title: Identification of drug- resistance mutations in majority and minority subpopulations of HIV-1 quasispecies

status: Public on Nov 30 2016

city: Torrejón de Ardoz

first: Carlos

last: Briones

state: Madrid

address: Ctra de Torrejón a Ajalvir, km 4

department: Department of Molecular Evolution

institute: Centro de Astrobiología (CAB, CSIC-INTA)

summary: The response of human immunodeficiency virus type 1 (HIV-1) quasispecies to antiretroviral therapy is influenced by the ensemble of mutants that composes the evolving population. Low-abundance subpopulations within HIV-1 quasispecies may determine the viral response to the administered drug combinations. However, routine sequencing assays available to clinical laboratories do not recognize HIV-1 minority variants representing less than 25% of the population. Although several alternative and more sensitive genotyping techniques have been developed, including next-generation sequencing (NGS) methods, they are usually very time consuming, expensive and require highly trained personnel, thus becoming unrealistic approaches in daily clinical practice. Here we describe the development and testing of a HIV-1 genotyping DNA microarray that detects and quantifies, in majority and minority viral subpopulations, relevant mutations and amino acid insertions in 42 codons of the pol gene associated with resistance and multidrug resistance to protease (PR) and reverse transcriptase (RT) inhibitors. A customized bioinformatics protocol has been implemented to analyze the microarray hybridization data by including a new normalization procedure and a stepwise filtering algorithm which resulted in the highly accurate (96.33%) detection of positive/negative signals. This microarray has been tested with 57 subtype B HIV-1 clinical samples extracted from multi-treated patients, showing an overall identification of 95.53% and 89.24% of the queried PR and RT codons, respectively, and enough sensitivity to detect minority subpopulations representing as low as 5-10% of the total quasispecies. Such a genotyping platform represents an efficient diagnostic and prognostic tool useful to personalize antiviral treatments in clinical practice.

overall_design:
We describe a novel genotyping DNA microarray platform that contains a panel of 160 optimized oligonucleotide probes complementary to HIV PR and RT genomic regions involved in resistance to NRTIs, NNRTIs and PIs. This platform has been developed using 17 clonal HIV-1 samples and selected mixtures of them at different ratios, and further tested with 57 HIV-1 clinical samples extracted from multi-treated infected patients.

Please note that
[1] The array has two blocks that can be independently hybridized and thus, several raw data files were duplicated with the file name correponding to each sample (indicated in the sample description field). For example, 6.95c8-PRRT-2.1 normalized data is derived from Block/Array Column: 1 (in 6.95c8-PRRT-2.1.csv) and 6.95c8-PRRT-2.2 from Block/Array Column: 2 (in the same raw file but renamed as 6.95c8-PRRT-2.2.csv). In the normalized matrix, non corresponding block is filled with the 'null' label.
[2] The Sequences reported in the sample 'Characteristics:Sequence(s)' column are the PR, RT or PR-RT regions from the considered wild type proteins or the mutated counterparts, cloned into plasmids, used to characterize the hybridization signal of the probes, or the consensus sequences extracted from the patients.
[3] Some of the arrays have been analyzed with the ScanArray software, and the rest with the GenePix software (as indicated in the 'characteristics: Scanner' column).
[4] Probes positions in GenePix raw files are identified by labels 'Block','Row' and 'Column', while the equivalent labels in ScanArray raw files are 'Array Column','Spot Row' and 'Spot Column'.
[5] The number of rows in each raw data file depends on 3 factors, the scanner used (GenePix or ScanArray), the included regions (PR,RT or PRRT) and if it includes 1 or 2 blocks. For example,
pWT_pINS-RT-0-1.csv = GenePix file including PR-RT regions and 2 blocks (800 rows)
pWT-RT-7.2.csv = ScanArray file with only the RT region and 1 block (325 rows)
A47-PR-1.csv = ScanArray file with only the PR region and 1 block (157 rows)
5.96c9-PRRT-1.1.csv = ScanArray file with the PR-RT regions and 1 block (421 rows)
5.96c9-PRRT-1.2.csv = ScanArray file with the PR-RT regions and 2 blocks (781 rows)

first: Veronica

last: Martin

first: Celia

last: Perales

first: Maria

last: Fernandez-Algar

first: Helena

last: Dos Santos

first: Patricia

last: Garrido

first: María

last: Pernas

first: Victor

last: Parro

first: Miguel

last: Moreno

first: Javier

last: Garcia-Perez

first: Jose

last: Alcami

middle: L

last: Toran

first: David

last: Abia

first: Esteban

last: Domingo


title: Transcriptome profiling of madin-darby canine kidney cells with canine parvovirus 2a persistent infection

status: Public on Dec 01 2016

city: Lanzhou

first: Y

last: Gao

address: Xujiaping 1

country: China

institute: LVRI

summary: It has been demonstrated that parvovirus infection causing cytotoxicity and immune activation effect in many virus-induced cell lines, however, the underlying mechanisms are not fully understood. To investigate the gene expression signature of host cell after CPV-2 infection, we performed transcriptome profiling of MDCK after persistent infection of CPV-2a  using microarray analysis. Uninfected MDCK cells act as negative control. The data show the genes regulated by CPV-2 infection..

overall_design: The monolayer MDCK cells were digested with trypsin and plated into new cell culture flasks, supplement with 1/10 (v/v) CPV-2 virus solution (MOI=1) in DMEM containing 5% FBS. The infected MDCK cells were cultured at 37°C with 5% CO2, and passage for ten generation. MDCK F10 cells infected with CPV-2a and mock-treatment were harvest for microarray analysis.

first: Long

last: Shu

first: Shiqi

last: Sun

first: Huichen

last: Guo


title: Real-time quantitative PCR analysis of human T cells

city: Brasilia

first: Isabel

middle: Garcia

last: Sousa

state: Distrito Federal

address: Campus Universitario Darcy Ribeiro

department: Cell Biology

country: Brazil

institute: Univerty of Brasilia

summary: Human peripheral blood mononuclear cells were purified from healthy volunteers' blood and were cultured in the presence of the monoclonal antibody OKT3 or a recombinant fragment of humanized anti-CD3. After 72 hours, CD3+ T cells were isolated by negative selection using beads.

overall_design: qPCR miRNA expression profiling.  T cell from five donors were used and treated separately as indicated in the summary. Equal amount total RNA from each donor was used to miRNA expression analysis.


title: Differential regulation of telomere associated transcriptome homeostasis by Translin and Trax is linked to Argonaute-mediated chromosome stability control

city: Bangor

first: Ramsay

last: Mcfarlane

state: Gwynedd

address: Brambell Building, Deiniol Road

department: North West Cancer Research Institute

country: United Kingdom

institute: Bangor University

summary: RNA interference is required to form the centromeric heterochromatin needed for chromosome segregation fidelity. Central to this is Argonaute protein, which processes small interfering RNAs (siRNAs) within a self-enforcing feedback mechanism that utilizes the guidance of siRNAs to nucleate heterochromatin-mediators. siRNA processing by Argonaute-containing complexes is enhanced by Translin and Trax proteins. Current dogma purports that impairment of Argonaute drives centromeric heterochromatin dysregulation and chromosome instability. We used the fission yeast to demonstrate that loss of Trax can suppress the chromosomal instability conferred by loss of Argonaute in a Translin-dependent fashion, without restoring centromeric heterochromatin. Extended analysis of Trax and Translin defective cells revealed a conserved role for Trax and Translin in telomeric transcription. This not only identified a novel telomere regulatory activity, but also demonstrates that under conditions of centromeric dysfunction telomeric transcriptional stasis can negatively impact chromosome segregation.

overall_design: In total 24 samples: 8 strains in triplicates; S. pombe wildtype strain (wt_1, wt_2, wt_3), S. pombe Δago1 (ago1_1, ago1_2, ago1_3), S. pombe Δtfx (trax_1, trax_2, trax_3),  S. pombe ΔtfxΔago1 (traxago1_1, traxago1_2, traxago1_3), S. pombe ΔtfxΔtsn1 (traxtsn1_1, traxtsn1_2, traxtsn1_3), S. pombe Δtsn1 (tsn1_1, tsn1_2, tsn1_3), S. pombe ΔtsnΔago1 (tsn1ago1_1, tsn1ago1_2, tsn1ago1_3), S. pombe ΔtfxΔtsn1Δago1 (traxtsn1ago1_1, traxtsn1ago1_2, traxtsn1ago1_3)

last: McFarlane

first: Julia

last: Feichtinger

first: Stephane

last: Thiry


title: Gene expression profiling of differentially treated hematopoietic stem cells (LSK SLAM)

status: Public on Oct 21 2016

city: Frankfurt

first: Darja

last: Karpova

address: Sandhofstrasse 1

department: Cell Therapeutics

country: Germany

institute: German Red Cross Blood Donor Service

summary: Expression prolile of POL5551 treated (continuos infusion, 2 wks, 100 mg/kg/day) HSC was compared to that of G-CSF (100 ug/kg/injection, q12h, 2 vs. 5 days) and sham-op treated cells in order to identify potential inherent differences between the specimen. The cells were isolated from the BM of differentially treated mice.

overall_design: Mice were treated with G-CSF (2 days and 5 days), POL5551 (2 wks) or sham-op. BM was isolated and enriched for kit (CD117)+ progenitors and LSK SLAM cells (HSC) were then flow sorted from the positive cell fraction.

first: Darlene

last: Monlish


title: CAZyChip: Dynamic assessment of exploration of glycoside hydrolases in microbial diversity ecosystems.

city: Toulouse

first: Anne

last: Abot

address: 135 route de Narbone

department: LISBP

country: France

institute: INSA/INRA/CNRS

summary: Microorganisms constitute a reservoir of enzymes involved in environmental carbon cycling and degradation of plant polysaccharides since they produce a vast variety of glycoside hydrolases. The CAZyChip was developed to allow a rapid characterization at transcriptomic level of these GHs and to identify enzymes acting on hydrolysis of polysaccharide or glycans. This DNA biochip contains the signature of 55,220 bacterial GHs available in the CAZy database. Probes were designed using two softwares and microarrays were directly synthetized using the in situ ink-jet technology. CAZyChip specificity and reproducibility was validated by hybridization of known GHs RNA extracted from recombinant E. coli strains, previously characterized by a functional metagenomic approach. The GHs arsenal was also studied in bioprocess conditions using rumen derived microbiota. The CAZyChip appears to be a user friendly tool for profiling the expression of a large variety of GHs. It can be used to study temporal variations of functional diversity, thereby facilitating the identification of new efficient candidates for enzymatic conversions from various ecosystems.

overall_design: 26 plasmidic GH were tested once time, 23 fosmids were tested in triplicate

first: Gregory

last: Arnal

first: Lucas

last: Auer

first: Adèle

last: Lazuka

first: Delphine

last: Labourdette

first: Sophie

last: Lamarre

first: Lidwine

last: Trouilh

first: Elisabeth

last: Laville

first: Vincent

last: Lombard

first: Gabrielle

last: Potocki-Veronese

first: Bernard

last: Henrissat

first: Michael

last: O’Donohue

first: Guillermina

last: Hernandez-Raquet

first: Claire

last: Dumon

first: Véronique

middle: A

last: Leberre


title: Chemical induction of liver progenitor cells from mature hepatocytes

status: Public on Nov 15 2016

city: Philadelphia

first: Takeshi

last: Katsuda

state: PA

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

country: USA

institute: University of Pennsylvania

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

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Ethephon- and AVG-induced transcriptional changes at the onset of sugarcane ripening

status: Public on Oct 31 2016

city: Campinas

first: Camila

middle: Pinto da

last: Cunha

state: Sao Paulo

address: Rua Monteiro Lobato, 255, bloco H

institute: UNICAMP

summary: Transcriptional profiling of sugarcane leaf+1 and upper internode harvested at one and five days after chemical (ethephon and AVG) application (DAA) compared to control (mock) samples. Co-hybridization of chemical-treated samples with control samples as reference (one or five DAA chemical treated-samples against one DAA control sample; and five DAA chemical treated-sample against five DAA control sample) was performed to monitor gene expression changes in a two-color Agilent custom microarray, using a dye-swap design. Our goal was to determine the effect of ethylene on global gene expression of sugarcane plants at the maturation stage.

