title: Murine IgD+ B Cells transcriptome analysis when stimulated with LPS and LPS+anti-CD40 [72 hours]

status: Public on Dec 25 2012

city: Hyderabad

first: Tushar

last: Vaidya

address: Uppal Road Habshiguda

country: India

institute: Centre for Cellular and Molecular Biology

summary:
The effect of LPS and LPS+antiCD40 on the Transcriptome of IgD+ B Cells was analysed here at 72 hours after the stimulation.
B-lymphocytes constitute an important aspect of mammalian immune systems by virtue of their ability to produce highly specific antibodies in response to foreign antigens and pathogens. When B-lymphocytes encounter the particular antigen that they are responsive to, they differentiate into two types of cells:  short-lived antibody-secreting plasma cells and long-lived memory cells. While the plasma B cells are responsible for the rapid resolution of a current infection or immune challenge, the memory B cells are responsible for mounting a rapid response to subsequent exposures. Previous work had demonstrated that treatment of mice with a single dose of anti-CD40 at the time of immunization lead to improved secondary responses, suggesting an enhancement of the memory B cell pool. We are currently studying the molecular mechanisms underlying the generation of memory B cells, using CD40 signalling as a tool. We have carried out a Microarray analyses of genome wide gene expression patterns in naïve B-lymphocytes following CD40 signalling, over multiple time points.

overall_design: Analysis used LPS treated IgD+ B cells as control for comparison to LPS+anti-CD40 treated cells (test).Indirect comparisons were made across multiple arrays with raw data pulled from different channels for data analysis and comparison to the control data.

first: Mala

last: Upadhyay

first: G

last: Krishnapriya


title: Murine IgD+B Cells transcriptome analysis -untreated and when stimulated with LPS

summary:
Transcriptome comparison of untreated murine IgD+B cell with LPS treated IgD+B cell
B-lymphocytes constitute an important aspect of mammalian immune systems by virtue of their ability to produce highly specific antibodies in response to foreign antigens and pathogens. When B-lymphocytes encounter the particular antigen that they are responsive to, they differentiate into two types of cells:  short-lived antibody-secreting plasma cells and long-lived memory cells. While the plasma B cells are responsible for the rapid resolution of a current infection or immune challenge, the memory B cells are responsible for mounting a rapid response to subsequent exposures. Previous work had demonstrated that treatment of mice with a single dose of anti-CD40 at the time of immunization lead to improved secondary responses, suggesting an enhancement of the memory B cell pool. We are currently studying the molecular mechanisms underlying the generation of memory B cells, using CD40 signalling as a tool. We have carried out a Microarray analyses of genome wide gene expression patterns in naïve B-lymphocytes following CD40 signalling, over multiple time points.

overall_design: Analysis used untreated IgD+B  cells as control for comparison to LPS treated cells  as test. Indirect comparisons were made across multiple arrays with raw data pulled from different channels for data analysis and comparison to the control data.


title: S. aureus gene expression following growth in media containing oleic acid

status: Public on Dec 21 2012

city: Memphis

first: Matthew

middle: Wilmer

last: Frank

state: TN

address: 262 Danny Thomas Place

department: Infectious Diseases

country: USA

institute: St Jude Children's Research Hospital

summary:
S. aureus response to exogenous fatty acid (oleic acid)
Gene expression profiles were generated by microarray analysis of S. aureus cells grown in media without or with oleic aicd

sample_organism: Staphylococcus aureus subsp. aureus RN4220

overall_design:
Comparison of expression profiles after growth of S. aureus in exogenous fatty acid
S. aureus was grown in media with and without oleic acid to an OD600nm of 0.5, and RNA was extracted to look at the gobal gene expression.

middle: W

first: Pam

last: Jackson

first: Charles

middle: O

last: Rock


title: Microarray analysis of normal and abnormal chick myocardial development

status: Public on Dec 28 2012

city: Prague

first: David

last: Sedmera

address: U nemocnice 3

country: Czech Republic

institute: Charles University

summary: The goal of this study was to determine developmental differences in gene expression between left and right ventricle, and to assess the differential effect of altered hemodynamic loading on left and right ventricle. Chick ventricles from different developmental stages were isolated for assessment of normal developmental profiles. Conotruncal banding or partial ligation of the left atrial appendage was performed in ovo at embryonic day 4 and ventricles were isolated at embryonic day 5 (banding) or 8 (ligation) for assessment of altered loading effects.

overall_design: Normal heart and ventricle tissues were collected from chicks at embryonic day 4, 5, 6, 8, or 10 (Hamurger-Hamilton stages 29, 34, and 36). Conotruncal banding (CTB) or left atrial ligation (LCL) was performed for experimental groups in ovo at embryonic day 4 and tissues isolated at embryonic day 5 (CTB) or day 8 (LAL). For each sample type, tissues were carefully dissected, collected and stored in RNAlater, and then pooled for RNA isolation. Each sample contained 6 to 12 separate biological specimens. A single pooled RNA sample was generated for each normal and experimental condition.  Following preparation of labeled samples for hybridization, samples were split and hybridized in duplicate to separate microarrays (i.e., technical replicates).

first: Jeremy

middle: L

last: Barth


title: TAF15 protein regulates CDKN1A through miRNAs

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

country: France

institute: IGBMC

summary: TAF15 (formerly TAFII68) is a member of the TET family of RNA and DNA binding proteins whose genes are frequently translocated in sarcomas. Consistent with a functional role in cell viability, TAF15 depletion had a growth-inhibitory effect and increased apoptosis. Interestingly, one of the genes affected by TAF15 depletion is CDKN1A/p21, a key regulator of cell cycle. Here we show that TAF15 down-regulates CDKN1A/p21 expression through a pathway involving miRNAs.

overall_design: We performed a gene expression profiling upon TAF15 knock down by RNA interference.Total RNAs purified from four biological replicates of HeLa GL3 luc cells transfected either with si-TAF15 or control  si-LUC were hybridized to the array.

first: Monica

last: Ballarino

first: L

last: Jobert

first: Tora

last: Laszlo


title: Real-time quantitative PCR analysis of MDA MB 231 cells

status: Public on Dec 31 2012

city: Charleston

first: Dennis

last: Watson

address: 68 President Street

institute: Medical Univeristy of South Carolina

overall_design: qPCR gene expression profiling of MDA-MB-231 breast cancer cells were infected with either Ad-GFP, Ad-FLI1, or Ad-PDEF.


title: MiR expression profiles in M1-polarized compared with unstimulated (MФ) bone marrow-derived macrophage cells

status: Public on Dec 26 2012

city: Munich

first: Andreas

last: Schober

state: Bavaria

address: Pettenkoferstr. 9

department: Institute for Cardiovascular Prevention

country: Germany

institute: Ludwig-Maximilians-University

summary: The global change of the miR expression profile during atherosclerosis is due to the infiltration of different types of leukocytes into the arterial vessel wall in addition to disease-specific regulation in vascular cells. Monocyte-derived macrophage accumulation in the subintimal region is critical in the formation of atherosclerotic plaques. It is currently unknown which miRs are involved in the atherogenic macrophage response. The comparison of the miR expression profile in LPS/Interferon-gamma activated mouse macrophages with the miR expression in the unstimulated mouse macrophages was performed to detect M1-type macrophage-enriched miRs. This screening combined with our miR profiling in atherosclerotic vessels may help to identify M1-type macrophage-enriched miRs in atherosclerotic vessels that may play a role in the macrophage function during atherogenesis.

overall_design: Bone marrow cells were harvested from femura of 6- to 8-week-old female C57BL/6 mice, re-suspended in DMEM-F12/10% FCS/10% L929-conditioned medium, and cultured for 7 days to differentiate into primary macrophages. F4/80 and CD11b expression was determined by flow cytometry to confirm the macrophage phenotype. Macrophages were stimulated with LPS (100ng/ml, 14 hours) and INF-g (10ng/ml, 6 hours), and the M1 polarization was verified by quantification of mannose receptor C type 1 (MRC1), arginase II (ArgII), inducible nitric oxide synthase (iNOS), and arginase I (ArgI) by qRT-PCR. Total RNA (M1-type and unstimulated (MФ) macrophages) was isolated using the mirVana microRNA Isolation Kit.

first: Malihe

middle: N

last: Jahantigh

first: Yuanyuan

last: Wei


title: Genovul-Ssc_atresie_060510

city: Castanet-Tolosan Cedex

first: Gwenola

last: Tosser-Klopp

address: Chemin de Borde-Rouge  BP 52627

institute: INRA

summary:
In mammals, ovarian folliculogenesis leading to the ovulation of completely mature oocytes is a long and complex process that is regulated at different levels. The mechanisms that underlie the selection of one or several dominant follicles as well as the regulation of the number of ovulating follicles are largely unknown. Atresia is a phenomenon which affects the majority of developing follicles. In this project, we proposed to study the gene regulation of small antral follicles that are either healthy or undergoing atresia in pigs).  Towards this purpose, we made a comparative transcriptomics study on granulosa cells, using a 9K nylon pig microarray (GPL3729) on granulosa cells from either small healthy antral follicles (SHF) or small antretic follicles (SAF). The images were quantified using AGscan software and the data were managed with BASE software. Statistical analysis was performed using R software. Transcriptomic analysis evidenced 1682 (912) differentially expressed genes with a 5% (1%) FDR between the two follicle classes.     This research project which implicated three laboratories from INRA: "Laboratoire de Genetique Cellulaire" (UMR444-LGC), "Station d'Amelioration Genetique des Animaux" (UR 631-SAGA) and "Physiologie des Comportements et de la reproduction" (UMR 85-PRC) benefited from both European funding through SABRE project and French ANR funding through  GenOvul project.

