title: Comparison of mouse and human retinal pigment epithelium gene expression profiles reveals interspecies similarities and differences

status: Public on Nov 23 2015

city: Amsterdam

first: Anna

last: Bennis

address: Meibergdreef 9

department: Clinical Genetics

country: Netherlands

institute: Amsterdam Medical Centre Amsterdam

summary:
To determine mouse retinal pigment epithelium (RPE) specific gene expression, we compared the gene expression profile of the RPE to the gene expression of its adjacent layers: the choroid (CH) and photoreceptors (PR). We collected the tissues using the meticulous laser dissection microscopy. Next, we performed RNA isolation, amplification, labeling and hybridization against 44k Agilent microarrays.
Compared RPE gene expression with CH gene expression, and with PR gene expression

overall_design: We performed the microarrays against a common reference sample, namely mouse RPE/choroid RNA. We performed 3 replicates of  every tissue: CH, RPE and PR.

first: Arthur

last: Bergen


title: LncVSM (AK098656) up/down-regulation in Vascular Smooth Muscle cells

status: Public on Dec 12 2015

city: Beijing

first: Lei

last: Yang

address: No.8 Gongtinanlu

department: Medical Research Center

country: China

institute: Beijing Chaoyang Hosptial, Capital Mediacal Unversity

summary: Long non-coding RNAs (LncRNAs) in hypertensives and their mechanisms in regulating blood pressure still remain unexplored.  The aim of present study is to construct the profiles of LncRNAs in blood of patients with essential hypertension and healthy controls.   Methods and results, LncRNA microarray identified up-regulated, anddown-regulated LncRNAs, in hypertensives compared to their healthy controls. Among them, one vascular smooth muscle (VSM)-specific LncRNA AK096656 (LncVSM) was quantitated in plasma of patients with hypertension and their healthy controls using the real-time qRT-PCR.  LncVSM shows specific expression in human arterial vascular smooth muscle cells (HASMCs) and promote its proliferation and migration. Expression profiles and Ingenuity Pathway Analysis (IPA) revealed that LncVSM activated Renin-Angiotensin Signaling (RAS). the overexpression of LncVSM would result hypertension related complications.

overall_design: LncVSM (AK098656) transfection

first: Cai

last: Jun

first: Geng

last: Bin

first: Qinghua

last: Cui


title: Gene expression analyses of expandable hepatocytes in culture

status: Public on Nov 18 2015

city: shanghai

first: yan

last: hexin

address: No. 1630 East Road

institute: Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine

summary: To compare the global expression profiles among primary hepatocytes and expandable hepatocytes with or without in vitro differentiation.

overall_design: Expandable hepatocytes were derived from 3 mice and cultured in expansion medium or differentiation medium for 21 days. Primary mouse hepatocytes were isolated using a two-step collagenase perfusion technique.

first: He-Xin

last: Yan

first: Gong-Bo

last: Fu


title: Gene expression profiles of human iPSC derived podocytes

status: Public on Nov 24 2015

city: Kumamoto

first: Atsuhiro

last: Taguchi

state: Kumamoto

department: IMEG

country: Japan

institute: Kumamoto Univ.

summary: The gene expression profile of human iPSC derived podocytes were analyzed by utilizing NEPHS1-GFP knock-in human iPS cell line. The induced podocytes shows characteristic gene expression pattern that overlap with those of mouse and human podocytes in vivo.

overall_design: Kidney tissue was induced from human iPSC by our originally established protocol. NEPHS1-GPF knock-in human iPSC was used to isolate podocytes from induced kidney tissues. To identify the molecules which are specifically expressed in induced podocytes, NEPHS1-GFP positive and negative fractions were sorted by FACS and compared. RNA was isolated from cells and the gene expression profiles were determined by microarrays.

first: Sazia

last: Sharmin

first: Ryuichi

last: Nishinakamura


title: Development of gene expression signature for primary epidermal neonatal keratinocytes treated with mature IL-36B cytokine

status: Public on Dec 15 2015

city: Dublin

first: Seamus

middle: J

last: Martin

address: Linclon Place

department: Genetics

country: Ireland

institute: Trinity College Dublin

summary: Stimulated primary keratinocytes with mature IL-36B cytokine and analysed differential mRNA expression at 8 h timepoint.

overall_design: IL-36B induced gene expression in primary human neonatal keratinocytes was measured at 8 hours after exposure to dose IL-36B (5 nM).

first: Conor

middle: M

last: Henry


title: PRMT6 knockdown effects on the early zebrafish development

status: Public on Nov 25 2015

city: Shanghai

first: xin

middle: xi

last: zhao

address: Yueyang Road, 320#, new building 615

institute: Shanghai Institute of Biochemistry and Cell Biology

summary:
Zygotic genome activation (ZGA), which is according to the midblastula transition in zebrafish, is an important event during the maternal-zygotic transition in animals. Our preliminary study and other group’s works indicate that epigenetic regulations play an essential role in ZGA.
Morpholino was employed to knockdown PRMT6. We used microarrays to analyze the global gene expression in prmt6 morphants.

overall_design: prmt6 MO (0.3mM) was injected into the one-two cell zebrafish, prmt6 cMO (0.3mM) injection as a control. At 6 hpf, embryos were classified into three subtypes (normal, mild and severe) and prepared for global gene expression analysis with Affymetrix Zebrafish Genome Arrays. The severe subtype and the control were repeated three times.

first: Xinxi

last: Zhao

first: Yiping

last: Li


title: SSEA4 is a marker for chemotherapy resistance

status: Public on Nov 19 2015

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

country: Germany

institute: Miltenyi Biotec GmbH

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

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

overall_design: Refer to individual Series


title: Donor dependent variations in hematopoietic differentiation among embryonic and induced pluripotent stem cell lines.

status: Public on Nov 17 2015

city: Chilly-Mazarin

first: Dominique

last: Lesuisse

address: 1, avenue Pierre Brossolette

department: Rare and neurologic diseases therapeutic area

country: France

institute: Sanofi

summary: Hematopoiesis generated from human embryonic stem cells (ES) and induced pluripotent stem cells (iPS) are unprecedented resources for cell therapy. We compared hematopoietic differentiation potentials from ES and iPS cell lines originated from various donors and derived them using integrative and non-integrative vectors. Significant differences in differentiation toward hematopoietic lineage were observed among ES and iPS. The ability of engraftment of iPS or ES-derived cells in NOG mice varied among the lines with low levels of chimerism. iPS generated from ES cell-derived mesenchymal stem cells (MSC) reproduce a similar hematopoietic outcome compared to their parental ES cell line. We were not able to identify any specific hematopoietic transcription factors that allow to distinguish between good versus poor hematopoiesis in undifferentiated ES or iPS cell lines. However, microarray analysis showed genes differentially expressed in ES and iPS cell lines according to their hematopoietic potential. These results demonstrate the influence of genetic background in variation of hematopoietic potential rather than the reprogramming process.

overall_design: Microarray gene expression analysis on EB’s from five pluripotent stem cells (PSC), with good (H1, PB11, PB7) versus poor hematopoietic potential (PB6, PB12). The gene expression profiling was performed on biological replicates of the five cell lines except for the EB derived from PB7 cell line for which one sample was excluded from the transcriptome analysis due to a low RNA yield. The genes were selected on the basis of two criteria p-value ≤ 0.05 and an absolute FC ≥ 2.

first: Olivier

last: Féraud

first: Yannick

last: Valogne

first: Michael

last: Melkus

first: Yanyan

last: Zhang

first: Noufissa

last: Oudrhiri

first: Rima

last: Haddad

first: Aurélie

last: Daury

first: Corinne

last: Rocher

first: Aniya

last: Larbi

first: Philippe

last: Duquesnoy

last: Divers

first: Emilie

last: Gobbo

last: Brunet de la Grange

first: Fawzia

last: Louache

first: Annelise

last: Bennaceur-Griscelli

first: Maria-Teresa

last: Mitjavila-Garcia


title: Gene expression profile of two colorectal cancer HT29 and DLD-1 cell lines treated with single or fractionated ionizing radiation doses under 3D cell culture conditions.

city: Vilnius

first: Vaidotas

last: Stankevicius

state: Lithuania

address: Santariskiu 1

country: Lithuania

institute: National Cancer Institute

summary: Tumor cell response to irradiation also depends on their microenvironment. Therefore ongoing investigation of three-dimensional (3D) cell culture models provide researchers with essential data studying and remodeling radiotherapeutic implications in cancer treatment. 3D culture models were shown to mimic in vivo cell microenvironment more accurately than the standard two-dimensional cell monolayer (2D) cultures. Growing evidence suggests that 2D and 3D cultured cell gene expression pattern discrepancies following irradiation is highly dependent on cell-ECM interactions.  It has been shown that laminin-rich-extracellular matrix (lr-ECM) used in 3D cultures not only alters cancer cell phenotype and response to external stimuli but also affects their differentiation, migration and survivability. Thus, a change in these fundamental cell properties demands us to reconsider data previously collected using 2D in vitro models.

overall_design: RNA was harvested from two colorectal cancer cell lines cultivated under 3D cell culture conditions, 4h after treatment of single (2 Gy or 10 Gy) or fractionated (5x2 Gy) ionizing radiation dose.

first: V

first: K

last: Suziedelis


title: A validated gene regulatory network and GWAS identifies early regulators of T-cell associated diseases (Th17 Treg)

status: Public on Nov 12 2015

city: Linköping

first: Danuta

last: Gawel

address: Garnisonsvägen

country: Sweden

institute: Linköping University

summary: In this work we present an analytical strategy to systematically identify early regulators by combining gene regulatory networks (GRN) with GWAS.  We hypothesized that early regulators in T-cell associated diseases could be found by defining upstream transcription factors (TFs) in T-cell differentiation. Time series expression and DNA methylation profiling of T-cell differentiation identified several upstream TFs, of which TFs involved in Th1/2 differentiation were most enriched for disease associated SNPs identified by GWAS.

overall_design: Naïve CD4+ T cells were isolated from buffy coat of four healthy donors using a naïve CD4+ T cell isolation kit (Miltenyi, Bergisch-Gladbach, Germany). Naïve CD4+ T cells were stimulated with TGF-β (1 ng/mL), IL-1β (10 ng/mL), IL-6 (25 ng/mL), IL-21 (25 ng/mL) and IL-23 (25 ng/mL) for Th17, and TGF-β (10 ng/mL) and IL-2 (10 ng/mL) for Treg. Cells were cultured for six days in Iscove’s modified Dulbecco medium (IMDM) supplemented with 2 mM L-glutamine (PAA Laboratories, Linz, Austria), 10% heat-inactivated FCS (PAA Laboratories, Linz, Austria), 5 µM β–mercaptoethanol (Sigma-Aldrich, St. Louis, Missouri, USA) and 50 ug/mL gentamicin (Sigma-Aldrich, St. Louis, Missouri, USA). Cells were cultured for 6 days and then re-stimulated with plate-bound anti-CD3 and soluble anti-CD28 in the presence of corresponding polarizing cytokines and antibodies for another 2 days (Zhang et al. 2013). RNA was extracted using a miRneasy Mini Kit (Qiagen). The RNA concentrations were analysed with NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies). For the gene expression microarray analysis, The cRNA was prepared using a Low Input QuickAmp Labeling Kit. For Th17 and Treg cells the gene expression microarray analysis was performed using SurePrint G3 Human Gene Expression 8x60K v2 microarray kit, according to the manufacture’s instruction (Agilent Technologies).