overall_design: Twelve-condition experiment: control at one DAA (CTL1) vs. ethephon at one DAA (ET1), control at one DAA (CTL1) vs. AVG at one DAA (AVG1), control at one DAA (CTL1) vs. ethephon at five DAA (ET5), control at one DAA (CTL1) vs. AVG at five DAA (AVG5), control at five DAA (CTL5) vs. ethephon at five DAA (ET5), control at five DAA (CTL5) vs. AVG at five DAA (AVG5). Upper internode samples are identified by “c”. Technical replicates: 2 replicates.

middle: P

first: Carolina

middle: G

last: Lembke

first: Glaucia

middle: M

last: Souza

first: Marcelo

last: Menossi


title: Transcriptome analysis of genome-reduced Bacillus subtilis strains

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

institute: University Medicine Greifswald

summary: In this study two genome-reduced Bacillus subtilis strains lacking about 36% of dispensable genetic information were constructed using a markerless and scarless deletion method. In order to analyze the consequences of the deletions for the bacteria, a multi-omics characterization of the reference strain Δ6 (Westers et al., 2003; PMID 12949151) and the two deletion strains was carried out. Bacteria were cultivated in complex medium supplemented with glucose, and samples of the same cultures were subjected to metabolome, proteome, and transcriptome analyses.These revealed a massive re-organization of metabolism as well as substantial changes in the transcriptome and the proteome.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design:
Global gene expression changes between the reference strain Δ6 and the deletion strains PG10 and PS38, grown to mid-exponential phase in LB medium supplemented with glucose, were examined using whole-genome tiling arrays.
Hybridizations were performed in quadruplicate using RNA isolated from independent cultures.

first: Daniel

last: Reuss

first: Hermann

last: Rath

first: Pierre

last: Nicolas

first: Josef

last: Altenbuchner

first: Uwe

last: Völker

first: Jörg

last: Stülke


title: Analysis of the role for TgAP2IV-3 in regulating gene expression in Toxoplasma development

status: Public on Nov 03 2016

city: Tampa

first: Dong-Pyo

last: Hong

state: Florida

address: 3720 Spectrum Blvd, Suite304

institute: University of south florida

summary:
Analysis of TgAP2IV-3 overexpression (pH7.0, pH7.8) and knockout parasites(ph8.2) in the developmental CTG (Type III) genetic background, in vitro, 32-48hrs
The role for TgAP2IV-3 was evaluated  in the overexpression system of ddFKBP(DD) fusion protein with a-tubulin promotor controlled by Shield 1 (100nM)

overall_design: 12 total samples.  Each condition presented as 2 biological replicates

first: Joshua

middle: B

last: Radke

middle: W

last: White


title: transcriptomic analysis of the effects of low levels of atrazine and by-products-Molecular analysis of signal transduction mechanisms involved in plant – organic pollutant interactions.

status: Public on Nov 01 2016

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: au15-04_xeno - transcriptomic analysis of the effects of low levels of atrazine and by-products - Identification of xenobiotic direct sensing and of low chemical stress transduction networks in Arabidopsis thaliana. - Seeds of Arabidopsis thaliana (Columbia ecotype, Col-0) were surfaced-sterilized in bayrochlore/ethanol (1/1, v/v), rinsed in absolute ethanol and dried overnight. Germination and growth were carried out under axenic conditions in square Petri dishes. After seeds were sowed, Petri dishes were placed in the dark at 4 °C for 72 h in order to break dormancy and homogenize germination, and were then transferred to a control growth chamber at 22 °C/20 °C under a 16 h light (6000 lux)/8 h dark regime. Growth medium consisted of 0.8% (w/v) agar in Hoagland basal salt mix (H2395, Sigma-Aldrich) adjusted to pH 6. After 13 days of growth under optimal conditions, seedlings were transferred to fresh growth medium containing pesticides during 24 h (Control, Atrazine 1µM, Hydroxyatrazine 1µM or Desethylatrazine 1µM). Then control and treated seedlings were harvested and ground in liquid nitrogen until RNA extraction by RNeasy kit (Qiagen) and DNase digestion. RNA was extracted on at least 2 independent biological replicates of 30 pooled plantlets.

overall_design: 6 dye-swap - treated vs untreated comparison

first: Gwenola

last: Gouesbet-Jan

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Conversion of terminally committed mouse hepatocytes to culturable bipotent progenitor cells

first: Takeshi

last: Katsuda

summary:
A challenge for advancing approaches to liver regeneration is loss of functional differentiation capacity when hepatocyte progenitors are maintained in culture. Recent lineage-tracing studies have shown that mature hepatocytes (MHs) convert to an immature state during chronic liver injury, and we investigated whether this conversion could be recapitulated in vitro and if such converted cells could represent a source of expandable hepatocytes. We report that a cocktail of small molecules, Y-27632, A-83-01 and CHIR99021, can convert rat and mouse MHs in vitro into proliferative bipotent cells, which we term chemically induced liver progenitors (CLiPs). CLiPs can differentiate into both MHs and biliary epithelial cells that can form functional ductal structures. CLiPs in long-term culture did not lose their proliferative capacity or their hepatic differentiation ability, and rat CLiPs were shown to extensively repopulate chronically injured liver tissue. Thus our study advances the goals of liver regenerative medicine.
Transcriptomic analysis for mouse CLiPs at P1 which underwent hepatic induction (Matrix 1). Transcriptomic analysis for mouse CLiPs at P11-12 which underwent hepatic induction (Matrix 2).

overall_design: Hepatic induction was performed for P1 mouse CLiPs or CLiPs that underwent 11-12 passages.

first: Takahiro

last: Ochiya


title: Role of annexin A2 in muscle repair

status: Public on Oct 04 2016

city: Washington D. C.

first: Jyoti

middle: K.

last: Jaiswal

address: 111 Michigan Av NW

department: Center for Genetic Medicine Research

institute: Children’s National Health System

summary: Repair of injured muscle involves repair of injured myofibers through the involvement of dysferlin and its interacting partners, including annexin. Studies with mice and patients have established that dysferlin deficit leads to chronic inflammation and adipogenic replacement of the diseased muscle. However, longitudinal analysis of annexin deficit on muscle pathology and function is lacking. Here we show that unlike annexin A1, but similar to dysferlin, lack of annexin A2 (AnxA2) causes poor myofiber repair and progressive weakening with age. However, unlike dysferlin-deficient muscle, AnxA2-deficient muscles do not exhibit chronic inflammation or adipogenic replacement. Deletion of AnxA2 in dysferlin deficient mice reduces inflammation, adipogenic replacement, and loss in muscle function caused by dysferlin deficit. These results show that: a) AnxA2 facilitates myofiber repair, b) chronic inflammation and adipogenic replacement of dysferlinopathic muscle requires AnxA2, and c) inhibiting AnxA2-mediated inflammation is a novel therapeutic avenue for dysferlinopathy.

overall_design: For this study total RNA was extracted from the gastrocnemius muscle of 24 weeks old mouse samples (Wild type n=4 and Anxa2 knockout n=4).

first: Aurelia

last: Defour

first: Sushma

last: Medikayala

first: Jack

middle: H

last: Van der Meulen

first: Marshall

last: Hogarth

first: Nicholas

last: Holdreith

first: Apostolos

last: Malatras

first: William

last: Duddy

first: Jessica

last: Boehler

first: Kanneboyina

last: Nagaraju

middle: K


title: Genome-wide analysis of gene expression regulated by VRK1 kinase in cancer cell lines [Illumina]

status: Public on Oct 07 2016

city: Nagasaki

first: TAKEYA

last: NAKAGAWA

address: 1-12-4 sakamoto

department: Biochemistry

country: Japan

institute: Nagasaki unversity

summary: Histone H2A T120 phosphorylation promotes oncogenic transformation via upregulation of cyclin D1

overall_design: Total RNA obtained from cancer cell lines treated with siRNA for VRK1knockdown

first: Ito

last: Takashi

first: Cheung

last: Edwin

first: Mizusaki

last: Hirofumi

first: Aihara

last: Hitoshi


title: The role of Hoxa9 and Meis1 in development of acute myeloid leukemia (mRNA)

status: Public on Sep 01 2016

city: Gothenburg

first: Lars

last: Palmqvist

address: Sahlgrenska University Hospital

department: Institute of Biomedicine

country: Sweden

institute: University of Gothenburg

summary: OBJECTIVE: MEIS1, a HOX cofactor, collaborates with multiple HOX proteins, such as HOXA9, to accelerate the onset of acute myeloid leukemia (AML) through largely unknown molecular mechanisms. To further resolve these mechanisms, we conducted a structure-function analysis of Meis1 and gene expression profiling, in the context of Hoxa9 leukemogenesis. RESULTS: We show, in a murine bone marrow transplantation model, that the homeodomain of Meis1 is required for leukemogenic collaboration with Hoxa9. Gene expression profiling of a Hoxa9 preleukemic cell line transduced with wild-type or Meis1 homeodomain mutant reveal deregulation of multiple genes including a set not previously implicated as Meis1 targets.

overall_design: Murine bone marrow cells transduced with Hoxa9-GFP + empty MIY vector were compared to Hoxa9+Meis1 cells or Hoxa9+Meis1 with deleted homeodomain (DHD) cells and cultured for three or four weeks before harvest for miRNA expression array. Four independent experiments were performed for each of the three different conditions included in the study. Cells from all samples were also transplanted into lethally irradiated mice to test for their transforming and leukemic potential.


title: SOX7-enforced expression promotes the expansion of adult blood progenitors and blocks B cell development

status: Public on Aug 09 2016

city: Manchester

first: Valerie

last: Kouskoff

address: Wilmslow Road

institute: Cancer Research UK Manchester Institute

summary: Here we use a microarray approach to define at the molecular level the consequences of SOX7-mediated effect on B lymphopoiesis and progenitor proliferation. Transcriptome profiling analysis was performed on two subpopulations expressing low and high level of SOX7::GFP.

overall_design: Bone marrow cells extracted from iSox7 transgenic mice were treated with and without dox in duplicate

first: Sara

last: Cuvertino


title: Human polar body transfer eliminates the transmission of inherited mitochondrial DNA variants [mRNA]

status: Public on Sep 11 2016

city: Shanghai

first: Hongying

last: Sha

state: Shanghai

address: 220 Handan Rd, WuJiaoChang, Yangpu Qu

institute: Fudan University

summary: Although polar body transfer (PBT) has the potential to prevent the transmission of inherited mitochondrial DNA (mtDNA) diseases, the PBT technique is still at an early stage, as no human data are publicly available for PBT. Here, we investigated the comparative values of first and second PBT (PB1T, PB2T), spindle-chromosome and pronuclear transfer (ST, PNT), modified ST and PNT (mST and mPNT) to explore the efficiency and safety of these approaches. A comparative analysis confirmed that PB1T, mST, PB2T and mPNT could be used to donate mtDNA without resulting in significant heteroplasmy or alterations in the methylation profile and gene expression. Importantly, PB1T produced reconstructed embryos and embryonic stem cells (ESCs) in every generation with undetectable donor mtDNA. However, donor mtDNA seems to have a tendency to be amplified in generations of mPNT-ESCs with up to 3% heteroplasmy. These results suggest that PB1T holds great potential in eliminating mtDNA variants.

