a cell type-specific expression atlas of the early Arabidopsis embryo

status: Public on Nov 06 2017

first: Joakim

last: Palovaara

state: Gelderland

institute: Wageningen Univeristy

summary:
SuperSeries contain expression data from the nuclei of cell types involved in patterning events, with focus on root apical stem cell formation, at 16-cell stage, early globular stage and late globular stage in the early Arabidopsis embryo (atlas). Expression data comparing nuclear and cellular RNA isolated from whole 16-cell stage Arabidopsis embryos is also included.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Expression analysis of breast cancer cell lines SKBR-3 and ZR-75-1 upon treatment of LMO2 overexpression or knocking-down

city: Tianjin

first: Wei

last: Sun

address: No.94 Weijin Road

department: School of Medicine

institute: Nankai University

summary: Investigation of whole genome gene expression level changes in ZR-75-1 cells with knocking-down of LMO2, and in SKBR-3 cells with overexpression of LMO2, compared to their relative control cells.

overall_design: A total of 4 microarray assays were performed with total RNA from ZR-75-1_ctrl, ZR-75-1_sh-LMO2, SKBR-3_LMO2 and SKBR-3_ctrl cells. Samples were compared between each treatment and control in each cell lines.


title: Transcriptomic analysis of Hyperphyllin-treated Arabidopsis seedlings [ATH1 array]

summary: ALTERED MERISTEM PROGRAM1 (AMP1) is a member of the M28 family of carboxypeptidases with a pivotal role in plant development and stress adaptation. Its most prominent mutant defect is a unique hypertrophic shoot phenotype combining a strongly increased organ formation rate with enhanced meristem size and the formation of ectopic meristem poles. However, so far the role of AMP1 in shoot development could not be assigned to a specific molecular pathway nor is its biochemical function resolved. We used a chemical genetic approach to identify the drug hyperphyllin (HP), which specifically mimics the shoot defects of amp1, including plastochron reduction and enlargement and multiplication of the shoot meristem. To further assess whether hyperphyllin acts in an AMP1-dependent manner we compared the transcriptonal responses of hyperphyllin-treated wild-type Arabidopsis seedlings with those of untreated amp1 mutant seedlings.

overall_design: Wild-type Arabidopsis seedlings were germinated and grown for 10 d in liquid medium in the presence of either DMSO (solvent) or 30 µM hyperphyllin, whereas amp1-13 seedlings were grown under the same conditions in medium containing only DMSO (solvent). For each treatment three biological replicates were used for RNA extraction and subsequent hybridization on Affymetrix microarrays.


title: Transcriptomic responses of Arabidopsis wild-type and amp1 seedlings after hyperphyllin treatment

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