first: Mika

last: Gustafsson

middle: R

first: Sandra

last: Hellberg

first: Aelita

last: Konstantinell

first: Daniel

last: Eklund

first: Jan

last: Ernerudh

first: Antonio

last: Lentini

first: Robert

last: Liljenström

first: Johan

last: Mellergård

first: Hui

last: Wang

first: Colm

middle: E

last: Nestor

first: Huan

first: Mikael

last: Benson


title: 3-anhydro-6-hydroxy-ophiobolin A inhibits the replication of influenza A virus in vitro and in vivo

status: Public on Nov 05 2015

city: fuzhou

first: xiaojuan

last: chi

address: cangshan NO:15

institute: Fujian Agriculture and Forestry University

summary:
Influenza is a major cause of morbidity and mortality worldwide, and the emerging drug resistance poses an increasing challenge to the treatment of influenza virus infection. Therefore, the development of a novel antiviral drugs has become an urgent task to combat against the influenza viruses that are resistant to the current therapeutic treatment. Here, by screening a small molecule chemical compound library, we identified 3-anhydro-6-epi-ophiobolin A (named L435) as a potent anti-influenza agent. Mechanistically, L435 markedly reduced influenza virus replication in vitro and in vivo. Importantly, L435 treatment improved the survival of influenza-virus-infected mice, suggesting that L435 may be a novel therapeutic agent for treatment of influenza virus infections.
This microarray experiment was carried out to explore gene expression changes in influenza-virus-infected A549 cells after L435 treatment, and find out why L435 could inhibit the replication of influenza A virus.

overall_design: Total RNAs were extracted from three different groups of A549 cells that were mock treated, or infected with WSN and treated with DMSO for 12h, or infected with WSN and treated with L435 for 12 h, using TRIzol reagent (Invitrogen, Carlsbad, CA). Three independent experiments were performed. Samples were amplified and labeled using the One-Color Quick Amp Labeling Kit (Agilent p/n 5190-2305).

first: Xiaojuan

last: Chi

first: Song

first: Xiaoqin

last: Luo

first: Jilong

last: Chen


title: Comparison of gene expression by sheep and human blood stimulated with the TLR4 agonists lipopolysaccharide and monophosphoryl lipid A [human]

status: Public on Dec 16 2015

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

country: USA

institute: GenUs BioSystems, Inc.

summary:
11,431 and 4,992 genes were determined in whole blood of healthy human volunteers and normal sheep, respectively following MPLA and LPS exposure
Following the exposure 1,029 human and 175 sheep genes were differentially expressed. Of those 175 sheep genes, 54 had a known human ortolog. The major inflammatory mediators, such as IL-1-6-8, TNFa, NFkB, ETS2, PTGS2, PTX3, CXCL18, KYNU, and CLEC4E were similarly (>2-fold) upregulated in both human and sheep blood.

overall_design: Six healthy human volunteers and six normal sheep blood was incubated with LPS or MPLA for 90 minutes, then the blood was transferred to the Paxgene blood RNA tubes and the gene expression microarrays were scanned with G2556 Microaaray Scanner.

first: Perenlei

last: Enkhbaatar

first: Christina

last: Nelson

first: John

last: Salsbury

first: Joseph

last: Carmical

first: Karen

last: Torres

first: David

last: Herndon

first: Donald

last: Prough

first: Liming

last: Luan

first: Edward

last: Sherwood


title: SSEA4 is a marker for chemotherapy resistance [mRNA]

first: Stefan

last: Tomiuk

summary: By coupling PDX and cell surface marker screening technologies, we have identified distinct tumor cell sub-populations that are associated with tumor resistance to chemotherapy. In the majority of relapsed tumors, the percentage of the marker-positive cells shifted back to pretreatment levels. SSEA4 is one of the cell surface molecules tested that could distinguish enriched residual tumor cells in all the different TNBC PDX models analyzed. The expression of SSEA4 is associated with tumor resistance to chemotherapy and SSEA4+ cells show increased gene expression of genes involved in response to toxins, cellular import/export, cell migration and EMT.

overall_design: The dataset comprises four different sample groups including SSEA4- and SSEA4+ cell fractions isolated from mouse xenografts of human breast cancer cells. Two technical replicates were generated for each cell fraction. Microarray analysis was performed on the Agilent Whole Human Genome Oligo Microarray 8x60K (v2) platform.

first: Andrea

last: Aloia

first: Evgeniya

last: Petrova

first: Stefano

last: Cairo

first: Silvia

last: Rüberg

first: Olivier

last: Deas

last: Agorku

first: Andreas

last: Bosio

first: Jean-Gabriel

last: Judde

first: Olaf

last: Hardt


title: Gene Expression Profiling of IL-17A-treated Synovial Fibroblasts from the Human Temporomandibular Joint

city: Chiba

first: Toshio

last: Hattori

address: 2-870-1, Sakaecho-Nishi, Matsudo

department: Maxillofacial Surgery

institute: Nihon University School of Dentistry at Matsudo

summary: Synovial fibroblasts contribute to the inflammatory temporomandibular joint under pathogenic stimuli. Synovial fibroblasts and T cells participate in the perpetuation of joint inflammation in a mutual activation feedback, via secretion of cytokines and chemokines that stimulate each other. IL-17 is an inflammatory cytokine produced primarily by Th17 cells that plays critical roles in the pathogenesis of numerous autoimmune and inflammatory diseases. Here, we investigated the roles of IL-17A in temporomandibular joint disorders (TMD) by using genome-wide analysis of synovial fibroblasts isolated from patients with TMD. We analyzed the gene expression profiles of synovial fibroblasts that were treated with or without IL-17A.

overall_design: IL-17 induced gene expression in synovial fibroblasts from human temporomandibular joint was measured at 4 hours after treated with IL-17A (10 ng/ml) and untreated control samples. This experiment used one donor sample.

first: Naomi

last: Ogura

first: Miwa

last: Akutsu

first: Mutsumi

last: Kawashima

first: Suguru

last: Watanabe

first: Ko

last: Ito

first: Toshirou

last: Kondoh


title: Acutely isolated murine cortical astrocytes and microglia: Alzheimer's disease vs wildtype- effect of gfap-/- and vim-/-

status: Public on Nov 04 2015

city: Utrecht

first: Elly

last: Hol

address: Universiteitsweg 100

department: Department of Translational Neuroscience

institute: University Medical Center Utrecht

summary:
GFAP and vimentin deficiency alters gene expression in astrocytes and microglia in wild-type mice and changes the transcriptional response of reactive glia in mouse model for Alzheimer's disease.
Reactive astrocytes with an increased expression of intermediate filament (IF) proteins Glial Fibrillary Acidic Protein (GFAP) and Vimentin (VIM) surround amyloid plaques in Alzheimer's disease (AD). The functional consequences of this upregulation are unclear. To identify molecular pathways coupled to IF regulation in reactive astrocytes, and to study the interaction with microglia, we examined WT and APPswe/PS1dE9 (AD) mice lacking either GFAP, or both VIM and GFAP, and determined the transcriptome of cortical astrocytes and microglia from 15- to 18-month-old mice. Genes involved in lysosomal degradation (including several cathepsins) and in inflammatory response (including Cxcl5, Tlr6, Tnf, Il1b) exhibited a higher AD-induced increase when GFAP, or VIM and GFAP, were absent. The expression of Aqp4 and Gja1 displayed the same pattern. The downregulation of neuronal support genes in astrocytes from AD mice was absent in GFAP/VIM null mice. In contrast, the absence of IFs did not affect the transcriptional alterations induced by AD in microglia, nor was the cortical plaque load altered. Visualizing astrocyte morphology in GFAP-eGFP mice showed no clear structural differences in GFAP/VIM null mice, but did show diminished interaction of astrocyte processes with plaques. Microglial proliferation increased similarly in all AD groups. In conclusion, absence of GFAP, or both GFAP and VIM, alters AD-induced changes in gene expression profile of astrocytes, showing a compensation of the decrease of neuronal support genes and a trend for a slightly higher inflammatory expression profile. However, this has no consequences for the development of plaque load, microglial proliferation, or microglial activation.

overall_design: 2 cell types from 6 conditions: cortical microglia and cortical astrocytes from 15-18 month old APPswe/PS1dE9 mice compared to wildtype littermates. Biological replicates: microglia from APPswe/PS1dE9, N=7, microglia from WT, N=7, astrocytes from APPswe/PS1dE9, N=4, microglia from WT, N=4

first: Willem

last: Kamphuis

first: Marie

last: Orre

first: Oscar

last: Stassen


title: Fasting response of mouse brain

status: Public on Nov 14 2015

city: Setagaya-ku

first: Kosuke

last: Tanegashima

state: Tokyo

address: 2-1-6 Kamikitazawa

institute: Tokyo Metropolitan Institute of Medical Science

summary:
Analysis of fasting-induced change of metabolites in mice confirmed that glucose level was reduced in the liver, but unaffected in the brain of fasted mice. To explore molecular mechanisms for the preferential glucose supply to the brain upon fasting, we compared gene expression profiles of the brain between fasted and fed mice. Gene ontology (GO) term analysis revealed the enrichment of one GO term, “active membrane transporters activity”.
We also showed that fasting enhances the expression of a glucose transporter Slc2a1 (Glut1) gene.

overall_design: Mice were fasted or fed for 17 hrs, and their brains were dissected for microarray analysis

first: Yasumasa

last: Nishito

first: Takahiko

last: Hara


title: Study of transcriptional effects of monosodium urate crystal (MSU) on HaCaT keratinocyte cell line.

status: Public on Oct 29 2015

city: Rennes

first: Cedric

last: Coulouarn

address: CLCC Eugène Marquis, Rue de la Bataille Flandres Dunkerque, Bat D, 1er étage

institute: INSERM

summary:
Aim of the study was to characterize at a molecular level (changes in transcriptomes) the effect of monosodium urate crystal (MSU) on HaCaT keratinocyte cell line.
This was adressed by using a culture model. The HaCaT cell line (human keratinocytes) was stimulated by MSU (1mg/mL) vs control for 12 hrs. By using genome-wide expression profiling, we identified deregulation of functionally relevant gene networks.

overall_design: HaCaT were obtained from Cell Lines Service (Eppelheim, Germany) and grown in DMEM medium (PAN biotech, Aidenbach, Germany) supplemented with 10% FBS (Life Technology, Grand Island, NY, USA), L-glutamine and non-essential amino acid. Before the treatment HaCaT cells were cultured in serum-free medium for 12hrs. HaCaT were treated with MSU (1mg/ml) vs DMEM control for 12hrs then submitted to RNA extration and gene expression profiling. Triplicate experiments were performed: HaCaT control (n=3), MSU-treated (n=3).

first: Thomas

last: Ondet


title: Transient transfection of miR-449 family in the hepatocellular carcinoma cell line HLE

status: Public on Nov 06 2015

city: Hannover

first: Maria

last: Sandbothe

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

summary: In this study, we comparatively analyzed the members of the miR-449 family (miR-449a, miR-449b, and miR-449c) with regards to their target genes and functional effects in hepatocellular carcinoma (HCC). Microarray analysis after transient transfection of miR-449a, miR-449b, and/or miR-449c in the HCC cell line HLE identified putative target genes of miR-449a, miR-449b, and miR-449c.

overall_design: For transient overexpression of miRNAs, the HCC cell line HLE was transfected with 50 nM Allstars Negative Control or miScript miRNA mimics. MiRNA mimics for miR-449a, miR-449b, and miR-449c were either single transfected or cotransfected in equimolar amounts (16.7 nM each). Global mRNA expression profiling was performed utilizing pooled RNA of three biological replicates per microarray and two microarrays per condition.