overall_design:
Nine samples, one negative control and one positive control were analyzed, each sample replicate three times.
Negative = human embryonic fibroblasts, and positive = IVF embryonic stem cells.


title: Diagnosis of childhood bacterial and viral infection using host RNA expression - Meningococcal validation cohort

status: Public on Aug 29 2016

city: London

first: Michael

last: Levin

address: South Kensington Campus

department: Paediatrics

institute: Imperial College London

summary: Genome-wide analysis of transcriptional profiles in children <17 years of age with bacterial or viral infections or with clinical features suggestive of infection.

overall_design: Patients were recruited at or after presentation to hospital. Blood was collected into PAX gene tubes (PreAnalytiX). Total RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Labeled cRNA was hybridized to Illumina Human Ref8 Beadchips. Numbers of arrays analysed were as follows: Meningococal disease (n=24), Healthy adult controls (n=21)


title: Identification of rare copy number polymorphic gains at 3q12.2 and 19q13.2 identifies candidate genes for familial endometriosis

status: Public on Aug 17 2016

city: Ribeirão Preto

first: Flavia

middle: Gaona de Oliveira

last: Gennaro

state: São Paulo

address: Av Bandeirantes, 3900, Depto. Genética, Bloco C

department: Genetics

institute: USP

summary: The association between endometriosis, genomic copy number variant polymorphisms and differential gene expression is still unclear. The rationale of this study was to identify regions of copy number change in familial endometriosis, which could contain genes that may be involved with the susceptibility and progression of this disease.

overall_design: The Agilent Human Genome CGH microarray 400K (Agilent Technologies, Inc) were used for array-CGH experiments.  1μg of Human Genomic DNA from multiple anonymous female donors (Promega Corporation) and  1μg of test genomic endometrium DNA sample were used, according to the Agilent Array Protocol. The references were labelled with Cy3-dUTP and endometrium DNA samples were labelled with Cy5-dUTP. Arrays were scanned using an Agilent microarray scanner (Agilent Technologies, Inc), and processed using Agilent’s Feature Extraction software.

first: Julio

middle: C

last: Silva

first: Alexandra

last: Gomes

first: Juliana

last: Meola

middle: D

last: Grzesiuk

first: Thiago

last: Vidotto

first: Rodrigo

last: Panepucci

first: Lucia

last: Martelli


title: Gene expression of extranodal NK/T cell lymphoma I

status: Public on Jul 26 2016

city: Singapore

first: Siok-Bian

last: Ng

address: National University Hospital, 5 Lower Kent Ridge Road, Main Building, level 3

department: Department of Pathology

country: Singapore

institute: National University Health System, Singapore

summary: Gene expression profiling of extranodal nasal-type NK/T cell lymphoma and other EBV-associated lymphoid proliferation disease patients was analyzed to elucidate association between JAK-STAT pathway and canonical or non-canonical PRC2/EZH2 target pathways using Illumina HumanRef-8 v3 chips.

overall_design: 6 samples in total in this data set. 3 from NKTL cell line, 3 from NKTL patient.  The non-normalized data were used for analysis. No normalization was performed.

first: Tae-Hoon

last: Chung


title: Gene expression of extranodal NK/T cell lymphoma II

overall_design: In total, 47  samples were assayed in this data set. The non-normalized data were used for analysis. No normalization was performed.


title: Gene expression of extranodal NK/T cell lymphoma


title: bigun transcriptomics-Functional characterization of BIGUN proteins in Arabidopsis thaliana

first: Stéphanie

last: Pateyron

summary: au14-03_bigun - bigun transcriptomics - What are the gene networks associated with BIGUN function during Hyaloperonospora arabidopsidis infection? - 5 weeks after germination of 12 seedlings of Arabidopsis thaliana Col-0,bigun 1 mutant and bigun 2 mutant genotypes(growth condition n°1),6 plants are infected by spraying a solution of Hyaloperonospora arabidopsidis spores,and 6 plants are left untreated,and all plants were cultivated under growth condition n°2.For each condition,leaves were sampled and pooled one week after infection.The experiment was repeated three times.

overall_design: 12 dye-swap - gene knock out,normal vs disease comparison

first: Pedro-Humberto

last: Castro

first: Jérome

last: Crouzet

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Gene expression analysis of pulmonary artery in a rabbit model of pulmonary thromboembolism

status: Public on Jul 23 2016

city: Nantong

first: Songshi

last: Ni

state: Jiangsu

address: No.20 Xisi Road Chongchuan District

department: Department of Respiratory Medicine

institute: Affiliated Hospital of Nantong University

summary: Acute pulmonary thromboembolism (PTE) refers to the obstruction of the pulmonary artery or its branches by thrombus.  Recent studies suggest that PTE-induced endothelium injury is the major physiological consequence of PTE, and PTE-induced endothelium injury can be used to stratify disease severity.  Several plasma biomarkers have been identified in PTE patients, but genome-wide gene expression has not been attempted in PTE.  In this study, using rabbit autologous thrombus PTE model, we applied gene expression array to identify genes and proteins changes in pulmonary arteries under PTE.

overall_design: Twenty healthy China big-ear rabbits, specific-pathogen-free (SPF) grade and weighing between 2.5 and 3 kg, were purchased from the Center of experimental animals of the Nantong University.  These rabbits were randomly divided into control (n=10) and experimental group (n=10).  One hour before the experiment, thrombi were generated by collecting 0.5 ml blood from the marginal ear vein and placing into a sterile petri dish for 45 minutes at room temperature.  The autologous blood clot was subsequently cut into 5 mm sized aliquots and suspended in sterile saline.  After anesthesia, a venous catheter was placed in the exposed and isolated femoral vein.  In the experimental group, the blood clot in 10 mL of saline was injected into the femoral vein. An additional 5 mL of saline were used to flush the catheter. In the control group, 15 mL of saline were injected into the femoral vein.  Afterwards, the animals were placed back in the cage.

first: Zhiyuan

last: Tang


title: CRISPR/Cas9-mediated genome editing in wild-derived mice; Generation of tamed wild-derived strains by mutation of the a (nonagouti) gene

status: Public on Jul 27 2016

city: Tsukuba

first: Shogo

last: Matoba

state: Ibaraki

address: 3-1-1, Koyadai

institute: RIKEN BioResource Research Center

summary: Wild-derived mice have contributed to mouse genetics by their genetic diversity that may increase the chance of identifying novel modifier genes responsible for specific phenotypes and diseases. However, gene-targeting using wild-derived mice has been unsuccessful due to the unavailability of stable embryonic stem cells. Here, we report that the CRISPR/Cas9-mediated gene-targeting can be applied to the Japanese wild-derived MSM/Ms strain. We targeted the nonagouti (a) gene encoding the agouti protein localized in hairs and the brain. We obtained three homozygous knockout mice as founders, all showing black coat color. While homozygous knockout offspring were physiologically indistinguishable from wild-type littermates, they showed specific domesticated behaviors; a high locomotion during the light period and a decline in the avoidance of a human hand. These phenotypes were consistent over the subsequent generations. Our findings support the empirical hypothesis that nonagouti is a domestication gene, which might repress aggressive behavior.

overall_design: Global gene expression patterns in the midbrain of wildtype and nonagouti (a) homogygous mutant MSM/Ms mice were analyzed by one-color Mouse Gene Expression 8x60K microarray. The midbrain tissues were manually isolated from 8-9 weeks old mice under dissecting microscope. Total RNA was purified from dissected midbrain using Trizol (Thermo Fisher Scientific). Purified total RNA was amplified and labeled with Cy3 using Low-Input QuickAmp Labeling Kit (Agilent Technologies). Cy3-labeled RNAs were hybridized to SurePrint G3 Mouse Gene Expression v2 8x60K Microarray Kit (Agilent Technologies) at 65 °C for 17h. After wash, the hybridized slides were scanned with DNA microarray scanner (Agilent Technologies). The scanned images were processed with Feature Extraction software (Agilent Technologies) to extract signal intensities of each probe. The extracted signal data were imported into the Gene Spring GX 13.1.1 software (Agilent Technologies) and normalized using the default settings. Two and six biological replicates were performed in wildtype and mutant group, respectively.

first: Michiko

last: Hirose

first: Ayumi

last: Hasegawa

first: Keiji

last: Mochida

first: Yuki

last: Hatanaka

first: Kimiko

last: Inoue

first: Tatsuhiko

last: Goto

first: Hideki

last: Kaneda

first: Ikuko

last: Yamada

first: Tamio

last: Furuse

first: Kuniya

last: Abe

first: Yoshihisa

last: Uenoyama

first: Hiroko

last: Tsukamura

first: Shigeharu

last: Wakana

first: Arata

last: Honda

first: Atsuo

last: Ogura


title: Differential role of HNF4α isoforms in colitis and colitis-associated colon cancer

status: Public on May 23 2016

city: Riverside

first: Eugene

last: Bolotin

state: CA

address: 900 university ave

department: Cell Biology and Neuroscience

institute: UC Riverside

summary:
Hepatocyte nuclear factor 4alpha (HNF4α) is a nuclear receptor with an emerging role in the gut. While HNF4α has been implicated in colitis and colon cancer in humans, deciphering its functional role is complicated by the existence of two promoters (P1 and P2) in theHNF4A gene that drive the expression of multiple isoforms in the adult intestine. In this study we investigate the roles of P1- and P2-driven HNF4α under conditions of homeostasis, colitis and colitis-associated colon cancer (CAC).
P1- and P2-HNF4α are differentially expressed in the differentiated and proliferative compartments of the normal colonic crypt, respectively. Expression profiling of untreated exon swap mice suggests distinct functions of the isoforms that were corroborated in migration and ion transport assays.

overall_design: To investigate the function of the HNF4α isoforms in the colon we utilized HNF4α isoform-specific mice developed previously by an exon swap strategy (PMID: 16498401). WT mice express P1-HNF4α predominantly at the top of the crypt in the differentiated compartment and P2-HNF4α in the bottom, proliferative compartment. The exon swap mice express only P1-HNF4α (α1 HMZ) or P2-HNF4α (α7 HMZ) throughout the colonic crypt. To identify functional differences between the isoforms we performed microarray analysis on RNA isolated from the distal colon of untreated young adult males and found a significant change in a substantial number of genes in the isoform-specific mice compared to their respective WT controls

first: Karthikeyani

last: Chellappa

first: Frances

last: Sladek


title: Malnutrition-associated hepatic steatosis and ATP depletion is caused by peroxisomal and mitochondrial dysfunction and rescued by fenofibrate

status: Public on Jun 18 2016

city: Groningen

first: vincent

last: bloks

department: Pediatrics

country: Netherlands

institute: UMCG

summary:
Severe malnutrition in young children is associated with signs of hepatic dysfunction such as steatosis and hypoalbuminemia, but its etiology is unknown. To investigate the underlying mechanisms of hepatic dysfunction we used a rat model of malnutrition by placing weanling rats on a low protein or control diet (5% or 20% of calories from protein, respectively) for four weeks. Low protein diet-fed rats developed hypoalbuminemia and severe hepatic steatosis, consistent with the human phenotype. Hepatic peroxisome content was decreased and metabolomic analysis indicated impaired peroxisomal function. Loss of peroxisomes was followed by accumulation of dysfunctional mitochondria and decreased hepatic ATP levels. Fenofibrate supplementation restored hepatic peroxisome abundance and increased mitochondrial fatty acid β-oxidation capacity, resulting in reduced steatosis and normalization of ATP and plasma albumin levels. These findings provide important insight into the metabolic
disturbances associated with malnutrition and have potentially profound clinical consequences with respect to the management of malnourished children worldwide.