Keywords: transcriptome analysis, pig, cattle, ovary, folliculogenesis, gene expression, cDNA microarray

overall_design: The data were obtained from 13 RNA samples: 6 small healthy follicles samples and 7 small atretic follicles. They were hybridized on a 9K pig nylon microarray (GPL3729).


title: RpfF-dependent regulon of Xylella fastidiosa

city: Lake Alfred

first: Nian

last: Wang

state: Florida

address: 700 Experiment Station Road

department: Citrus Research and Education Center/Department of Microbiology and Cell Science

institute: University of Florida

summary: Xylella fastidiosa regulates traits important to both virulence of grape as well as colonization of sharpshooter vectors via its production of a fatty acid signal molecule known as DSF whose production is dependent on rpfF.  While X. fastidiosa rpfF mutants exhibit increased virulence to plants they are unable to be spread from plant to plant by insect vectors.  To gain more insight into the traits that contribute to these processes, a DNA microarray for this species was designed and utilized to determine the RpfF-dependent regulon by transcriptional profiling.  A total of 447 genes whose expression was significantly different between the wild type and an rpfF mutant (FDR<0.05) were identified when cells were grown in PW liquid medium. Among them, 165 genes were down-regulated in the rpfF mutant compared to the wild type strain whereas 282 genes were over-expressed.  RpfF function was required for regulation of eleven regulatory and sigma factors including rpfE, yybA, PD1177, glnB, rpfG, PD0954, PD0199, PD2050, colR, rpoH, and rpoD.  In general, RpfF is required for regulation of genes involved in attachment and biofilm formation, enhancing expression of hemagglutinin genes hxfA and hxfB and suppressing most type IV pili and gum genes.  A large number of other RpfF-dependent genes that might contribute to virulence or insect colonization were also identified such as those encoding hemolysin, colicin V, as well as genes with unknown functions.

platform_organism:
Xylella fastidiosa 9a5c
Xylella fastidiosa Temecula1

overall_design: Two samples and one time-points experiment. Two biological and dye-swap replicates of each strain were used.

first: Steven

middle: E

last: Lindow


title: Treg_Chip_Expression_Profile_Healthy_vs_Crohns_Disease

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary:
Regulatory T cells from patients with Crohn´s disease show  an inadequate increase of their frequency in inflamed mucosa.  Using a self-developed mRNA-array (Treg Chip), we wanted to identified candidate genes for a disturbed Treg migration

Keywords: cell type comparison

overall_design: To obtain individual transcription profiles, we isolated CD4+CD25+ and CD4+CD25-  T cells from peripheral blood of 6 patients with Crohn´s disease  (3 patients each with active (aCD) and inactive disease (iCD)) and 11 healthy control (HC) using magnetic cell sorting. Micoarray analysis was done using our self-developped human TReg Chip. RNA from  CD4+CD25+ T cells was isolated. After ethanol precipitation, quality and integrity of the total RNA was controlled. Samples were prepared by applying a double-linear amplification method. Briefly, the first round of RNA-amplification was performed without biotinylated nucleotides. After clean-up of the precipitated aRNA synthesis of second round, first-strand cDNA. Subsequent second-strand cDNA was prepared like in the first round but integrating an additional RNAse H incubation step to digest the aRNA before annealing of the T7T23V primer. The second round of RNA amplification was performed as an in vitro transcription assay in the presence of biotinylated UTP. The concentration of the obtained biotin-labelled cRNA was determined by UV absorbance and its quality as means of product length distribution was again checked. In all cases, 15 µg of each biotinylated cRNA preparation were fragmented and placed in a hybridization cocktail containing four biotinylated hybridization controls (BioB, BioC, BioD, and Cre). Samples were hybridized to individual Human TReg Chips for 16 hours at 42°C. After hybridisation the microarrays were washed, stained with Cy5-streptavidin and read .  Signal intensities were qualified and quantified by means. Spots of poor quality (flag = 3) were excluded from further analysis. To adjust arrays from different experiments, data normalisation based on median signal intensities of the housekeeping genes was carried out. In addition, to adjust the data set from HC (11 donors, 29 chips) to aCD or iCD (3 patients each, 6 chips), median normalised signal intensity for each gene and donor was calculated (MV), standard derivation (SD) was assigned and normalised (CV = SD/MV). Statistical Analysis of Microarrays (SAM) was used to ascertain gene expression changes in CD4+CD25+ regulatory and CD4+CD25- naïve T cells. For this, only genes with a CV < 0.3 in 8/11 HC were evaluated.

first: R

first: S

last: Pfoertner

first: J

last: Maul


title: Genetic variation in parthenogenetic collembolans is associated with differences in fitness and cadmium-induced transcriptome responses

city: Amsterdam

first: Benjamin

last: Nota

state: Noord Holland

address: Plesmanlaan 125

department: Research Facilities

country: Netherlands

institute: Sanquin

summary: Ecotoxicological tests may be biased by the use of laboratory strains that usually contain very limited genetic diversity. It is therefore essential to study how genetic variation influences stress tolerance relevant for toxicity outcomes. To that end we studied sensitivity to cadmium in two distinct genotypes of the parthogenetic soil ecotoxicological model organism Folsomia candida. Clonal lines of both genotypes (TO1 and TO2) showed divergent fitness responses to cadmium exposure; TO2 reproduction was 20% less affected by cadmium. Statistical analyses revealed significant differences between the cadmium-affected transcriptomes; i) the number of genes affected by cadmium in TO2 was only minor (~22%) compared to TO1; ii) 97 genes showed a genotype × cadmium interaction and their response to cadmium showed globally larger fold changes in TO1 when compared to TO2; iii) the interaction genes showed a concerted manner of expression in TO1 while a less coordinated pattern was observed in TO2. We conclude that (1) there is genetic variation in parthenogenetic populations of F. candida, and (2) this variation affects life-history and molecular endpoints relative to cadmium toxicity. This sheds new light on the sources of biological variability in test results, even when the test organisms are thought to be genetically homogeneous because of their parthenogenetic reproduction.

overall_design: Gene expression was measured in two different clones (TO1 and TO2) of the springtail Folsomia candida, after exposure of 2 days to soil containing cadmium (Cd+) and non-spiked (Cd-) soil. A 2 x 2 factorial analysis was performed, to examine the effect of clone (TO1, TO2), of treatment (Cd+, Cd-), and the clone x treatment interaction.

first: Maarten

last: de Korte

first: Bauke

last: Ylstra

first: Nico

middle: M

last: van Straalen

first: Dick

last: Roelofs


title: Helicobacter pylori-mediated Epigenetic Dysregulation of FOXD3 Tumor-suppressive Cascade In Gastric Carcinogenesis [ChIP]

city: Hong Kong

first: Alfred

middle: S

last: Cheng

address: Rm 707, LiKaShing Medical Sciences Building, Prince of Wales Hospital, Shatin

country: Hong Kong

institute: Institute of Digestive Disease, The Chinese University of Hong Kong

type: Genome binding/occupancy profiling by genome tiling array

type: Methylation profiling by genome tiling array

summary:
Forkhead box (Fox) proteins constitute an evolutionarily conserved family of transcriptional regulators whose deregulations lead to tumorigenesis. However, their regulation and function in gastric cancer are unknown. Promoter hypermethylation occurs during Helicobacter pylori (H pylori)-induced gastritis, but whether the deregulated genes contribute to the multi-step gastric carcinogenesis remains unclear. FOXD3 was found to be hypermethylated in a mouse model of H pylori infection and possess tumor-suppressive functions in gastric cancer cell lines. In order to characterize the direct targets of FOXD3 that confer its actions, we performed ChIP-chip in N87 gastric cancer cell line which express low level of FOXD3 in the nuclei of a sub-population of cells.
Promoter hypermethylation occurs during Helicobacter pylori (H pylori)-induced gastritis, but whether the deregulated genes contribute to the multi-step gastric carcinogenesis remains unclear. We used MethylCap-microarray to identify hypermethylated genes in a mouse model of H pylori infection.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
human Samples: Human gastric tumor cell line, N87 was grown in RPMI1640 supplemented with 10% fetal bovine serum. ChIP assays were performed using anti-FOXD3 antibody. The immunoprecipitated-FOXD3 and -IgG DNA were used to probe the Agilent human ChIP-chip arrays.
mouse Samples: Two-condition experiment, H pylori-infected vs. control gastric tissues. 2 dye-swap replicates.


title: Genovul-Bt-Ssc_020410

summary:
In mammals, ovarian folliculogenesis leading to the ovulation of completely mature oocytes is a long and complex process that is regulated at different levels. The mechanisms that underlie the selection of one or several dominant follicles as well as the regulation of the number of ovulating follicles are largely unknown. In this project, we proposed to study the genetic determinism that underlies the difference of ovulation rate between species (cattle and pigs), by studying two processes that exist in ovary: follicular development and follicular atresia.  Towards this purpose, we made a comparative transcriptomics study on granulosa cells.  Pig and cattle comparison was achieved by a transcriptome analysis with a 9K nylon pig microarray (GPL3729) on granulosa cells from either small healthy antral follicles (SHF), small atretic follicles (SAF) or large healthy antral follicles (LHF). The images were quantified using AGscan software and the data were managed with BASE software. Statistical analysis was performed using R software. Transcriptomic analysis on pig and cattle evidenced 997 differentially expressed genes (FDR1%) between the three follicle classes and/or the two species. This research project which implicated three laboratories from INRA: "Laboratoire de Genetique Cellulaire" (UMR444-LGC) , "Station d'Amelioration Genetique des Animaux" (UR 631-SAGA) and "Physiologie des Comportements et de la reproduction" (UMR 85-PRC) benefited from both European funding through SABRE project and French ANR funding through  GenOvul project.

Keywords: transcriptome analysis, pig, cattle, ovary, folliculogenesis, gene expression, cDNA microarray

overall_design: The data were obtained from 34 RNA samples: 10 small healthy follicles samples (6 for sows and 4 for cows), 13 small atretic follicles samples (7 for sows and 6 for cows) and 11 samples for large healthy follicles (6 for sows and 5 for cows). They were hybridized on a 9K pig nylon microarray (GPL3729).


title: WRKY45-dependent rice genes

city: Tsukuba

first: Hiroshi

last: Takatsuji

state: Ibaraki

address: 2-1-2 Kannondai

department: Division of Plant Sciences

country: Japan

institute: National Institute of Agrobiological Sciences

summary: WRKY45-dependent rice genes:  Mock- and benzothiadiazole (BTH)-treated wild-type (Nipponbare NB) rice and mock- and BTH-treated WRKY45-knockdown (W45-kd) rice (line #15) were analyzed in four biological replicates at 12 and 24 h after the treatment.  Mock- and benzothiadiazole (BTH)-treated wild-type (Nipponbare NB) rice and mock- and BTH-treated WRKY45-knockdown (W45-kd) rice (line #3) were analyzed in four biological replicates at 24 h after the treatment.

first: Akira

last: Nakayama


title: Changes in miR expression profile carotid plaques induced by acutely induced flow disturbances in apoe-/- mice on a high fat diet.

first: Andreas

last: Schober

summary: Atherosclerosis is causally related to disturbed flow through low and oscillatory shear stress. In order to study the miR expression profile in atherosclerotic plaques induced by disturbed flow, partial ligation of the carotid artery was performed. This procedure results acutely in severly reduced blood flow and in stenotic lesion formation within 6 weeks in apoe-/- mice on a high fat diet. We compared the miR expression profile  in partially ligated left carotid arteries with the untreated right carotid artery to identify miRs which are involved in plaque formation through flow disturbances.

overall_design: The left carotid arteries of 6 female apoe-/- mice (6-8 weeks) were partially ligated (i.e. the external and internal carotid artery as well as the occipital artery were occluded; blood flow out of the common carotid artery occurs mainly through the superior thyroid artery). Following partial ligation the animals were fed a high fat diet for 6 weeks. Total RNA was isolated from partially ligated left carotid arteries and untreated right carotid arteries (control). MiRs expression profile of the partially ligated carotid arteries  were compared with the control group. Biological replicates: 6 per group. One replicate per array.