first: Reena

last: Buurman

first: Luisa

last: Greiwe

first: Beate

last: Vajen

first: Vera

last: Schäffer

first: Marlies

last: Eilers

last: Illig

first: Brigitte

last: Schlegelberger

first: Britta

last: Skawran


title: Identification of a potent and selective chemical probe for exploring the role of Mediator complex-associated protein kinases CDK8 and CDK19 in human disease

status: Public on Oct 26 2015

city: Sutton

first: Robert

middle: te

last: Poele

state: Surrey

address: 15 Cotswold Road

department: Cancer Reserach UK Unit for Cancer Therapeutics

country: United Kingdom

institute: The Institute of Cancer Research

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Natural circular RNA encodes regulatory small peptides in Mammalian cells

city: Guangzhou

first: Maolei

last: Zhang

state: Guangdong

address: Zhongshan two Road 58，Guangzhou City，Guangdong Province

department: Neurosurgery

institute: The 1st Affiliated Hospital of Sun Yat-sen University

summary: To test the hypothesis that circRNAs might encode functional peptides in mammalian cells, we studied the long intergenic non-protein coding RNA, p53 induced transcript (LINC-PINT), which was previously reported as a tumor suppressor and connected p53 activation with polycomb repressive complex 2 (PRC2). We selected this long noncoding RNA (lncRNA) for further analysis because LINC-PINT has a long exon 2 which in accordance with the bioinformatical analyzed circular RNA standard.The following immunoblotting showed 87aa peptide level also decreased, indicating that this peptide is encoded by circPINTexon2. We name this circRNA encoded peptide PINT87aa.

overall_design: To investigate the possible regulatory role of PINT87aa, we did the expression micro array in PINT87aa stably transfect U251 or U87 glioblastoma cells and their control cells. The array analysis reveals that PINT87aa may involve in the cell cycle regulation, anti-apoptosis effects and multiple oncogenic signaling pathway activation.

first: Nu


title: Changes in gene expression in primary human white preadipocytes in response to knockdown of DPP4

city: Bonn

first: Peter

last: Mayer

address: Kurt-Georg-Kiesinger-Allee 3

institute: BfArM

summary: Transcriptional profiling of primary human white preadipocytes after infection with lentiviral vector either containing shRNA directed against dipeptidypeptidase 4 (DPP4) or unspecific shRNA as negative control

overall_design: Treatment of cells with DPP4 shRNA or control shRNA was done in 4 biological replicates, the first sample of DPP4 KD was hybridized against the first sh-control sample, the second DPP4 smple against the second control sample and so on


title: Modulator of Apoptosis 1 (MOAP-1) is a highly regulated tumor suppressor protein

status: Public on Nov 02 2015

city: Edmonton

first: Kathryn

last: Graham

state: Alberta

address: 11560 University Ave

department: Oncology

country: Canada

institute: University of Alberta

summary: Modulator of apoptosis 1 (MOAP-1) is a BH3-like protein that plays key roles in both the intrinsic and extrinsic modes of cell death or apoptosis. It is an integral partner to the tumor suppressor Ras association domain family 1A (RASSF1A) and functions to activate the Bcl-2 family pro-apoptotic protein Bax. Although RASSF1A is now considered a bona fide tumor suppressor protein, the role of MOAP-1 as a tumor suppressor is yet to be determined. In this study, we present several lines of evidence from cancer databases, immnoblotting of cancer cells, proliferation and xenograft assays to demonstrate the role of MOAP-1 as a tumor suppressor. MOAP-1 overexpressed tumors display upregulation of multiple genes including several pro-apoptotic members that may influence the role of MOAP-1 in cell death. Frequent loss of MOAP-1 expression, in at least some cancers, appears to be attributed to enhanced proteasomal degradation. The loss of RASSF1A is an early marker of tumorigenesis and we speculate that the additional loss of function of MOAP-1 may be a second “hit” to functionally compromise the RASSF1A/MOAP-1 death receptor dependent pathway and drive tumorigensis.

overall_design: RNA was isolated mouse xenographs generated with the HCT116 cell line transfected with wild type Myc-tagged MOAP-1, empty Vector  or the Myc-tagged MOAP-1 mutants K278R or K264R in triplicate. Pairwise gene expression differences were compared  the two samples.  Features selected had more than 1.5-fold up-or down-regulated (P values of >05, unpaired Student’s  t-test).

first: Shaiaz

last: Baksh


title: Human DLD1 Cells: shRNA_Control vs. shRNA_FOXQ1

status: Public on Oct 22 2015

city: Kunming

first: Hui

last: Tang

state: Yunnan

address: No.157 Jinbi Street

department: Institute of Clinical and Basic Medical Sciences

institute: The First People’s Hospital of Yunnan Province.

summary: Transcriptional profiling of human colorectal cell DLD1 transfected by shRNA_Control or shRNA_FOXQ1 respectively.

overall_design: Two-condition experiment, DLD1_shRNA_Control cell vs. DLD1_shRNA_FOXQ1 cell. Biological replicates: 2 DLD1_shRNA_Control replicates, 2 DLD1_shRNA_FOXQ1 replicates.

first: Qiang

last: Guo


title: Identification of a potent and selective chemical probe for exploring the role of Mediator complex-associated protein kinases CDK8 and CDK19 in human disease [Colo205]

summary:
There is an unmet need for chemical tools to explore the role of the Mediator complex in human pathologies ranging from cancer to cardiovascular disease.  Here we determine that CCT251545
a WNT-pathway inhibitor discovered by cell-based screening
is a potent and selective chemical probe for the Mediator complex-associated protein kinases CDK8 and CDK19.  CCT251545 is an ATP competitive inhibitor with >100-fold selectivity over 291 other kinases. X-ray crystallography demonstrates Type 1 binding involving insertion of the CDK8 C-terminus into the ligand binding site.  In contrast to Type II inhibitors of CDK8/19
CCT251545 displays potent cell-based activity.  We show that CCT251545 and close analogues not only alter WNT-pathway regulated gene expression
but also other CDK8/19 targets including STAT1-regulated gene expression.   Consistent with this we find that phospho-STAT1SER727 is a biomarker of CDK8 kinase activity in vitro and in vivo.  Finally
we demonstrate in vivo activity of CCT251545 in WNT-dependent tumours.

overall_design:
Colo205 colon cancer cells were treated with 350 nM of Compound 1 or with vehicle (DMSO) for 2 or 6h. Four samples with four biological repeats each. Samples were hybridized against human reference.
Compound 1 is a close analogue of a 3,4,5-trisubstituted pyridine series identified from a high-throughput cell-based reporter assay of WNT signalling. It was shown to be potent and selective inhibitor of the Mediator complex-associated protein kinases CDK8 and CDK19.  Its is ATP competitive inhibitor with >100-fold selectivity over 291 other kinases. X-ray crystallography demonstrates Type 1 binding involving insertion of the CDK8 C-terminus into the ligand-binding site.

first: Trevor

last: Dale

first: Paul

middle: A

last: Clarke

first: Christina

last: Esdar

first: Dennis

last: Waalboer

first: Olajumoke

last: Adeniji-Popoola

first: Maria-Jesus

last: Ortiz-Ruiz

first: Aurelie

last: Mallinger

first: Rahul

last: Samant

last: Czodrowski

first: Djordje

last: Musil

first: Daniel

last: Schwarz

first: Klaus

last: Schneider

first: E

middle: V

first: A

last: Lammens

first: Mark

last: Stubbs

first: Ken

last: Ewan

first: Elizabeth

last: Fraser

middle: H

last: te Poele

first: Will

last: Court

first: Gary

last: Box

first: Melanie

last: Valenti

first: Alexis

last: de Haven Brandon

first: Sharon

last: Gowan

first: Felix

last: Rohdich

first: Florence

last: Raynaud

first: Richard

first: Oliver

last: Poeschke

first: Andree

last: Blaukat

last: Workman

first: Kai

last: Schiemann

first: Suzanne

last: Eccles

first: Dirk

last: Wienke

first: Julian

last: Blagg


title: Genome-wide Expression Profiling in Peripheral Models of XDP

status: Public on Oct 16 2015

city: Luebeck

first: Aloysius

last: Domingo

address: Maria Goeppert Str. 1

institute: Institute of Neurogenetics

summary:
We performed genome-wide expression profiling using an Agilent microarray in blood- and fibroblast-derived samples from XDP patients and ethnicity-matched Filipino controls.
The hypothesis was that TAF1 is dysregulated in peripheral models of XDP and this dysregulation has a concomitant downstream effect on expression genome-wide.

overall_design: Cross-sectional, XDP affecteds vs controls. In blood-derived RNA: 10 from affecteds, 12 from controls. In fibroblast-derived RNA: 15 from affecteds, 10 from controls


title: Development of gene expression signatures for IGF-1 overexpressing human umbilical cord-derived mesenchymal stem cells

status: Public on Oct 06 2015

first: Pengfei

last: Liu

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences

summary: As a key factor for differentiation and development, IGF-1 has attracted scientists’ attention gradually in recent years. However, its exact effects in human umbilical cord-derived mesenchymal stem cells (UC-MSCs) are still unclear. In this study, we mainly investigated whether IGF-1 could affect some biological functions of UC-MSCs.

overall_design: UC-MSCs were isolated from the human umbilical cord. IGF-1 overexpressing UC-MSCs (UC-MSCs-IGF-1) were established through retroviral infection. Whole genome expression of UC-MSCs-IGF-1 was analyzed with RNA microarray.


title: Gene expression profile of Randall's Plaque tissue

status: Public on Oct 03 2015

city: Nagoya

first: Kazumi

last: Taguchi

address: Kawasumi-1, Mizuho-cho, Mizuho-ku

department: Nephro-urology

institute: Nagoya City University Graduate School of Medical Sciences

summary: Randall’s plaque (RP) is the origin of renal calcification on which idiopathic calcium oxalate (CaOx) kidney stones develop. To establish genomic pathogenesis of RP, we performed the microarray analysis for comparing the gene expressions among renal papillary RP and normal tissue of 23 CaOx and 6 calcium phosphate (CaP) stone formers, and normal papillary tissue of 7 control patients. Compare to normal papillary tissue, RP tissue contained up-regulation of lipocalin 2, interleukin 11, prostaglandin-endoperoxide synthase 1, glutathione peroxidase 3, and monocyte to macrophage differentiation, whereas down-regulation of solute carrier family 12 member 1  and sodium leak channel non selective (either > 2.0- or 0.5-fold, p <0.01). The network and toxicity analysis showed these genes had association with activated mitogen-activated protein kinase, Akt/ phosphatidylinositol 3-kinase pathway, and pro-inflammatory cytokines, which caused renal injury and oxidative stress.

overall_design: Human renal papillary tip tissues were biopsied during endoscopic kidney stone surgery. Tissues including Randall's Plaque from calcium stone former was designed as P group, normal papillary tissue from calcium stone former was designed as N group, and normal papillary tissue from control patients without any kidney stone was designed as C group. Comparison among P, N, and C group was performed.