overall_design: 24 rats in 4 groups of 6 animals per group where placed on a normal  20%  or low protein 5% diet for a period of 4 weeks

first: Tim

last: van Zutphen

first: Jolita

last: Ciapaite

first: Roberta

last: Allgayer de Moraes

first: Dirk

middle: J

last: Reijngoud

first: Angelika

last: Jurdzinski

first: Cameron

last: Ackereley

first: Justina

last: Wolters

first: Ronald

last: Wanders

first: Sander

last: Houten

first: Vincent

last: Bloks

first: Dana

last: Bronte-Tinkew

first: Albert

last: Groen

first: Johan

last: Jonker

first: Barbara

last: Bakker

first: Peter

last: Kim

first: Robert

last: Bandsma

first: Ling

last: Zhang

last: Gerding

first: Tatiana

last: Shatseva

first: Gary

middle: F

last: Lewis

first: Rainer

last: Bischoff


title: Trancriptional profiling of rat liver after short-term (up tp 14 days) administration of carcinogenic and non-carcinogenic chemicals

status: Public on Apr 27 2016

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

summary: The carcinogenic potential of chemicals is currently evaluated with rodent life-time bioassays, which are time consuming, and expensive with respect to cost, number of animals and amount of compound required. Since the results of these 2-year bioassays are not known until quite late during development of new chemical entities, and since the short-term test battery to test for genotoxicity, a characteristic of genotoxic carcinogens, is hampered by low specificity, the identification of early biomarkers for carcinogenicity would be a big step forward. Using gene expression profiles from the livers of rats treated up to 14 days with genotoxic and non-genotoxic carcinogens we previously identified characteristic gene expression profiles for these two groups of carcinogens. We have now added expression profiles from further hepatocarcinogens and from non-carcinogens the latter serving as control profiles. We used these profiles to extract biomarkers discriminating genotoxic from non-genotoxic carcinogens and to calculate classifiers based on the support vector machine (SVM) algorithm. These classifiers then predicted a set of independent validation compound profiles with up to 88% accuracy, depending on the marker gene set. We would like to present this study as proof of the concept that a classification of carcinogens based on short-term studies may be feasible.

overall_design: Male Wistar rats were treated by oral gavage with the nongenotoxic hepatocarcinogens, genotoxic carcinogens and non-hepatocarcinogens. Depending on the administered compound, rats were treated daily for 1, 3, 7, or 14 days and livers were taken 1 day each after the last treatment for histopathological evaluation. From the five animals per treatment group three animals were selected based on the histopathological findings and subjected to molecular profiling using Affymetrix RG-230A arrays.

first: Michael

last: Römer

first: Heidrun

last: Ellinger-Ziegelbauer


title: Association between in vivo bone formation and ex vivo migration capacity of human bone marrow stromal cells

status: Public on Jun 01 2016

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

summary: Introduction: There is a clinical need for developing systemic transplantation protocols for use of human skeletal stem cells (also known bone marrow stromal stem cells) (hBMSC) in tissue regeneration. In systemic transplantation studies, only a limited number of hBMSC home to injured tissues suggesting that only a subpopulation of hBMSC possess “homing” capacity. Thus, we tested the hypothesis that a subpopulation of hBMSC defined by ability to form heterotopic bone in vivo, is capable of homing to injured bone.  Methods: We tested ex vivo and in vivo homing capacity of a number of clonal cell populations derived from telomerized hBMSC (hBMSC-TERT) with variable ability to form heterotopic bone when implanted subcutaneously in immune deficient mice. In vitro transwell migration assay was used and in vivo homing ability to bone fractures in mice was visualized by bioluminescence imaging (BLI). In order to identify the molecular phenotype associated with enhanced migration, we carried out comparative DNA microarray analysis of gene expression of hBMSC-derived high bone forming (HBF) clones versus low bone forming (LBF) clones.  Results: In this study, clonal cell populations forming in vivo bone were shown to exhibit higher ex vivo transwell migration and following intravenous infusion, enhanced in vivo homing ability to bone fractures. Comparative microarray analysis of LBF versus HBF clones identified a significant enrichment of gene categories of cell chemo-attraction, adhesion and migration. Among these genes, platelet-derived growth factor receptor (PDGF-R) α and β were highly expressed in HBF clones. Further studies showed that the chemoattractive effects of PDGF in vitro was more enhanced in HBF clones compared to LBF clones and this effect was abolished in presence of a PDGFR-β-specific inhibitor: SU-16f. Sorted PDGFR-β+ cells from LBF clones showed that the PDGFR-β+ enriched cell population exhibited strong chemoattractance towards PDGF.   Conclusion: Our data demonstrate phenotypic and molecular association between in vivo bone formation and migratory capacity of hBMSC. PDGFR-β can be used as a potential marker for the prospective selection of hBMSC populations with high migration and bone formation capacities suitable for clinical trials for enhancing bone regeneration.

overall_design: Total RNA obtained from telomerized human bone marrow derived mesenchymal stromal cells (T4P38a) with high in vivo bone forming capacity and (T4P74a) with low bone forming capacity and three single cell clones with high bone forming capacities (DD8, AD10 and BB10) and three clones with low bone forming capacities (CF1, CB4 and CD4). All cells were cultured under standard conditions and RNAs were isolated at baseline with no induction. each sample was represented in doublicate as a and b.

first: Rikke

last: Andersen

first: Walid

last: Zaher

first: Kenneth

last: Larsen

first: Nicholas

last: Ditzel

first: James

last: Adjaye

first: Katharina

last: Drews

first: Moustapha

last: Kassem

first: Basem

last: Abdallah


title: Gene expression profile in cells treated with different oligonucleotides

status: Public on Mar 30 2016

city: Carlsbad

first: Sagar

middle: S

last: Damle

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

summary: Oligonucleotides are normally used to down regulate gene expression via RISC or RNase H dependent mechanisms. However, properly designed oliognucleotides can be used to specifically increase translation of proteins by targeting certain regions of mRNAs. To determine if this type of oligonucleotide that does not activate RNA cleavage causes off-targeted effects, microarray was performed to evaluate the gene expression in cells treated with different oligonucleotides.

overall_design: HeLa cells were treated for 15 hr with oligonucleotides at 30 nM final concentration, under this condition the targeted protein level was increased. RNA was perpared from treated cells and analyzed by microarray.

first: Xue-hai

last: Liang

first: Wen

last: Shen

first: Hong

last: Sun

middle: T

last: Migawa

first: Timothy

last: Vickers

first: Stanley

last: Crooke


title: Normalization of whole-genome SNP data from non-Hodgkin lymphoma patients for copy number variation.

status: Public on May 24 2016

first: Fan

last: YANG

address: 197, Rui Jin Er Road

institute: Shanghai Institute of Hematology

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

summary: With the whole genome SNPs array information, we could evaluate the copy number variation of samples so as to find out specific DNA aberrations in non-Hodgkin lymphma comparing with reactive hyperplasia patients.

overall_design: To find out lymphoma-related copy number variations in 45 non-Hodgkin lymphoma patients comparing with 8 reactive hyperplasia patients.

first: Wei-Li

last: Zhao


title: Interleukin-6 is a Potential Therapeutic Target in Interleukin-6 Dependent Estrogen Receptor-alpha Positive Breast Cancer [patient tumor tissue]

status: Public on Feb 04 2016

city: Beerse

first: Tine

last: Casneuf

address: Turnhoutseweg 30

department: Oncology Translational Research

country: Belgium

institute: Janssen R&D

summary: Interleukin-6 (IL-6) is an important growth factor for estrogen receptor-alpha (ERα) positive breast cancer, and elevated serum IL-6 is associated with poor prognosis. We firstly demonstrated that pSTAT3 is the primary downstream IL-6 signaling pathway in ERα-positive breast cancer, using ten different breast cancer cell lines.  Three-dimensional cultures of these cell lines were also used to develop a 17-gene IL-6 specific gene signature that could be used to identify IL-6 driven disease. This signature included a variety of genes involved in immune cell function and migration, cell growth and apoptosis, and the tumor microenvironment. To further validate this IL-6 signature, we obtained 36 human ERα-positive breast cancer tumor samples with matched serum for gene expression profiling and determination of an IL-6 pathway activation score (PAS).  Patients with high IL-6 PAS were also enriched for elevated serum IL-6 (>=10 pg/ml).  We then utilized a murine MCF-7 xenograft model to determine the role of IL-6 in ERα-positive breast cancer and potential anti-IL-6 therapy in vivo. When IL-6 was administered in vivo, MCF-7 cells engrafted without the need for estrogen supplementation.  Subsequently, we prophylactically treated mice at MCF-7 engraftment with an anti-IL-6 antibody (siltuximab), fulvestrant or combination therapy.  Siltuximab alone was able to blunt MCF-7 engraftment.  Similarly, when tumors were allowed to grow to 125 mm3 before treatment, siltuximab alone demonstrated tumor regressions in 90% (9/10) of tumors.  Given the established role for IL-6 in ERα+ breast cancer, this data demonstrates the potential for anti-IL-6 therapeutics.

overall_design: Matched formalin-fixed paraffin-embedded (FFPE) tissue and serum from 36 ERα-positive breast tumors were purchased from Asterand USA (Detroit, MI, USA).

first: Tineke

first: Amy

middle: E

last: Axel

first: Peter

last: King

first: J

last: Alvarez

first: Jillian

middle: L

last: Werbeck

first: Tinne

last: Verhulst

first: Karin

last: Verstraeten

first: Brett

last: Hall

first: A

last: Sasser


title: Gene expression profiling of THP-1 cells on treatment with vitamin C

status: Public on Feb 15 2016

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: The present study reports the temporal transcriptional response of THP-1 cells to physiological levels (100 μM) of vit C treatment. An extensive modulation of gene expression occurs from early to late time-points, which is reflected in a gamut of functional responses regulated by vit C, as determined by enrichment analysis. The study reveals the pleiotropic activity of vit C with diverse implications on biological processes. vit C mediates responses that encompass a range of cellular processes, and span regulation of gene expression, signal transduction, cell cycle, immune system, cAMP metabolic process and signaling and ion homeostasis. Thus vit C modulates a plethora of physiological functions, that emphasize its key role in maintaining equilibrium.

overall_design: Agilent one-color experiment,Organism: Homo sapiens  ,Agilent Custom Human Whole Genome Array 8x60k designed by Genotypic Technology Private Limited (AMADID: 027114) Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Sakshi

last: Batra

first: Malobi

last: Nandi

first: Kriti

last: Sikri

first: Jaya

last: Tyagi


title: ADAM9 Up-regulates N-Cadherin via MiR-218 Suppression in Lung Adenocarcinoma Cells [mRNA]

status: Public on Jan 01 2016

city: Taipei

first: Mong-Hsun

last: Tsai

address: 4F, No. 81, Chang-Xing St.

