title: Differential Gene Expression Profile in Bovine Blastocysts Resulting from Hyperglycemia Exposure during Early Cleavage Stages

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

institute: CHU Sainte Justine

summary: IVP blastocysts exposed to hyperglycaemia during early phase of development, i.e from zygote to 8-16 cells stages. Genes expression analysis is done at day 7.5 (7 days of embryo culture).

overall_design: Total RNA form glucose treated blastocysts (4 replicates of 10 embryos each) and control treated blastocysts (4 replicates of 10 embryos each) were compared on a 2-color micro-array design and dye swap.

first: Isabelle

last: Dufort

first: Christian

last: Vigneault

first: Marc-André

last: Sirard


title: Expression analysis of Candida albicans WO-1 grown in glucose or xylose

status: Public on Oct 20 2011

city: Carlisle

first: Dana

middle: Jasmine

last: Wohlbach

state: PA

department: Biology

country: USA

institute: Dickinson College

type: Expression profiling by genome tiling array

summary: Investigation of whole genome gene expression level changes in Candida albicans WO-1 grown aerobically in xylose, compared to the same strain grown aerobically in glucose.

overall_design: A six array study using total RNA recovered from three separate cultures of Candida albicans WO-1 grown in glucose and three separate cultures of Candida albicans WO-1 grown in xylose.  Each array measures the expression level of 373,067 probes (average probe length 55.2 +/- 4.0 nt) tiled across the Candida albicans WO-1 genome with a median spacing distance of 31 nt.  During data processing, probes are filtered to include only those probes corresponding to annotated protein-coding genes.

middle: J

first: Audrey

middle: P

last: Gasch


title: Expression analysis of Candida tenuis NRRL Y-1498 grown in glucose or xylose

summary: Investigation of whole genome gene expression level changes in Candida tenuis NRRL Y-1498 grown aerobically in xylose, compared to the same strain grown aerobically in glucose.

overall_design: A six array study using total RNA recovered from three separate cultures of Candida tenuis NRRL Y-1498 grown in glucose and three separate cultures of Candida tenuis NRRL Y-1498 grown in xylose.  Each array measures the expression level of 363,196 probes (average probe length 53.1 +/- 3.8 nt) tiled across the Candida tenuis NRRL Y-1498 genome with a median spacing distance of 24 nt.  During data processing, probes are filtered to include only those probes corresponding to annotated protein-coding genes.


title: Expression analysis of Lodderomyces elongisporus NRRL YB-4239 grown in glucose or xylose

summary: Investigation of whole genome gene expression level changes in Lodderomyces elongisporus NRRL YB-4239 grown aerobically in xylose, compared to the same strain grown aerobically in glucose.

overall_design: A six array study using total RNA recovered from three separate cultures of Lodderomyces elongisporus NRRL YB-4239 grown in glucose and three separate cultures of Lodderomyces elongisporus NRRL YB-4239 grown in xylose.  Each array measures the expression level of 371,451 probes (average probe length 54.1 +/- 4.1 nt) tiled across the Lodderomyces elongisporus NRRL YB-4239 genome with a median spacing distance of 33 nt.  During data processing, probes are filtered to include only those probes corresponding to annotated protein-coding genes.


title: Chromosomal aberrations and aneuploidy in oral potentially malignant lesions: distinctive features for tongue.

city: Genova

first: PAOLA

last: SCARUFFI

state: GE

address: LARGO R. BENZI, 10

country: Italy

institute: "San Martino" Hospital

type: Genome variation profiling by genome tiling array

summary: The mucosae of the oral cavity are different at the histological level but are all exposed to common genotoxic agents. As a result of this exposure, changes in the mucosal epithelia develop giving rise to Oral Potentially Malignant Lesions (OPMLs), which with time may in turn progress to Oral Squamous Cell Carcinomas (OSCCs). Therefore, much effort should be devoted to identify features able to predict the likeliness of progression associated with an OPML. Such features may be helpful in assisting the clinician to establish both appropriate therapies and follow-up schedules. Here, we report a pilot study that compared the anatomical subsites of OPMLs development with occurrence of DNA aneuploidy and chromosomal copy number aberrations (CNAs). Multiple samples from histologically diagnosed OPMLs were processed for high resolution DNA flow cytometry (hr DNA-FCM) in order to determine the relative DNA content expressed by the DNA index (DI). Additionally, array-Comparative Genomic Hybridization (a-CGH) analysis was performed on FCM-sorted nuclei subpopulations based on DI values. Tongue OPMLs were more frequently associated with DNA aneuploidy and CNAs than OPMLs arising from all the other mucosal subsites. We suggest that the follow-up and the management of the patients with tongue OPMLs should receive a distinctive special attention. Clearly, this conclusion should be validated in a prospective clinical study.  exposed to common genotoxic agents. As a result of this exposure, changes in the  mucosal epithelia develop giving rise to Oral Potentially Malignant Lesions (OPMLs),  which with time may in turn progress to Oral Squamous Cell Carcinomas (OSCCs).  Therefore, much effort should be devoted to identify features able to predict the  likeliness of progression associated with an OPML. Such features may be helpful in  assisting the clinician to establish both appropriate therapies and follow-up  schedules. Here, we report a pilot study that compared the anatomical subsites of  OPMLs development with occurrence of DNA aneuploidy and chromosomal copy  number aberrations (CNAs). Multiple samples from histologically diagnosed OPMLs were processed for high resolution DNA flow cytometry (hr DNA-FCM) in order to determine the relative DNA content expressed by the DNA index (DI). Additionally, array-Comparative Genomic Hybridization (a-CGH) analysis was performed on FCM-sorted nuclei subpopulations based on DI values. Tongue OPMLs were more frequently associated with DNA aneuploidy and CNAs than OPMLs arising from all the other mucosal subsites.  We suggest that the follow-up and the management of the patients with tongue  OPMLs should receive a distinctive special attention. Clearly, this conclusion should  be validated in a prospective clinical study.

overall_design: We analyzed: 19 samples (4 aneuploid and 15 diploid components) deriving from oral potentially malignant lesions without dysplasia obtained of 16 patients; 14 samples (2 aneuploid and 12 diploid components) deriving from oral potentially malignant lesions with dysplasia obtained from 11 patients (two patients had multiple dysplastic lesions); 2 samples from visually normal mucosa in the near field obtained from two patients with dysplastic lesions. All the aneuploid samples had a purity of at least 90%.

first: Paola

last: Scaruffi

first: Simona

last: Coco

first: GianPaolo

last: Tonini

first: Massimo

last: Maffei

first: Alessandra

last: Donadini

first: Walter

last: Giaretti


title: Expression analysis of Pichia stipitis CBS 6054 grown in glucose or xylose

summary: Investigation of whole genome gene expression level changes in Pichia stipitis CBS 6054 grown aerobically in xylose, compared to the same strain grown aerobically in glucose.

overall_design: A six array study using total RNA recovered from three separate cultures of Pichia stipitis CBS 6054 grown in glucose and three separate cultures of Pichia stipitis CBS 6054 grown in xylose.  Each array measures the expression level of 374,100 probes (average probe length 53.6 +/- 4.1 nt) tiled across the Pichia stipitis CBS 6054 genome with a median spacing distance of 33 nt.  During data processing, probes are filtered to include only those probes corresponding to annotated protein-coding genes.


title: Chlamydomonas growth under nitrogen starvation

status: Public on Oct 19 2011

city: Bielefeld

first: Jörg

last: Toepel

address: Universitätsstrasse 27

country: Germany

institute: University of Bielefeld

summary: Comparison of gene expression for Chlamydomonas cells grown for 24h, 48h, 72h, 96h under nitrogen starvation

overall_design: Two-condition experiment, 3 Biological replicates (pooled samples experiment)


title: Sun and shade leaves_2x ambient ozone_020806

status: Public on Oct 21 2011

city: Neuherberg

first: Maren

last: Olbrich

address: Ingolstädter Landstr. 1

institute: Helmholtz Zentrum München

summary: Tropospheric ozone causes severe oxidative stress in plants. To investigate the transcriptional responsiveness of adult trees to ozone, fully-expanded sun and shade leaves of mature beech trees were harvested at four time points over the entire vegetation period in 2005 and 2006. Microarray analyses were conducted on leaves from trees grown in the field under ambient and twice-ambient ozone concentrations at Kranzberger Forst (Bavarian). Beech trees changed their transcript levels in response to ozone. In the years 2005 and 2006 different transcription patterns were observed; this may have been a result of different weather conditions and ozone uptake. Furthermore, we obtained differences in mRNA expression patterns between shade and sun leaves. In the ozone-treated sun leaves of 2005, slightly up- and down-regulated transcript levels were detected, particularly in the spring and autumn, whereas shade leaves clearly exhibited reduced mRNA-levels, particularly at the end of the vegetation period. In 2006, this pattern could not be confirmed, and in the autumn, four other transcripts were slightly up-regulated in ozone-treated shade leaves. In addition, two additional transcripts were found to be influenced in sun leaves in the spring/summer. While we detected changes in the levels of only a few transcripts, the observed effects were not identical in both years. In conclusion, elevated ozone exhibited very small influence on the transcription levels of genes of mature beech trees.

overall_design:
The study was carried out at the Kranzberger Forst research site (near Freising, Germany: 48°25’08’’N, 11°39’41’””E, 485m (Pretzsch et al., 1998) in a mixed 60-year old stand (closed canopy) with about 30m high European beech (Fagus sylvatica) and Norway spruce (Picea abies) trees. Free-air ozone fumigation started in May 2000 at double the ambient ozone concentrations with a cut-off at 150 nl l-1 (Werner and Fabian, 2002), thereby avoiding acute damage to the leaves. The ozone concentrations were measured at four heights within the fumigated space and were additionally monitored with 200 passive samplers (Werner and Fabian, 2002). In 2005 the AOT40 value under twice ambient ozone was 64.3 μmol mol-1 h and in 2006 69.0 μmol mol-1 h. Detailed ozone concentration data over the growing seasons have been reported elsewhere (Gielen et al., 2007; Kitao et al., 2009).  Sun and shade leaves from 60-year-old European beech trees were harvested in a total of 8 sampling campaigns in 2005 and 2006. Using scaffolding, five leaves of sun crown (height of about 25 m) and five shade (height of about 19 m) leaves were taken from each of five control and ozone-treated trees. The sampling was carried out in May, June, August, and September of 2005 and in June, August, September and October of 2006. To avoid diurnal effects, the samples were always taken around 11 a.m. For each tree, the four leaves (sun or shade) were combined, frozen in liquid nitrogen and stored at -80 °C until RNA isolation.