first: Shuzo

last: Hamamoto


title: Microarray data of human MLLr AML cells with or without CD93 expression

status: Public on Oct 02 2015

city: Stanford

first: Masayuki

last: Iwasaki

state: CA

address: 265 Campus Drive

department: Pathology

institute: Stanford University School of Medicine

summary: Leukemia stem cells (LSCs) share several crucial properties with hematopoietic stem cells (HSCs) including self-renewal, cell cycle quiescence, and expression of a CD34+CD38- immunophenotype, which complicates efforts to eradicate AML by therapeutically targeting LSCs without adversely affecting HSCs.  Here we report that CD93, a C-type lectin transmembrane receptor, is preferentially expressed on the cell surface of LSCs compared with HSCs in the genetic subtype of AML with genomic rearrangements of the MLL gene.  LSCs that selectively express CD93 are actively cycling, and highly enriched for xeno-engraftment potential, yet comprise a minor component of an otherwise quiescent CD34+CD38- compartment of human AML. Notably, CD93 is required for LSC function in MLL leukemogenesis, and is not simply a passive surface marker co-expressed on LSCs.  Thus, CD93 selectively marks and essentially maintains LSCs, and identifies them as predominantly cycling, non-quiescent leukemia-initiating cells in MLL-rearranged AML.

overall_design: Comparison of gene expression profiles of the LSC-enriched (CD34+CD38-CD93+) versus LSC-depleted (CD34+CD38-CD93-) populations from within individual MLLr leukemias

first: Michael

middle: L

last: Cleary


title: Human KASUMI-1 cells: Control vs Radotinib (RD) 5uM

status: Public on Sep 11 2015

city: Ulsan

first: Sook-Kyoung

last: Heo

address: 877 Bangeojinsunhwan-doro

department: Biomedical Research Center

country: South Korea

institute: University of Ulsan College of Medicine

summary: Transcriptional profiling of KASUMI-1 cells comparing between control (DMSO-treated) and radotinib treated Kasumi-1 cells at 48hr

overall_design: one-condition experiment, Control vs RD 5 uM. Biological replicates: 1.

first: Sook

middle: K

first: Eui

last: Noh


title: Microarray analysis of Salmonella-infected or uninfected in vitro M cells and Caco-2 cells

status: Public on Oct 10 2015

city: Taipei

first: Ke-Chuan

last: Wang

address: 250 Wu-Hsing Street

country: Taiwan

institute: Taipei medical university

summary: To investigate what genes are differently expressed between in vitro M cells and Caco-2 cells, and how S. Typhimurium and speG aﬀect gene expression of both cells.

overall_design: We established an in vitro M cell model using transwell co-culture of Caco-2 cells and Raji B lymphocytes and infected in vitro M cells and Caco-2 cells with S. Typhimurium wild-type (WT), its ΔspeG mutant (MOI 25), or uninfected for 1 hour for RNA microarrays. Transcriptomes among the 6 pools (uninfected, WT-infected or ΔspeG -infected Caco-2 cells and M cells) were pairwise compared.

first: Shiuh-Bin

last: Fang

first: Chih-Hung

last: Huan

first: Ching-Rou

last: Huang


title: Global mRNA expression profiling of patient derived pancreatic carcinoma xenograft Bo63 following JQ1-SAHA combination therapy

status: Public on Sep 20 2015

city: Munich

first: Jens

middle: T

last: Siveke

address: Ismaninger Str. 22

department: 2. Med. Klinik

institute: Klinikum rechts der Isar, Technical University Munich

summary: Global mRNA expression profiling of patient derived pancreatic carcinoma xenograft Bo63 were collected using Agilent human whole genome array (G4845A AMADID 026652, cRNA 4x44k V2) . Two different sources of RNA were analyzed: 1.) Bo63 xenograft tumors grown on nude mice treated with vehicle only as control. 2.) Bo63 xenograft tumor grown on nude mice treated with JQ1 and SAHA (SAHA 25 mg/kg 1-0-0 and JQ1 50 mg/kg 0-0-1, treatment was imitated when tumor size reached 200 mm³ +/- 20 mm³.

overall_design: Two conditions (vehicle vs JQ1-SAHA treatment), each condition is represented by 3-4 biological replicates

first: Stephan

last: Hahn


title: Storage time does not modify the gene expression profile of cryopreserved human metaphase II oocytes

status: Public on Sep 19 2015

city: Genova

first: Sara

last: Stigliani

address: largo R Benzi 10

country: Italy

institute: IRCCS AOU San Martino-IST

summary: Study question: Does storage time impact on transcriptome of slowly frozen cryopreserved human metaphase II (MII) oocytes? Summary answer: For the first time, we demonstrate that the length of cryostorage has no effect on the gene expression profile of human metaphase II oocytes. What is known already: Oocyte cryopreservation is a largely-used technique in IVF for storage of surplus oocytes, as well as for fertility preservation (i.e., women undergoing gonadotoxic therapies) and oocyte donation programs. Although it is known that cryopreservation negatively impacts on oocyte physiology and it is associated with decrease of transcripts, no experimental data about the effect of storage time on the oocyte molecular profile are available to date.  Study design, size, duration: This study included 27 women undergoing IVF treatment, < 38 years aged, without any ovarian pathology. Surplus MII oocytes were donated after written informed consent. A total of 31 non-cryopreserved oocytes and 68 surviving slow-frozen/rapid-thawed oocytes (32 oocytes cryostored for 3 years and 36 cryostored for 6 years) were analyzed. Participants/materials, setting, methods: Pools of ≈10 oocytes for each group were prepared. Total RNA was extracted from each pool, amplified, labeled and hybridized on 4x44K v2 microarrays (Agilent). Analyses were performed by R v3.1.3 software using the limma package v3.22.7. Main results and the role of chance: Comparison of gene expression profiles between surviving thawed oocytes after 3 and 6 years of storage in liquid nitrogen found no differently expressed genes. The expression profiles of cryopreserved MII oocytes significantly differed from those of non-cryopreserved oocytes in 107 probe sets corresponding to 73 down-regulated and 29 up-regulated unique transcripts. Gene Ontology analysis by DAVID bioinformatics resource disclosed that cryopreservation deregulates genes involved in oocyte function and early embryo development, such as chromosome organization, RNA splicing and processing, cell cycle process, response to DNA damage stimulus, cellular response to stress and DNA repair, calcium ion binding, malate dehydrogenase activity, mitochondrial membrane respiratory chain. Among the probes significantly up-regulated in cryopreserved oocytes, 2 corresponded to ovary-specific expressed large intergenic noncoding (linc)RNAs.

first: Paola

last: Scaruffi

first: Stefano

last: Moretti


title: Alectinib-resistant NSCLC harboring EML4-ALK cells: Parental vs. Alectinib-resistant

status: Public on Sep 18 2015

city: Okayama

first: Hideko

last: Isozaki

address: 2-5-1 Shikatacho

department: Department of Hematology, Oncology and Respiratory Medicine

institute: Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences

summary: Transcriptional profiling of NSCLC harboring EML4-ALK comparing parental H2228 cells with alectinib resistant H2228 cells.

overall_design: Two-condition experiment, H2228 vs. H2228/CHR cells. Biological replicates: 1 parental replicates, 3 alectinib-resistant replicates.

first: Katsuyuki

last: Kiura

first: Nagio

last: Takigawa


title: Equivalent Gene Expression Profiles between Glatopa and Copaxone

status: Public on Sep 26 2015

city: Cambridge

first: Jay

middle: Lawrence

last: Duffner

state: MA

address: 675 West Kendall St.

department: Research

institute: Momenta Pharmaceuticals

summary: Glatopa is a generic glatiramer acetate recently approved for the treatment of patients with relapsing forms of multiple sclerosis. Gene expression profiling was performed as a means to evaluate equivalence of Glatopa and Copaxone. Microarray analysis containing 39,429 unique probes across the entire genome was performed in murine glatiramer acetate–responsive Th2-polarized T cells, a test system highly relevant to the biology of glatiramer acetate. A closely related but nonequivalent glatiramoid molecule was used as a control to establish assay sensitivity. Multiple probe-level (Student’s t-test) and sample-level (principal component analysis, multidimensional scaling, and hierarchical clustering) statistical analyses were utilized to look for differences in gene expression induced by the test articles. The analyses were conducted across all genes measured, as well as across a subset of genes that were shown to be modulated by Copaxone. The following observations were made across multiple statistical analyses: the expression of numerous genes was significantly changed by treatment with Copaxone when compared against media-only control; gene expression profiles induced by Copaxone and Glatopa were not significantly different; and gene expression profiles induced by Copaxone and the nonequivalent glatiramoid were significantly different, underscoring the sensitivity of the test system and the multiple analysis methods. Comparative analysis was also performed on sets of transcripts relevant to T-cell biology and antigen presentation, among others that are known to be modulated by glatiramer acetate. No statistically significant differences were observed between Copaxone and Glatopa in the expression levels (magnitude and direction) of these glatiramer acetate-regulated genes. In conclusion, multiple methods consistently supported equivalent gene expression profiles between Copaxone and Glatopa.

overall_design: 48 samples were tested for gene expression by Agilent oligonucleotide array. The samples include 17 Copaxone samples from 9 different lots of material, 18 Glatopa samples from 4 different lots of material, 8 AcN acetonitrile nonconforming copolymer samples from one lot and one Media only sample that was treated with an amount of mannitol equivalent to that in the Copaxone or Glatopa samples.  Samples were randomized prior to labelling and application to the microarray.

first: Josephine

middle: S

last: D'Alessandro

first: Joel

last: Pradines

first: Ishan

last: Capila

first: Kevin

last: Garofalo

first: Ganesh

last: Kaundinya

first: Benjamin

last: Greenberg

first: Daniel

last: Kantor

first: Tanmoy

last: Ganguly


title: Haploinsufficiency in bromodomain containing 2 (Brd2) gene remodels synaptic transmission in male mouse striatum

status: Public on Sep 01 2015

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: Our previous work confirmed that Brd2+/- mouse presents the sex specific characteristics of juvenile myoclonic epilepsy, a subsyndrome of idiopathic generalized epilepsy. Here, we investigated the role of Brd2 gene in modulating the genomic fabrics responsible for the glutamatergic, GABAergic, dopaminergic, cholinergic and serotonergic transmission in the front cortex striata of male mice. Agilent two-color gene expression arrays and the genomic fabric paradigm were used to determine whether the expression and networking of genes involved in the synaptic transmission differ between Brd2+/- and wildtype mice. We found relatively few regulated genes in Brd2+/-mice with respect to their wildtype counterparts. However, most of the regulated genes were directly related to control of anxiety and seizures, justifying the role of Brd2 upstream control of these traits.

overall_design: Agilent mouse two-color gene expression arrays to profile striata of the prefrontal cortices of wildtype (W) and Brd2+/- (H) mouse male (M) adult C57Bl/6j mice. Differently labeled biological replicates were cohybridized with each array. Results of similarly labeled different conditions were compared then averaged for the two fluorescent labels. For instance: MW1 & MW3 were compared with MH1 & MH3, MW2 & MW4 were compared  with MH2 & + MH4, and the results of the comparisons averaged. This design uses 100% of the resources, has a better normlaiztion and allows all possible comparisons among the conditions.

first: Sanda

first: Jana

last: Veliskova

first: Libor

last: Velisek


title: miRNA expression patterns in immature and CpG stimulated murine BMDCs

status: Public on Sep 04 2015

city: Portland

first: Evan

middle: F.