first: Malihe

last: Nazari Jahantigh


title: Kidney transplantation (SMD set)

city: Stanford

first: Minnie

last: Sarwal

state: CA

address: 703 Welch Road

department: Pediatric Nephrology

institute: Stanford University

summary:
In this study, we examined transcriptional profiles from 3 different microarray platforms, across 103 peripheral blood samples with and without acute rejection, to find a critical gene-set for the diagnosis of acute renal rejection that matched biopsy diagnosis, irrespective of patient demographics, clinical confounders, concomitant infection, immunosuppression usage or sample processing methods. We hypothesized that changes in peripheral blood expression profiles correlate with biopsy-proven rejection, and that these changes could be used as biomarkers for the diagnosis and prediction of acute rejection.
Disease State: Acute Rejection (AR#sampleid) or Stable (S#sampleid) samples

overall_design: We performed cross-sectional microarray analysis of 103 matched peripheral blood samples collected at a single time point, timed with a biopsy where acute rejection was either confirmed as present (60 AR samples) or absent (62 STA samples). The samples were hybridized to one of 3 microarray platforms: Affymetrix (n=75 the 54K HG-U133_Plus2 Array), Agilent (n=26, 44K oligo Array) and cDNA array (n=21, ~30K cDNA).  Of 103 samples, 14 were used on both Affy and Agilent arrays; 1 was used in cDNA and Agilent array and 2 were used across 3 array platforms.   Microarray data generated from 3 array platforms were cross-compared, by mapping common and overlapping transcripts to Human Gene Organization (HUGO) gene names. Significant gene lists on each platform were identified using Significant Analysis of Microarray (SAM, ref) with a common significance threshold of a false discovery rate (FDR) of <10%. This set contains the data for samples hybridized to cDNA arrays.


title: Murine female muscle 4 month old: control vs Calsequestrin1 genetic ablated (calsequestrin1 null)

status: Public on Dec 24 2012

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

summary: Transcriptional profiling of mouse Extensior Digitorum Longus muscle  comparing control Wilde type (WT)  C57BL/6J, 4 month old female with Calsequestrin 1-null muscles of the same age and gender without any treatment

overall_design: Two-condition experiment, KO vs. WT muscle. Biological replicates: 1 pool with 6 WT controls, 4 KO independently grown. Two replicates per array and dye swap.

first: A

last: Nori

first: M

last: Tomasi

last: Cagnin

first: B

last: Pacchioni

first: C

last: Millino

last: Celegato

last: De Pittà

first: L

last: Tombolan

first: G


title: In the livers of rats treated with thioacetamide for 28 days

city: Fuchu-shi

first: Atsunori

last: Yafune

state: Tokyo

address: 3-5-8 Saiwai-cho

institute: Tokyo University of Agriculture and Technology

summary:
To clarify the regulatory molecular mechanisms behind cell cycle aberrations related to the early stages of hepatocarcinogenesis.
We investigated the early stage of hepatocarcinogenesis using global expression analyses.

overall_design: Livers from rats treated with thioacetamide were subjected to microarray analysis. Results were compared with livers from rats untreated controls (n = 4 animals/group).

first: Eriko

last: Taniai

first: Makoto

last: Shibutani


title: Helicobacter pylori-mediated Epigenetic Dysregulation of FOXD3 Tumor-suppressive Cascade In Gastric Carcinogenesis

last: Cheng

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

overall_design: Refer to individual Series


title: EVALUATION IN A MOUSE PROSTATE CANCER XENOGRAFT MODEL OF THE EFFECTIVENESS OF CYCLOPHOSPHAMIDE METRONOMIC REGIMEN

status: Public on Dec 30 2012

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

summary: The aim of this study was to evaluate in a mouse prostate cancer xenograft model the effectiveness of cyclophosphamide metronomic regimen, as single agent or in combination with standard docetaxel therapy. We used a human prostate cancer cell line to establish tumours in mice and we treated the animals with the combination of 50 mg/kg of cyclophosphamide (per os) and 30 or 10 mg/kg of docetaxel (intraperitoneally) or with the two drugs alone. We found that metronomic cyclophosphamide alone is as efficient as docetaxel in blocking tumor growth (respectively 18% and 21% of the tumor volume reached by control group in 25 days of treatment). Immunohistochemical analysis on tumours and in vitro proliferation and FACS analyses revealed that cyclophosphamide acts downregulating cell proliferation, both in vitro and in vivo. Through microarray analysis we found the upregulation of p21 that probably together with an action on the micro-environment may explain the induction of apoptosis seen in tumor xenografts. Moreover, we found 107 genes differentially expressed upon treatment with the active metabolite of cyclophosphamide and associated with functions such as cellular movement, growth, and proliferation.

overall_design: Cells (2 x 10^6) were seeded in T150 flasks and then treated with vehicle (ctrl), with inactive cyclophosphamide (trt) or with 5.5 μM of active 4-Hydro peroxy cyclophosphamide (trtA) for 10, 24, and 48 hours.

first: Irene

last: Cardillo

first: Enrico

middle: P

last: Spugnini

first: Paola

last: Galluzzo

first: Maria

last: Dell'Anna

first: Mauro

last: Picardo

first: Stefania

last: Crispi

middle: T

last: Piccolo

first: Maddalena

last: Arigoni

first: Daniela

last: Cantarella

first: Gennaro

last: Citro

first: Gianluigi

last: Ferretti

first: Alfonso

last: Baldi


title: SABRE-Bt-Ssc_020410

first: Gwenola

last: Tosser-Klopp

summary:
In mammals, ovarian folliculogenesis leading to the ovulation of completely mature oocytes is a long and complex process that is regulated at different levels. The mechanisms that underlie the selection of one or several dominant follicles as well as the regulation of the number of ovulating follicles are largely unknown. In this project, we proposed to study the genetic determinism that underlies the difference of ovulation rate between species (cattle and pigs).  Towards this purpose, we made a comparative transcriptomics study on granulosa cells.  Pig and cattle comparison was achieved by a transcriptome analysis with a 9K nylon pig microarray (GPL3729) on granulosa cells from either small healthy antral follicles (SHF) or large healthy antral follicles (LHF). The images were quantified using AGscan software and the data were managed with BASE software. Statistical analysis was performed using R software. Transcriptomic analysis on pig and cattle evidenced 252 differentially expressed genes (FDR5%) between the two follicle classes and/or the two species.     This research project which implicated three laboratories from INRA: « Laboratoire de Génétique Cellulaire » (UMR444-LGC) , « Station d’Amélioration Génétique des Animaux » (UR 631-SAGA) and « Physiologie des Comportements et de la reproduction » (UMR 85-PRC) benefited from both European funding through SABRE project and French ANR funding through  GenOvul project.

Keywords: transcriptome analysis, pig, cattle, ovary, folliculogenesis, gene expression, cDNA microarray

overall_design: The data were obtained from 21 RNA samples: 10 small healthy follicles samples (6 for sows and 4 for cows) and 11 samples for large healthy follicles (6 for sows and 5 for cows). They were hybridized on a 9K pig nylon microarray (GPL3729).


title: Murine IgD+ B cells transcriptome analysis when stimulated with LPS and LPS+anti-CD40

first: Tushar

last: Vaidya


title: MEK inhibition exhibits efficacy in human and mouse neurofibromatosis tumors, despite transcriptional feedback onto ERK.

city: Cincinnati

first: Nancy

last: Ratner

state: OH

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hospital Medical Center

summary: Neurofibromatosis Type 1 (NF1) patients develop benign neurofibromas and malignant peripheral nerve sheath tumors (MPNST). These incurable peripheral nerve tumors result from loss of NF1 tumor suppressor gene function, causing hyperactive Ras signaling. Activated Ras controls numerous downstream effectors, but specific pathways mediating effects of hyperactive Ras in NF1 tumors are unknown. Cross-species transcriptome analyses of mouse and human neurofibromas and MPNSTs identified global negative feedback of genes that regulate Ras-Raf- MEK- extracellular signal-regulated protein kinase (ERK) signaling in both species. Nonetheless, activation of ERK was sustained in mouse and human neurofibromas and MPNST. PD0325901, a highly selective pharmacological inhibitor of MEK, was used to test whether sustained Ras-Raf-MEK-ERK signaling contributes to neurofibroma growth in the Nf1fl/fl;Dhh-cre mouse model or in NF1 patient MPNST cell xenografts. PD0325901 treatment reduced aberrantly proliferating cells in neurofibroma and MPNST, prolonged survival of mice implanted with human MPNST cells, and shrank neurofibromas in >80% of mice tested. PD0325901 also caused effects on tumor vasculature. Our data demonstrate that deregulated Ras/ERK signaling is critical for the growth of NF1 peripheral nerve tumors and provide strong rationale for testing MEK inhibitors in NF1 clinical trials.

overall_design:
83 microarrays: Mouse control (15), Mouse neurofibroma (15), Mouse MPNST (18); Human nerve (3), Human neurofibroma (26), Human MPNST (6)

We used the same human tumor samples as in series GSE14038 (dNF, pNF and MPNST). However, instead of referencing gene expression changes to the normal human Schwann cell samples (NHSC) as we did in series GSE14038, we generated three (new) normal nerve samples (samples jan-N1-3) and referenced gene expression changes to those samples.
Moreover, the analysis of series GSE14038 evaluated changes in expression between NHSC, benign tumor subtypes (dNF and pNF), and malignant tumors (MPNST), while our present submission evaluated changes between normal nerve, benign tumors (combined dNF and pNF),and malignant tumors (MPNST).

The Series supplementary 'merged_data.txt' file contains the data for 9,891 transcripts that were statistically different in at least one of the two species and present in both mouse and human data sets.

first: Walter

last: Jessen


title: Murine IgD+ B Cells transcriptome analysis when stimulated with LPS and LPS+anti-CD40 [48 hours]

city: Hyderabad

address: Uppal Road Habshiguda

institute: Centre for Cellular and Molecular Biology

summary:
The effect of LPS and LPS+antiCD40 on the Transcriptome of IgD+ B Cells was analysed here at 48 hours after the stimulation
B-lymphocytes constitute an important aspect of mammalian immune systems by virtue of their ability to produce highly specific antibodies in response to foreign antigens and pathogens. When B-lymphocytes encounter the particular antigen that they are responsive to, they differentiate into two types of cells:  short-lived antibody-secreting plasma cells and long-lived memory cells. While the plasma B cells are responsible for the rapid resolution of a current infection or immune challenge, the memory B cells are responsible for mounting a rapid response to subsequent exposures. Previous work had demonstrated that treatment of mice with a single dose of anti-CD40 at the time of immunization leads to improved secondary responses, suggesting an enhancement of the memory B cell pool. We are currently studying the molecular mechanisms underlying the generation of memory B cells, using CD40 signalling as a tool. We have carried out a Microarray analyses of genome wide gene expression patterns in naïve B-lymphocytes following CD40 signalling, over multiple time points.

overall_design: Analysis used LPS treated IgD+B  cells as control for comparison to LPS+anti-CD40 treated cells (test).Indirect comparisons were made across multiple arrays with raw data pulled from different channels for data analysis and comparison to the control data.

first: Mala

last: Upadhyay

first: G

last: Krishnapriya


title: Systems Modeling of the Rho Signaling Network

city: Cambridge

first: Michael

last: Baym

state: MA

address: MIT 32-G572 / 32 Vassar St.

department: Mathematics

institute: MIT

summary:
Describing the architecture of robust, nonlinear cell signaling networks is essential to gain a predictive understanding of cellular behavior.  The structure of the Drosophila Rho-signaling network, comprised of Rho-family GTPases, RhoGTP Exchange Factors (RhoGEFs), and RhoGTPase Activating Proteins (RhoGAPs), has been particularly difficult to infer due to the highly overlapping function and substrate specificity of network components.  We developed a parameterized modeling approach to predict connectivity amongst components of the Rho-signaling network that was driven by hundreds of mRNA expression profiles derived from RNAi-mediated inhibition or overexpression of component genes. Our model incorporated rate kinetics, transcriptional feedback, and noise. We biochemically validated several novel predicted connections, and used this model to predict Rho-signaling response to particular conditions. While functional redundancy is a feature of all signaling systems that often prevents classical genetic methods from elucidating relationships between components, the methods described here provide the basis for describing any complex network architecture.