For one time point we had five microarrays and five dye-swaps for each of sun and shade leaves. The probes of the trees under ambient ozone were labelled with Cy3 and probes of the trees under 2x ambient were labelled with Cy5. For every pair of trees a dye control were carried out, where the control trees were labelled with Cy5 and the ozone-treated one with Cy3. For statistical analysis a coefficient of variation about all microarrays of one time point was calculated using Acuity 4.0 microarray informatics software [Axon Instruments]. We used only those spots that had a coefficient of variation < 50 and were present on at least half of identical slides. The ozone-changed transcript level of genes were expressed in the median values as log2 ratios.

The following Samples are missing from this submission:
Sun leaves, rep.2 (non-dye-swap)
Sun leaves, rep.2 (dye-swap)
Sun leaves, rep.3 (non-dye-swap)
Sun leaves, rep.4 (non-dye-swap)

first: Dieter

last: Ernst


title: Transgenerational epigenetic inheritance of longevity in Caenorhabditis elegans

city: Palo Alto

first: Eric

middle: Lieberman

last: Greer

state: CA

address: Alway M314 300 Pasteur Drive

department: Genetics

institute: Stanford University

summary: Chromatin modifiers regulate lifespan in several organisms, raising the question of whether changes in chromatin states in the parental generation could be incompletely reprogrammed in the next generation and thereby affect the lifespan of descendents. The histone H3 lysine 4 trimethylation (H3K4me3) complex composed of ASH-2, WDR-5, and the histone methyltransferase SET-2 regulates C. elegans lifespan. Here we show that deficiencies in the H3K4me3 chromatin modifiers ASH-2, WDR-5, or SET-2 in the parental generation extend the lifespan of descendents up until the third generation. The transgenerational inheritance of lifespan extension by members of the ASH-2 complex is dependent on the H3K4me3 demethylase RBR-2, and requires the presence of a functioning germline in the descendents. Transgenerational inheritance of lifespan is specific for the H3K4me3 methylation complex and is associated with epigenetic changes in gene expression. Thus, manipulation of specific chromatin modifiers only in parents can induce an epigenetic memory of longevity in descendents.

overall_design: There are 35 samples in total. We found that genetically WT descendents from mutants of the H3K4me3 modifying complex had extended longevity up until the F4 generation. Their lifespan returned to WT levels in the F5 generation. We performed microarrays to examine what gene expression differences there were between N2(WT) worms, +/+ (from wdr-5 mutant) worms, and wdr-5/wdr-5 in the F4 and the F5 generation. We analyzed L3 samples from the first and second days of egg laying in triplicate each. Samples consist of ~1000 worms each.

middle: L

first: Anne

last: Brunet


title: Insight into the response of Bacillus cereus towards the polysaccharide chitosan

city: Jena

first: Akos

middle: T

last: Kovacs

address: Neugasse 23

department: Institute of Microbiology

institute: Friedrich Schiller University of Jena

summary: Comparison of chitosan-treated B. cereus ATCC 14579 cells with non-treated B. cereus ATCC 14579 cells. 2 chitosans with similar molecular weight (Mw) but different degrees of acetylation (Fa) were used: chitosan B (Mw: 28.4 kDa, Fa: 0.16) (samples 1-3) and chitosan A (Mw: 36.0 kDa, Fa: 0.01) (samples 4-6).

overall_design: One-condition design comparision of treated vs. non-treated control. 3 biological replicates, including a dye swap.

first: Hilde

last: Mellegard

first: Toril

last: Lindback

first: Bjorn

middle: E

last: Christensen

first: Oscar

last: Kuipers

first: Per

last: Granum


title: Sun and shade leaves_2x ambient ozone_270606

overall_design:
The study was carried out at the Kranzberger Forst research site (near Freising, Germany: 48°25’08’’N, 11°39’41’””E, 485m (Pretzsch et al., 1998) in a mixed 60-year old stand (closed canopy) with about 30m high European beech (Fagus sylvatica) and Norway spruce (Picea abies) trees. Free-air ozone fumigation started in May 2000 at double the ambient ozone concentrations with a cut-off at 150 nl l-1 (Werner and Fabian, 2002), thereby avoiding acute damage to the leaves. The ozone concentrations were measured at four heights within the fumigated space and were additionally monitored with 200 passive samplers (Werner and Fabian, 2002). In 2005 the AOT40 value under twice ambient ozone was 64.3 μmol mol-1 h and in 2006 69.0 μmol mol-1 h. Detailed ozone concentration data over the growing seasons have been reported elsewhere (Gielen et al., 2007; Kitao et al., 2009).  Sun and shade leaves from 60-year-old European beech trees were harvested in a total of 8 sampling campaigns in 2005 and 2006. Using scaffolding, five leaves of sun crown (height of about 25 m) and five shade (height of about 19 m) leaves were taken from each of five control and ozone-treated trees. The sampling was carried out in May, June, August, and September of 2005 and in June, August, September and October of 2006. To avoid diurnal effects, the samples were always taken around 11 a.m. For each tree, the four leaves (sun or shade) were combined, frozen in liquid nitrogen and stored at -80 °C until RNA isolation.

For one time point we had five microarrays and two dye-swaps for shade leaves, and three microarrays and two dye-swaps for sun leaves. The probes of the trees under ambient ozone were labelled with Cy3 and probes of the trees under 2x ambient were labelled with Cy5. For every pair of trees a dye control were carried out, where the control trees were labelled with Cy5 and the ozone-treated one with Cy3. For statistical analysis a coefficient of variation about all microarrays of one time point was calculated using Acuity 4.0 microarray informatics software [Axon Instruments]. We used only those spots that had a coefficient of variation < 50 and were present on at least half of identical slides. The ozone-changed transcript level of genes were expressed in the median values as log2 ratios.


title: Sun and shade leaves_2x ambient ozone_120906

overall_design:
The study was carried out at the Kranzberger Forst research site (near Freising, Germany: 48°25’08’’N, 11°39’41’””E, 485m (Pretzsch et al., 1998) in a mixed 60-year old stand (closed canopy) with about 30m high European beech (Fagus sylvatica) and Norway spruce (Picea abies) trees. Free-air ozone fumigation started in May 2000 at double the ambient ozone concentrations with a cut-off at 150 nl l-1 (Werner and Fabian, 2002), thereby avoiding acute damage to the leaves. The ozone concentrations were measured at four heights within the fumigated space and were additionally monitored with 200 passive samplers (Werner and Fabian, 2002). In 2005 the AOT40 value under twice ambient ozone was 64.3 μmol mol-1 h and in 2006 69.0 μmol mol-1 h. Detailed ozone concentration data over the growing seasons have been reported elsewhere (Gielen et al., 2007; Kitao et al., 2009).  Sun and shade leaves from 60-year-old European beech trees were harvested in a total of 8 sampling campaigns in 2005 and 2006. Using scaffolding, five leaves of sun crown (height of about 25 m) and five shade (height of about 19 m) leaves were taken from each of five control and ozone-treated trees. The sampling was carried out in May, June, August, and September of 2005 and in June, August, September and October of 2006. To avoid diurnal effects, the samples were always taken around 11 a.m. For each tree, the four leaves (sun or shade) were combined, frozen in liquid nitrogen and stored at -80 °C until RNA isolation.

For one time point we had five microarrays and five dye-swaps for each of sun and shade leaves. The probes of the trees under ambient ozone were labelled with Cy3 and probes of the trees under 2x ambient were labelled with Cy5. For every pair of trees a dye control were carried out, where the control trees were labelled with Cy5 and the ozone-treated one with Cy3. For statistical analysis a coefficient of variation about all microarrays of one time point was calculated using Acuity 4.0 microarray informatics software [Axon Instruments]. We used only those spots that had a coefficient of variation < 50 and were present on at least half of identical slides. The ozone-changed transcript level of genes were expressed in the median values as log2 ratios.


title: Sun and shade leaves_2x ambient ozone_091006


title: ChIP with anti-H3K27me3  to compare binding in salivary glands of WT and SuUR Drosophila

status: Public on Oct 18 2011

city: Cambridge

first: Terry

middle: L.

last: Orr-Weaver

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

type: Genome binding/occupancy profiling by genome tiling array

summary: ChIP was performed to identify regions of gDNA bound by H3K27me3 in third instar salivary glands of Drosophila WT and SuUR mutants.  This demonstrated that H3K27me3 binds differently in under-replicated in SuUR mutant third instar salivary glands.

overall_design: Comparison of H3K27me3 ChIP sample relative to input DNA or control IgG pulldown for two different Drosophila strains

first: Noa

last: Sher


title: Sun and shade leaves_2x ambient ozone_190905

overall_design:
The study was carried out at the Kranzberger Forst research site (near Freising, Germany: 48°25’08’’N, 11°39’41’””E, 485m (Pretzsch et al., 1998) in a mixed 60-year old stand (closed canopy) with about 30m high European beech (Fagus sylvatica) and Norway spruce (Picea abies) trees. Free-air ozone fumigation started in May 2000 at double the ambient ozone concentrations with a cut-off at 150 nl l-1 (Werner and Fabian, 2002), thereby avoiding acute damage to the leaves. The ozone concentrations were measured at four heights within the fumigated space and were additionally monitored with 200 passive samplers (Werner and Fabian, 2002). In 2005 the AOT40 value under twice ambient ozone was 64.3 μmol mol-1 h and in 2006 69.0 μmol mol-1 h. Detailed ozone concentration data over the growing seasons have been reported elsewhere (Gielen et al., 2007; Kitao et al., 2009).  Sun and shade leaves from 60-year-old European beech trees were harvested in a total of 8 sampling campaigns in 2005 and 2006. Using scaffolding, five leaves of sun crown (height of about 25 m) and five shade (height of about 19 m) leaves were taken from each of five control and ozone-treated trees. The sampling was carried out in May, June, August, and September of 2005 and in June, August, September and October of 2006. To avoid diurnal effects, the samples were always taken around 11 a.m. For each tree, the four leaves (sun or shade) were combined, frozen in liquid nitrogen and stored at -80 °C until RNA isolation.
For one time point we had five microarrays and five dye-swaps for each of sun and shade leaves. The probes of the trees under ambient ozone were labelled with Cy3 and probes of the trees under 2x ambient were labelled with Cy5. For every pair of trees a dye control were carried out, where the control trees were labelled with Cy5 and the ozone-treated one with Cy3. For statistical analysis a coefficient of variation about all microarrays of one time point was calculated using Acuity 4.0 microarray informatics software [Axon Instruments]. We used only those spots that had a coefficient of variation < 50 and were present on at least half of identical slides. The ozone-changed transcript level of genes were expressed in the median values as log2 ratios.