last: Lind

state: OR

address: Mail Code L220, 3181 SW Sam Jackson Park Road

department: Molecular Microbiology and Immunology

institute: Oregon Health & Science University

summary: Toll-like receptor (TLR)-induced maturation of dendritic cells (DCs) leads to the production of proinflammatory cytokines as well as the upregulation of various molecules involved in T cell activation. These are believed to be the critical events that account for the induction of the adaptive immune response. Here, we have examined the role of micro-RNA-155 (miR-155) in DC function and the induction of immunity. Using a model where the transfer of self-antigen-pulsed, TLR-matured DCs can induce a functional CD8 T cell response and autoimmunity, we find that DCs lacking miR-155 have an impaired ability to break immune tolerance. Importantly, transfer of self- antigen-pulsed DCs overexpressing miR-155 was sufficient to break tolerance in the absence of TLR stimuli. Although these unstimulated DCs induced T cell function in vivo, there was no evidence for the upregulation of costimulatory ligands or cytokine secretion. Further analysis showed that miR-155 influenced the level of the phosphatase SHIP1 in DCs, and that the lack of SHIP1 in DCs was sufficient to break T cell tolerance in vivo, again in the absence of TLR induced DC maturation. Our study demonstrates that the overexpression of miR-155 in DCs is a critical event that is alone sufficient to break self tolerance and promote a CD8-mediated autoimmune response in vivo. This process is independent of the induction of conventional DC maturation markers, indicating that miR-155 regulation of SHIP represents a unique axis that regulates DC function in vivo.

overall_design: Dendritic cell culture: Bone marrow was flushed from tibias and femurs of mice with HBSS. Bone marrow cells were cultured at 2x106 cells/ml in 10 ml non-tissue culture treated dishes in RPMI 1640 containing 10% LPS-free FBS, Penicillin:streptomycin glutamine 2-mercaptoethanol (cRPMI), with 40ng/ml murine GM-CSF (Peprotech). On day 3 of cultures 10ml of fresh media was added also containing 40ng/ml GM-CSF. On days 6 and 8, 10ml of media was removed and centrifuged to collect cells, which were resuspended in 10ml fresh media containing GM-CSF and were added back to dishes. Non-adherent cells were isolated on day 9. DCs were plated in 24-well plates at 2x106 cells/ml in 1ml of cRPMI with or without the class B CpG ODN1826 (ACGT DNA Technologies corporation, Toronto, ON, Canada) at 10μM final concentration overnight. Array analysis of mi-RNA expression: BMDCs from WT mice were either stimulated with CpG or left in media alone overnight. Whole RNA was isolated using mirVana miRNA isolation kit following the manufacturers instructions. RNA samples were labeled and hybridized to Agilent mouse miRNA 8x15K arrays (Agilent). Data was generated from 8 individual samples (4 unstimulated and 4 CpG-treated).

middle: F

first: Douglas

middle: G

last: Millar

first: Dilan

last: Dissanayake

first: Jonathan

last: Savage

first: William

last: Kerr

first: Pamela

last: Ohashi


title: IL6-STAT3 downstream targets in MCF10A/MCF10A.ErbB2* cells

status: Public on Sep 03 2015

city: Memphis

first: Jiyang

last: Yu

state: TN

address: 262 Danny Thomas Place, MS 1135

department: Computational Biology

institute: St. Jude Children's Research Hospital

summary: Overexpression in IL6 in MCF10A vs. WT, MCF10A.ErbB2* with/without shRNA targeting STAT3

overall_design: Overexpression in IL6 in MCF10A vs. WT, MCF10A.ErbB* with/without shSTAT3, duplicates, two STAT3 shRNAs

first: Ruth

last: Rodriguez-Barrueco

first: Andrea

last: Califano

first: Jose

middle: M

last: Silva


title: Transcriptomic effects of law salt diet on the mouse left ventricle

summary: Low salt diet is a constant recommendation to hypertensive patients. Here we investigated the impact of prolonged reduced sodium feeding on the geneomic fabrics responsible for heart contraction in adult male mice. Although only 166 (0.59%) of the 27901 quantified transcripts in all samples were significantly up- and 88 (0.32%) down-regulated, the synergistic coupling of the heart contraction genes increased by 22% while their antagonistic coupling decreased by 43%. This substantial remodeling of the heart contraction genomic fabric justifyes the low salt diet recommendation.

overall_design: Agilent mouse two-color gene expression arrays were used to profile the left heart ventricles of 16 weeks old C57Bl/6j male mice subjected for the last 8 weeks of their lives to normal (N, 0.4% Na) or low (L, 0.05%Na) salt diet. Differently labeled biological replicates were cohybridized with each array. Results of similarly labeled different conditions were compared then averaged for the two fluorescent labels. Thus, MW1 & MW3 were compared with MH1 & MH3, MW2 & MW4 were compared  with MH2 & + MH4, and the results of the comparisons averaged. This design uses 100% of the resources, has a better normlaiztion and allows all possible comparisons among the conditions.

first: Yester

last: Ervolina

first: Thomas

last: Hintze


title: Gene expression profile of mock and FLT3-ITD-expressing K562 cells.

status: Public on Sep 09 2015

city: Isehara-shi

first: Anar

middle: Damdinsuren

last: Damdinsuren

state: Kanagawa

address: 143 Shimokasuya

department: Department of Laboratory Medicine

institute: Tokai University, School of Medicine

summary: We used whole genome microarray expression profiling as a discovery platform to identify genes regulated by FLT3-ITD activity.

overall_design: Viral particles with pMY-puro, pMY-puro-FLT3-ITD-1 or pMY-puro-FLT3-ITD-2, were generated using PLAT-gp packaging cells and infected to K562 cells. The vector-transduced cells were selected with 2µg/ml puromycin treatment.

first: Damdinsuren

last: Anar

first: Hiromichi

last: Matsushita

first: Masatoshi

last: Ito


title: The effects of exogenous RNAs on transcriptome

status: Public on Sep 30 2015

city: Seattle

first: Kai

last: Wang

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary:
To explore the potential functions of exogenous RNAs in circulation, we transfected several synthetic, double-stranded mature microRNA-like molecules selected from observed exogenous miRNA sequences and some highly abundant exogenous sequences (bacterial rRNAs) that have potential to form pre-miRNA-like secondary structures into a mouse, Dicer-deficient, fibroblast cell line.
This provides a good tool for studying the function of miRNAs. By introducing individual miRNA into these cells and avoiding multiple interactions of microRNA and mRNA (Wang et al in preparation) it is possible to interrogate the cells for mRNA levels, which are informative as to specific miRNA function.

overall_design: A mouse, Dicer-deficient, fibroblast cell line transfected with several synthetic, double-stranded mature microRNA-like molecules selected from observed exogenous miRNA sequences and some highly abundant exogenous sequences (bacterial rRNAs)

first: Hong

last: Li

first: Yue

last: Yuan

first: Alton

last: Etheridge

first: Yong

last: Zhou

first: David

last: Huang

first: Paul

last: Wilmes

last: Galas


title: Detection of metastasis-specific miRNA for metastatic lesion of colorectal cancer

city: okayama city

first: Tomokazu

last: Fuji

state: Okayama

address: 2-5-1 Shikata-cho

department: Department of Gastroenterological Surgery

institute: Okayama University Graduate School of Medicine Dentistry and Pharmaceutical Sciences

summary:
We carried out comprehensive analysis for the miRNA profiling of primary tumor and metastatic lesion which seems to be source of circulating miRNA. We picked up two patients who treated with primary tumor resection initially and received chemotherapy followed by surgical resection of liver metastasis.
The total miRNA was isolated from frozen tissue specimens. SurePrint G3 Human miRNA microarray kit Rel.21.0 (Agilent Technologies) contains 2549 human microRNA probes.   As previously reported, hsa-miR200c revealed specifically high expression in metastatic sites at both two cases.

overall_design: In two colorectal cancer patients, the frozen primary tumor, normal mucosa and liver-metastatic lesion were analyzed by microRNA microarray.

first: Takeshi

last: Nagasaka


title: Haploinsufficiency in bromodomain containing 2 (Brd2) gene remodels synaptic transmission in female mouse striatum in a sex-specific manner

first: Dumitru

last: Iacobas

summary: Our previous work showed that Brd2+/- mouse models the sex specific characteristics of juvenile myoclonic epilepsy, a subsyndrome of idiopathic generalized epilepsy. Here, we investigated a role of Brd2 gene in modulating the genomic fabrics responsible for the glutamatergic, GABAergic, dopaminergic, cholinergic and serotonergic transmission in the striatum of female mice. Agilent two-color gene expression arrays and the genomic fabric paradigm were used to determine whether the expression and networking of genes involved in the synaptic transmission differ between Brd2+/- and wildtype mice and whether these differences are sex-specific. As in Brd+/- male mice we found relatively few regulated genes in Brd2+/-female mice with respect to their wildtype counterparts. However, most of the regulated genes were directly related to control of anxiety and seizures, justifying the role of Brd2 upstream control of these traits. Remarkably, the sets of regulated genes in the two sexes did not overlap, supporting the conclusion of sex-specific control of traits by Brd2.

overall_design: Agilent mouse two-color gene expression arrays to profile striata of the prefrontal cortices of wildtype (W) and Brd2+/- (H) mouse female (F) adult C57Bl/6j mice. Differently labeled biological replicates were cohybridized with each array. Results of similarly labeled different conditions were compared then averaged for the two fluorescent labels. For instance: FW1 & FW3 were compared with FH1 & FH3, FW2 & FW4 were compared  with FH2 & + FH4, and the results of the comparisons averaged. This design uses 100% of the resources, has a better normlaiztion and allows all possible comparisons among the conditions.

first: Sanda

first: Jana

last: Veliskova

first: Libor

last: Velisek


title: Abnormal differentiation and activation of Pla2g2f-/- keratinocytes in primary culture

status: Public on Aug 08 2015

city: Setagaya

first: Kei

last: Yamamoto

address: 2-1-6 kamikitazawa

department: Lipid Metabolism Project

institute: Tokyo Metropolitan Institute of Medical Science

summary: Primary keratinocytes from Pla2g2f-/- mice were defective in proper differentiation and activation.

overall_design: Pla2g2f+/+ and Pla2g2f-/- keratinocytes after culture for 48 h with (differentiated) or without (control) 1 mM CaCl2. Equal amounts of total RNA were pooled from keratinocytes from 6 mice for each genotype.

first: Yasumasa

last: Nishito

first: Makoto

last: Murakami


title: Expression data from fetal sheep immunocytes

status: Public on Aug 21 2015

city: Darlinghurst

first: Tim

last: Molloy

state: NSW

address: Level 8, 405 Liverpool St

department: Haematology

country: Australia

institute: St Vincent's Centre for Applied Medical Research

summary:
study investigating the initiation of systemic inflammatory signaling in fetuses exposed to TLR-4 agonist lipopolysaccharides from E.coli
microarray was used to determine the inflammatory transcriptome in circulating fetal immunocytes

overall_design: fetal sheep at 92d GA were catheterised prior to intraamniotic exposure fo saline or lipopolysaccharides for 48h prior to euthanasia

first: M

middle: W

last: Kemp

first: T

middle: J


title: Retinoic acid signaling targets within the embryonic zebrafish eye during photoreceptor differentiation

status: Public on Aug 28 2015

city: Moscow

first: Deborah

middle: Lynn

last: Stenkamp

state: Idaho

address: 875 Perimeter Drive, MS 3051

department: Biological Sciences

institute: University of Idaho

summary: The signaling molecule retinoic acid (RA) regulates rod and cone photoreceptor fate, differentiation, and survival. The purpose of this study was to identify eye-specific genes controlled by RA during photoreceptor differentiation in the zebrafish.