department: Institute of Biotechnology

country: Taiwan

institute: National Taiwan University

summary: Lung cancer is the leading cause of cancer death worldwide. Brain metastasis is a major cause of morbidity and mortality in lung cancer. CDH2 (N-cadherin, a mesenchymal marker in epithelial-mesenchymal transition) and ADAM9 (a member of type I transmembrane proteins) have been reported relating to lung cancer brain metastasis, however, it is still not clear whether any interaction between them to mediate lung cancer brain metastasis. Since microRNAs were discovered to regulate many biological functions and disease processes (e.g., cancer) by down-regulating their target genes, microRNA microarrays were used to identify ADAM9 regulated miRNAs that target CDH2 in aggressive lung cancer cells. Luciferase assays and immunoblotting proved that CDH2 was a target gene of miR-218. The expression of miR-218 was generated from pri-mir-218-1, located in SLIT2, in low invasive lung adenocarcinoma while it was inhibited in aggressive lung adenocarcinoma. Down-regulation of ADAM9 could up-regulate SLIT2 and miR-218, thus down-regulate CDH2 expression. This study elucidated the mechanism of ADAM9 activating CDH2 may be due to release the inhibition of miR-218 on CDH2 in lung adenocarcinoma.

overall_design: For each of the cell lines bm#2, bm#7, and F4, one microarray was analyzed.

first: Yuh-Ping

last: Sher

first: Li-Ju

last: Wang

first: Ting-Ting

last: Kuo

first: Eric

middle: Y

last: Chuang

first: Liang-Chuan

last: Lai


title: Hypertrophy induced KIF5B controls mitochondrial localization and function in neonatal rat cardiomyocytes

status: Public on Apr 21 2016

first: vincent

last: bloks

summary:
Cardiac hypertrophy is associated with growth and functional changes of cardiomyocytes,including mitochondrial alterations, but the latter are still poorly understood. Here we investigated mitochondrial function and dynamic localization in neonatal rat ventricular cardiomyocytes (NRVCs) stimulated with insulin like growth factor 1 (IGF1) or phenylephrine (PE), mimicking physiological and pathological hypertrophic responses,respectively.

A decreased activity of the mitochondrial electron transport chain (ETC) (state 3) was observed in permeabilized NRVCs stimulated with PE, whereas this was improved in IGF1 stimulated NRVCs. In contrast, in intact NRVCs, mitochondrial oxygen consumption rate
(OCR) was increased in PE stimulated NRVCs, but remained constant in IGF1 stimulated NRVCs. After stimulation with PE, mitochondria localized to the periphery of the cell.

To study the differences in more detail, we performed gene array studies. IGF1 and PE stimulated NRVCs did not reveal major differences in gene expression of mitochondrial encoding proteins, but we identified a gene encoding amotor protein implicated in mitochondrial localization, kinesin family member 5b (Kif5b ), which was clearly elevated in PE stimulated NRVCs but not in IGF1 stimulated NRVCs.

We confirmed that Kif5b gene and protein expression was elevated in animal models with pathological cardiac hypertrophy.

 Silencing of Kif5b reverted the peripheral mitochondrial localization in PE stimulated NRVCs and diminished PE induced increases in mitochondrial OCR, indicating that KIF5B dependent localization affects cellular responses to PE stimulated NRVCs.

 These results indicate that KIF5B contributes to mitochondrial localization and function in cardiomyocytes and may play a role in pathological hypertrophic responses in vivo.

overall_design: NRVCs were isolated from 12 neonatal (Sprague Dawley) rats of 1-3 days old.  4 control, 4 PE, and 4 IGF1 stimulated NRVCs were used and arrayed.

first: Wardit

last: Tigchelaar

first: Anne

last: de Jong

first: Vincent

last: Bloks

first: Wiek

last: van Gilst

first: Rudolf

middle: A

last: de Boer

first: Herman

last: Silljé


title: Breast cancer tumor promoting cell transcriptome

status: Public on Nov 23 2015

city: Milan

first: Maurizio

last: Callari

address: Via Amadeo, 42

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

summary: In this study we obtained gene expression profiles of MCFS and parental MCF7 cell lines using Illumina microarrays

overall_design: Transcriptome analysis of tumor promoting mammospheres (MCFS) and parental MCF7 breast cancer cell line was run in triplicate on microarrays

first: Maria

middle: G

last: Daidone


title: Pathways of retinoid synthesis in mouse macrophages and bone marrow cells

status: Public on Dec 17 2015

city: St Louis

first: John

last: Welch

state: MO

address: 660 South Euclid Ave

institute: Washington University

summary:
In vivo pathways of natural retinoid metabolism and elimination have not been well characterized in primary myeloid cells, even though retinoids and retinoid receptors have been strongly implicated in regulating myeloid maturation. Using a UAS-GFP reporter transgene, and retrovirally expressed Gal4-RARA in primary mouse bone marrow cells, we identified two distinct enzymatic pathways utilized by mouse myeloid cells ex vivo to synthesize RARA ligands from free vitamin A metabolites (retinyl acetate, retinol, and retinal). Bulk Kit+ bone marrow progenitor cells utilize diethylaminobenzaldehyde (DEAB)-sensitive enzymes, whereas bone marrow-derived macrophages use DEAB-insensitive enzymes to synthesize natural RARA-activating retinoids (all-trans retinoic acid). Bone marrow-derived macrophages do not express the DEAB-sensitive enzymes Aldh1a1, Aldh1a2, or Aldh1a3, but instead express Aldh3b1, which we found is capable of DEAB-insensitive synthesis of all trans-retinoic acid. However, under steady-state and stimulated conditions in vivo, diverse bone marrow cells and peritoneal macrophages showed no evidence of intracellular RARA-activating retinoids despite expression of these enzymes and a vitamin A sufficient diet, suggesting that the enzymatic conversion of retinal is not the rate limiting step in the synthesis of intracellular RARA-activating retinoids in myeloid bone marrow cells and that that RARA remains in an un-liganded configuration during adult hematopoiesis.
In order to identify additional enzymes that might contribute to DEAB-insensitive retinoid synthesis in bone marrow-derived macrophages, we compared gene expression in Kit+ progenitor cells vs bone marrow macrophages by Affymetrix array profiling.

overall_design: We analyzed 3 biological samples each of mouse bone marrow-derived macrophages and Kit+ progenitor cells


title: Potential biomarker genes for crowding stress in maraena whitefish Coregonus maraena

status: Public on Jan 06 2016

city: Dummerstorf

first: Alexander

last: Rebl

address: Wilhelm-Stahl-Allee 2

department: Institute of Genome Biology

institute: Research Institute for Farm Animal Biology

summary: Stress represents a major factor negatively affecting fish welfare in aquaculture. The objective of the present study was to identify and evaluate informative indicators for the welfare and particular health status of maraena whitefish (Coregonus maraena) farmed at four different stocking densities. Transcriptome profiling revealed that numerous stress-related signaling pathways were activated in liver and kidney under ED and HD conditions, such as ERK/MAPK, mTOR, glucocorticoid receptor, SAPK/JNK and JAK/Stat signalling, as well as p38 and p53 signalling. Moreover, several stress-relevant effector pathways were found to be overexpressed including glycolysis and glycogen degradation. Strikingly, a high number of upregulated genes in kidney and in liver of fish kept at HD (compared to MD fish) were related to immunological processes, such as Acute-phase response signalling, B cell receptor signaling, CD28 signaling in T helper cells, and Interleukin-6 signaling.

overall_design: Four stocking density conditions were investigated: an uncrowded “moderate” density (MD: 33 kg trout/m³) , an elevated density (ED: 60 kg/m³ ), a low density (LD: 10 kg/m³ ), and high density (HD: 100 kg/m³). The experiment was performed twice, randomly assigned to identical glass tanks with MD (100 individuals), ED (180 individuals),  LD (30 individuals), and HD (300 individuals). Trout were sampled 8 d after experimental onset.

first: Simone

last: Altmann

first: Judith

last: Köbis

first: Mareen

last: Nipkow

first: Tom

last: Goldammer


title: Potential biomarker genes for crowding stress in rainbow trout Oncorhynchus mykiss

status: Public on Oct 24 2015

summary: Stocking density is considered as a key factor determining the productivity of fish aquaculture systems. The transcriptomic response to crowding stress is, however, still poorly investigated. We aimed at the identification of potential biomarker genes via microarray analyses to get insight into molecular pathways modulated through density-induced stress in farmed rainbow trout Oncorhynchus mykiss. Transcriptome profiling in liver, kidney, and gills was complemented with behaviarol observation and analysis of classical plasma parameters. Individuals of two trout strains were exposed for eight days to definite stocking densities, 1 kg/m³ (low density); 10 kg/m³ (moderate); 18 kg/m³ (elevated); and 35 kg/m³ (high). Whereas stocking density had no significant effect on cortisol levels, plasma glucose levels were elevated in trout kept at high density. Pathway enrichment analyses confirmed the upregulation of HIF1a signaling in liver contributing to glucose homeostasis during stress conditions, while mTOR and PI3K/AKT signaling pathways were downregulated. Further perturbed hepatic pathways were involved in protein ubiquitination and the biosynthesis of cholesterol, retinol and glutathione.

overall_design: Three stocking density conditions were investigated: an uncrowded “moderate” density (MD: 10 kg trout/m³) , an elevated density (ED: 18 kg/m³ ), and high density (HD: 35 kg/m³). The experiment was performed twice with two strains of Steelhead rainbow trout (Troutlodge and Born trout), randomly assigned to identical glass tanks with MD (30 and 34 individuals), ED (60 and 64 individuals), and HD (120 and 140 individuals). Trout were sampled 8 d after experimental onset.

first: Andreas

last: Borchel

first: Marieke

last: Verleih


title: The effect of age on alternative splicing in different tissues of wild-type mice

status: Public on Nov 01 2015

city: Huddinge

last: Eriksson

address: Hälsovägen 7

department: Biosciences and Nutrition

institute: Karolinska Institutet

summary:
Exon level expression analysis for the physiological aging study data set to analyze the effect of age on alternative splicing in different tissues and age groups of wild-type mice
Analysis of the effect of age on alternative splicing (AS) using exon microarrays to interrogate the differential exon usage  of the entire genome of aging wild-type male C57BL/6J mice (4- and 18-month-old) in five tissues (skin, skeletal muscle, bone, thymus, and white adipose tissue) and in an additional 28-month-old age group, which allowed for age-related AS analysis of the skin, skeletal muscle and bone tissues. We found AS genes with age in all tissue, we show that the number of AS genes increased with age and that AS genes across all tissues are involved in RNA processing. Note: This dataset is one of the 2 datasets in the overall study. An additional data set series is available with exon expression analysis of HGPS mice to analyze the effect of progerin expression on alternative splicing. The two datasets are linked together in the SuperSeries GSE67289. A link to the SuperSeries is available at the bottom of this page.

overall_design: 65  tissue samples from wild-type male  C57BL/6J mice; from  5 different tissues (ventral skin, skeletal muscle, bone, muscle, and white adipose tissue) and from 3 different age groups: 4, 18 and 28 months  (for skin skeletal muscle and bone ) and from 2 different age groups: 4 and 18 months (for ventral skin, skeletal muscle, bone, thymus and white adipose tissue)

first: Sofia

last: Rodriguez

first: David

last: Brodin


title: The effect of progerin expression on alternative splicing in keratinocytes of HGPS mice

summary:
Exon level expression analysis for the HGPS pathological aging study data set to analyze the effect of progerin expression on alternative splicing in keratinocytes of HGPS mice.
Analysis of the effect of pathological aging (transgenic progerin expression)  on alternative splicing (AS) using exon microarrays to interrogate the differential exon usage  of the entire genome of HGPS mice (postnatal day 24 and 35) and their wild-type litter mates. Our results suggests that early expression of progerin impairs developmental splicing but that as progerin accumulates, the number of genes with AS increases, similar to what is observed in aging wild-type mice. This dataset is one of the 2 datasets in the overall study. An additional data set series is available with exon expression analysis of aging wild-type mice to analyze the effect of age on alternative splicing during physiological aging. The two datasets are linked together in the SuperSeries GSE67289. A link to the SuperSeries is available at the bottom of this page.