title: replication experiment

summary: Testing for labeling efficiency and Replication effeciency of the microarray (Chlamydomonas cells grown for 24 h under sulfur starvation)

overall_design: Two-condition experiment, 3 Biological replicates


title: An antioxidant response phenotype is shared between hereditary and sporadic type 2 papillary renal cell carcinoma

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: Fumarate hydratase (FH) mutation causes hereditary type 2 papillary renal cell carcinoma (HLRCC, Hereditary Leiomyomatosis and Renal Cell Cancer (MM ID # 605839)). The main effect of FH mutation is fumarate accumulation. The current paradigm posits that the main consequence of fumarate accumulation is HIF-a stabilization. Paradoxically, FH mutation differs from other HIF-a stabilizing mutations, such as VHL and SDH mutations, in its associated tumor types. We identified that fumarate can directly up-regulate antioxidant response element (ARE)-controlled genes. We demonstrated that AKR1B10 is an ARE-controlled gene and is up-regulated upon FH knockdown as well as in FH-null cell lines. AKR1B10 overexpression is also a prominent feature in both hereditary and sporadic PRCC2. This phenotype better explains the similarities between hereditary and sporadic PRCC2.

overall_design: Expression profiling renal normal and tumor tissue


title: Sun and shade leaves_2x ambient ozone_120505

overall_design:
The study was carried out at the Kranzberger Forst research site (near Freising, Germany: 48°25’08’’N, 11°39’41’””E, 485m (Pretzsch et al., 1998) in a mixed 60-year old stand (closed canopy) with about 30m high European beech (Fagus sylvatica) and Norway spruce (Picea abies) trees. Free-air ozone fumigation started in May 2000 at double the ambient ozone concentrations with a cut-off at 150 nl l-1 (Werner and Fabian, 2002), thereby avoiding acute damage to the leaves. The ozone concentrations were measured at four heights within the fumigated space and were additionally monitored with 200 passive samplers (Werner and Fabian, 2002). In 2005 the AOT40 value under twice ambient ozone was 64.3 μmol mol-1 h and in 2006 69.0 μmol mol-1 h. Detailed ozone concentration data over the growing seasons have been reported elsewhere (Gielen et al., 2007; Kitao et al., 2009).  Sun and shade leaves from 60-year-old European beech trees were harvested in a total of 8 sampling campaigns in 2005 and 2006. Using scaffolding, five leaves of sun crown (height of about 25 m) and five shade (height of about 19 m) leaves were taken from each of five control and ozone-treated trees. The sampling was carried out in May, June, August, and September of 2005 and in June, August, September and October of 2006. To avoid diurnal effects, the samples were always taken around 11 a.m. For each tree, the four leaves (sun or shade) were combined, frozen in liquid nitrogen and stored at -80 °C until RNA isolation.

For one time point we had five microarrays and five dye-swaps for each of sun and shade leaves. The probes of the trees under ambient ozone were labelled with Cy3 and probes of the trees under 2x ambient were labelled with Cy5. For every pair of trees a dye control were carried out, where the control trees were labelled with Cy5 and the ozone-treated one with Cy3. For statistical analysis a coefficient of variation about all microarrays of one time point was calculated using Acuity 4.0 microarray informatics software [Axon Instruments]. We used only those spots that had a coefficient of variation < 50 and were present on at least half of identical slides. The ozone-changed transcript level of genes were expressed in the median values as log2 ratios.

The following Sample is missing from this submission:
Sun leaves, rep.5 (non-dye-swap)


title: Integrated transcriptomic and proteomic profiling of white spruce stems during the transition from active growth to dormancy.

status: Public on Oct 17 2011

city: Edmonton

first: Chelsea

last: Ju

state: Alberta

address: CW 405, Biological Sciences Centre

department: Biological Sciences

country: Canada

institute: University of Alberta

summary: In the autumn, stems of woody perennials such as forest trees undergo a transition from active growth to dormancy. We used microarray transcriptomic profiling in combination with a proteomics analysis to elucidate processes that occur during this growth-to-dormancy transition in a conifer, white spruce (Picea glauca [Moench] Voss). Several differentially expressed genes were likely associated with the developmental transition that occurs during growth cessation in the cambial zone and the concomitant completion of cell maturation in vascular tissues. Genes encoding for cell wall and membrane biosynthetic enzymes showed transcript abundance patterns consistent with completion of cell maturation, and also of cell wall and membrane modifications potentially enabling cells to withstand the harsh conditions of winter. Several differentially expressed genes were identified that encoded putative regulators of cambial activity, cell development, and of the photoperiodic pathway. Reconfiguration of carbon allocation figured centrally in the tree’s overwintering preparations. For example, genes associated with carbon-based defenses such as terpenoids were downregulated, while many genes associated with proteinbased defenses and other stress mitigation mechanisms were upregulated. Several of these correspond to proteins that were accumulated during the growth-to-dormancy transition, emphasizing the importance of stress protection in the tree’s adaptive response to overwintering.

overall_design: Two year old white spruce (Picea glauca [Moench] Voss) seedlings were used for all experiments, which were conducted as described by El Kayal et al. (2011). Using a complete randomized block design, seedlings were grown in growth chambers under long days (LD; 16h day / 8h night, 20°C, 50 to 60% RH) for 8-10 weeks. Shortly before seedlings were to begin bud formation, the photoperiod was changed to short days (SD; 8h day / 16h night, 20°C, 50 to 60% RH) to induce rapid and synchronous bud formation. This was designated Day 0.  Lignified whole stems representing the current year’s growth (microarrays, microscopy) or previous year’s growth (protein analyses) were sampled at 0, 3, 7, 14, 28 and 70 d (10 wk) SD, and immediately frozen in liquid nitrogen.  Remaining plants were maintained in SD for an additional 8-15 wk, and then transferred to low temperatures (LT, 2 - 4°C) for 3 to 4 weeks with continuing SD prior to harvest.  These are referred to as LT samples.

first: Leonardo

middle: M

last: Galindo González

first: Walid

last: El Kayal

first: Carmen

middle: C

last: Allen

first: Susanne

last: King-Jones

first: Janice

last: Cooke


title: ChIP with anti-orc2 antibody to identify regions of orc binding in third instar salivary glands of WT and SuUR mutant Drosophila

summary: ChIP was performed to identify regions of gDNA bound by orc2 in third instar salivary glands of Drosophila WT and SuUR mutants.  This demonstrated that ORC does not localize to regions that are under-replicated in SuUR mutant third instar salivary glands.

overall_design: Comparison of ORC2 ChIP sample relative to input DNA or control IgG pulldown for two different Drosophila strains


title: Sun and shade leaves_2x ambient ozone_050805

first: Maren

last: Olbrich

first: Elke

last: Gerstner

first: Guenther

last: Bahnweg

first: Karl-Heinz

last: Haeberle

first: Rainer

last: Matyssek

first: Gerhard

last: Welzl

first: Werner

last: Heller

first: Dieter

last: Ernst


title: CGH to ascertain levels of gDNA in third instar salivary glands of various mutant Drosophila

first: Terry

last: Orr-Weaver

summary: Comparative genomic hybridization was performed to compare levels of gDNA in third instar salivary glands of Drosophila mutants/nulls in the SuUR and orc proteins, compared with 0-2hr diploid embryo gDNA.  This illustrates regions of differential replication in the genome.

overall_design: CGH of salivary gland DNA compared with diploid early embryonic samples for four different Drosophila strains

first: Sharon

last: Li


title: Expression analysis of Spathaspora passalidarum NRRL Y-27907 grown in glucose or xylose

first: Dana

last: Wohlbach

summary: Investigation of whole genome gene expression level changes in Spathaspora passalidarum NRRL Y-27907 grown aerobically in xylose, compared to the same strain grown aerobically in glucose.

overall_design: A six array study using total RNA recovered from three separate cultures of Spathaspora passalidarum NRRL Y-27907 grown in glucose and three separate cultures of Spathaspora passalidarum NRRL Y-27907 grown in xylose.  Each array measures the expression level of 362,487 probes (average probe length 54.5 +/- 4.0 nt) tiled across the Spathaspora passalidarum NRRL Y-27907 genome with a median spacing distance of 29 nt.  During data processing, probes are filtered to include only those probes corresponding to annotated protein-coding genes.

first: Audrey

last: Gasch


title: Representational Oligonucleotide Microarray Analysis (ROMA) array for Copy Number Variation Detection.

city: Cold Spring Harbor

first: Kazimierz

middle: O.

last: Wrzeszczynski

state: NY

address: One Bungtown Rd.

institute: Cold Spring Harbor Laboratory

summary:
The identification of genetic and epigenetic alterations from primary tumor cells has become a common method to identify genes critical to the development and progression of cancer. We provide a bioinformatic analysis of copy number variation and DNA methylation covering the genetic landscape of ovarian cancer tumor cells. We individually examined the copy number variation and DNA methylation for 44 primary ovarian cancer samples and 7 ovarian normal samples using our MOMA-ROMA technology and Affymetrix expression data as well as 379 tumor samples analyzed by The Cancer Genome Atlas. We have identified 346 genes with significant deletions or amplifications among the tumor samples. Utilizing associated gene expression data we predict 156 genes with significantly altered copy number and correlated changes in expression. We identify changes in DNA methylation and expression for all amplified and deleted genes. We predicted 615 potential oncogenes and tumor suppressors candidates by integrating these multiple genomic and epigenetic data types.
This ROMA experiment was performed on Ovarian Tumor samples using the same platform as previously reported by Navin, N. et. al. Genome Res. 2010 Jan;20(1):68-80 (PMID: 19903760). Analysis of the array data was performed as previously reported in Chen, S. et. al. Cancer Biol Ther. 2008 Nov;7(11):1793-802. (PMID: 18836286 ).

overall_design: The genomic DNA from each tumor was labeled with Cy5 and hybridized to an 85K Bgl2 ROMA Microarray. A normal reference male fibroblast was labeled with Cy3 as a control. The value data repesents a log ratio. (As previously reported Chen, S. et. al. Cancer Biol Ther. 2008 Nov;7(11):1793-802. PMID: 18836286 ).