overall_design: 6 samples; 3 replicates of 2 conditions

first: Craig

last: Stevens


title: Transcriptomic signatures of Auger electron radioimmunotherapy using nuclear targeting 111In-trastuzumab for potential combination therapies

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

institute: National Institutes for Quantum and Radiological Science and Technology

summary: The aim of this study was to identify targetable molecular signatures for enhancing the cytotoxic effects of In-111-trastuzumab-NLS using microarray technology.

overall_design: Changes in gene expression in SKBR3 cells untreated or treated with unlabeled or In-111-labeled antibodies for 7 days were measured. Three independent experiments in each condition were performed.

first: Huizi

last: Li

first: Yukie

last: Morokoshi

last: Daino

first: Takako

last: Furukawa

first: Tadashi

last: Kamada

first: Tsuneo

last: Saga

first: Sumitaka

last: Hasegawa


title: Gene expression profile in HCAECs transfected with RNF213 siRNA

status: Public on Aug 10 2015

city: Fukuoka

last: Ohkubo

state: Fukuoka

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

department: Department of Pediatrics

institute: Graduate School of Medical Sciences, Kyushu University

summary: We performed transcriptome analysis of HCAECs upon treatment with siRNF213 or with a control siRNA. Overall, a total of 217 genes were up-regulated (> 2.0-fold change in expression), while 499 genes were down-regulated (< 0.5-fold change in expression), in the siRNF213-treated cells when compared to the control. Expression of four genes (RNF213, CyclinA, B and E) from this signature was quantified in the same RNA samples by real-time PCR.

overall_design: Gene expression in HCAECs upon treatment with siRNF213 or with a control siRNA. Two independent experiments were performed at each condition.


title: Impacts of reprogramming method and culture conditions in trophoblast differentiation of induced pluripotent stem cells

status: Public on Aug 31 2015

city: Columbia

first: Toshihiko

last: Ezashi

state: MO

address: 240a CS Bond Life Sciences Center

department: Animal Sciences

institute: University of Missouri-Columbia

summary:
Trophoblast differentiation from human ESC has been achieved by exposing the cells to BMP4 with or without supplementation of ALK4/5/7 inhibitor (A83-01) and FGF2 signaling inhibitor (PD173074) (BAP). Here the two differentiation conditions, BMP4 and BAP were applied to two sets of human PSC lines, H1 ESC and iPSC that latter was generated by DOX-inducible lentiviral (V) transductions of umbilical cord mesenchymal cells. The V-iPSC showed residual transgene expressions from the viral vectors in DOX-free culture condition. When the both ESC and iPSC lines were differentiated simultaneously, similar time dependent morphological changes were observed but BMP4 treated V-iPSC showed a minor yet consistent lag in the differentiation progression compared to BMP4 treated hESC.
Although both differentiated ESC and V-iPSC showed dominant trophoblast phenotypes, the BMP4 treated V-iPSC also expressed gene markers consistent with the presence of mesoendoderm. The BAP condition provided more efficient differentiation than BMP4 alone, and the BAP-differentiated iPSC and ESC never expressed mesoendoderm markers.

overall_design: Five samples, one control of undifferentiated V-iPSC (FGF2) and four differentiated samples included two H1 ESC (treated with BMP4 or BMP4+A83-01) and similarly treated two V-iPSC were analyzed. Trophoblast differentiation was conducted with BMP4 (10 ng/ml) with or without supplementation of ALK4/5/7 inhibitor (A83-01; 1 μM) to H1 ESC and V-iPSC, respective reagents were added to FGF2-free MEF-CM from the second day culture of following passages for up to six additional days.

first: R

last: Roberts


title: Global changes in gene expression in Caco-2 cell line by treatment with extract from iodine-biofortified carrot and lettuce

status: Public on Aug 01 2015

city: Warsaw

first: Magdalena

last: Łój

address: Nowoursynowska 166

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

summary: Whole genome microarray data were analyzed to describe the changes in gene transcription profile in human Caco-2 cancer cells under the influence of the extract from iodine-biofortified and non-fortified carrot and lettuce. These iodine-biofortified vegetables can be used as a functional food.

overall_design: Four-condition experiment: iodine-biofortified carrot, non-fortified carrot, iodine-biofortified lettuce, non-fortified lettuce vs. Caco-2 colorectal adenocarcinoma cell line.    Three biological replicates and three technical replicates.

first: Aneta

middle: A

last: Koronowicz

last: Kopeć

first: Sylwester

last: Smoleń

first: Roksana

last: Rakoczy

first: Adam

last: Master

first: Teresa

last: Leszczyńska

first: Ewa

last: Piątkowska

first: Renata

last: Bieżanowska-Kopeć

first: Mirosław

last: Pysz

first: Joanna

last: Kapusta-Duch

first: Łukasz

last: Skoczylas

first: Iwona

last: Ledwożyw-Smoleń


title: Expression analysis of Vitis Vinifera clones differing for compactness

city: Logrono

first: Jérôme

last: Grimplet

address: C/ Madre de Dios 51

country: Spain

institute: Instituto de Ciencias de la Vid y del Vino

summary: Grapevine cluster compactness is a multi-componential trait of agronomical interest; it greatly influences the vineyard management and the visual aspect of table grape. Clusters with greater compactness are more susceptible to disease. The compactness can be break down in a patchwork of agronomical traits, each having agronomical importance that includes parameters related to inflorescence and cluster architecture (cluster length and width, length of pedicels, etc.), fruitfulness (number of berries, number of seeds) and berry (size, shape, volume...). Through visual evaluation of a collection of 730 clones from the cultivar Tempranillo and 501 clones from Garnacha Tinta we identified and fully phenotyped distinct clones which transcriptomes were compared at key developmental stages in order to identify the genes playing a role in mechanisms involved in cluster compactness such as the ones determining number of berries, cluster length or berry size. Key genes involved in this process were identified. The findings lead us to hypothesize that berry size and/or number at ripening are greatly influenced by the rate of cell replication in flowers during the first stages after pollination.

overall_design:
A total of 57 samples were hybridized. Comparison G1 was performed between clones showing differences in the cluster compactness and in the total number of berries per cluster and berries size (compact: clone 1134. loose: clone 0368).
Comparison G2 was performed between two compact clones (Garnacha Tinta 147 and 1134) significantly differing for cluster length and number of nodes (branches) of the rachis.
Comparison G3 was performed with two loose clones (Garnacha Tinta 681 and 1154) differing in the number of nodes of the rachis (p<0.01).
Comparisons G4 and T were performed between clones showing differences in the cluster compactness and in the total number of berries per cluster (compact: clones 0906 and 0126. loose: clones 1154 and 1041).

first: Jerome

first: Javier

last: Tello

first: Natalia

last: Laguna

last: Ibanez


title: Placental transcriptomic pattern of murine advanced paternal age model of autism

status: Public on Jul 25 2015

city: Magdalenka

first: Adrian

middle: Mateusz

last: Stankiewicz

state: Mazovia

address: Jastrzebiec, ul. Postepu 36A

department: Animal Behaviour

institute: Institute of Genetics and Animal Breeding of the Polish Academy of Sciences

summary: Advanced paternal age has been shown to be a significant risk factor for neurodevelopmental psychiatric disorders, particularly autism. We have recently shown that mice conceived by old fathers display behavioral abnormalities which resemble key diagnostic symptoms of human autism. De novo mutations and epigenetic alterations increase in the male germ line during ageing and are thought to mediate the effect of paternal age on occurrence of diseases occurrence. Because the placenta carry a predominantly fetal genetic background, age-related mutagenesis and epigenetic errors might negatively influence placental physiology and in turn perturb fetal brain development. Here, we examined the impact of paternal age on placental mRNA transcriptome.    This work was supported by Programme FP7-KBBE-2012.1.3-04, GA no. 312097 Acronym: FECUND, to GEP; MIUR/CNR, Programme FIRB. GA n. B81J12002520001 Acronym: GenHome, to PL. This study was also partially financed by the IGAB PAS project (S.III.1.3), Polish Scientific Committee Grant 2011/03/N/NZ29/05222, Polish Ministry of Science and Higher Education Grants N N519 657940 and N N311 604938.

overall_design: We compared gene expression patterns of mouse placentas harvested from either advanced paternal age model (APA) of autism or control animals. We included 2 comparisons: 1) placenta of female APA vs placenta of female control; 2) placenta of male APA vs placenta of male control. Each comparison was composed of 3 biological replicates. To minimize family bias, poolings contained at most one placenta per sex from each dam to a minimum of one and a maximum of three placentas per group/sex.

last: Goscik

first: Artur

last: Swiergiel

first: Pasqualino

last: Loi

first: Jacek

last: Modlinski

first: Grazyna

middle: E

last: Ptak

first: Silvestre

last: Sampino


title: Human pulmonary microvascular endothelial cells (HPMECs): Control siRNA vs HSP27 siRNA

status: Public on Aug 29 2015

city: Seoul

first: Yoon-Jin

last: Lee

address: Nowon GU

institute: Korea Institute of Radiological & Medical Sciences

summary: Transcriptional profiling of HPMECs comparing Control siRNA treated  with HSP27 siRNA

overall_design: Two-condition experiment, control siRNA vs HSP27 siRNA ; 3 controlsiRNA transfected replicates , 3HSP27 siRNA replicates. Replicates were pooled and hybridized to a single array.

first: Seo

middle: H

last: Choi


title: Genes regulated by SET7/9 knockdown in gastric cancer cells

status: Public on Jul 24 2015

city: Tokyo

first: Yoshimitsu

last: Akiyama

address: 1-5-45 Yushima, Bunkyo-ku

department: Molecular Oncology

institute: Tokyo Medical and Dental University

summary: Expression of SET7/9, a histone methyltransferase, was frequently reduced in cultured and primary gastric cancers. To identify the SET7/9 target genes in gastric cancer, we performed siRNA-based knockdown of SET7/9 in MKN74 and MKN45 cells and then examined significant expression changes of genes by microarray.

overall_design: Transfection of SET7/9 siRNA into MKN74 and MKN45 cells were performed by electroporation. After 48hrs, cells were harvested. Total RNA was used for cDNA microarray.

first: Y

first: S

last: Shimada

first: T

last: Nishikawaji

last: Yuasa


title: The effect of THADA knockdown on Huh7 cells

city: Kurume

first: Takafumi

last: Yoshida

address: 67, asahi-machi

department: Department of Medicine

institute: Kurume University

summary: We use lentivirus carrying shRNA for THADA to evaluate the efect of THADA knockdown in Huh7 cells.

overall_design: The pGIPZ shRNA plasmid specific to human THADA (clone ID V3LHS_318037 Open Biosystems, Inc.) or the pGIPZ non-silencing shRNAmir lentiviral plasmid (as a control) was cotransfected with the pPACKH1 plasmid mix in HEK 293 cells. Stable clones of Huh7 cells with THADA knockdown were routinely maintained in a medium containing of puromycin (500ng/ml)


title: Tribbles-1 regulates hepatic lipogenesis through post-transcriptional regulation of C/EBPα [array]

status: Public on Jul 14 2015

city: Philadelphia

first: Robert

middle: C

last: Bauer

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary:
Comparison of gene expression in livers of either WT mice or mice with hepatic specific deletion of the gene Tribbles1. Animal groups were both Trib1 cKO mice homozygous for a floxed allele of Trib1. Mice aged 8-10 weeks were treated with adeno associated virus (AAV) encoding Cre recombinase (AAV_Cre) or no gene (AAV_null). The WT group is mice treated with AAV_Null, the liver-specific KO group treated with AAV_Cre.
Gene expression data was then used in Ingenuity Pathway analysis to attempt to identify upstream transcription factors that might be responsible for the gene expression changes observed.