Keywords: Genetic modification, RNAi-mediated gene inhibition

overall_design: 129 samples analyzed. Experiments were peformed in batches of 4 containing 1 control/reference sample (transfection of GFP alone) that was prepared in parallel with experimental samples. There are 30 reference samples. The majority of experiments were replicated 2-6 times.

first: Chris

last: Bakal

first: Bonnie

last: Berger

first: Norbert

last: Perrimon


title: Expression of obese mice subjected to diet induced weight loss for 60 days

city: Seattle

first: Zhi

last: Wang

state: WA

address: 1100 Fairview Ave N, M1-C108

institute: Sage Bionetworks

summary:
We used microarrays to study the gene expression dynamics during caloric restricted weight loss in obese mice after feeded with high fat diet.
C57BL/6J male mice were placed on a high fat diet at 10-11 weeks of age in individual cages and kept on the diet until they reached ~ 41 g.
After all the baseline (41g) measurement were made, each mouse  was fed 75% of their ad libitum food intake in two divided daily "meals".  The high fat diet was maintained.

overall_design: Mice were sacrificed after 0, 1, 3, 7, 14, 21 or 42 day of caloric restriction. Hypothalamus, liver, abdominal subcutaneous adipose, mesenteric adipose, perirenal adipose and perigonadal adipose tissues were collected for RNA extraction and hybridization on Affymetrix microarrays.


title: Murine IgD+ B cells transcriptome analysis when stimulated with LPS and LPS+anti-CD40 [24 hours]

summary: B-lymphocytes constitute an important aspect of mammalian immune systems by virtue of their ability to produce highly specific antibodies in response to foreign antigens and pathogens. When B-lymphocytes encounter the particular antigen that they are responsive to, they differentiate into two types of cells:  short-lived antibody-secreting plasma cells and long-lived memory cells. While the plasma B cells are responsible for the rapid resolution of a current infection or immune challenge, the memory B cells are responsible for mounting a rapid response to subsequent exposures. Previous work had demonstrated that treatment of mice with a single dose of anti-CD40 at the time of immunization leads to improved secondary responses, suggesting an enhancement of the memory B cell pool. We are currently studying the molecular mechanisms underlying the generation of memory B cells, using CD40 signalling as a tool. We have carried out a microarray analysis of genome-wide gene expression patterns in naïve B-lymphocytes following CD40 signalling over multiple time points.

overall_design:
The effect of LPS and LPS+antiCD40 on the transcriptome of IgD+ B cells was analyzed 24 hours after stimulation.
The analysis used LPS-treated IgD+B cells as the control for comparison to LPS+anti-CD40-treated cells (test). Indirect comparisons were made across multiple arrays with raw data pulled from different channels for data analysis and comparison to the control data.


title: p100 deficiency alone is insufficient for full activation of the alternative NF-κB pathway: TNF signaling cooperates with p52-RelB activation in the transcriptional regulation of the enpp2/autotaxin promoter

city: Jena

last: Albrecht

address: Wildenbruchstr. 15

institute: BioControl Jena GmbH

summary:
Background: Constitutive activation of the alternative NF-κB pathway leads to marginal zone B cell expansion and disorganized spleen microarchitecture. Furthermore, uncontrolled alternative NF-κB signaling results in the development and progression of cancer. We aimed here to learn about the mechanisms how does the constitutively active alternative NF-κB pathway exert its effects in these malignant processes.
Methodology/Principal Findings: To explore the consequences of constitutive alternative NF-κB activation on genome-wide transcription, we compared gene expression profiles of wild-type and NF-kB2/p100-deficient (p100-/-) primary mouse embryonic fibroblasts (MEFs) and spleens. Microarray experiments revealed 73 differentially regulated genes in p100-/- vs. wild-type MEFs. Chromatin immunoprecipitation (ChIP) assays showed in p100-/- MEFs direct binding of RelB and p52 to the promoter of the enpp2 gene encoding Enpp2/Autotaxin, a protein with an important role in lymphocyte homing and cell migration. Gene ontology analysis revealed upregulation of genes with anti-apoptotic/proliferative activity (enpp2, serpina3g, traf1, rrad), chemotactic/locomotory activity (enpp2, ccl8), and lymphocyte homing activity (enpp2, cd34). Most importantly, biochemical analyses of MEFs and gene expression analyses of mice indicated a crosstalk between classical and alternative NF-κB pathways.
Conclusions/Significance: The present results show that uncontrolled alternative NF-κB signaling is further enhanced by classical NF-κB activation, indicating that p100 deficiency alone is insufficient for full induction of a subset of genes by the alternative NF-κB pathway.

overall_design: cell type comparison (wt vs p100-/-) after genetic modification

first: Agnes

last: Lovas


title: Whole blood-derived miRNA signatures in mice exposed to lipopolysaccharide

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

summary: To profile the expression of microRNAs (miRNAs) in the whole blood of mice in exposure to intraperitoneal lipopolysaccharide (LPS) injection. C57BL/6 mice which received intraperitoneal injections of different concentration (ranged from 10 to 1000 μg) of LPS originated from different bacteria, including E. coli, Klebsiella pneumonia, Pseudomonas aeruginosa, Salmonella enterica, and Serratia marcescens were sacrificed at indicated survival times (2, 6, 24, and 72 h) following LPS injection. The whole blood was drawn and the tissues including lung, brain, liver and spleen were harvested for miRNAs expression analysis with miRNA array (Phalanx Mouse & Rat miRNA OneArray® 1.0). These differentially expressed miRNAs were applied for hierarchical cluster analysis using average linkage and Pearson correlation as a measure of similarity.

overall_design: lung, brain, liver, spleen, blood in experiment mice exposed to 100 ug lipopolysaccharide or control mice exposed to PBS solution were harvested 6 h later (n=3 in each specimens, total 5(tissues)*3(n=3)*2(experiment vs control)=30 arrays were used)

first: Johnson-Chia-Shen

last: Yang

first: Cheng-Shyuan

last: Rau


title: Helicobacter pylori-mediated Epigenetic Dysregulation of FOXD3 Tumor-suppressive Cascade In Gastric Carcinogenesis [MMASS]

first: Alfred

last: Cheng

summary: Promoter hypermethylation occurs in human gastric cancers, but whether the deregulated genes contribute to the multi-step Helicobacter pylori (H pylori)-induced gastric carcinogenesis remains unclear. We used Microarray-based Methylation Assessment of Single Samples (MMASS) to identify differential methylated genes in 10 human gastric cancer tissues.

overall_design: Two-condition experiment, gastric cancers from patients (n = 5 per group) who survived 5 years or more (long-term survivors group) and who died of disease prior to 5 years (short-term survivors group)


title: Dystrophic single myofibers vs control single myofibers

city: Milano

first: Yvan

last: Torrente

address: Francesco Sforza 35

department: Neuroscience

institute: University of the Studies of Milan

summary:
MicroRNA-expression profile of dystrophic single fibres vs wild type single fibers isolated from different muscle of mdx and c57bl mice.
Myofibers were isolated from different muscle type (tibialis, diaphragm and quadriceps of gender- (male) and age- (3 month old and half) matched wt and dystrophic mice).

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: 9 total samples per animal model, 3 replicates per muscle type sample


title: Clear cell sarcoma human HEEBO microarray data

status: Public on Dec 20 2012

city: Houston

first: Hao

last: Hu

state: Texas

address: 1155 Pressler Blvd, Unit 1340

department: Epidemiology

institute: MD Anderson Cancer Center

summary:
Clear cell sarcoma (CCS) of tendons and aponeuroses is a deadly soft-tissue malignancy resembling melanoma, with a predilection for young adults. EWS-ATF1, the fusion product of a balanced chromosomal translocation between chromosomes 22 and 12, is considered the definitional feature of the tumor. Conditional expression of the EWS-ATF1 human cDNA in the mouse generates CCS-like tumors with 100 percent penetrance. Tumors, developed through varied means of initiating expression of the fusion oncogene, model human CCS morphologically, immunohistochemically, and by genome-wide expression profiling. We also demonstrate that while fusion oncogene expression in later stages of differentiation can transform mesenchymal progenitor cells and generate tumors resembling CCS generally, expression in cells retaining stem cell markers permits the full melanoma-related phenotype.

Nielsen et al. ("Molecular characterisation of soft tissue tumours: a gene expression study"; PMID 11965276) used microarray to compare a variety of soft-tissue neoplasms morphologically similar to clear cell sarcoma. In our study, we use their expression data (not previously submitted) in the profiling of our mouse mutant that models clear cell sarcoma.

overall_design: The mRNA profiles of a variety of soft-tissue neoplasm samples are examined by HEEBO microarrays. Included here are a total of 6 different types of tumors, and 5 of them have at least one biological replicate. The authors of "Molecular characterisation of soft tissue tumours: a gene expression study" (PMID 11965276) performed these microarray experiments, including data processing and normalization. We obtained these expression data, and used them to train a support vector machine, which was later used to characterize our mouse model of clear cell sarcoma (data submitted elsewhere).