first: Robert

last: Lucito

first: Douglas

middle: A

last: Levine

middle: O

first: Sitharthan

last: Kamalakaran

first: James

last: Byrnes

first: Mark

last: Joinnides

first: Elena

last: Lum


title: RNAPolII ChIP to find differences between third instar salivary glands of WT and SuUR

summary: ChIP was performed to identify regions of gDNA bound by RNA polymerase II in third instar salivary glands of Drosophila WT and SuUR mutants.  This demonstrated that RNAPolII does not localize to regions that are under-replicated in SuUR mutant third instar salivary glands.

overall_design: Comparison of RNAPolII ChIP from third instar salivary glands relative to control IgG pulldown for two different Drosophila strains

first: Noa

last: Sher


title: Sulfur starvation experiment in Chlamydomonas

first: Jörg

last: Toepel

summary: Comparison of gene expression for chlamydomonas cells grown for 24 h, 48 h 72 h, 96 h in sulfur depleted media against

overall_design: Two-condition experiment, 3 different Chlamydomonas wt strains plus npq 4 mutant (3 pooled biological samples)


title: Methylation detection Oligonucleotide Microarray Analysis: high resolution method for CpG island methylation detection 3.

type: Methylation profiling by genome tiling array

summary: The identification of genetic and epigenetic alterations from primary tumor cells has become a common method to identify genes critical to the development and progression of cancer. We provide a bioinformatic analysis of copy number variation and DNA methylation covering the genetic landscape of ovarian cancer tumor cells. We individually examined the copy number variation and DNA methylation for 44 primary ovarian cancer samples and 7 ovarian normal samples using our MOMA-ROMA technology and Affymetrix expression data as well as 379 tumor samples analyzed by The Cancer Genome Atlas. We have identified 346 genes with significant deletions or amplifications among the tumor samples. Utilizing associated gene expression data we predict 156 genes with significantly altered copy number and correlated changes in expression. We identify changes in DNA methylation and expression for all amplified and deleted genes. We predicted 615 potential oncogenes and tumor suppressors candidates by integrating these multiple genomic and epigenetic data types.

overall_design: We have developed a method to profile genome wide methylation. 7 ovarian normal samples and 44 tumor samples from other individuals were analyzed for CpG methylation. After inter array normalization, the tumor samples were taken together and the methylation compared to that of the normal samples to identify regions of the CpG islands that are significantly altered between the two datasets. Some of these regions were validated for their methylation as a proof of principle for the method. Kamalakaran S., et. al. Mol Oncol. 2011;5:77-92 (PMID: 21169070).


title: miRNA profiling of Melanoma Cell lines and Normal Melanocytes

city: Brisbane

first: Mitchell

last: Stark

address: 300 Herston Rd Herston

country: Australia

institute: QIMR

summary: To identify microRNAs potentially involved in melanomagenesis we compared microRNA transcription profiles between melanoma cell lines and cultured melanocytes.

overall_design: miRNA microarrays were manufactured by Agilent Technologies (Santa Clara, CA), and contain 20-40 features targeting each of 470 human miRNAs (Agilent design ID 016436). Sequences of the 470 miRNAs were obtained from the Sanger miRBase, release 9.1. Labeling and hybridization of total RNA samples were performed according to the manufacturer’s protocol. 100ng total RNA was used as input into the labeling reaction, and the entire reaction was hybridized to the array for 20 hours at 55°C. The labeling and hybridizations of the nine human tissues were done 4-5 times using the same starting RNA sample for each tissue. Total RNA was extracted from 51 melanoma cells and 2 pools of melanocytes using the QIAGEN miRNA kits.

first: Glen

last: Boyle

first: Susan

last: Woods

first: Vanessa

middle: F

last: Bonazzi

middle: S

first: Elke

last: Hacker

first: Lauren

middle: G

last: Aoude

first: Nicholas

middle: K

last: Hayward


title: Liver transcriptome comparison of divergently selected Lean and Fat mouse lines in cholesterol homeostasis, bile acids, glucose and lipoprotein metabolism

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

summary: This study aimed to identify molecular basis of obesity-resistant mechanisms in the Lean line with the emphasis on lipid homeostasis. Expression profiling using custom Steroltalk v2 microarray demonstrated that Lean mice exhibit a higher hepatic expression of cholesterol synthesis genes compared to the Fat line. A significant difference between the strains was also found in the bile acid metabolism. We identified novel candidate molecular targets by which we can at least in part explain resistance to obesity development in the Lean line.

overall_design: Direct comparison of 10 Lean and 10 Fat mouse samples. For 7 out of 10 comparisons dye-swap technical replication were performed.

first: Matjaž

last: Simončič

first: Tadeja

last: Režen

first: Damjana

last: Rozman

first: Simon

last: Horvat


title: The YbjN regulon in Escherichia coli

status: Public on Oct 15 2011

city: Urbana

first: Frank

last: Zhao

state: IL

address: 1210 Gregory Dr.

department: Crop Sciences

institute: University of Illinois

summary: YbjN, an enterobacteria-specific protein, is a multicopy suppressor of ts9 temperature sensitivity in Escherichia coli.  Microarray study revealed that the expression level of ybjN was inversely correlated with the expression of flagellar, fimbrial and acid resistance genes. Over-expression of ybjN significantly down-regulated genes involved in the citric acid cycle, glycolysis, the glyoxylate shunt, oxidative phosphorylation, and amino acid and nucleotide metabolism. On the other hand, over-expression of ybjN up-regulated toxin-antitoxin modules, the SOS responsive pathway, cold shock proteins and starvation-induced transporter genes. Our results collectively suggest that YbjN may play important roles in regulating bacterial multicellular behaviors, metabolism and survival under various stress conditions in Es. coli.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: A total of 8 samples were analyzed: E. coli wild type strain (2 replicates); E. coli ybjN mutant strain (3 replicates); E. coli ybjN over-expression strain (3 replicates).

first: Dongping

last: Wang

first: Youfu


title: Blimp1 expression predicts embryonic stem cell development in vitro

city: Houston

first: Thomas

middle: Paul

last: Zwaka

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Comparing global transcriptional profile between standard or 2i derived ES cell lines.

overall_design: RNA extracted from established ES cell lines either from standard derivation condition or 2i derivation condition, all cultured without 2i after derivation.

first: Li-Fang

last: Chu

first: M.

last: Surani

first: Rudolf

last: Jaenisch


title: Catabolite repression of phosphoenolpyruvate carboxykinase by a zinc finger protein under biotin- and pyruvate carboxylase-deficient conditions in Pichia pastoris

status: Public on Oct 14 2011

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: We have identified a methanol- and biotin-starvation-inducible zinc finger protein named ROP  [repressor of phosphoenolpyruvate carboxykinase (PEPCK)] in the methylotrophic yeast Pichia  pastoris. When P.pastoris strain GS115 (wild-type, WT) is cultured in biotin-deficient, glucose ammonium  (Bio-) medium, growth is suppressed due to the inhibition of anaplerotic synthesis of  oxaloacetate, catalysed by the biotin-dependent enzyme pyruvate carboxylase (PC). Deletion of  ROP results in a strain (∆ROP) that can grow under biotin-deficient conditions due to  derepression of a biotin- and PC-independent pathway of anaplerotic synthesis of oxaloacetate.  Northern analysis as well as microarray expression profiling of RNA isolated from WT and ∆ROP  strains cultured in Bio(-) medium indicate that expression of the phosphoenolpyruvate  carboxykinase gene (PEPCK) is induced in ∆ROP during biotin- or PC-deficiency even under  glucose-abundant conditions. There is an excellent correlation between PEPCK expression and  growth of ∆ROP in Bio(-) medium, suggesting that ROP-mediated regulation of PEPCK may have  a crucial role in the biotin- and PC-independent growth of the ∆ROP strain. To our knowledge,  ROP is the first example, of a zinc finger transcription factor involved in the catabolite repression  of PEPCK in yeast cells cultured under biotin- or PC-deficient and glucose-abundant conditions.

overall_design: Agilent one-color experiment,Organism: Pichia pastoris ,Custom Pichia pastoris Gene Expression 8x15k  array designed by Genotypic Technology Pvt. Ltd. (Agilent -AMADID: 25088 )  , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Nallani

middle: V

last: Kumar

first: Pundi

middle: N

last: Rangarajan


title: Analysis of copy number changes in primary and metastatic colorectal cancer samples

status: Public on Oct 12 2011

city: Utrecht

first: Wigard

last: Kloosterman

address: Universiteitsweg 100

country: Netherlands

institute: University Medical Center Utrecht

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

summary: Structural rearrangements form a major class of somatic variation in cancer genomes. Local chromosome shattering, termed chromothripsis, is a mechanism proposed to be the cause of clustered chromosomal rearrangements and was recently described to occur in a small percentage of tumors. The significance of these clusters for tumor development or metastatic spread is largely unclear. We used genome-wide long mate-pair sequencing and SNP array profiling to reveal that chromothripsis is a widespread phenomenon in primary colorectal cancer and metastases. We find large and small chromothripsis events in nearly every colorectal tumor sample and show that several breakpoints of chromothripsis clusters and isolated rearrangements affect cancer genes, including NOTCH2, EXO1 and MLL3. We complemented the structural variation studies by sequencing the coding regions of a cancer exome in all colorectal tumor samples and found somatic mutations in 24 genes, including APC, KRAS, SMAD4 and PIK3CA. A pairwise comparison of somatic variations in primary and metastatic samples indicated that in many chromothripsis clusters, isolated rearrangements and point mutations are exclusively present in either the primary tumor or the metastasis and may affect cancer genes in a lesion-specific manner. We conclude that chromothripsis is a prevalent mechanism driving structural rearrangements in colorectal cancer and show that a complex interplay between point mutations, simple copy number changes and chromothripsis events drive colorectal tumor development and metastasis.

overall_design: We analyzed 16 tissue samples from four patients. For each patient we analyzed the DNA of a primary colon tumor sample, a normal colon tissue sample, a metastatic liver tumor sample and a normal liver tissue sample. The normal colon and normal liver samples serve as a control for the primary and metastatic tumor samples.