overall_design: All animals were 8-10 weeks of age, and all animals were homozygous for the floxed allele of Trib1. WT animals were treated with AAV_Null, Trib1 liver specific KO mice were treated with AAV_Cre. Mice were euthanized at 1-week post injection of AAV, and RNA collected from whole liver tissue.

first: Daniel

last: Rader


title: A comparison of whole genome gene expression profiles of GFP/CD19-Cre and LMP2A/CD19-Cre mouse splenic B220+ B cells

status: Public on Jul 07 2015

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Analysis of gene expression profiling change by expression of Epstein-Barr virus latent membrane protein 2A (LMP2A) in B cells

overall_design: A Dye-swapped experiment was performed by hybridizing complimentary RNA (cRNA) labeled with either Cyanine (Cy) -3 or Cy-5 onto 4X44K ver.2 Agilent Whole Mouse Genome Oligo Microarray (G4846A).

first: Takeharu

last: Minamitani


title: Flavivirus antagonism of type I interferon signaling reveals prolidase as a regulator of IFNAR1  trafficking and expression

status: Public on Jul 08 2015

first: Michael

last: Katze

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: Type I interferon (IFN-I) signals through two receptor subunits, IFNAR1 and IFNAR2, to regulate sterile and infectious immunity. IFNAR1 expression is tightly regulated to prevent autoimmunity although the mechanisms governing this are incompletely understood. We investigated the strategies used by two flaviviruses, tick-borne encephalitis virus and West Nile virus, to antagonize IFN-I signaling. Infection with these viruses resulted in depletion of IFNAR1 associated with the function of the viral IFN-I antagonist, NS5. NS5 function was dependent on its ability to associate with prolidase (PEPD), a cellular dipeptidase. PEPD was required for IFNAR1 maturation and accumulation, as well as gene induction following IFNAR1 stimulation. The relevance of PEPD to human biology was confirmed in fibroblasts derived from patients with genetic prolidase deficiency that expressed low IFNAR1 and exhibited reduced responses to IFNAR1. Thus, by understanding flavivirus IFN-I antagonism, PEPD is revealed as a central regulator of IFN-I responses in humans.

overall_design: RNA was isolated from replicates of 4 cultured dermal fibroblast lines derived from patients with genetic prolidase deficiency (PEPD), as well as from 4 cultured dermal fibroblast lines derived from normal healthy donors.  These were run on Agilent microarrays to compare differences in gene expression observed in PEPD fibroblasts compared with normal fibroblasts.

first: Angela

middle: L

last: Rasmussen

first: Richard

last: Green

first: Sonja

last: Best


title: A Comparison of Whole Genome Gene Expression Profiles of 0p-EpSCs and 15p-EpSCs

summary: To investigate successful maintenance of skin epithelial stem cells (EpSCs) in vitro using Wnt-3a, we prepared CD49f+CD34+ cells, an EpSC-rich population from adult mouse skin and cultured for 10 days in the presence of Wnt-3a. Sorted CD49f+CD34+ cells proliferated markedly in the presence of Wnt-3a. Those cells were then subjected to a second 10-day culture with Wnt-3a and sorted, with the same procedures repeated until fifteen 10-day cultures were performed.

overall_design: A dye-swapped experiment was performed by hybridizing complimentary RNA (cRNA) labeled with either Cyanine (Cy) -3 or Cy-5 onto 4X44K ver.2 Agilent Whole Mouse Genome Oligo Microarray (G4846A).

first: Yukiteru

last: Ouji


title: An Artificial Interfering lncRNA Mediated by Oncolytic Adenovirus Competitively Consumes OncomiRs to Exert Antitumor Efficacy in Hepatocellular Carcinoma (microRNA)

status: Public on Jul 21 2015

city: Shanghai

first: Changqing

last: Su

address: 225 Changhai Rd.

department: Department of Molecular Oncology

institute: National Center of Liver Cancer

summary: The study generated an artificially-designed interfering long non-coding RNA (lncRNAi). The adenovirus-expressed lncRNAi with high level in hepatocellular carcinoma (HCC) cells competes with OncomiR target genes to bind to and consume OncomiRs, thereby achieving the targeted anti-HCC efficacy.

overall_design: High expression of an artificially-designed lncRNAi mediated by oncolytic adenovirus can compete with the mRNAs of OncomiR target genes to bind to and consume OncomiRs, thereby achieving the targeted anticancer effect of HCC.

first: Xiaoya

last: Li

first: Yinghan


title: Early gene expression of regenerating zebrafish hearts following water or atropine treatment

status: Public on Jun 11 2015

city: Cambridge

first: Caitlin

last: O'Meara

address: 65 landsdowne street

department: Medicine

institute: Brigham and Women's hospital

summary: We report global RNA expression profiles from whole zebrafish hearts 24 hours after ventricle amputation.  Zebrafish were exposed to atropine or water following surgery.

overall_design: 15 zebrafish hearts were pooled per microarray chip.  Amputated hearts of zebrafish exposed to atropine was compared to hearts of zebrafish exposed to water.


title: Therapeutic intervention of monocytes to LPS challenge

status: Public on Jul 02 2015

city: Borstel

first: Sebastian

last: Marwitz

address: Parkallee 3a

department: Histology

institute: Research Center Borstel - Leibniz Lung Center

summary: To investigate the possible therapeutic effects of ibuprofen and Pep19-2.5 alone or in combination on the LPS-response of human monocytes.

overall_design: Human monocytes were challenged with 0.1ng/ml LPS and/or 10ng/ml Pep19-2.5 LPS. Medium controls served as unstimulated samples. LPS and Pep19-2.5 was used either alone or together to LPS-challenged samples. RNA was extracted after 4 hrs of stimulation. Three biological replicates were conducted

first: Lena

last: Heinbockel

first: Torsten

last: Goldmann

first: Klaus

last: Brandenburg


title: Vascularized And Complex Organ Buds From Diverse Tissues Via Mesenchymal Cell-Driven Condensation

status: Public on Jul 01 2015

city: Yokohama City

first: Yasuharu

last: Ueno

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

department: Graduate School of Medicine

institute: Yokohama City University

summary: Here, we demonstrate a generalized method for organ bud formation from diverse tissues by combining pluripotent stem cell-derived tissue-specific progenitors or relevant tissue samples with endothelial cells and mesenchymal stem cells (MSCs). The MSCs initiated condensation within these heterotypic cell mixtures, which was dependent upon substrate matrix stiffness. Defining optimal mechanical properties promoted formation of 3D, transplantable organ buds from tissues including kidney, pancreas, intestine, heart, lung, and brain. Transplanted pancreatic and renal buds were rapidly vascularized and self-organized into functional, tissue-specific structures. These findings provide a general platform for harnessing mechanical properties to generate vascularized, complex organ buds with broad applications for regenerative medicine.

overall_design: Gene expression profiles of development-related gene expression in kidney bud transplants and murine kidneys.

first: Takanori

last: Takebe

first: Hideki

last: Taniguchi


title: Regulation of gene expression by miR-101 in U2OS cells

status: Public on May 22 2015

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: miR-101 is a tumor suppressive microRNA. Besides EZH2, a well known EZH2 target, miR-101 should have other targets, which might also contribute to its tumor suppressive function. Thus, we performed array hybridization to determine changes in gene expression upon miR-101 overexpression in U2OS cells.

overall_design: U2OS were transfected with synthetic miRNA negative control (NC) or miR-101 for 48hrs, and then harvested for RNA preparation.  Three independent experiments were performed. One NC sample were repeated twice for the microarray.

first: Xin

last: Zhang

first: Matthias

last: Dobbelstein


title: Expression profiles of liver tissues from wild-type and AID transgenic mice exposed to thioacetamide hepatotoxicity

status: Public on Jul 10 2015

first: Tomonori

last: Matsumoto

address: 3-1 Yamadaoka

institute: Osaka University

summary: AID is an intrinsic DNA mutator enzyme and contributes to tumorigenesis through the accumulation of genetic aberrations. To examine whether mutagenesis induced by AID during inflammation-associated hepatocarcinogenesis depends on the transcriptional levels of the target genes, we performed the gene expression profiling of liver tissues from AID transgenic mice and wild-type mice with and without thioacetamide treatment.

overall_design: AID transgenic mice and wild-type mice were administered with thioacetamide in drinking water for 6 months, and the gene expression levels of their livers are compared.

first: Hiroyuki

last: Marusawa


title: Gene expression profile regulated by leptin

status: Public on Jul 06 2015

city: Buffalo

first: AC

last: CHANG

address: Elm and Carlton

institute: RPCI

summary: Global gene expression profiling compared between MCF7 cells with treatment of vehicle and leptin

overall_design: Whole human genome 4x44K array analysis was performed following the manufacturers protocol (Agilent, 3 triplicates each sample)

first: Chun-Ju

last: Chang


title: Increased resistance to proteasome inhibitors in multiple myeloma mediated by cIAP2 overexpression - implications for a combinatorial treatment

status: Public on May 18 2015

city: Uppsala

first: Prasoon

last: Agarwal

state: Sweden

address: Dag Hammarshkojlds vag 20

department: IGP

institute: Rudbeck Laboratory, Uppsala University

summary: In this study we wanted to investigate the role of cIAP2 in drug resistance, the plausible mechanisms underlying this resistance and possible strategies to overcome this by combinatorial treatment in human MM cell lines containing a TRAF3 mutation

overall_design: Gene expression profiling of the human MM cell line LP-1 under 6 different experimental perturbations: untreated  or treated with bortezomib (10nM), 2 different timepoints (6 and 24 hours) and cIAP2 overexpression or endogenous cIAP2 level.

first: Charlotte

last: Fristedt

first: Helena

last: Wiklund


title: Gene expression in metronomic cyclophosphamide-treated glioma xenografts

status: Public on May 04 2015

city: Boston

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

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

sample_organism:
Homo sapiens
Rattus norvegicus

overall_design: Refer to individual Series


title: Expression data from rice roots treated with Gln

status: Public on Jun 30 2015

city: Taipei

first: Ming-Hsiun

last: Hsieh

address: 128 Academia Road, Section 2

department: Institute of Plant and Microbial Biology

institute: Academia Sinica

summary:
We used GeneChip Rice Genome Array (Affymetrix, Santa Clara, CA, USA) to identify genes that were rapidly induced by glutamine in rice roots.
Transcriptomic analysis of rice roots revealed that the expression of at least 35 genes involved in metabolism, transport, signal transduction, and stress responses was rapidly induced by glutamine within 30 minutes.

overall_design: Total RNA from –N and Gln-treated roots (2.5 mM Gln, 30 min) was extracted using a phenol extraction protocol. RNA samples from two biological repeats were sent to the Affymetrix Gene Expression Service Lab at Academia Sinica, Taipei, Taiwan (http://ipmb.sinica.edu.tw/affy/) for target preparation, and hybridization to the GeneChip Rice Genome Array.