title: Methylome analysis of nerd1-1 mutant seedlings

city: Lyon

first: François

last: ROUDIER

address: 46 Allée d'Italie

department: Biologie

institute: Ecole Normale Supérieure de Lyon

summary: DNA methylation profiling in nerd1-1 mutant seedlings

overall_design: 2 biological replicates in dye-swap - MeDIP-chip

last: Roudier

first: Vincent

last: Colot

first: Thierry

last: Lagrange


title: Defining a molecular roadmap of cellular reprogramming into iPS cells [miRNA profiling]

city: Boston

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

summary: Factor induced reprogramming is a slow and inefficient process with only rare cells progressing towards induced pluripotent stem cells (iPSCs). Owing to these restraints, mechanistic studies have been limited to analyses of heterogeneous bulk populations undergoing reprogramming and partially reprogrammed cell lines. Here, by combining surface markers (Thy1, SSEA1) and an Oct4-GFP fluorescent reporter allele, we analyzed defined intermediate cell populations poised to becoming iPSCs at the transcriptional and epigenetic levels using genome-wide and single cell technologies. We found that factor-induced reprogramming elicits two discernible transcriptional waves that are characterized by the initial extinction of the somatic gene expression program and the concomitant acquisition of an ESC-like proliferative and metabolic state, followed by the activation of an embryonic pluripotent state primed for differentiation. The first wave is mostly driven by gene activation through c-Myc and gene repression by Klf4, whereas the second wave is a result of gradually activated Oct4/Sox2 targets in cooperation with Klf4 targets and other downstream regulators. While microRNA expression and enrichment for individual histone modifications (H3K4me3 or H3K27me3 enriched promoters) mirrored the observed biphasic transcriptional pattern, the establishment of bivalent domains (H3K4me3/H3K27me3 enriched promoters) occurred more gradually. In contrast, changes in DNA methylation took place predominantly at the end of reprogramming when cells assumed a stable pluripotent state. Cells that became refractory to reprogramming activated the first but failed to initiate the second transcriptional wave. However, introduction of additional copies of the reprogramming transgenes into these cells rescued their ability to form iPSCs, indicating that suboptimal transcription factor levels are a limiting factor for efficient iPSC formation. This integrative analysis allowed us to identify novel genes and microRNAs that enhance reprogramming and surface markers that further subdivide intermediate cell populations. Collectively, our data offer new mechanistic insights into the nature and sequence of molecular events inherent to cellular reprogramming and provide a valuable resource of molecules that may act as roadblocks during iPSC formation.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Time series design with samples sorted into subpopulations according to surface markers. 18 Samples total

first: Jose

last: Polo

first: Endre

last: Anderssen

first: Ryan

last: Walsh

first: Benjamin

last: Schwarz

first: Christian

last: Nefzger

first: Sue

last: Lim

first: Marti

last: Borkent

first: Effie

last: Apostolou

first: Sara

last: Alaei

first: Jeniffer

last: Cloutier

first: Ori

last: Bar-Nur

first: Sihem

last: Cheloufi

first: Matthias

last: Stadtfeld

first: Maria

last: Figueroa

first: Daisy

last: Robinton

first: Sridaran

last: Natesan

first: Ari

last: Melnick

first: Jinfang

last: Zhu

first: Sridhar

last: Ramaswamy

first: Konrad

last: Hochedlinger


title: Airn transcriptional overlap but not its lncRNA products induce imprinted Igf2r silencing.

city: Klosterneuburg

first: Florian

last: Pauler

address: Am Campus 1

country: Austria

institute: IST Austria

type: Expression profiling by genome tiling array

summary:
To test if the imprinted long non-coding RNA (lncRNA) Airn transcription or its product silences the protein-coding Igf2r gene, we shortened the endogenous lncRNA to four different lengths by inserting polyadenylation (polyA) cassettes on the paternal chromosome via homologous recombination in ES cells.
ES cell differentiation was used to recapitulate the developmental onset of Airn and Igf2r imprinted expression and polyA cassettes inserted before (T3, T16, T27) or after (T31, T51) the Igf2r promoter successfully truncated Airn, with the exception of T27.
RNA hybridization to a tiling array (MIRTA) demonstrated loss of Airn upstream of the Igf2r promoter (except T27) and absence of novel spliced variants in all truncation alleles.

To further test the transcriptional overlap model we moved the Airn promoter ~700bp before the Igf2r TSS in ES cells that lack an endogenous paternal Airn promoter and called this cell line FAP (Forward-Airn-Promoter).
RNA hybridization to a tiling array (MIRTA) demonstrated that the moved Airn promoter expresses Airn in wildtype orientation and terminates at the wildtype 3' end.

overall_design: ES cell lines expressing different Airn variants were differentiated on gelatinized dishes after feeder cell depletion and LIF withdrawal by 0.27µM retinoic acid for 5 days and Airn length was assayed.

first: Paulina

last: Latos

first: Martha

middle: V

last: Koerner

first: H

middle: B

last: Şenergin

first: Denise

last: Barlow


title: Transcriptome analysis of nerd1-1 mutant seedlings

first: François

last: ROUDIER

summary: Expression profiling in nerd1-1 mutant seedlings

overall_design: 2 biological replicates in dye-swap - RNA-chip

last: Roudier

first: Vincent

last: Colot

first: Thierry

last: Lagrange


title: Comparison of gene expression profile of bovine muscle samples

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

summary: A bovine oligo microarray platform (GPL7053) was used to profile gene expression from twenty-five (25) bovine biceps brachii samples randomly collected at the slaughterhouse. Four (4) of these animals were suspected for corticosteroids treatment at tymus histological analyses. Eighteen (18) negative controls animals were also included. Analysis with PAM (Prediction Analysis of Microarray) identified ten (10) genes as potential biomarkers that best discriminated control animals from the animals suspected for corticosteroids treatment.

overall_design: In this study, we analyzed forty-three (43) bovine muscle samples, twenty-five (25) unknown samples and eighteen (18) negative controls. Gene expression profiling was performed using the Agilent-015354 Bos taurus Oligo Microarray platform (GPL7053) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Sara

last: Pegolo

first: Luca

last: Bargelloni


title: Transcriptional analysis of prebiotic uptake and catabolism by Lactobacillus acidophilus NCFM

city: Raleigh

first: Todd

middle: Robert

last: Klaenhammer

state: NC

department: Department of Food, Bioprocessing, and Nutrition Sciences

institute: North Carolina State University

summary: The global transcriptome of the wild type Lactobacillus acidophilus NCFM strain (NCK56) was measured during exponential growth on 11 prebiotic carbohydrates and glucose to identify the specific gene cluster differentially upregulated in response to each carbohydrate.

overall_design: Oligoarray hybridization experiments were performed to compare the differential transcriptional profiles of the NCK56 at the early-log (OD600nm 0.3-0.5) phase when cultured in semi-synthetic medium (SSM, Barrangou et al., 2003 PNAS. 100:8957-8962, supplemented with a range of 1% (w/v) carbohydrates, at 37 °C and harvested by centrifugation and flash freezing.     A total of 12 NCK56 cultures were prepared by growing in SSM supplemented with each one of the 12 tested carbohydrates.  Each culture was grown in fresh carbohydrate supplemented SSM with a 1% inoculum from an overnight culture for a total of five subcultured passages. Aliquots of cells were collected at OD600nm of 0.3-0.5 (early log-phase) for total RNA extraction and cDNA synthesis. Labeled cDNA samples from NCK56 were coupled with mono-reactive Cy3 and Cy5 dyes (GE Healthcare Bio-Sciences Corp., Piscataway, NJ),  for two technical replicates on each carbohydrate (e.g. cy3-GOS and cy5-GOS). Comparative hybridizations were performed on samples representing two different carbohydrate cultures at same growth phases labeled with either cy3 or cy5 using a loop design for 12 hybridizations.

first: Joakim

last: Andersen

first: Yong

middle: J

last: Goh

middle: R


title: Preliminaly gene transcriptional profiling of the oesophageal gland of male S. mansoni

status: Public on Dec 19 2012

city: Brisbane

first: Geoffrey

last: Gobert

address: 300 Herston Rd

country: Australia

institute: QIMR

summary: This study provides a transcriptomic analysis of the oesophageal gland of S. mansoni male. The results obtained will help direct future research on the functional aspects of this  tissue, and will allow the characterisation of currently unannotated genes in S. mansoni

overall_design: Quantification of gene expression of S. mansoni male oesophageal gland was achieved by a combination of laser microdissection microscopy (LMM) and oligonucleotide microarray analysis. We compared the gene expression profile of the adult male oesophageal glands with whole male worm controls.

first: Sujeevi

last: Nawaratna

first: Candy

last: Chuah

first: Malcolm

middle: K

last: Jones


title: ChIP-on-chip data from human ES cells-derived CD34+CD43+CD45low cells (hemogenic endothelium-like cells) overexpressing 3xFLAG-Sox17-ERT

status: Public on Dec 14 2012

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

summary: Overexpression of transcription factor Sox17 in human ES cells-derived endothelial cells enhances expansion of hemogenic endothelium-like cells.

overall_design: Human ES cells were differentiated for 6 days in EBs, then CD34+CD43-CD45- endothelial cells were isolated, plated onto OP9 cells, and transduced with the 4OH-tamoxifen (4OHT)-inducible 3×FLAG-tagged Sox17-ERT retrovirus. The cells were seeded on OP9 stromal cells and cultured in the presence of 4OH-tamoxifen. At day 27 of  the co-culture with OP9 cells, CD34+CD43+CD45low hemogenic endothelium-like cells overexpressing Sox17-ERT were collected by CD34 magnetic-activated cell sorting (MACS) and subjected to a ChIP-chip analysis.

first: Yaeko

last: Nakajima-Takagi

first: Atsushi

last: Iwama

first: Mitsujiro

last: Osawa


title: Expression analysis of the effects of methyl-donor deficient diet on male mice

status: Public on Dec 13 2012

city: Leicester

first: Yuri

last: Dubrova

address: University Road

department: Genetics

country: United Kingdom

institute: University of Leicester

summary:
BALB/c male mice were maintained for 8 weeks on a synthetic diet lacking in choline and folic acid and sacrificed 0, 2 and 6 weeks after the end of dietary restrictions. The design of this study is further described in Voutounou, M., C .D. Glen, and Y. E. 2012. The effects of methyl-donor deficiency on mutation induction and transgenerational instability in mice. Mutat. Res. 734(1):1-4 (PMID: 22569175)
The pattern of gene expression in liver and kidney of mice sacrificed immediatelly after the end of dietary restrictions is significatly altered.

overall_design: A ten 12x135K chip study using total RNA extracted from kidney and liver of control and treated BALB/c male mice. The expression of 42,575 genes was measured with two-fold technical redundancy.


title: Expression analysis of the first-generation offspring of irradiated male mice

status: Public on Dec 17 2012

summary:
Investigation of whole genome gene expression level changes in kidney, brain, liver and spleen of the offspring of CBA/Ca and BALB/c male mice exposed to 1 Gy of acute X-rays
The pattern of gene expression of a number of circadian rhythm genes in the offspring of irradiated males is compromised

overall_design: A twenty-two 12x135K chip study using total RNA extracted from kidney, brain, liver and spleen of control CBA/Ca and BALB/c male mice and the first-generation offspring of male mice exposed to 1 Gy of acute X-rays. The expression of 42,575 genes was measured with two-fold technical redundancy.