middle: P

first: Marlous

last: Hoogstraat

first: Oscar

last: Paling

first: Masoumeh

last: Tavakoli-Yaraki

first: Ivo

last: Renkens

first: Joost

last: Vermaat

first: Markus

middle: J

last: van Roosmalen

first: Stef

last: van Lieshout

first: Ies

last: Nijman

first: Wijnand

last: Roessingh

first: Ruben

last: van 't Slot

first: José

last: van de Belt

first: Victor

last: Guryev

first: Marco

last: Koudijs

first: Emile

last: Voest

first: Edwin

last: Cuppen


title: FUR- mutant vs. WT

city: St. Cloud

first: Ryan

middle: Cristiano

last: Fink

state: MN

address: 720 4th Ave S

institute: St. Cloud State University

summary: Ferric uptake regulator (Fur) is the major regulator of iron acquisition in Escherichia coli and other bacteria. In the present study, the role of Fur in anaerobic S. enterica serovar Typhimurium was determined by transcriptome analysis, reporter assays, and enzymatic assays. In anaerobic Δfur, 298 genes were differentially expressed. In general, Fur repressed genes required for iron acquisition/storage, metabolism, electron transport, oxidative/nitrosative stress, and modulators of virulence. There were 73 genes whose expression required Fur, eleven of which contain a putative Fur box 5‟ of the gene. Transcription of sodA was >9-fold higher in Δfur but there was no corresponding increase in the activity of SodA.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design:
Anaerobic cultures of the fur mutant and the WT were used to inoculate two sets of three independent flasks each containing 150 ml of anoxic LB-MOPS-X. The three independent cultures were grown to an optical density at 600 nm (OD600) of 0.25 to 0.35, pooled, and treated with RNAlater (QIAGEN, Valencia, CA) to fix the cells and preserve the quality of the RNA. Total RNA was extracted with the RNeasy RNA extraction kit (QIAGEN), and the samples were treated with RNase-free DNase (Invitrogen, Carlsbad, CA). The absence of contaminating DNA and the quality of the RNA was confirmed by PCR amplification of known genes and by using agarose gel electrophoresis. Aliquots of the RNA samples were kept at –80°C for use in the microarray and quantitative real-time reverse transcription-PCR (qRT-PCR) studies.

The SuperScript Indirect cDNA labeling system (Invitrogen) was used to synthesize the cDNA for the hybridizations. Each experiment consisted of two hybridizations, on two slides, and was carried out in Corning Hybridization Chambers at 42°C overnight. Dye swapping was performed to avoid dye-associated effects on cDNA synthesis. The slides were washed at increasing stringencies (2x SSC [1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate], 0.1% sodium dodecyl sulfate [SDS], 42°C; 0.1% SSC, 0.1% SDS, room temperature; 0.1% SSC, room temperature). Following hybridization, the microarrays were scanned for the Cy3 and Cy5 fluorescent signals with a ScanArray 4000 microarray scanner from GSI Lumonics (Watertown, MA). The intensity of every spot was codified as the sum of the intensities of all the pixels within a circle positioned over the spot itself and the background as the sum of the intensities of an identical number of pixels in the immediate surroundings of the circled spot.
Cy3 and Cy5 values for each spot were normalized over the total intensity for each dye to account for differences in total intensity between the two scanned images. The consistency of the data obtained from the microarray analysis was evaluated by a pair-wise comparison, calculated with a two-tailed Student's t test and analyzed by the MEAN and TTEST procedures of SAS-STAT statistical software (SAS Institute, Cary, NC) . The signal intensity at each spot from the fur mutant and the WT were background subtracted, normalized, and used to calculate the ratio of gene expression between the two strains. All replicas were combined, and the median expression ratios and standard deviations were calculated for open reading frames (ORFs) showing 2.5-fold change.

first: Bryan

last: Troxell

first: Steffen

last: Porvollik

first: Michael

last: McClelland

first: Hosni

last: Hassan


title: Apoptosis pathway analysis of genes from macropahges infected with Histoplasma capsulatum

city: Cincinnati

first: George

middle: Samuel

last: Deepe

state: Ohio

address: 231 Albert Sabin Way

department: Dept. of Medicine/Division of Infectious Diseases

institute: University of Cincinnati College of Medicine

summary: Analyzed 84 genes from macrophages infected with Histoplasma capsulatum for changes in expression over 24 hours

overall_design: Macrophages infected with Histoplasma capsulatum were analyzed for alterations in apoptosis genes, 5 biological replicate (rep1-5)


title: Identification of Alpha Interferon-Induced Genes Associated with Antiviral Activity in Daudi Cells and Characterization of IFIT3 as a Novel Antiviral Gene

city: Bethesda

first: Hana

last: Schmeisser

state: MD

address: 50 Center Drive

department: CBS

institute: NIAID

summary: A novel assay was developed for Daudi cells in which the antiviral (AV) and antiproliferative (AP) activities of interferon (IFN) can be measured simultaneously. Using this novel assay, conditions allowing IFN AV protection but no growth inhibition were identified and selected. Daudi cells were treated under these conditions, and gene expression microarray analyses were performed. The results of the analysis identified 25 genes associated with IFN-alpha AV activity. Upregulation of 23 IFN-induced genes was confirmed by using reverse transcription-PCR. Of 25 gene products, 17 were detected by Western blotting at 24 h. Of the 25 genes, 10 have not been previously linked to AV activity of IFN-alpha. The most upregulated gene was IFIT3 (for IFN-induced protein with tetratricopeptide repeats 3). The results from antibody neutralizing experiments suggested an association of the identified genes with IFN-alpha AV activity. This association was strengthened by results from IFIT3-small interfering RNA transfection experiments showing decreased expression of IFIT3 and a reduction in the AV activity induced by IFN-alpha. Overexpression of IFIT3 resulted in a decrease of virus titer. Transcription of AV genes after the treatment of cells with higher concentrations of IFN having an AP effect on Daudi cells suggested pleiotropic functions of identified gene products.

overall_design: Gene expression was initially measured in four Daudi cell groups (3 x 10(6) in 10 ml of RPMI) treated for 24 h at IFN concentrations selected to allow comparison of gene activity in AV activity environments with environments in which no AV activity was observed. These treatment groups were: (i) 0.0036 ng of IFN-alpha2c/ml (n=5) (allowing AV activity only); (ii) 0.00036 ng of IFN-alpha2c/ml (n=5) (no AV observed); (iii) 0.036 ng of HY-2/ml (n=3) (allowing AV activity); and (iv) 0.0036 ng of HY-2/ml (n=3) (no AV observed). To refine the list of genes associated with AV activity, samples showing AP phenotype (achieved by treatment with IFN-alpha2c [0.36 ng/ml] (n=3) or HY-2 [36 ng/ml]) (n=3) were compared to identically treated samples manipulated to display the AV phenotype through subsequent neutralization with anti-IFNAR1 MAb 64.10 (1 ug/ml) (n=6). Further analysis of gene expression profiles after 6 h of incubation helped indicate genes associated with early roles in IFN-induced AV mechanisms (n=6).


title: Effects of elevated seawater pCO2 on gene expression patterns in the gills of the green crab, Carcinus maenas

status: Public on Oct 10 2011

city: Winnipeg

first: Sandra

last: Fehsenfeld

state: MB

address: 509 Buller Building, 45 Chancellors Circle

department: Biological Science

institute: University of Manitoba

summary: In order to promote our understanding of the responses of green crab acid-base regulatory epithelia to high pCO2, Baltic Sea green crabs were exposed to a pCO2 of 400 Pa for 3 and 7 days after which posterior gills 7 and 9 were sampled. Gills were then subsequently screened for differentially expressed gene transcripts using a 4,462-feature microarray developed by Towle et al. 2010.

overall_design: For each experimental block (gill7-day3, gill7-day7, gill9-day3, gill9-day7), 6 replicate samples were obtained for control (= 39 Pa) and  elevated (= 400 Pa) pCO2 exposed animals. Each microarray slide included 4 technical replicates for each transcript and was hybridized with one control pCO2 (labelled with AlexaFluor555) and one elevated pCO2 cDNA (labelled with AlexaFluor647). Lowess-normalized gene expression was calculated as the log2 of the ratio of the fluorescence intensity of the CO2-treatment cDNA to the fluorescence intensity of the control cDNA (log2 ratio=F635/F532).

first: David

middle: W

last: Towle

first: Rainer

last: Kiko

first: Martin

last: Zimmer

first: Frank

last: Melzner


title: Molecular characterization of the chromosome 7 in SMZL

status: Public on Oct 11 2011

city: Salamanca

first: Cristina

last: Robledo

address: Campus Miguel de Unamuno

country: Spain

institute: CIC

summary: Splenic marginal zone lymphomas (SMZL) are an uncommon type of B-cell non-Hodgkin’s lymphoma (NHL-B) in which no specific chromosomal translocations have been described. In contrast, the most frequent cytogenetic abnormality is the loss of the long arm of chromosome 7 (7q). Previous reports have located this loss in the 7q32 region. In order to better characterize the genomic imbalances in SMZL, molecular studies were carried out in 73 patients with SMZL. To gain insight into the mapping at 7q a tiling array was also used. Our results confirmed the presence of a new region of loss on chromosome 7 in these NHL.

overall_design: In order to better characterize the genomic imbalances in SMZL, molecular studies were carried out in 69 patients with SMZL.

first: Jesus

middle: M

last: Hernandez

first: Juan

middle: L

last: Garcia


title: Transcriptional changes during photoperiodic tuber induction in Solanum tuberosum ssp andigena

status: Public on Oct 06 2011

city: Cantoblanco

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

summary: For expression profiling analyses of early stages of tuber induction, plants of Solanum tuberosum ssp andigena (7540) were used. This wild subspecies is strictly dependent on photoperiod for tuberisation, such that short days (SD) inductive conditions are required in order to trigger tuber induction in the stolons. Andigena plants were grown in the greenhouse under LD non-inductive conditions until a 10-leaf stage. They were subsequently transferred to inductive SD conditions (8 h light/16 h dark), and sampled at 0, 2, 4, 6 and 8 days after transfer to SDs. Tuber swelling was visible approximately 6-8 days after transfer to inductive conditions. The apical region of the stolons (2 cm) was collected one hour before the beginning of the light period.

overall_design: All collected stolons (LD; and 2d, 4d, 6d and 8d under SD) were processed as described. Hybridization scheme with a loop design was applied to compare one sample against the rest of the samples in the induction time course.

first: José

last: Abelenda

first: Salomé

last: Prat


title: Effects of StSP6A overexpression and silencing on potato stolons

summary: Summary  StSP6A is a protein with sequence homology to the Arabidopsis FLOWERING LOCUS T (FT). FT is a main component of the long range flowering promoting signal or florigen that induces photoperiodic flowering under long days (LDs). In potato, short days (SDs) promote tuber induction, and wild subspecies like Solanum tuberosum ssp andigena (wild type line 7540) are strictly dependent on SDs to tuberize. StSP6A transcription is induced in leaves and stolons at early stages upon transfer to SD inductive conditions, priotr to visible solon swelling. Transgenic andigena lines over-expressing the StSP6A gene under the control of the 35S promoter are able to tuberize under LD non-inductive conditions, whereas silencing of this gene by means of an specific RNAi construct are strongly delayed in tuber induction in SD inductive conditions. This data indicate that StSP6A plays a central role in the control of tuber induction.