overall_design: 16 skin keratinocyte samples from 2 different age groups: postnatal day 24 and postnatal day 35, from 8 HGPS samples and 8 genotype negative (wild-type) littermates.

first: Tomas

last: McKenna


title: The effect of age and progerin expression on alternative splicing in selected tissues in mice

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

overall_design: Refer to individual Series


title: Alteration of gene expression in MCF-7 cells induced by king cobra venom L-amino acid oxidase (OH-LAAO)

status: Public on Dec 31 2015

city: KUALA LUMPUR

first: LI

middle: MUI

last: LEE

address: JALAN PANTAI BARU

department: MOLECULAR MEDICINE

country: Malaysia

institute: UNIVERSITY OF MALAYA

summary: Alteration of gene expression in MCF-7 cells using array-based whole genome gene expression technology . Results provide useful information on the molecular events leading to cell death induced by L-amino acid oxidase enzyme.

overall_design: MCF-7 cells were treated with IC20 value of OH-LAAO or PBS (control). Treated and control cells were harvested and the RNA were extracted. RNAs were pooled from three independent experiments (n=3) (Replicate 1 and replicate 2) and were subjected to microarray analyses.

first: MUI-LI

last: Lee

first: NGET-HONG

last: Tan

first: SHIN-YEE

last: Fung


title: Gfi1 proteins regulate the emergence of HSCs and blood precursors in the  AGM through recruitment of LSD1 [Affymetrix]

status: Public on Nov 30 2015

city: Manchester

first: Roshana

last: Thambyrajah

address: Wilmslow Road

department: Stem Cell Biology

institute: CRUK Manchester

summary:
Transcriptome analysis of sorted hemogenic endothelial cells with and without Lsd1 inhibition with 300nM of compound B.
Transcriptome analysis to detect the global changes in gene expression upon LSD1 inhibition.

overall_design: Bry-GFP ES line derived FLK1+ mesodermal were differentiated to Cdh5/CD41 positive HE cells with/out the compound B. CD41 compartment of both populations were FACS sorted and processed for Affymetrix.

first: Milena

last: Mazan

first: Rahima

last: Patel

first: Victoria

last: Moignard

first: Monika

last: Stefanska

first: Thomas

last: Clapes

first: Tarik

last: Möröy

first: Catherine

last: Robin

first: Shaun

last: Cowley

first: Berthold

last: Göttgens

first: Valerie

last: Kouskoff

first: Georges

last: Lacaud


title: Transcriptome analysis of FOXF1 expressing cells at E7.5 of embryonic development

status: Public on Oct 10 2015

first: Maud

last: Fleury

institute: Cancer Research UK Manchester Institute

summary: Comparison of the transcriptional profile of cells expressing FOXF1::VENUS and/or FLK1 in E7.5  mouse embryos carrying a foxf1::venus knock-in allele

overall_design: Foxf1::venus E7.5 embryos were sorted based on FLK1 and FOXF1::VENUS expression (3 sorted populations, 2 biological replicates)


title: Copy number analysis in melanoma tumor samples from E2603

city: Philadelphia

first: Katherine

last: Nathanson

address: 421 Curie Blvd

institute: Perelman School of Medicine at the University of Pennsylvania

type: Genome variation profiling by genome tiling array

summary:
Blinded study, melanoma tumor samples from patients treated with carboplatin and paclitaxel +/- sorafenib are compared
aCGH of human melanoma tumor samples

overall_design:
Tumor cells and commercially available pooled, control female DNA were labeled, processed, and analyzed per life technologies protocol, agilent protocol, and Nexus program respectively
---------------------------------------------------
drug treatments blinded and are not yet available

first: Melissa

last: Wilson

first: Bradley

last: Wubbenhorst


title: Effects of dexamethasone on gene expression in rat pancreatic AR42J cell line

status: Public on Sep 11 2015

city: Kansas City

first: Robert

last: De Lisle

state: KS

address: 3901 Rainbow Blvd

department: Anatomy & Cell Biology

institute: Univ Kansas Med Ctr

summary: The rat pancreatic cell line AR42J is relatively undifferentiated under normal culture conditions. When the glucocorticoid dexamethasone is added to the medium the cells display a dramatic decrease in proliferative rate and are induced to a more exocrine phenotype that includes increased expression of exocrine pancreas products (digestive enzymes) and more developed regulated secretion. We used microarray to determine changes in gene expression comparing control (without dexamethasone) vs induced (plus dexamethasone).

overall_design: Three independent pairs of control and dexamethasone-induced cultures were prepared followed by total RNA extraction and microarray analysis using the Affymetrix Rat 230A chip.

first: Donna

last: Ziemer


title: PML-RARA fusion gene requires Dnmt3a to induce acute promyelocytic leukemia in mice

status: Public on Oct 01 2015

first: Timothy

last: Ley

address: 660 S Euclid Avenue

department: Internal Medicine

institute: Washington University School of Medicine

summary:
Loss of function mutations in the DNA methyltransferase DNMT3A are highly recurrent in acute myeloid leukemia (AML).  DNMT3A and DNMT3B encode the two methyltransferases that are primarily responsible for the de novo methylation of specific DNA sequences during cellular differentiation. DNMT3A mutations are rarely found in AML patients with translocations that create oncogenic fusion genes (e.g. PML-RARA, RUNX1-RUNX1T1, CBFB-MYH11, and MLL-X). To begin to define the reasons why these mutations do not occur together, we used retroviral vectors to express PML-RARA, RUNX1-RUNX1T1, and MLL-AF9 in the bone marrow cells of wild type (WT) or Dnmt3a deficient mice; we also examined the hematopoietic phenotypes of Ctsg-PML-RARA animals (which express PML-RARA in early hematopoietic progenitors and myeloid precursors) with and without Dnmt3a.
We demonstrated that the methyltransferase activity of Dnmt3a (but not Dnmt3b) is required for aberrant self-renewal ex vivo that is driven by PML-RARA (but not RUNX1-RUNX1T1 or MLL-AF9); furthermore, the PML-RARA-driven competitive transplantation advantage and leukemia generation both required Dnmt3a. Together, these findings demonstrate that PML-RARA is specifically dependent on Dnmt3a to initiate APL in mice, and may explain why loss-of-function DNMT3A mutations are not found in patients with acute promyelocytic leukemia.

overall_design: Samples were specific sorted progenitor populations (CMP, common myeloid progenitors;  GMP, granulocyte-monocyte progenitor) isolated from wild-type or Dnmt3a-/- mice on the C57Bl/6J background.

first: Christopher

last: Cole


title: ATF7 mediates lipopolysaccharide-induced epigenetic changes in macrophages involved in innate immunological memory (ChIP)

status: Public on Aug 31 2015

city: Tsukuba

first: Keisuke

last: Yoshida

address: 3-1-1 Koyadai,

institute: RIKEN

type: Genome binding/occupancy profiling by genome tiling array

summary: Immunological memory is generally thought to be mediated exclusively by lymphocytes such as memory T and B cells. However, enhanced innate immune responses caused by a previous infection increase protection against reinfection suggesting the presence of innate immunological memory. Here, we describe 3,811 ATF7 binding sites in mouse peritoneal macrophages, and 95% of the ATF7 signals in wild-type macrophages are lost in ATF7 knockout macrophages. ATF7 suppresses a group of innate-immunity genes in macrophage by recruiting H3K9 dimethyltransferase G9a. TLR ligands induce ATF7 phosphorylation, leading to release of ATF7 from chromatin and reduction in H3K9me2 level. Partially disrupted chromatin structure and increased basal expression on target genes are maintained for a long period, increasing resistance pathogens. Therefore we speculate ATF7 is important factor in controlling innate immunological memory.

overall_design: This series contains one set of whole genome ChIP-chip data and 2 sets of promoter array ChIP-chip data. For all sample, we use three IP .CEL files and three WCE .CEL files (they are triplicated experiments) to make one profile.

first: Toshio

last: Maekawa

first: Claire

last: Renard-Guillet

first: Bruno

last: Chatton

first: Katsuhiko

last: Shirahige

first: Shunsuke

last: Ishii


title: Changes in Expression of Genes Regulating Airway Inflammation Following a High-Fat Mixed Meal in Asthmatics

status: Public on Oct 16 2015

city: Newcastle

first: QIAN

last: LI

address: University drive

country: Australia

institute: University of Newcastle

summary: Consumption of a high fat meal can increase neutrophilic airway inflammation in asthma. This study investigates the molecular mechanisms driving airway neutrophilia following a high fat meal in asthma.

overall_design: a subset of subjects (asthmatics, n=5; healthy controls, n=3) were examined by microarray. A total of 500 ng of sputum RNA was amplified and labelled with biotin-uridine triphosphate using the Total Prep RNA amplification kit as per manufacturer’s instructions (Life Technologies). 750 ng cRNA was hybridised to Illumina Sentrix HumanRef-8 V3 Expression BeadChips (Illumina, San Diego, CA, USA) using standard protocols. Each BeadChip measured the expression of 24,354 genes and was scanned using the Illumina Bead Station and captured using BeadScan 3.5.11 (Illumina)

first: Qian

last: Li

last: Baines

first: Peter

last: Gibson

first: Lisa

last: Wood


title: Renal Expression of Dahl SS/Jr (S) and Congenic Rats after 24 hours of Dietary Salt Loading

status: Public on Aug 28 2015

city: Toledo

first: Andrew

middle: John

last: McSweeny

state: OH

address: 3000 Arlington Avenue Room # 209, Mail Stop #1008

department: Physiology & Pharmacology: CVMD Track

institute: University of Toledo College of Medicine

summary:
The overlap of congenic regions in an earlier substitution mapping study suggested the location of two blood pressure quantitative trait loci (QTL)-containing regions in the q-terminus of rat chromosome 3, QTL1 and the more distal, QTL2.  Male SS/jr rats and two congenic substrain rats S.R(D3Mco36-D3Mco46) and S.R(D3Mco36-D3Got166) were maintained on a low salt (0.4% NaCl Harlan Teklad diet TD7034) diet until 39-41 days of age.  These 3 rat strains will be hereafter referred to as S, S.R(ET3x1), and S.R(ET3x2), respectively.  At 39-41 days of age, half of the rats from each strain were fed a high (4% NaCl Harlan Teklad diet TD83033) salt diet and water ad libitum for 24 hours.  Both congenic substrains carry SR/jr (R)-rat alleles for QTL2 on an S-rat genetic background, while S.R(ET3x2) also carries R-rat alleles for QTL1. Renal gene expression analysis was used to identify differentially expressed genes or genes with altered activity within the S.R(ET3x2) congenic region.