title: CCND2 rearrangements are the most frequent genetic events in Cyclin D1-negative mantle cell lymphoma [Agilent]

city: Barcelona

first: Sílvia

last: Beà

state: Barcelona

address: Rossello, 153

department: HematoPathology

country: Spain

institute: Hospital Clinic

type: Genome variation profiling by genome tiling array

summary: Cyclin D1-negative mantle cell lymphomas (MCL) are not well characterized, in part due to the difficulties in their recognition. SOX11 has been recently identified as a reliable biomarker of MCL, also expressed in the cyclin D1-negative variant. We investigated 40 lymphomas with MCL morphology and immunophenotype, negative for cyclin D1 expression/t(11;14)(q13;q32) but SOX11-positive. These tumors presented clinically with generalized lymphadenopathy, advanced stage, and had a poor outcome (5-year overall survival 48%). Chromosomal rearrangements of the CCND2 locus were detected in 55% of the cases, with an IG gene as partner in 18/22 cases, in particular with light chains (10 IGK@, 5 IGL@). No mutations in the phosphorylation motifs of CCND1, CCND2 and CCND3 were detected. The global genomic profile and the high complexity of the 32 cyclin D1-negative SOX11-positive MCL analyzed by copy number arrays were similar to the conventional cyclin D1/SOX11-positive MCL. 17p deletions and high Ki67 expression conferred a significantly worse outcome to the patients. This comprehensive characterization of a large series of cyclin D1-negative MCL indicates that these tumors are clinically and biologically similar to the conventional cyclin D1-positive MCL and provides a basis for the proper identification and clinical management of these patients.

overall_design: Copy number analysis of Agilent 1*1M arrays was performed for 27 MCL, with sex-matched control DNAs and without duplicates or dye-swapt.

first: Itziar

last: Salaverria

first: Silvia


title: Canine lymphoma tissues

status: Public on Dec 10 2012

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

summary: Tumor tissues from canine lymphomas with accompanying survival and breed  data.

overall_design: Gene expression analysis of samples representing common histologic subtypes of canine lymphoma.

first: Aric

last: Frantz


title: Characterization of PlcRa, a new PlcR-like regulator involved in oxidative stress response and cysteine metabolism during early stationary phase in Bacillus cereus

city: Guyancourt

first: Eugenie

last: HUILLET

address: La Minière INRA

department: MICA

institute: INRA institute

summary: PlcR, the major virulence transcriptional regulator in the Bacillus cereus group belongs to the RNPP quorum sensor family and is activated through interaction with the secreted heptapeptide PapR7 used as a signalling molecule. We identified using modeling analysis a structural homologue of PlcR, PlcRa, in B. cereus. Whole-genome comparative microarrays identified 119 genes (threshold >3) differentially expressed at the onset of stationary phase in a plcRa mutant. phBC6A51 and phBC6A52 prophage genes were up-expressed in a plcRa mutant. Genes involved in oxidative stress response and in cysteine metabolism, including genes which belong to the CymR regulon, were down-regulated in a plcRa mutant. Accordingly, deletion of plcRa resulted in increased sensitivity to hydrogen peroxide and disulfide induced stresses. We also characterized a major target of PlcRa, the (BC2444) abrB2 gene, encoding a putative regulator belonging to AbrB family. PlcRa controlled CymR-regulated genes through AbrB2 and deletion of abrB2 gene resulted in increased sensitivity to hydrogen peroxide and disulfide induced stresses. In conclusion, we identified a new early stationary transcriptional regulator specific to B. cereus group members involved in oxidative stress response and CymR regulon activation.

overall_design: Two different comparisons were performed (both in biological duplo and Cy5-Cy3 dye-swapped) using 2 different time points: (1) B.cereus WT versus B. cereus plcRa overexpression strain at T1 (one hour after the onset of stationary phase) and T2 (two hours after the onset of stationary phase). (2) B.cereus WT versus B.cereus plcRa deletion strain at T1 and T2

first: Eugénie

last: Huillet

first: Marcel

middle: H

last: Tempelaars

first: Tjakko

last: Abee

first: Didier

last: Lereclus


title: Transcriptome and methylome analyses of the nerd1-1 mutant

first: François

last: ROUDIER

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

overall_design: Refer to individual Series


title: Tomato ripe fruits:Lycb-1 transgenic line vs Wild type

status: Public on Dec 12 2012

city: wuhan

first: Fei

last: Guo

address: shizishan

country: China

institute: Huazhong Agricultural Univesity

summary: The enzyme lycopene β-cyclase (LYCB) is responsible for the synthesis of β-carotene, a valuable component of the human diet. To understand the effect of the high β-Carotene content accumulation on plants carotenoid biosynthesis and global genes expression，a tomato engineered to constitutively express Lycb-1 accumulated a high level of β-carotene was used in this reasearch.Microarray analysis in the ripe stage revealed that the constitutive expression of Lycb-1 differentially regulated a number of genes involved in the synthesis of fatty acids, flavones, flavonols, flavonoids and phenylpropanoids, in the degradation of limonene and pinene, in starch and sucrose metabolism and in photosynthesis.

overall_design: Two-condition experiment, Lycb-1 transgenic lines vs. Wild type. Biological replicates, independently grown and harvested. One replicate per array.


title: Linalool-responsive genes in rice

city: miki

first: kenji

last: gomi

state: kagawa

institute: Kagawa University

summary: The plant volatile linalool plays important roles in the regulation of defense responses in rice. To clarify the response to linalool in rice at gene expression level, we performed a microarray analysis using the Agilent Rice Oligo Microarray (44k, custom-made; Agilent Technologies, Redwood City, CA, USA). As a result, treatment of linalool caused high upregulation of many defense-related genes including pathogenesis-related (PR) genes in rice.

overall_design: An Agilent Rice Oligo Microarray (44k, commercial-made; Agilent Technologies,　Redwood City, CA, USA) was used for the microarray analysis. Total RNA was extracted from leaf blades of five-leaf stage rice plants that had been treated with 10 μM linalool for 1 day. For each biological replicate, material from at least three rice plants was pooled to provide a single sample for RNA extraction. We performed 4 biological replicates for each treatment. All microarray procedures and data analyses were performed according to the manufacturer’s instructions. RNA integrity was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Redwood City, CA, USA). Total RNA (100 ng) was labeled with Cy-3 using an Agilent Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies). Fluorescently labeled targets were hybridized to Agilent Rice Oligo Microarrays for 17 h at 65°C. After hybridization, following wash processes were performed according to the manufacturer’s instructions, and hybridized microarrays were scanned using an Agilent Microarray Scanner (G2565CA; Agilent Technologies). Feature extraction software (Agilent Feature Extraction; Agilent Technologies) was used to delineate and measure the signal intensity of each spot in the array, and to normalize intensities. The background was measured around each spot as local background, calculated by the Feature Extraction software. Statistical data extraction processes were performed according to the manufacturer’s instructions.

first: Kenji

last: Gomi

first: Shiduku

last: Taniguchi

first: Yumi

last: Hosokawa-Shinonaga

first: Akihito

last: Kano

first: Kazuya

last: Akimitsu


title: Identification of avian RIG-I responsive genes during influenza infection

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary: Transcriptional profiling of chicken embryonic fibroblasts (DF-1 cells) comparing the effects of chicken cells transfected with duck RIG-I compared to empty-vector transfected cells following with low or highly pathogenic avian influenza. Goal was to determine the effects of duck RIG-I on influenza-induced immune gene expression.

overall_design: Two-condition experiment. Biological replicates for low pathogenic avian influenza infection: 3 empty-vector transfected replicates, 3 RIG-I transfected replicates. Biological replicates for highly pathogenic influenza infection: 2 empty-vector transfected replicates, 2 RIG-I transfected replicates.

first: Megan

last: Barber


title: Root and shoot Jamonic Acid induction in Brassica oleraceae

status: Public on Dec 18 2012

city: Nijmegen

first: Tom

last: Tytgat

address: Heyendaalseweg 135

department: Ecogenomics

institute: Radboud University Nijmegen

summary:
Brassica oleraceae plants were treated with jasmonic acid either at the roots or two leaves. An acidic (HCl) water sollution with the same pH as the jasmonic acid sollution was also applied to two leaves of the root jasmonic acid treated plants, and to the roots of leaf jasmonic acid treated plants. Control plants received a mock treatment on roots and leaves with acidic water of the same pH as the jasmonic acid sollution.
The whole root system and two systemic leaves were harvested separately at 6, 18 and 30 h after treatment. For each time point, tissue and treatment, three biological replicates (except two replicates for 'Root-Cont-18h' sample) were made consisting of pooled tissue samples from 10 plants. Gene expression was analyzed in both tissues using the 29,000 element Arabidopsis Oligonucleotide Microarrays (Qiagen-Operon Arabidopsis Genome Array Ready Oligo Set version 3.0).

overall_design: Two treatments (root and leaf jasmonic acid) and control treatment. For each treatment, three biological replicates (except two replicates for 'Root-Cont-18h' sample) were taken of two tissues (roots and leaves). Samples were taken at three time points (6, 18 and 30 h). Single color hybridizations were performed, which lead to 53 slides in total.

middle: O


title: Identification of ABA regulated genes in sunflower

status: Public on Dec 09 2012

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

summary: Abiotic stress and more specifically drought is the major limiting factor for sunflower production. ABA is a key hormone for drought stress response in plants and sunflower. This experiment aims at identifying ABA responsive pathways in order to better understand sunflower responses to drought. We studied in parallel microRNA profiles on the same samples and we will try to identify sunflower microRNA regulated genes in response to ABA. The ultimate goal will be improve sunflower breeding through selection of key drought response genes.-The experiment consisted of 3 repeats of four 12-day-old-plantlets of sunflower genotype SF193 (INRA code: XRQ) grown in growth chamber conditions and submitted to a 6-hour-treatment of 10 µM absissic acid or not. Growth conditions were 14h light at 23°C and 10h night at 20°C under fluorescent bulbs. Plants were grown in 6 hydroponic boxes containing 20 litres of aerated liquid culture medium (as described in Massonneau et al., 2001 Planta). Leaves (not cotyledons) 1 to 4 were harvested 4 hours after light onset and frozen immediately in liquid nitrogen.

overall_design: 6 arrays - SUNFLOWER; treated vs untreated comparison

first: Sandrine

last: Arribat

last: Balzergue

first: Nicolas

last: Langlade

first: Marie-Laure

last: Martin-Magniette


title: Effects of a 8-week training on human skeletal muscle

city: Toulouse

first: Nathalie

last: Viguerie

address: Avenue Poulhes

institute: INSERM

summary:
Context:  Exercise training is a plausible model for identification of molecular mechanisms that cause metabolic-related changes in human skeletal muscle.

Objective: The goal was to explore the molecular basis of the adaptation of skeletal muscle to exercise training.

Design and Intervention: Obese male subjects were subjected to an individualized supervised training program targeted in order to optimize lipid oxidation during 8 weeks.