overall_design: For each sample of the two comparisons (35S-StSP6A versus Wild Type and StSP6A-RNAi versus Wild Type) two biological replicates were prepared. In the case of 35S-StSP6A and StSP6A-RNAi each replicate was composed by a pool of several transgenic lines.

middle: A


title: Juvenile rainbow trout exposed in situ at site receiving different concentrations of municipal wastewater effluent (MWWE) and an upstream reference site

status: Public on Oct 07 2011

city: Waterloo

first: Jennifer

last: Ings

state: Ontario

address: 200 University Ave West

institute: University of Waterloo

summary: Juvenile rainbow trout were exposed to MWWE in a caging study, with cages held upstream and downstream of a MWWE outfall for two weeks in the fall of 2007. Whole tissues were sampled and analyzed. Microarray analysis was conducted on liver samples.

overall_design: Four condition experiment, Control (0%),10%, 50% and 100% MWWE. Four independent pooled samples for each treatment, hybridized against a reference pool. The reference pool and test sample were randomly assigned for each array.

first: Mathilakath

last: Vijayan

first: Mark

middle: R

last: Servos


title: Expression analysis of channel catfish anterior kidney at 48h post immersion challenge of vaccinated fish (28 days post vaccination with attenuated Edwardsiella ictaluri) with virulent E. ictaluri

status: Public on Oct 05 2011

city: AUBURN

first: julia

last: pridgeon

state: AL

address: 990 WIRE ROAD

department: AAHRU

institute: USDA, ARS

summary:
To determine the global gene transcriptional changes in vaccinated channel catfish anterior kidney after immersion challenge with a virulent Edwardsiella ictaluri compared to sham vaccinated catfish control.
The attenuated Edwardsiella ictaluri used for vaccination was Aquavac-ESC which was commercially available, the virulent strain of Edwardsiella ictaluri is the AL93-58 strain.

overall_design: A six chip study using total RNA samples including 3 controls (no vaccination, no challenge) and 3 treated groups (challenge after vaccination). Each RNA sample used for microarray was pooled fish anterior kidney samples (5 fish anterior kidney samples were pooled as one). Each chip measrues the expression level of 65,182 genes. For each sequence, 3 probes were selected. Two copies were prepared on arrays.

first: Julia

last: Pridgeon

first: Hung-Yueh

last: Yeh

first: Craig

last: Shoemaker


title: Differences in the genomic content of Bordetella pertussis strains before and after vaccine introduction in European countries

status: Public on Oct 04 2011

city: Turku

first: Teemu

last: Kallonen

address: Kiinamyllynkatu 13

department: Derpartment of Infectious Disease Surveillance and Control

country: Finland

institute: National Institute for Health and Welfare

summary: Resurgence of pertussis has been observed in many countries with high vaccination coverage and clonal expansion of certain Bordetella pertussis strains has been associated with recent epidemics in Europe. It is known that vaccinations have selected strains which are different from those used for vaccine production. However, little is known about the differences in genomic content of strains circulating before the vaccination was introduced. In this study, we compared the genomes of 39 vaccine strains and old clinical isolates collected from Finland (N=5), Poland (N=14), Serbia (N=10) and the UK (N=10). The analysis included genotyping, pulsed-field gel electrophoresis (PFGE) and comparative genomic hybridisation (CGH). Compared to the strain Tohama I, the European strains analyzed have lost three major regions of difference (RD3, 5 and 29). However, difference in frequency of the absent RDs 3, 5 or 29 was observed among the four countries. Of the strains with absent RD5, half had also a duplicated region in the genome. All four RDs (RD22, 23, 24 and 26) absent in Tohama I were present in majority of the tested strains. Results obtained from PFGE analysis correlated well with those of CGH. Recently a novel pertussis toxin promoter allele (ptxP3) was described. Strains with ptxP3 have replaced resident ptxP1 strains. When the recent strains (N=22) selected from the four countries were examined, the ptxP3 allele was found in all countries except Poland. Our result indicates that at least three clusters of B. pertussis circulated in Europe in pre-vaccine era and their genomes were distinct from that of the reference strain Tohama I. Although progressive gene loss occurs in B. pertussis population with time, difference in frequency of the lost genes were observed among the countries. The observed differences in genomic content might be vaccine-driven.

overall_design:
The strains were serotyped for the fimbriae, genotyped with LightCycler RT-PCR for pertussis toxin subunit 1 (ptxA), pertussis toxin promoter (ptxP) (Kallonen et al 2011, unpublished data, submitted) and pertactin (prn). The vaccine and old strains were assigned to profiles according to the PFGE results. From every PFGE profile from all countries at least 1 strain was selected and tested for CGH. Altogether 29 strains were analysed with CGH from Poland, Serbia and the United Kingdom, 12, 7 and 10, respectively. In addition 5 old previously published Finnish strains were included in the analysis as well as the reference strain Tohama I (Heikkinen et al., 2007).

The hybridisations were performed as previously described (Heikkinen et al., 2007).

Microarray data analysis was performed with R/Bioconductor (R Development Core Team, 2008). Print-tip-loess normalization was performed with default parameters and the gains/losses were filtered with Limma package. The regions of difference (RDs) found in this study are presented with the nomenclature defined by Brinig et al. (2006). The RDs which were not described by Brinig et al are indicated by RDs and the consequent unused number.

first: Kirsi

last: Gröndahl-Yli-Hannuksela

first: Annika

last: Elomaa

first: Anna

last: Lutynska

first: Norman

last: Fry

first: Jussi

last: Mertsola

first: Qiushui

last: He


title: Expression of placental genes in STOX1 overexpressing mice at 16.5 days of gestation versus WT mice

status: Public on Oct 08 2011

city: Paris

first: Daniel

last: Vaiman

address: 24 rue du Faubourg St Jacques

department: Genetics and Development

country: France

institute: INSERM

summary: Two pools of three placentas from transgenic mice of the TG13 strain and WT mice were hybridized on Nimblegen Arrays. TG13 mice overexpress the gene STOX1 and have the symptoms of severe preeclamsia.

overall_design: Total RNA was used

first: Ludivine

last: Doridot


title: Lhx2 ChIP-chip from primary mouse keratinocytes

city: Bradford

first: Andrei

last: Mardaryev

address: Richmond Road

country: United Kingdom

institute: University of Bradford

summary: The Lhx2 transcription factor plays essential roles in morphogenesis and patterning of ectodermal derivatives, as well as in controlling stem cell activity. Lhx2 is expressed in the hair follicle (HF) buds, while in postnatal telogen HFs Lhx2+ cells reside in the stem cell-enriched epithelial compartments (bulge, secondary hair germ) and co-express selected stem cell markers (Sox9, Tcf4 and Lgr5). Lhx2+ cells represent the vast majority of cells in the bulge and secondary hair germ that proliferate in response to skin injury. This is functionally important, since the wound re-epithelialization is significantly retarded in heterozygous Lhx2 knockout (+/-) mice, while anagen onset in the HFs located closely to the wound is accelerated compared to wild-type mice. Cell proliferation in the bulge and the number of Sox9+ and Tcf4+ cells in the HFs closely adjacent to the wound in Lhx2+/- mice are decreased in comparison to wild-type controls, while expression of Lgr5 and cell proliferation in the secondary hair germ are increased. Furthermore, acceleration of wound-induced anagen development in Lhx2+/- mice is inhibited by administration of Lgr5 siRNA. In addition, Chip-on-chip/ChIP-qPCR and reporter assay analyses reveal Sox9, Tcf4 and Lgr5 as direct Lhx2 targets in keratinocytes. These data strongly suggest that Lhx2 positively regulates Sox9 and Tcf4 in the bulge cells and promotes wound re-epithelization, while it simultaneously negatively regulates Lgr5 in the secondary hair germ and inhibits HF cycling. Thus, Lhx2 operates as a regulator of epithelial stem cell activity during skin response to injury.

overall_design: Chromatin form primary mouse keratinocytes (PMK) was subjected to ChIP analysis with Lhx2 antibody; input and ChIP DNA were  labelled with Cy3 and Cy5 respectivly and used form Nimblegen MM8 Mouse Promoter Array

first: Vladimir

last: Botchkarev


title: HeLa cell mitochondrial microRNAs

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: MACSmolecular Business Unit

institute: Miltenyi Biotec GmbH

summary:
MicroRNAs (miRNAs) are small non-coding RNAs that associate with Argonaute 2 protein to regulate gene expression at the post-transcriptional level in the cytoplasm. However, recent studies have reported that some miRNAs localize to and function in other cellular compartments. Mitochondria harbour their own genetic system that may be a potential site for miRNA-mediated post-transcriptional regulation. We aimed at investigating whether nuclear-encoded miRNAs can localize to and function in human mitochondria.
To enable identification of mitochondrial-enriched miRNAs, we profiled the mitochondrial and cytosolic RNA fractions from the same HeLa cells by miRNA microarray analysis. Mitochondria were purified using a combination of cell fractionation and immunoisolation, and assessed for the lack of protein and RNA contaminants. We found 57 miRNAs differentially expressed in HeLa mitochondria and cytosol. Of these 57, a signature of 13 nuclear-encoded miRNAs was reproducibly enriched in mitochondrial RNA and validated by RT-PCR for hsa-miR-494, hsa-miR-1275 and hsa-miR-1974.
This study provides the first comprehensive view of the localization of RNA interference components to the mitochondria. Our data outline the molecular bases for a novel layer of crosstalk between nucleus and mitochondria through a specific subset of human miRNAs that we termed ‘mitomiRs’.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: To assess whether nuclear-encoded miRNA are detectable in human mitochondria, we performed the following four steps approach. First, cultured HeLa cells were allowed to reach  80-100% confluence and subjected to  fractionation in order to isolate the cytosolic fraction. From the same HeLa cells, mitochondria were isolated by immunomagnetic Anti-TOM22 MicroBeads from the Mitochondria Isolation Kit (Miltenyi Biotec). In total, six mitochondria preparations were perfromed, three of these were additionally treated with RNase A. Second, total RNA was extracted from the mitochondrial and cytosolic fractions. Third, mitochondrial and cytosolic RNA were respectively profiled by microRNA microarray analysis. Last, data were analyzed and normalized.Three independent assays were performed.