Keywords: strain differences in response to dietary changes

overall_design: Age-matched male S (n=10), S.R(ET3x1) (n=8), and S.R(ET3x2) (n=8) rats were bred, housed, and studied concomitantly to minimize envi¬ronmental effects. Rats were weaned at 30 days of age onto a low salt diet (0.4% NaCl, Harlan Teklad diet TD7034) and water ad libitum. At 39-41 days of age one-half of rats from each strain group were switched to a 4% NaCl diet (Harlan Teklad diet TD83033) and water ad libitum for 24 hours.  Rats were then killed with pentobarbitol overdose.  Gene expression data from Affymetrix Rat RAE230 A and B GeneChips, hybridized with kidney cRNA, was used to identify genes with altered activity within the S.R(ET3x2) congenic region.

first: Soon

last: Jin Lee

first: George

last: Cicila


title: Renal Expression of Dahl SS/Jr (S) and Congenic Rats after 28 days of dietary salt elevation

summary:
The overlap of congenic regions in an earlier substitution mapping study suggested the location of two blood pressure quantitative trait loci (QTL)-containing regions in the q-terminus of rat chromosome 3, QTL1 and the more distal, QTL2.  Male SS/jr rats and two congenic  substrain rats S.R(D3Mco36-D3Mco46) and S.R(D3Mco36-D3Got166) were maintained on a low salt (0.4% NaCl Harlan Teklad diet TD7034) diet until 39-41 days of age and then fed an intermediate (2% NaCl Harlan Teklad diet TD94217) salt diet for 28 days. These 3 rat strains will be hereafter referred to as S, S.R(ET3x1), and S.R(ET3x2), respectively. Both congenic substrains carry SR/jr (R)-rat alleles for QTL2 on an S-rat genetic background, while S.R(ET3x2) also carries R-rat alleles for QTL1. Renal gene expression analysis was used to identify differentially expressed genes or genes with altered activity within the S.R(ET3x2) congenic region.

Keywords: strain differences in response to dietary changes

overall_design: Rats of each strain were divided into 4 groups: S, n=2 rats/group; S.R(ET3x1), n=3 rats/group; and S.R(ET3x2), n=3 rats/group. Equal amounts of left kidney RNA from each rat in a group were pooled, such that four different pools of kidney RNA (biological replicates) were prepared for each of the three rat strains.  Total RNA was isolated from the kidneys of each rat separately. Gene expression data were analyzed from Affymetrix Rat RAE230 A and B GeneChips.


title: Dietary Salt effects on Renal Expression of Dahl SS/Jr (S) and Congenic Rats

overall_design:
Refer to individual Series

GSE12423 and GSE12424 represent the results of two separate analyses.


title: The methylome of Alu repeats in colon cancer (CGH)

status: Public on Sep 08 2015

city: Badalona

first: Miguel

middle: A.

last: Peinado

address: Can Ruti Campus

country: Spain

institute: IGTP

summary: Next Generation Sequencing of Unmethylated Alu (NSUMA) interrogation of more than 130,000 individual Alus for differential methylation with concomitant analysis of copy number variations applied to the study of hypomethylation in colorectal cancer.

overall_design: normal colon tissues, matched primary tumors, and colon derived cell lines

first: Mireia

last: Jordà

first: Anna

last: Díez-Villanueva

first: Berta

last: Martín

first: Sergi

last: Lois

first: Izaskun

last: Mallona


title: Gene expression of rat cerebellum in a new animal model of hepatic encephalopathy (HE)

status: Public on Jul 29 2015

city: Barcelona

first: Teresa

last: García-Lezana

address: Paseo de la Vall d'hebron 119-129

institute: Vall d'Hebron Research Institute

summary:
Identify differentially expressed genes related to the neurodegenerative process in a new animal model of hepatic encephalopathy (HE).
The animal model consists on the simulation of several bouts of HE in PCA rats, being the precipitant factors of the episodes ammonia (NH3) and/or lipopolisaccharide (LPS) or saline.

overall_design: Regular administration (one every two weeks up to 10 infussion) of NH3 (20 μl/min along 3h) and/or LPS (5mg/kg) or in PCA rats. Sham rats were used as a surgery control.

first: Jordi

last: Romero

last: García

first: Laia

last: Chavarria


title: Renoprotective Effects of Valproic Acid and Dexamethasone in Acute Kidney Ischemia-Reperfusion Injury

status: Public on Jul 06 2015

city: Ft. Detrick

first: Christine

last: Baer

state: MD

address: 568 Doughten Drive

department: Environmental Health Program

institute: Excet, Inc. / USACEHR

summary: Introduction: Renal ischemia-reperfusion (IR) causes acute kidney injury (AKI) with high mortality and morbidity. The objective of this study was to ameliorate kidney IR injury and identify novel biomarkers for kidney injury and repair. Methods: Left renal ischemia was induced in rats by clamping renal artery for 45 minutes, followed by reperfusion and right nephrectomy. Thirty minutes prior to ischemia, rats (n=8/group) received Valproic Acid (150 mg/kg; VPA), Dexamethasone (3 mg/kg; Dex) or Vehicle (Saline) intraperitoneally. Animals were sacrificed at 3h, 24h or 120h post- IR and blood, urine and kidney were collected. Results: Serum creatinine (mg/dL) at 24 h IR in VPA (2.7±1.8) and Dex (2.3±1.2) was reduced (P<0.05) compared to Vehicle (3.8±0.5). At 3h post-IR, urine albumin (mg/ml) was higher in Vehicle (1.47±0.10), VPA (0.84±0.62) and Dex (1.04±0.73) compared to uninjured/untreated control (0.14±0.26) group. At 24h post-IR urine Lipocalin-2 (µg/ml) was significantly higher (P<0.05) in VPA, Dex and Vehicle groups (9.61-11.36) compared to uninjured/untreated control (0.67±o.29); also, Kidney Injury Molecule-1 (KIM-1; ng/ml) was significantly higher in VPA, Dex and Vehicle groups (13.7-18.7) compared uninjured/untreated control (1.7±1.9). KIM-1 levels were significantly (P<0.05) higher in all groups compared to uninjured/untreated control levels. Histopathology at 3h post IR demonstrated (P<0.05) reduction in ischemic injury in the renal cortex in VPA (Grade 1.6± 1.5) compared to Vehicle (Grade 2.9±1.1) group. Inflammatory cytokines IL1β and IL6 were down-regulated in VPA and Dex groups. BCL2 was higher in VPA group. DNA microarray analysis demonstrated reduced stress response and injury, and improved recovery related gene expression in the kidneys of VPA treated animals. Conclusions: VPA administration reduced kidney IR injury and improved regeneration. KIM-1 and Lipocalin-2 appear to be promising early urine biomarkers of acute ischemic kidney injury.

overall_design: We had three experimental groups. Group A, VPA treatment; Group B, Dexamethasone treatment; and Group C, No treatment (vehicle saline control). Treatments were administered prior to the induction of left renal ischemia. Animals underwent 45 minutes of left renal ischemia, followed by reperfusion, and right nephrectomy as described above. Following reperfusion, animals were sacrificed at 3, 24 or 120 hours (n=8/group). In the 3 hour group, rats were maintained under anesthesia after surgery until sacrifice. In the 24 and 120 hour groups, the rats were recovered and returned to the cages for normal housing. Analgesic buprenorphine (0.05mg/kg) was administered every 12 h for three days post-operatively. After animal sacrifice, urine, blood, and kidney were collected for kidney functional biomarker assays, histology and / or molecular analyses. Urine was obtained via cystocentesis and blood was obtained via the left renal vein. Tissue and urine samples collected from normal (naïve) animals (n=5) were used for baseline measurements. A subset of 46 animals (n = 4-5 per group) were selected for microarray analysis.

first: Shashikumar

last: Salgar

first: Jonathan

last: Stallings


title: Germline duplication of ATG2B and GSKIP predisposes to familial essential thrombocythemia rapidly progressing to acute leukemia

status: Public on Aug 05 2015

city: VILLEJUIF

first: Bastien

last: Job

address: 39 rue Camille Desmoulins

institute: Institut Gustave Roussy

summary: No major predisposing gene for familial myeloproliferative neoplasms (MPN) has been identified. Here, we demonstrate that the autosomal dominant transmission of a 700 kb duplication in four geographically-related families predisposes to MPN rapidly progressing to acute leukemia. Using induced pluripotent stem and primary cells to explore hematopoietic differentiation, we demonstrate that overexpressed ATG2B and GSKIP enhance hematopoietic progenitor differentiation, including megakaryocytic through increasing their sensitivity to TPO. ATG2B and GSKIP cooperate with acquired JAK2, MPL and CALR mutations during MPN development. Thus, the germline duplication changes the fitness of cells harboring signaling mutations and increases the probability of disease development.

overall_design: 14 samples corresponding to iPSC and control cases (Cy5) where hybridized in dual color against commercial normal reference DNA (Cy3) of matched sex, except for samples with unknown gender for which male normal was used as reference.

first: Joseph

last: Saliba

first: Cécile

last: Saint-Martin

first: Antonio

last: Di Stefano

first: Gaëlle

last: Lenglet

first: Caroline

last: Marty

first: Boris

last: Keren

first: Folrence

last: Pasquier

first: Véronique

last: Della Valle

first: Lise

last: Secardin

first: Gwendoline

last: Leroy

first: Emna

last: Mahfoudhi

first: Sarah

last: Grosjean

first: Nathalie

last: Droin

first: Khadija

middle: M

last: Diop

first: Sabine

last: Charrier

first: Aberta

last: Palazzo

first: Jane

last: Merlevede

first: Jean-Côme

last: Mediane

last: Delaunay-Darivon

first: Pascal

last: Fuseau

first: Françoise

last: Isnard

first: Nicole

last: Casadevall

first: Eric

last: Solary

first: Najet

last: Debili

first: Olvier

last: Bernard

first: Hana

last: Raslova

first: Albert

last: Najman

first: William

last: Vainchenker

last: Bellanné-Chantelot

first: Isabelle

last: Plo


title: miRNA profiles regulated by PLD1 inhibitor in Wnt-relevant colon cancer cells

status: Public on Jun 03 2015

city: Busan

first: Do Sik

last: Min

address: 30 Jangjeon-dong, Geumjeong-gu

department: Molecular Biology

country: South Korea

institute: Pusan National University

summary: To identify potential miRNA effectors responsible for anti-tumorigenesis by targeting PLD1, we performed miRNA microarray in Wnt-relevant colon cancer cells and analyzed miRNAs that were differently expressed by inhibition of PLD1

overall_design: Total RNA obtained from isolated DLD1 cells in Vehicle or PLD1-Inh groups under 1% heat-inactivated fetal bovine serum condition for 36 hours, respectively.

first: Do

first: Dong

middle: W

last: Kang


title: Expression data from mouse perigonadal white adipose tissue - various mutant conditions [exon-level analysis]

status: Public on Jun 05 2015

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: Progerin-expressing mice (HGPS-like) demonstrated increased energy metabolism and lipodystrophy. Increased mitochondrial biogenesis was found in adipose tissue from HGPS-like mice, whereas lamin C-only mice had fewer mitochondria. Thus we analyse which molecular pathways mediated the changes in adipose tissue caused by lamin C and progerin expression and the roles of these pathways in energy metabolism and aging.

overall_design: 10 cDNAs samples were analysed. We compared the mean fold change of 2 to 4 biological replicates. We performed an unpaired Student’s t-test to compare intensities in the different biological replicates. Genes were considered significantly regulated when the fold change was ≥ 1.5, and the p-value was ≤0.05.