Main Outcome Measures: Primary outcome measures were gene expression profiling of skeletal muscle. Body composition, oral glucose tolerance test, Resting metabolic rate, respiratory quotient, maximal oxygen uptake and metabolic biochemistry were also assessed.

overall_design:
Overall Design
The obese (BMI 30-36) male volunteers (age 32-42)  were asked to refrain from vigorous physical activity 48h before presenting to the clinical investigation centre, and ate a weight-maintaining diet consisting of 35% fat, 16% protein, and 49% carbohydrates two days before the experiment. Muscle biopsies of Vastus Lateralis weighing 60–100 mg were obtained using the Bergstrom technique, cleaned and snap-frozen in liquid nitrogen. Resting metabolic rate, respiratory quotient and maximal oxygen uptake were assessed. The subjects were investigated at baseline and after 8 weeks of supervised aerobic exercise training program consisting of daily sessions of 45-60 min of endurance exercise, 5 days a week, at least 48-72h after the last acute exercise bout. Skeletal muscle biopsies were obtained at the beginning and at the end of the protocol. Transcriptome analysis compared 8 subjects before vs. after training using arrays using a common reference design (Cy5 dye was incorporated into all muscle RNA samples, while a reference RNA pool made of the mix of commercial human liver, adipose tissue and skeletal muscle RNA was labelled with Cy3 dye (Applied Biosystems/Ambion, Foster City, USA)( and whole genome 4x44k oligonucleotide arrays (Agilent Technologies).

first: Emilie

last: Montastier

first: Aurele

last: Besse-Patin

first: Marion

last: Combes

first: Cedric

last: Moro

first: Dominique

last: Langin


title: Microarray Analysis of Toxicogenomic Effects of Triclosan on Mycobacterium bovis BCG

city: Ft. Meade

first: Prashanthi

last: Mulinti

state: MD

address: 701 Mapes Road

department: OPP/BEAD

institute: USEPA

summary: Global gene expression analysis of Mycobacterium bovis BCG following Triclosan treatment using Affymetrix GeneChip arrays. Results from this study provide insight into the molecular mechanisms underlying the cellular response of Mycobacterium bovis BCG to Triclosan

sample_organism: Mycobacterium tuberculosis variant bovis BCG

overall_design: We conducted three independent microarray experiments (biological replicates) in the absence (control) and the presence (experimental) of triclosan. Fold change was calculated as a ration between the signal averages of three untreated (control) and three triclosan-treated (experimental) cultures for 0, 10 and 60min exposures.

first: C

last: San Miguel

first: P

first: H

last: Jang

first: F

last: Toghrol


title: Yeast spore germination: time course

city: Gothenburg

first: Abraham

last: Ericsson

address: Medicinaregatan 9C

department: Cell and Molecular Biology

country: Sweden

institute: Gothenburg University

summary: The process of Saccharomyces cerevisiae spore germination includes breakage of dormancy, morphological changes and resumption of vegetative growth. We have determined the global transcriptional response during the first two hours of spore germination in response to rich growth medium and glucose alone, and identified possible transcription factors regulating the different transcriptional programs.

overall_design: Saccharomyces cerevisiae Y55 spores subjected to YPD and glucose 2%. Samples are taken in triplicates (except for glucose 0 min were duplicates were taken) in time course series after glucose and nutrient addition. Total of 18 samples. RNA from dormant spores was used as reference RNA for all microarrays.

first: Cecilia

last: Geijer

first: Ivan

last: Pirkov

first: Wanwipa

last: Wongsangnak

first: Marcus

last: Krantz

first: Jens

last: Nielsen

first: Stefan

last: Hohmann


title: AIM2-responsive genes in colorectal tumor cells

city: Mannheim

first: Li

last: Li

address: Theodor-Kutzer-Ufer

institute: University Heidelberg

summary:
Absent in Melanoma 2 (AIM2) is a member of the HIN-200 family of hematopoietic, IFN-inducible nuclear proteins associated with infection defense and tumor pathology. Recently, AIM2 was found to act as a DNA sensor in innate immunity. In addition, a high frequency of AIM2-alterations was observed in microsatellite unstable tumors. To elucidate AIM2 function in colorectal tumors, we here addressed AIM2-responsive genes by microarray. Among genes up-regulated by AIM2, there were a number of interferon-stimulated genes (ISGs: IFIT1, IFIT2, IFIT3, IFI6, IRF7, ISG15, HLA-DRA, HLA-DRB, TLR3 and CIITA) as well as genes involved in intercellular adhesion and matrix remodeling. Expression of ISGs correlated with expression of AIM2 in ten different IFN-γ treated colorectal cancer cell lines. Moreover, knock-down of AIM2 resulted in reduced expression of HLA-DRA, HLA-DRB, and CIITA in IFN-γ treated cells. IFN-γ independent induction of HLA-DR genes and their encoded proteins was also demonstrated upon transient induction of AIM2. STAT-signaling was not involved in IFN-γ independent induction of ISGs, arguing against participation of cytokines released in an autocrine manner. Our data indicate that AIM2 mediates IFN-γ dependent and independent induction of several Interferon stimulated genes (ISGs) including genes encoding the MHC II antigens HLA-DRα and β.
we used microarray techniques to define genes responsive to AIM2 expression in colorectal tumor cells.

overall_design: HCT116 is a colorectal tumour cell line with no evidence for AIM2 expression which served as background for gene transfection. B8 and D1 were transfected subclones with persisting expression of AIM2. Gene expression of B8 and D1 was compared with that of mock transfected control cells.

first: Norbert

last: Gretz

first: Johannes

last: Gebert

first: Susanne

last: Dihlmann


title: Methylome analysis of Arabidopsis thaliana Col-0 primary root

status: Public on Dec 07 2012

city: Lyon

first: François

last: ROUDIER

address: 46 Allée d'Italie

institute: Ecole Normale Supérieure de Lyon

summary: DNA methylation profiling in Col-0 wild type primary root

overall_design: 2 biological replicates in dye-swap - MeDIP-chip

first: Vincent

last: Colot

first: Francois

last: Roudier


title: Expression changes in MEL cells upon differentiation and Ldb1 knockdown

status: Public on Dec 11 2012

city: Bethesda

first: Ryan

last: Dale

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: Carbonic anhydrase 1 (Car1), an early specific marker of the erythroid differentiation, has been used to distinguish fetal and adult erythroid cells since its production closely follows the γ- to β-globin transition, but the molecular mechanism underlying transcriptional regulation of Car1 is unclear. Here, we show that Car1 mRNA decreases significantly when erythroid differentiation is induced in MEL cells. The Ldb1 protein complex including GATA1/SCL/LMO2 binds to the Car1 promoter in uninduced cells and reduced enrichment of the complex during differentiation correlates with loss of Car1 expression. Knockdown of Ldb1 results in a reduction of Ser2 phosphorylated RNA Pol II and Cdk9 at the Car1 promoter region, suggesting that Ldb1 is required for recruitment of Pol II as well as the transcription regulator P-TEFb to enhance elongation of Car1 transcripts. Taken together, these data show that Ldb1 forms a regulatory complex to maintain Car1 expression in erythroid cells.

overall_design: Expression analysis of induced and uninduced MEL cells after control or Ldb1 shRNA knockdown.

first: Ann

last: Dean


title: ChIP analysis on a custom tiling array of U251 human glioblastoma cell line

city: Hamburg

first: Genrich

last: Tolstonog

department: Department of Tumor Virology

institute: Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology

summary: Missense mutations in the TP53 gene are frequent genetic alterations in human tumor tissue and cell lines. In contrast to wild-type p53, the mutant p53 (mutp53) protein has lost the transcriptional activity towards pro-apoptotic and growth arrest genes, but retained the property to interact with DNA in a structure-specific fashion. Expression of mutp53 is advantageous for tumor cells, however the molecular mechanism of mutp53 action is still not known. We used the glioblastoma-derived U-251 MG human cell line to analyze DNA binding of mutant p53 (R273H mutation) on a Nimblegen custom 135k tiling array and to correlate mutp53 binding regions with the epigenetic state and occupation by other transcription factors (ETS1 and SP1). We found that mutp53-binding regions are G/C-rich and are located around transcriptional start sites (TSS) of many protein-coding genes, which in most cases are active, but are not always regulated upon transient mutp53 depletion. We propose a model which does not only rely on interactions of mutp53 with diverse transcriptional regulators at active promoters, but primarily is based on a DNA binding activity of mutp53.

overall_design: We designed a Nimblegen custom 135k tiling array that covers a large set of putative and known p53 (wild-type and mutant) target genes in the human genome. For analysis of the epigenetic state of genes covered by the tiling array in control and mutant p53-depleted U251 cells we focused on changes in active histone marks, H3K4me3 and H3K9Ac, and RNA polymerase II recruitment and processivity. H3K4me3 and H3K9Ac marks are enriched in active promoter regions and the phosphorylation of serine 5 (S5-P) and serine 2 (S2-P) in the CTD of RNA polymerase II have been described to define initiated and elongating complexes, respectively. We performed the ChIP-chip experiments for H3K4me3, H3K9Ac, RNA polymerase II (S5-P) and RNA polymerase II (S2-P) from U251 cells transfected with p53-specific siRNA or control siRNA (2 biological replicates each). To analyze binding of mutant p53 to the genes covered by the tiling array we performed mutant p53 ChIP-chip experiments in 4 biological replicates of. In addition, we analyzed the distribution of SP1 and ETS1 binding sites in 3 biological replicates.

first: Timo

last: Quante

first: Benjamin

last: Otto

first: Wolfgang

last: Deppert


title: RNAs binding to the nucleoid protein HU in Escherichia coli

first: Andrei

middle: Nikolai

last: Trostel

state: Maryland

address: 9000 Rockville Pike, Building 37, Room 5138

department: Laboratory of Molecular Biology

summary: HU is a conserved prokaryotic nucleoid-associated protein known for its role in DNA binding and maintaining negative supercoils in DNA. HU also binds to a few RNAs but the natural targets are unknown. To understand the biology of HU interactions with RNA in Escherichia coli, potential HU-RNA in vivo complexes were immunoprecipitated and bound RNAs were examined by hybridization to whole-genome tiling arrays. We observed HU associations with rRNA, multiple tRNAs, a few sRNAs and a small, distinct set of mRNAs. More importantly, we also identified associations between HU and ten intragenic non-coding (nonc) RNAs, two of which are homologous to the annotated Bacterial Interspersed Mosaic Elements (BIME) and boxC elements; the other eight RNAs have not been annotated. We confirmed binding of HU to BIME RNA in vitro. Since HU and some unidentified RNAs have been implicated in the nucleoid structure, we explored an idea that HU, along with some or all of the nonc RNA species discovered here bind to BIME and/or boxC repeats to condense chromosomal DNA in a specific fashion. We propose that nonc RNAs may interact with both HU and DNA repeats to form ternary complexes, which are the anchoring points separating different chromosomal domains.

overall_design: RNAs binding to HU were isolated from the strain containing HUb protein tagged with eight myc tags using anti-myc antibody. Total RNA and RNA untreated with anti-myc antibody served as controls.

first: Mirjana

last: Macvanin

first: Rotem

last: Edgar

first: Feng

last: Cui

first: Victor

last: Zhurkin

first: Sankar

last: Adhya


title: Expression analysis of wildtype (OregonG) and upSET mutant ovaries.