first: Simonetta

last: Bandiera

last: Rüberg

first: Murie

last: Girard

first: Nicolas

last: Cagnard

first: Sylvain

last: Hanein

first: Dominique

last: Chrétien

first: Arnold

last: Munnich

first: Stanislas

last: Lyonnet

first: Alexandra

last: Henrion-Caude


title: Sun and shade leaves_2x ambient ozone_210605

city: Neuherberg

first: Maren

last: Olbrich

address: Ingolstädter Landstr. 1

institute: Helmholtz Zentrum München

summary: Tropospheric ozone causes severe oxidative stress in plants. To investigate the transcriptional responsiveness of adult trees to ozone, fully-expanded sun and shade leaves of mature beech trees were harvested at four time points over the entire vegetation period in 2005 and 2006. Microarray analyses were conducted on leaves from trees grown in the field under ambient and twice-ambient ozone concentrations at Kranzberger Forst (Bavarian). Beech trees changed their transcript levels in response to ozone. In the years 2005 and 2006 different transcription patterns were observed; this may have been a result of different weather conditions and ozone uptake. Furthermore, we obtained differences in mRNA expression patterns between shade and sun leaves. In the ozone-treated sun leaves of 2005, slightly up- and down-regulated transcript levels were detected, particularly in the spring and autumn, whereas shade leaves clearly exhibited reduced mRNA-levels, particularly at the end of the vegetation period. In 2006, this pattern could not be confirmed, and in the autumn, four other transcripts were slightly up-regulated in ozone-treated shade leaves. In addition, two additional transcripts were found to be influenced in sun leaves in the spring/summer. While we detected changes in the levels of only a few transcripts, the observed effects were not identical in both years. In conclusion, elevated ozone exhibited very small influence on the transcription levels of genes of mature beech trees.

overall_design:
The study was carried out at the Kranzberger Forst research site (near Freising, Germany: 48°25’08’’N, 11°39’41’””E, 485m (Pretzsch et al., 1998) in a mixed 60-year old stand (closed canopy) with about 30m high European beech (Fagus sylvatica) and Norway spruce (Picea abies) trees. Free-air ozone fumigation started in May 2000 at double the ambient ozone concentrations with a cut-off at 150 nl l-1 (Werner and Fabian, 2002), thereby avoiding acute damage to the leaves. The ozone concentrations were measured at four heights within the fumigated space and were additionally monitored with 200 passive samplers (Werner and Fabian, 2002). In 2005 the AOT40 value under twice ambient ozone was 64.3 μmol mol-1 h and in 2006 69.0 μmol mol-1 h. Detailed ozone concentration data over the growing seasons have been reported elsewhere (Gielen et al., 2007; Kitao et al., 2009).  Sun and shade leaves from 60-year-old European beech trees were harvested in a total of 8 sampling campaigns in 2005 and 2006. Using scaffolding, five leaves of sun crown (height of about 25 m) and five shade (height of about 19 m) leaves were taken from each of five control and ozone-treated trees. The sampling was carried out in May, June, August, and September of 2005 and in June, August, September and October of 2006. To avoid diurnal effects, the samples were always taken around 11 a.m. For each tree, the four leaves (sun or shade) were combined, frozen in liquid nitrogen and stored at -80 °C until RNA isolation.

For one time point we had five microarrays and five dye-swaps for each of sun and shade leaves. The probes of the trees under ambient ozone were labelled with Cy3 and probes of the trees under 2x ambient were labelled with Cy5. For every pair of trees a dye control were carried out, where the control trees were labelled with Cy5 and the ozone-treated one with Cy3. For statistical analysis a coefficient of variation about all microarrays of one time point was calculated using Acuity 4.0 microarray informatics software [Axon Instruments]. We used only those spots that had a coefficient of variation < 50 and were present on at least half of identical slides. The ozone-changed transcript level of genes were expressed in the median values as log2 ratios.

first: Elke

last: Gerstner

first: Guenther

last: Bahnweg

first: Karl-Heinz

last: Haeberle

first: Rainer

last: Matyssek

first: Gerhard

last: Welzl

first: Werner

last: Heller

first: Dieter

last: Ernst


title: Non-additive gene expression in the natural allopolyploid Coffea arabica is massively affected by growth temperature

city: MONTPELLIER

first: Benoit

last: Bertrand

address: 911 Avenue Agropolis - BP 64501 F

department: RPB

institute: IRD - CIRAD

summary:
Background: Polyploidy has long been recognized as an important mechanism in eukaryotes evolution. Recent studies have documented dynamic changes in plant polyploid gene expression, which reflects genomic and functional plasticity of duplicate genes and genomes in plants. Genomewide approaches in a variety of allopolyploids, mostly synthetics, reveal a trend of non-additive gene expression. The aim of the study was to document expression divergence between a relatively recently formed natural allopolyploid (Coffea arabica) and its ancestral parents (Coffea canephora and Coffea eugenioides) and to verify if the divergence was ‘environment-dependent’.Results: Employing a microarray platform designed against 15,522 unigenes, we assayed gene expression levels in allopolyploid and its two parental diploids. For each gene, we determined expression variation levels between the three species grown under two sets of temperature conditions (26-22°C/30-26°C). More than 35% of genes were differentially expressed in each comparison at both temperatures, except for ‘allopolyploid versus Canephora’ at the ‘hottest’ temperature where an unexpected low gene expression divergence (<9%) were observed. Genes were binned in categories: ‘no change’, ‘additivity’, ‘transgressive’ and ‘dominance’ (‘Canephora-like’ and ‘Eugenioides-like’). The totally new phenomenon revealed by our study was a drastic modification of proportions between the allopolyploid and its parents when environmental conditions were modified. At the ‘hottest’ temperature, we found a virtual disappearance of gene categories classed as ‘transgressive’, ‘Eugenioides-like dominance’ or ‘additivity’ and a major increase in genes classed in the ‘Canephora-like dominance’ category. At this set of growing conditions, we therefore found very high bias that suggested a phenomenon of ‘dominance’ of C. canephora transcription profile. The Canephora genome parental expression state seems exhibited in strong preference to the Eugenioides genome parental state.
Conclusion: Our data constitute evidence for a transcription profile divergence between allopolyploid and its parental species, massively affected by environmental conditions. The parental origin of the transcription profiles was not consistently biased towards one parental species, but appeared to be affected by environmental conditions. This phenomenon indicates the plasticity of allopolyploids and might ultimately explain better adaptation to environmental conditions.

overall_design: Two leaves were pooled per plant from three plants to form three biological replicates, which were subjected to RNA extraction and hybridized in microarrays. We used 72 slides [i.e., 3 (replicates) x 2 (dye-swaps) x 6 (comparisons) x 2 (growth temperature conditions)] following a ‘saturated’ design.

first: Amélie

last: Bardil

first: Marie-Christine

last: Combes

first: Philippe

last: Lashermes

first: Benoît


title: Recessive resistance to Watermelon mosaic virus in melon is associated with a defense response as revealed by microarray analysis

status: Public on Oct 03 2011

city: Espinardo

first: Daniel

last: Gonzalez-Ibeas

state: Murcia

address: Campus de Espinardo s/n

department: Biologia Estres y Patologia Vegetal

institute: CEBAS-CSIC

summary: Virus resistances that are recessively inherited are associated with loss-of-susceptibility resistance alleles. Resistance to Watermelon mosaic virus (WMV) of melon accession TGR-1551 is expressed as a drastic reduction of the virus titer, and is recessively inherited. In this work, viral RNA accumulation was measured in TGR-1551 and in susceptible WMV-infected melon plants by real time quantitative PCR (qPCR), and gene expression of 17,443 unigenes represented in a melon microarray was monitored in a time-course experiment. Virus accumulation was higher in inoculated cotyledons of the resistant genotype up to 7 days post-inoculation; from this time on, virus accumulation was much higher in plants of the susceptible genotype. Microarray experiments were carried with samples from inoculated cotyledons at 1 and 3 dpi to monitor early changes in response to virus infection, and at 7 dpi. Samples from systemically infected leaves harvested at 15 dpi were also included in the analysis. Results showed much more profound transcriptomic alterations in resistant plants compared to susceptible ones. Analyses of gene expression profiles reveal deep and extensive transcriptomic alterations in TGR-1551 plants, many of them involving pathogen response-related genes. Overall, data suggested that resistance to WMV in TGR-1551 is associated with a defense response, contrasting with its recessive nature.

overall_design: Two melon genotypes have been used to analyse transcriptomic responses to infection by Watermelon mosaic virus: Tendral (susceptibel to WMV) and TGR-1551 (resistant to WMV). For each genotype, 60 melon seedlings were inoculated with WMV-M116 and another 60 were mock-inoculated. Cotyledons of 10 plants were harvested at 1, 3, 5, 7, 9 and 15 dpi. At 15 dpi, the systemically infected second true leaf was also harvested.  To reduce variability, each biological replicate used in this study was prepared by mixing the RNA extracts from 2 or 4 mock or WMV-inoculated cotyledons, respectively, or from 3 melon leaves. Samples (WMV infected and mock inoculated) corresponding to cotyledons at 1, 3 and 7 dpi, and leaves at 15 dpi were used for microarray hybridisations, three biological replicates for each one, leading to a total of 48 samples.

first: Joaquin

last: Cañizares

first: Miguel

last: Aranda


title: Hydrogen peroxide Stress in Desulfovibrio vulgaris Hildenborough (REPLACED BY GSE21438)

city: Berkeley

first: Adam

middle: P.

last: Arkin

address: 1 Cyclotron Road

department: Physical Biosciences Division

institute: Virtual Institute for Microbial Stress and Survival

summary:
Using data from microarray experiments, we investigated the effects of excess hydrogen peroxide on D. vulgaris.