first: J

last: Tazi


title: microRNA expression profiling of human nasopharyngeal Carcinoma tissues and Chronic Nasopharyngitis specimens

status: Public on Jun 30 2015

city: Guangzhou

first: Xin

last: Li

state: Province

address: Southern medical university

department: Cancer research institute

country: China

institute: Southern medical university

summary:
Epstein-Barr virus (EBV) has been etiologically linked to human malignancies including Nasopharyngeal Carcinoma (NPC). Although EBV-encoded miRNAs have been shown to contribute to viral latency, host cell survival and immune evasion, their direct impact on cancer progression in their human host remains unclear. In the current study, based on a miRNA expression profiling analysis of a larger number of clinical specimens using a miRNA array platform containing human, EBV  and other species miRNA probes., we found that some EBV-miR-BARTs were highly expressed in NPC. Accordingly, further exploration of the potential roles and regulatory mechanisms of some important EBV-miR-BARTs in NPC progression was carried out.
We applied a miRNA expression profiling analysis in 20 poor or undifferentiated NPC (Nasopharyngeal Carcinoma) matched with 20 benign chronic nasopharyngitis (CNP) specimens using a miRNA array platform containing human, EBV and other species miRNA probes.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human gammaherpesvirus 8
Macacine gammaherpesvirus 4
Betapolyomavirus macacae

overall_design: Two-group experiment, NPC vs CNP. Biological repelicates: 20 NPCs, 20 CNPs. One replicate per array.

first: Yanfen

last: Ye


title: Expression of V3 Versican by Arterial Smooth Muscle Cells Promotes Differentiated and Anti-inflammatory Phenotypes

status: Public on Jul 07 2015

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: Arterial smooth muscle cells (ASMCs) undergo phenotypic changes during development and pathological processes in vivo and during cell culture in vitro. Our previous studies demonstrated that retrovirally-mediated expression of the versican V3 splice variant (V3) that lacks glycosaminoglycan chains by ASMCs retards cell proliferation and migration in vitro and reduces neointimal thickening, macrophage and lipid accumulation in animal models of vascular injury and atherosclerosis. However, the molecular pathways induced by V3 expression that are responsible for these changes are not yet clear. In the present study, we employed a microarray approach to examine how expression of V3 induced changes in gene expression and the molecular pathways in ASMCs. We found that forced expression of V3 by ASMCs affected expression of 521 genes by more than 1.5 fold. Gene ontology (GO) analysis shows that components of extracellular matrix were the most significantly affected by V3 expression, indicating that V3 expression elicits profound remodeling of extracellular matrix. In addition, genes regulating the formation of the cytoskeleton which also serve as markers of contractile smooth muscle cells were significantly upregulated. On the other hand, components of the complement system, chemokines, chemokine receptors, and transcription factors crucial for regulating inflammatory processes were among the genes most downregulated. Consistently, we found that the level of myocardin, a key transcription factor promoting contractile ASMC phenotype, was greatly increased while proinflammatory transcription factors NFkappaB1 and C/EBPβ were significantly attenuated in V3-expressing SMCs. Such results indicate that V3 expression reprograms ASMC into differentiated and anti-inflammatory phenotypes. Overall, these findings demonstrate that expression of V3 reprograms ASMCs promoting anti-inflammatory and differentiated smooth muscle cell phenotypes potentially by altering cell-ECM interaction and focal adhesion signaling pathways.

overall_design: Fischer rat ASMCs were transduced with either a retroviral vector expressing the Versican V3 splice variant (LV3SN) or an empty control vector (LXSN) in three independent experiments. In the first experiment, V3 and control transductions were performed with four technical replicates. In the subsequent two experiments, individual transductions were done for the V3 or control treatments. For data analysis, the technical replicates from the first experiment were averaged, and then data from the three experiments was evaluated in a paired manner.

first: Thomas

middle: N

last: Wight


title: Myc and PI3-k induced gene expression in RWPE1

status: Public on May 20 2015

city: singapore

first: Zhen Ning

last: Wee

address: 60 Biopolis

institute: Genome Institute of Singapore

summary: Analysis of transcriptional changes during Myc or PI3K induced oncogenic transformation in RWPE1 cells (benign prostate epithelial cell line). The aim of the present study was to identify key epigenetic gene silencing events that occur during the oncogenic transformation events, hence emphasis was placed on downregulated genes. Results provide important information on which are the tumor suppressive pathways or genes that will be epigenetically silenced by during Myc or PI3K induced oncogenic transformation.

overall_design: Total RNA obtained from oncogenic transformed RWPE1 cells which were either overexpressing Myc or constitutive active mutant of PI3K (E545K) as compared to RWPE1 cells expressing the empty vector control PMN.

first: Zhenning

first: Qiang

last: Yu


title: Comparison of protein profiles in the serum of NPC patients with different prognosis by high-throughput protein microarrays

status: Public on May 12 2015

first: Liangru

last: Ke

state: Guangdong

address: 651 Dongfeng Road East

department: Department of Nasopharyngeal Carcinoma

institute: Sun Yat-sen University

summary: High levels of c-Src in serum of patients with NPC was independent prognostic indicators for poor outcome of patients.

overall_design: In this study, eight NPC patients with or without distant metastasis, followed up more than five years, was used to acquire protein profiles in serum to find out serum biomarkers to predict outcome in NPC patients.

first: Xiang

last: Guo

first: Yanqun

last: Xiang

first: Xing

last: Lv


title: Multi-platform Characterization of Stage I Lung Adenocarcinoma (mRNA expression)

status: Public on Apr 30 2015

city: Bethesda

first: Ana

middle: I

last: Robles

address: 37 Convent Dr 37/3060D

institute: National Cancer Institute/NIH

summary: This dataset is the mRNA expression for Stage I Lung Adenocarcinoma and non-tumor adjacent tissues also characterized by Genome-wide DNA methylation profiling.

overall_design: Total cellular RNA was extracted from tumor and matching adjacent non-tumor lung and hybridized to Illumina HumanRef-8 v3 Expression Beadchip arrays.

first: Curtis

middle: C

last: Harris


title: Induced pluripotent stem cell-derived neurons from a sporadic Alzheimer disease donor as a model for investigating disease mechanisms

status: Public on Apr 21 2015

city: Berlin

first: Alessandro

last: Prigione

state: Berlin

address: Robert-Roessle-Str. 10

country: Germany

institute: Max Delbrueck Center for Molecular Medicine

summary: Gene expression analysis of control fibroblasts (NFH2), one AD-derived fibroblasts (NFH-46), NFH2-derived control-iPS cells (OiPS3, OiPS6), NFH46-derived AD-iPS cells (iPS5 and iPS 26B),  hESCs (H1 and H9).

overall_design: Total mRNA obtained from AD fibroblasts (NFH-46) and control fibroblasts (NFH-2), from pluripotent stem cells AD-iPS cells (iPS5 and iPS 26B), control-iPS cells (OiPS3, OiPS6), and hESCs (H1 and H9).


title: Gene Expression Profiling of Ischemic Stroke at 0-24 hours and 24-48 hours after known onset of symptoms

status: Public on Apr 25 2015

city: Morgantown

first: Taura

middle: L.

last: Barr

state: WV

address: One Medical Center Drive, BMRB Rm 119

department: School of Nursing

institute: West Virginia University

summary: The objective of this study was to provide insight to the molecular mechanisms chaging in the peripheral blood after acute ischemic cerebrovascular syndrome.

overall_design: Peripheral whole blood samples were collected from N=34 MRI diagnosed ischemic stroke patients >=18 years of age within 24 hours from known onset of symptom and again at 24-48 hours after onset. RNA was extracted from whole blood stabilized in Paxgene RNA tubes.


title: identification of the mis-regulated genes in mkk3 under aba treatment.-MKK3-ABA

status: Public on May 01 2015

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: Identification of the mis-regulated genes in mkk3 under ABA treatment

overall_design: 12 dye-swap - gene knock out,treated vs untreated comparison

first: Jean

last: COLCOMBET

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Detection of genome-wide copy number variations in two chicken lines divergently selected for abdominal fat content

city: Harbin

first: Hui

last: Zhang

state: Heilongjiang

address: Mucai street No. 59

department: College of Animal Science and Technology

institute: Northeast Agricultural University

summary: Background: The chicken (Gallus gallus) is an important model organism that bridges the evolutionary gap between mammals and other vertebrates. Copy number variations (CNVs) are a form of genomic structural variation widely distributed in the genome. CNV analysis has recently gained greater attention and momentum, as the identification of CNVs can contribute to a better understanding of traits important to both humans and other animals. To detect chicken CNVs, we genotyped 475 animals derived from two broiler chicken lines divergently selected for abdominal fat content using chicken 60K SNP array, which is a high-throughput method widely used in chicken genomics studies. Results: Using PennCNV algorithm, we detected 438 and 291 CNVs in the lean and fat lines, respectively, corresponding to 271 and 188 CNV regions (CNVRs), which were obtained by merging overlapping CNVs. Out of these CNVRs, 99% were confirmed also by the CNVPartition program. These CNVRs covered 40.26 and 30.60 Mb of the chicken genome in the lean and fat lines, respectively. Moreover, CNVRs included 176 loss, 68 gain and 27 both (i.e. loss and gain within the same region) events in the lean line, and 143 loss, 25 gain and 20 both events in the fat line. Ten CNVRs were chosen for the validation experiment using qPCR method, and all of them were confirmed in at least one qPCR assay. We found a total of 886 genes located within these CNVRs, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed they could play various roles in a number of biological processes. Integrating the results of CNVRs, known quantitative trait loci (QTL) and selective sweeps for abdominal fat content suggested that some genes (including SLC9A3, GNAL, SPOCK3, ANXA10, HELIOS, MYLK, CCDC14, SPAG9, SOX5, VSNL1, SMC6, GEN1, MSGN1 and ZPAX) may be important for abdominal fat deposition in the chicken. Conclusions: Our study provided a genome-wide CNVR map of the chicken genome, thereby contributing to our understanding of genomic structural variations and their potential roles in abdominal fat content in the chicken.

overall_design: In total, 475 birds (203 and 272 individuals from the lean and fat lines, respectively) from the 11th generation population of Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF) were used. These 475 birds were genotyped by the chicken 60k SNP chip and PennCNV method were used to perform genome-wide CNV detection.


title: Acquired resistance to mutant-selective EGFR inhibitor AZD9291 is associated with increased dependence on RAS signaling

status: Public on Apr 14 2015

city: Waltham

first: Aleksandra

last: Markovets

state: Massachusetts

address: 35 Gatehouse Dr.

department: Oncology, iMED

country: USA

institute: AstraZeneca

summary: To compare gene copy number in cell populations with acquired resistance to specified EGFR inhibitors to parental cell lines. The aim of the experiment was to determine whether gain or loss of copy number of particular genes was associated with resistance to particular EGFR inhibitors.

overall_design: Comparing gene copy number in PC9 parental cells to gene copy number in 5 cell populations resistant to AZD9291, 2 cell populations resistant to WZ4002, 2 cell populations resistant to afatinib and 4 cell populations resistant to gefitinib.

first: Cath

last: Eberlein

first: Zhongwu

last: Lai

first: Paul

last: Fisher

first: Garry

last: Beran


title: X-CGD iPS cells before and after genome editing by designer nucleases

status: Public on Feb 28 2015

city: Hannover

first: Doris

middle: Johanna

last: Steinemann

department: Institute of Human Genetics

institute: Hannover Medical School

summary: X-CGD (X-linked chronic granulomatous disease) patient derived CD34+ cells were reprogrammed into two X-CGD iPSC clones (7 and 25) and subsequently corrected using ZFN (clone 7) and TALEN (clone 25) by integrating a therapeutic gp91phox expression cassette into the AAVS1 "safe harbor" locus

overall_design: Three condition experiment: before and after reprogramming and before and after genome editing.

first: Anne

middle: K

last: Dreyer