first: Chia-Cheng

last: Kan

first: Tsui-Yun

last: Chung


title: Identification of time-dependent biomarkers and effects of exposure to volatile organic compounds using high-throughput analysis

status: Public on May 15 2015

city: Ansan

first: jiyoung

last: hong

address: Hanyang Univ.,55, Hanyangdaehak-ro, Sangrok-Gu

institute: hanyang university

type: Methylation profiling by genome tiling array


title: ALKBH3 Knockdown in PC3 prostate cancer cells

status: Public on Jun 05 2015

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg

summary:
Background: The oxidative DNA demethylase ALKBH3 targets single-stranded DNA (ssDNA) in order to perform DNA alkylation damage repair. ALKBH3 becomes up-regulated during tumorigenesis and is necessary for proliferation. However, the underlying molecular mechanism remains to be understood.
Methods: To further elucidate the function of ALKBH3 in cancer, we performed ChIP-seq to investigate the genomic binding pattern of endogenous ALKBH3 in PC3 prostate cancer cells coupled with microarray experiments to examine the expression effects of ALKBH3 depletion.
Results: We demonstrate that ALKBH3 binds to transcription associated locations, such as places of promoter-proximal paused RNA polymerase II and enhancers. Strikingly, ALKBH3 strongly binds to the transcription initiation sites of a small number of highly active gene promoters. These promoters are characterized by high levels of transcriptional regulators, including transcription factors, the Mediator complex, cohesin, histone modifiers and active histone marks. Gene expression analysis showed that ALKBH3 does not directly influence the transcription of its target genes, but its depletion induces an up-regulation of ALKBH3 non-bound inflammatory genes.
Conclusions: The genomic binding pattern of ALKBH3 revealed a putative novel hyperactive promoter type. Further, we propose that ALKBH3 is an intrinsic DNA repair protein that suppresses transcription associated DNA damage at highly expressed genes and thereby plays a role to maintain genomic integrity in ALKBH3-overexpressing cancer cells. These results raise the possibility that ALKBH3 may be a potential target for inhibiting cancer progression.

overall_design: PC3 cells were infected with ALKBH3 shRNA or Control shRNA for 48 hours and selected with puromycine. Cells were collected after 48h or 96h past selection.

first: Indra

last: Windhof

first: Jochen

last: Gaedcke

first: Grabriela

last: Salinas-Riester

first: Feizhen

last: Wu

first: Michael

last: Ghadimi

first: Sebastian

last: Dango


title: The function of ERRalpha in viral infection

status: Public on Jun 09 2015

city: beijing

first: Xiang

last: He

address: taiping road

institute: Beijing Institute of Biotechnology

summary: To explore the function of ERRalpha in viral infection, we compared the cDNA expression profile of ERRalpha knockdown 293T cells and control 293T cells.  The cells infected with VSV for 12 h or left uninfected were collected and RNA was extracted by Trizol.

overall_design: Viral infection induced gene expression in ERRalpha knockdown 293T cells or control  293T cells were measured at 0 and 12 hours.

first: Hui

last: Zhong

first: Shengli

last: Ma

first: Congwen

last: Wei


title: Gene expression of human blood Natural Killer (NK) cells directly after isolation and after manual or automated ex vivo expansion

status: Public on Apr 23 2015

city: Bergisch Gladbach

first: Jutta

last: Kollet

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

institute: Miltenyibiotec GmbH

summary: Ex vivo activation and expansion of natural killer (NK) cells is a strategy to produce sufficient numbers of these effector cells for adoptive immunotherapy. Therefore we aimed at the development of an automated, clinical scale NK cell expansion process and compared NK cells after manual and automated expansion.We found only a small subset of 124 genes that significantly varied between both sample groups. These genes were associated with movement of leukocytes were identified including a group of genes for NK cell movement (CMKLR1, CX3CR1, S1PR5, GNLY and CXCR1) which were slightly higher expressed after automated compared to manual expansion. Nevertheless, the expansion profiles of NK cells after automated or manual expansion were rather similar in comparison to the remarkable difference between primary and expanded NK cells in general represented by the vast majority of regulated genes between the analyzed sample groups. Pathway analysis revealed that most of regulated genes upon expansion were associated with cell cycle regulation, DNA replication, DNA recombination and DNA repair, regulation of apoptosis and cell survival as well as cytokine signaling. Furthermore, the expression of many NK cell relevant markers was changed upon expansion with the strongest effects on up regulation of TRAIL and FASL, inhibitory TIGIT and chemokine receptors CCR2, CCR5 and CXCR6. In addition, granzyme M was down regulated but other important effector molecules like TNFa, perforin and granzymes  A, B and K were up regulated. In summary we could show that manual and automatically expanded NK cells show a similar expansion profile while the differ significantly from primary NK cells. Up regulation of many NK cell relevant markers indicate for an enhanced NK cell functionaility after ex vivo activation and expansion.

overall_design: 24 samples were analyzed in total. 6 biological replicates represented by cells from different donors. 4 different samples per donor: freshly isolated NK cells (d0) and NK cells expanded for 14 days under 3 different conditions: in co-culture with EBV-LCL feeder cells and 500 U/mL IL2 either cultivated manually in T75 flasks (T) or automatically using the CliniMACS Prodigy system (P); NK cells cultured with 500 U/ml IL2 without feeder cells (I)

first: Markus

last: Granzin

first: Michail

last: Knauel

first: Silvia

last: Rüberg

first: Volker

last: Huppert


title: Role of Hopx in myogenesis and commitment [HopxKO+Wnt]

status: Public on Jun 01 2015

first: Kyoung Jae

last: Won

address: 3400 Civic Center Blvd

department: Genetics

institute: University of Pennsylvania

summary:
Progenitor cells require coordinated expression of lineage-specific genes to regulate differentiation into daughter cell types. Hopx labels cardiac progenitors that are commited to the cardiac myocyte lineage. Hopx-deficiency leads to thin myocardium in approximately mid-gestation lethality in approximately 50% of embryos (secondary to thin myocardium and presumed cardiac rupture). Hopx-/- EBs display impaired myogenesis during cardiac differentiation. ChIP-seq and RNA expression analysis suggests that Hopx down regulates Wnt signaling by directly occupying and repressing wnt ligand genes.
Analysis of embryoid bodies on day 8 of cardiac differentiation. RNA was made of from  Hopx +/- embryoid bodies or  Hopx -/- embryoid bodies treated with 12.5 uM XAV939. Heterozygous embryoid bodies included 0 uM XAV939, a well-characterized, known Wnt inhibitor. Embryonic stem cell lines were derived from littermate mouse blastocysts.  Results provide insight into gene programs regulated by Hopx in cardiac development.

overall_design: Three biological replicates of Hopx-/- + 12.5 uM XAV939 vs  3 biological replicates of Hopx+/- embryoid bodies, day 8 of cardiac differentiation.

first: Jonathan

last: Epstein

first: Rajan

last: Jain

last: Schug


title: Role of Hopx in myogenesis and commitment [HopxKO]

summary:
Progenitor cells require coordinated expression of lineage-specific genes to regulate differentiation into daughter cell types. Hopx labels cardiac progenitors that are commited to the cardiac myocyte lineage. Hopx-deficiency leads to thin myocardium in approximately mid-gestation lethality in approximately 50% of embryos (secondary to thin myocardium and presumed cardiac rupture). Hopx-/- EBs display impaired myogenesis during cardiac differentiation. ChIP-seq and RNA expression analysis suggests that Hopx down regulates Wnt signaling by directly occupying and repressing wnt ligand genes.
Analysis of embryoid bodies on day 8 of cardiac differentiation. RNA was made of from 1. Hopx +/- embryoid bodies, 2. Hopx -/- embryoid bodies, Embryonic stem cell lines were derived from littermate mouse blastocysts.  Results provide insight into gene programs regulated by Hopx in cardiac development.

overall_design: Three biological replicates of Hopx-/- vs 3 biological replicates of Hopx+/- embryoid bodies, day 8 of cardiac differentiation.


title: Identification of time-dependent biomarkers and effects of exposure to volatile organic compounds using high-throughput analysis (expression)

first: jiyoung

last: hong

summary: In this study, we examined the effects of VOCs exposure in humans on gene expression using microarray analysis. We recruited participants who had short-term exposure, long-term exposure, or no exposure. We then analyzed changes in gene expression in blood samples from these participants. A total of 866 genes were upregulated, while 366 genes were downregulated in the short-term exposure group. Similarly, in the long-term exposure group, a total of 852 and 480 genes were up- or downregulated, respectively. Hierarchical clustering analysis was used to divide the clustered genes into nine clusters to investigate the expression of variations in accordance with the exposure period. Further research is required to determine the time-dependent effects of VOCs on epigenetic regulation of gene expression.

overall_design: Gene expression of mRNA in human blood samples (IRB #AS 14039) divided into three groups: control (unexposed workers; n = 12), short-term exposure (workers exposed to VOCs for less than 10 years; n = 12), and long-term exposure (workers exposed to VOCs for more than 10 years; n = 12) was experimented by microarray analysis after exposure to VOCs

first: Ji-Young

last: Hong

first: So-Yeon

last: Yu

first: Gi-Won

last: Kim

first: Jeong-Jin

last: Ahn

first: Youngjoo

first: Seri

last: Lim

first: Sang-Wook

last: Son

first: Seung-Yong

last: Hwang


title: Human ex vivo Lung Perfusion: A Pre-Clinical Model for Lung Disease

status: Public on Jun 02 2015

city: Pittsburgh

first: Luai

last: Huleihel

address: 450 technology drive

department: Regenerative medicine

institute: University of Pittsburgh

summary:
We report the first use of ex vivo lung perfusion (EVLP) in the genetic and physiologic modification of lungs from deceased pulmonary arterial hypertension (PAH) patients and propose this as a translational platform to both (1) derive clinically relevant mechanistic insights into pulmonary pathophysiology and (2) to test treatments on human lungs.
The EVLP consist in the perfusion of the lungs out of the body during 6 hours. It is a well established protocol in where basically lungs are on a table connected to a close circuit containing a special perfusion solution that is circulated through the pulmonary vein and artery using a pump. The circuit contains also a deoxygenator. The perfusion temperature and flow are adjusted gradually and after 20 mins of perfusion the ventilation is initiated. Every hour lungs are recruited in order to assess pulmonary function and collect perfusate samples. In addition to perfusate, tissue samples from the lower lobe of the left lung and bronchial alveolar lavage (BAL) are collected at times T0, 3 and 6 hr.

overall_design: Two PAH donors (females; age 49 and 46 yr; with body mass index (BMI) 33.9 3.2 kg/m2) and two normal control donors (females; age 51 and 57 yr; BMI 28.5 1.6 kg/m2) were used for analysis. Gene expression profiling was also performed on tissue biopsies at several time points (T0, 3, and 6 hr).

first: Rojas

last: Mauricio


title: Gene expression in mouse blood following low dose-rate or acute x-ray exposure

status: Public on May 14 2015

city: New York

first: Sally

last: Amundson

state: NY

department: Center for Radiological Research

institute: Columbia University

summary: Radiation biodosimetry can play a critical role in the response to a large-scale radiologic emergency, and gene expression profiles have shown promise for providing biodosimetric information. This study was designed to test if gene expression could be used to distinguish between doses received from acute exposures and more protracted exposures, such as those that would result from fallout. Mice were exposed to whole body X-rays at low dose rate (LDR, 3.09 mGy/min) for 6, 12, or 24 hours (1.1, 2.2, or 4.4 Gy), or to equivalent doses delivered at high dose rate (HDR, 1.03 Gy/min). Global gene expression was measured in their blood 24 h after the start of exposure, and genes with the potential to classify samples by radiation dose and dose rate were identified.

overall_design: Data consist of 48 samples, representing 6 independent samples each from 3 doses delivered as either acute or low dose rate x-rays, plus 12 controls representing both acute and low dose rate sham treatments.

first: Sunirmal

last: Paul