city: Seattle

first: Hector

last: Rincon-Arano

state: Washington

address: 1100 Fairview Ave N

department: Basic Science Division

institute: Fred Hutchinson Cancer Research Center

summary: Developmental gene expression results from the orchestrated interplay between genetic and epigenetic mechanisms. Here, we describe upSET, a transcriptional regulator encoding a SET domaincontaining protein recruited to active and inducible genes in Drosophila. However, unlike other Drosophila SET proteins associated with gene transcription, UpSET is part of an Rpd3/Sin3-containing complex that restricts chromatin accessibility and histone acetylation to promoter regions. In the absence of UpSET, active chromatin marks and chromatin accessibility increase and spread to genic and flanking regions due to destabilization of the histone deacetylase complex. Consistent with this, transcriptional noise increases, as manifest by activation of repetitive elements and off-target genes. Interestingly, upSET mutant flies are female sterile due to upregulation of key components of Notch signaling during oogenesis. Thus UpSET defines a class of metazoan transcriptional regulators required to fine tune transcription by preventing the spread of active chromatin.

overall_design: A six chip study using total RNA recovered from three separate dissections wild-type ovaries and three separate dissections of epic mutant ovaries.  Each chip measures the expression level of 15,473 genes from Drosophila melanogaster with four 60-mer probes per target gene. Investigation of whole genome gene expression level changes in epic(e00365) mutants, compared to the wild-type strain (OregonG).  The mutation was generated by the insertion of the PBac{WH}CG9007e000365 transposon. The mutants analyzed in this study are further described in Rincon-Arano H., et al 2012. in Press.

last: Basom


title: Aberrant brain miRNA target and miRISC gene expression in the anx/anx anorexia mouse model

status: Public on Dec 08 2012

city: Badalona

first: Lauro

last: Sumoy

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

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

summary: The anorexia mouse model, anx/anx, carries a spontaneous mutation not yet identified and homozygous mutants are characterized by anorexia-cachexia, growth failure and abnormal behavior, such as head weaving, hyperactivity, and ataxia.  In order to test if miRNA machinery could influence the phenotype of these mice, RNA samples from mutant and wild type hypothalamus and cortex were hybridized to microarray chips based on LNA probes allowing the detection of 279 mouse miRNAs and to Agilent 44k chips to analyze the whole mRNA transcriptome.  In anx/anx hypothalamus we found that predicted miRNA targets were preferentially upregulated in a lineally dependent manner according to the number of miRNA target sites in each mRNA (p = 10-139). Conversely, we observed that in anx/anx cortex mRNAs predicted to be targeted by miRNAs were preferentially downregulated (p < 10-74), suggesting a de-regulation of genes targeted by miRNAs in two brain areas in anx/anx mice. A closer look to the mRNA transcriptome allowed us to identify upregulation of five miRISC genes, including Dgcr8 and Fmr1, and Ago2, which were later confirmed by Real Time PCR.   The results suggest that miRNA machinery might be impaired in anx/anx mice and propose its involvement in inflammatory/cancer-associated anorexia-cachexia. The data also support the previously reported link between miRNA machinery and ataxia. Further functional studies and the cloning of the anx gene should be done in order to elucidate the causality of miRNA machinery and miRNA target de-regulation, its relation with the anx/anx phenotype and to propose this mouse as a model for miRNA research.

overall_design: Total RNA expression profile comparison between 3 pairs of anx/anx mice and wild type littermates in brain neocortex. MicroRNA expression profile comparison between 3 pairs of anx/anx mice and wild type littermates in brain neocortex.

first: Josep

last: Mercader

first: Estivill

last: Xavier


title: Transcriptional changes associated to resistance to the cell wall active bacteriocin Lcn972

status: Public on Dec 06 2012

city: Villaviciosa

first: Beatriz

last: Martinez

address: Paseo Río Linares s/n

institute: IPLA-CSIC

summary: Lcn972 is a non-modified bacteriocin that targets exclusively Lactococcus sp. Addition of Lcn972 inhibits cell wall biosynthesis at the septum by binding to the cell wall precursor lipid II. Resistance to Lcn972 develops upon selection with subinhibitory concentrations. The transcriptome of the highly resistant L. lactis D1 derived from the susceptible strain L. lactis MG1614 was compared. Fourteen genes were significantly up-regulated and 29 were down-regulated (expression change > 2-fold, p<0.001). Down-regulation was mostly found in sugar catabolic genes. Up-regulated genes included members of the cell envelope stress (CesR) regulon, the penicillin-binding protein pbpX and llmg2447, which may encode a putative extracytoplasmic function (ECF) anti-sigma factor located downstream of a non-functional ECF-sigX. Up-regulation of llmg2447 was linked to integration of IS981 that exchanged the -35 promoter region of llmg2447. Over-expression of llmg2447 resulted in highly Lcn972-resistant L. lactis transformants.

platform_organism: Lactococcus cremoris subsp. cremoris MG1363

overall_design: The transcriptomes of Lactococcus lactis MG1614 susceptible to Lcn972 and L. lactis D1 resistant to Lcn972, grown under laboratory conditions, were compared using four biological replicates.

first: B

first: Anne

last: de Jong


title: Gene expression profiling in senescence leaves from senescence-inducible LEC2 in Arabidopsis

status: Public on Dec 05 2012

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

summary:
The profiling was conducted with the 385K Microarray manufactured at NimbleGen, Inc (http://www.nimblegen.com/) designed from 30,386 genes of Arabidopsis (TAIR v.6).
RNA samples of leaves of S1 (100% green leaf from 40 days plant) and S3 (more than 50% yellow leaf) senescence stages from senescence-inducible LEC2 transgenic plant, OIL21 were subjected for analysis of Arabidopsis 385K transcriptome. Expression of 3,025 genes were significantly changed with log2 ratios greater than 1.0 or less than -1.0 in S1 or S3 stage (p value <0.05), among which 1491 were up-regulated and 1534 were down regulated. Gene annotation revealed that 7.4% genes, 223 out of 3,025 changed by LEC2 were encoded transcription factors (TF). 106 TFs were up-regulated and 115 TFs were down-regulated.

overall_design: A total of 9 chips were used for microarray. Total RNAs were extracted from senescence leaves at S1 and S3 stages of wild-type and senescence-inducible LEC2 transgenic Arabidopsis. Experiments were triplicated.

first: Hyun

middle: U


title: Expression data from silkworm posterior silk glands at the late larval stages

city: Hangzhou

first: Bo-xiong

last: Zhong

address: 268 Kaixuan Road

institute: College of Animal Sciences, Zhejiang University

summary:
The silkworm silk gland is one of the most efficient protein synthesis systems among all organisms. Its amazingly efficient protein synthesis makes the silk gland a desirable object for basic studies on gene expression and regulation and for biotechnological applications. At the early stages of the fifth (final) instar, the cellular structures necessary for the synthesis of fibroin are rapidly formed, and at the later stage the synthesis of fibroin proceeds at a maximum rate. The posterior silk gland (PSG) is the longest suborgan and is responsible for the synthesis of the silk core protein fibroin, which is composed of heavy (H) and light (L) chains plus P25.
We used microarrays to detail the global programme of gene expression in silkworm PSG during the late larval stages, including the fourth molting (M4) and day 1 (V1), day 3 (V3), day 5 (V5), and day 7 (wandering stage, W) of the fifth instar, and to reveal the correlations of differential expression genes with the PSG development and fibroin synthesis.

overall_design: Silkworm PSGs were collected at M4, V1, V3, V5, and W stages for RNA extraction and hybridization on 23K Silkworm Genome Arrays (CapitalBio Corp., Beijing, China). Three groups of biological replicates were prepared at each time point.Dual-dye experiments were performed for the PSG at M4, V1, V3, V5, and W; a total of 15 samples were tested including three biological replicates at each stage. Aliquots of each test sample were pooled as a common reference sample (CKA). The test samples and CKA were labeled with Cy3 and Cy5, respectively.


title: Grain gene expression profile at early developmental stage

status: Public on Dec 03 2012

city: Tsukuba

first: Yutaka

last: Sato

state: Ibaraki

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

summary: Gene expression profiling of ovary at 1-10 days and embryo at 4-10 days after flowering (DAT) was performed to obtain an overall signature of the rice transcriptome during early grain development.

overall_design: After the onset of pollination, ovary samples at 1-10 DAT and embryo samples at 4-10 DAT with two replicates were collected and used for microarray analysis. A total of 20 microarray data for ovary and 14 microarray data for embryo were obtained.

first: Baltazar

last: Antonio

first: Hinako

last: Takehisa

first: Nobukazu

last: Namiki

first: Yoshiaki

last: Nagamura


title: Embryo and endosperm gene expression profile at ripening stage

summary: Gene expression profiling of embryo and endosperm at 7-42 days after flowering (DAT) was performed to obtain an overall signature of the rice transcriptome during grain development and maturation.

overall_design: After the onset of pollination, embryo and endosperm samples at 7, 10, 14, 21, 28 and 42 DAT with three replicates were collected and used for microarray analysis. A total of 36 embryo and endosperm microarray data were obtained.

first: Kazuhiko

last: Sugimoto


title: Gene expression profile of inflorescence at early developmental stage

summary: Gene expression profiling of infrorescence was performed to obtain overall signature of transcriptome at early developmental stages of inflorescence.

overall_design: After the reproductive stage transition, inflorescence samples corresponding to the early stages of development were collected based on the size. We obtained inflorescence samples ranging from 0.6 to 10 mm in two replicates representing 8  stages in inflorescence development. A total of 16 microarray data were obtained.


title: Rice global gene expression profile in response to plant hormones

summary: A time course gene expression profiling of rice treated with various plant hormones (abscisic acid, gibberelin, auxin, brassinosteroid, cytokinin and jasmonic acid)  was performed to obtain an overall signature of the rice transcriptome in response to each phytohormone.

overall_design: The transcriptome of rice seedlings treated with various plant hormones such as abscisic acid (ABA), gibberellic acid 3 (GA3), indole-3-acetic acid (IAA), brassinolide (BL), trans-zeatin (tZ), and jasmonic acid (JA) was characterized by microarray analysis. Seven-day old seedlings were transferred in culture solutions with specific hormones and in culture solution without hormone to serve as control (mock treatment). Root samples were collected and analyzed in three replicates at pretreatment (control) and after 15 min, 30 min, 1 h, 3 h and 6 h incubation in culture solutions with each hormone. Shoot samples were collected and analyzed in two replicates at pretreatment (control) and after 1 h, 3 h, 6 h and 12 h incubation culture solutions with each hormone. A total of 93 microarray data for root and 50 microarray data for shoot were obtained.


title: Continuous gene expression profile of root at daytime throughout the entire growth of rice in the field

summary: A continuous gene expression profiling of roots was performed during daytime at regular interval from transplanting until harvesting to characterize the transcriptional and physiological changes in the root system of rice throughout the entire growth under natural field conditions.

overall_design: Roots were sampled at daytime (12:00) at 7-day intervals encompassing 14 different growth stages. All samples were obtained from rice plants grown in the field during the 2008 cultivation season.