Keywords: stress response, time course

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: Comparison of wild type and deletion mutant cells treated with 1 mM H2O2 to untreated cells at times of 0 and 120 min. See also Series GSE4447 (http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE4447)


title: Genomic Loss of Penicillin-Binding Protein 3 in Burkholderia pseudomallei Confers Clinical Resistance to Ceftazidime

city: Singapore

first: Wen Fong

last: Ooi

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

summary: Array-CGH analysis and Burkholderia pseudomallei isolates pre and post ceftazidime relapse.

overall_design: Genomic DNA from both the parental strains and variant strains were labeled with Cy3 or Cy5 fluorescent dyes and hybridized onto a customized microarray with probes designed from the reference Bp K96243 genome. Log2 signal ratios of parental strain over the variant strains were then computed after normalization to find genomic loss or gain in the variant strains.

first: B

last: Sim

first: W

middle: F


title: Hydrogen peroxide Stress in Desulfovibrio vulgaris Hildenborough (REPLACED BY GSE21441)

platform_organism: Nitratidesulfovibrio vulgaris str. Hildenborough


title: RNA_Pol2_Ser5phospho_mES

city: Cambridge

first: Peter

last: Rahl

address: 9 Cambridge Center

institute: Whitehead Institute

summary: Mouse embryonic stem cells were used to study RNA Polymerase 2 phosphorylation of Ser 5 IP.

overall_design: Duplicate whole genome mouse arrays of embryonic stem cells. RNA Polymerase II phosphoCTD (Serine 5) antibody was used in the experiment.


title: Trimethoprim response in Escherichia coli in bacteriostatic and bactericidal conditions

city: Princeton

first: Dipen

last: Sangurdekar

state: NJ

address: 132 Carl Icahn laboratory, Princeton University

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

summary:
Transcriptional profiling of E. coli MG1655 to Trimethoprim in i) LB media, ii) M9 minimal media and iii) M9 minimal media with supplements to study the association of gene expression with corresponding lethal and non-lethal growth conditions.
Supplementation conditions in M9 media included addition of 50 microgram/ml of adenine, methionine, glycine or thymine in various combinations.

overall_design: For all growth conditions, TMP was added to E. coli in mid-log phase and samples were taken at regular intervals from 10 minutes to 120 minutes post treatment. 1 Biological replicate per time point.

first: D

first: Z

last: Zhang

first: A

middle: B

last: Khodursky


title: Signal-dependent dynamics of transcription factor translocation controls gene expression

last: Hao

address: 52 Oxford St. Rm.442

department: FAS Center for Systems Biology

institute: Harvard University

summary: Time course transcription profiling of S. cerevisiae in response to different dynamics of protein kinase A inhibition

overall_design: Time course experiments to analyze dynamics of whole-genome transcription in response to different temporal patterns of protein kinase A inhibition.

first: Erin

last: O'Shea


title: Spleen transcriptome response to infection with avian pathogenic Escherichia coli in broiler chickens

city: Ames

first: Susan

last: Lamont

state: IA

address: 2255 Kildee Hall

department: Animal Science

institute: Iowa State University

summary: Gene expression profiling of male broiler chickens exposed to APEC O1.  Comparisons were made between Day 1 and Day 5 of all treatment groups, between differences in pathology and effect of vaccine on spleen gene expression.  The goal was to determine expression differences that could convey genetic resistance to APEC O1.

overall_design: Chickens were either challenged or non-challenged with APEC, vaccinated or non-vaccinated, with spleens harvested 1 or 5 days post challenge.  The non-vaccinated, challenged group was further subdivided into mild and severe pathologay based on internal lesion scores.  This created 10 groups, done in 4 replicates.  The non-vaccinated, non-challenged, day 1 group was used as the reference for all other samples.

middle: E

last: Sandford

first: Megan

last: Orr

first: Emma

last: Balfanz

first: Nate

last: Bowerman

first: Xianyao

last: Li

first: Huaijun

last: Zhou

first: Timothy

last: Johnson

first: Subhashinie

last: Kariyawasam

first: Peng

last: Liu

first: Lisa

middle: K

last: Nolan


title: Promoter methylation data: OHT/ICI-sensitive vs. -resistant cell lines

city: Indianapolis

first: Jaesik

last: Jeong

address: 410 West 10th Street, Suite 3000

institute: IUPUI

summary:
MCF7 breast cancer cell lines: drug-resistant (OHT and ICI) cell lines vs. drug-sensitive (wild type) cell lines.
Assessment of association between gene expression and methylation.

overall_design:
Two comparisons: OHT-resistant vs. wild type, and ICI-resistant vs. wild type.

OHT: 4-hydroxytamoxifen
ICI: fulvestrant ((ICI 182780)

This submission represents the methylation component of the study.

first: Kenneth

last: Nephew


title: Expression profiling of 3D 2D MDCKII epithelial morphogenesis

status: Public on Oct 01 2011

city: Madrid

first: Manuel

last: Galvez-Santisteban

address: Nicolas Cabrera 1

department: Cell Biology and Immunology

institute: CSIC-CBM Severo Ochoa

summary:
Formation of epithelial tissues requires the generation of apical-basal polarity and the co-ordination of this polarity between neighboring cells to form a central lumen. MDCK cell line has proven to be a powerful model to study mammalian polarized epithelia in vitro. MDCK cells plated in extracellular matrix (ECM) form cysts, a spherical structure of polarized cells enclosing a central lumen which resembles epithelial tubular structures.
The morphogenetic process requires drastic changes in cell architecture, which are regulated by change in gene expression. We used microarrays to identify genes up-regulated in lumen formation. The identification of up-regulated genes could lead us to characterize novel pathways needed for this process.

overall_design: MDCKII cells were plated in two different conditions: Cells cultured in confluence in plastic dishes, forming polarized monolayers (2D); or cells cultured in plastic dishes covered with Matrigel (ECM) forming three dimensional cysts (3D). Comparison of both transcriptomic profiles would lead us to identify up-regulated genes in the 3D condition, which would be good candidates to be key regulators of novel processes involved in lumen morphogenesis.

first: Alejo

last: Rodriguez-Fraticelli

first: Fernando

last: Martin-Belmonte


title: Transcriptional and metabolomic consequences of luxS inactivation reveal a metabolic rather than quorum sensing role for LuxS in Lactobacillus reuteri 100-23

city: Oak Ridge

first: Charlotte

last: Wilson

state: Tennessee

address: 1 Bethel Valley Road

department: Biosciences Bldg 1520

country: New Zealand

institute: ORNL

summary: Autoinducer-2 (AI-2)-mediated quorum sensing has been extensively studied in relation to the regulation of microbial behaviour.  There are however two potential roles for the AI-2 synthase (LuxS).  The first is in the production of AI-2 and the second is as an enzyme in the activated methyl cycle where it catalyses the conversion of S-ribosylhomocysteine to homocysteine.  The by-product of the reaction catalysed by LuxS is (S)-4,5-dihydroxy-2,3-pentanedione (DPD), which spontaneously forms the furanones known collectively as AI-2.  The mammalian gastrointestinal tract contains a complex collection of bacterial species so a method of interspecies communication might influence community structure and function.  Lactobacillus reuteri 100-23 is an autochthonous inhabitant of the rodent forestomach where it adheres to the non-secretory epithelium of the forestomach forming a biofilm.  Microarray comparisons of gene expression profiles of the L. reuteri 100-23 wild type and a luxS mutant under different culture conditions revealed altered transcription of genes encoding proteins involved in cysteine biosynthesis, the oxidative stress response and cell wall proteins.  Metabolomic analysis revealed that the luxS mutation affected cellular levels of fermentation products, fatty acids and amino acids.  Cell density-dependent changes (log phase versus stationary phase growth) in gene transcription were not detected.  Overall, the results indicated that AI-2 was unlikely to be involved in gene regulation in L. reuteri 100-23 in a classical quorum-sensing type manner.

sample_organism: Limosilactobacillus reuteri subsp. rodentium

overall_design: Analysis of the microarray data was obtained from two or more independent biological replicates.

first: Paul

last: O'Toole

first: Silas

middle: V

last: Boas

first: Raphael

last: Aggio

first: Gerald

last: Tannock


title: ccpA mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + Galactose at MID-log growth phase

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

summary:
Comparison of Streptococcus pneumoniae D39 ccpA mutant compared to D39 wild type in CDM with galactose as sole carbon source to define the regulon of carbon catabolite control protein CcpA under this condition
Details described in Carvalho SM, Kloosterman TG, Neves AR, Kuipers OP. CcpA Ensures Optimal Metabolic Fitness of Streptococcus pneumoniae. Plos One 2011

overall_design: One condition design comparision of two strains including a dye swap

first: Sandra

last: Carvalho

first: Tomas

middle: G

last: Kloosterman

first: Oscar

last: Kuipers

first: Ana

last: Neves


title: ccpA mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + GLucose at transition-phase of growth (TS)

summary:
Comparison of Streptococcus pneumoniae D39 ccpA mutant compared to D39 wild type in CDM with glucose as sole carbon source to define the regulon of carbon catabolite control protein CcpA under this condition
Details described in Carvalho SM, Kloosterman TG, Neves AR, Kuipers OP. CcpA Ensures Optimal Metabolic Fitness of Streptococcus pneumoniae. Plos One 2011

middle: P


title: ccpA mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + Glucose at MID-log growth phase


title: ccpA mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + galactose at transition-phase of growth (TS)


title: Transcriptional profiling of Piriformospora indica colonizing living and dead barley roots

city: Regensburg

first: Urs

last: Lahrmann

address: Am Biopark 9

department: Project Group Personalized Tumor Therapy

institute: Fraunhofer ITEM

summary: Recent sequencing projects have provided deep insight into fungal lifestyle-associated genomic adaptations. Here we report on the 25 Mb genome of the mutualistic root symbiont Piriformospora indica (Sebacinales, Basidiomycota) and provide a global characterization of fungal transcriptional responses associated with the colonization of living and dead roots. Extensive comparative analysis of the P. indica genome with other Basidiomycota and Ascomycota fungi that have diverse lifestyles strategies identified features typically associated with both, biotrophism and saprotrophism. The tightly controlled expression of the lifestyle-associated gene sets during the onset of the symbiosis, revealed by microarrays analysis, argues for a biphasic root colonization strategy of P. indica. Our finding provides a significant advance in understanding development of biotrophic plant symbionts and suggests a series of incremental shifts along the continuum from saprotrophy towards biotrophy in the evolution of mycorrhizal association from decomposer fungi.

overall_design: P. indica (DSM 11827, DSMZ) was cultivated on complex medium agar plates or liquid medium as described before (Zuccaro et al., 2009). Barley seeds (Hordeum vulgare L. cv. Golden Promise) were surface sterilized with 3 % sodium hypochlorite, rinsed in water and pregerminated for 3 days. To address the experimental design four different treatments were done (P. indica on barley roots on 1/10 PNM medium, P. indica on autoclaved barley roots on 1/10 PNM medium, P. indica on 1/10 PNM medium and P. indica on CM medium), each in three independent biological replications. Root and fungal material was harvested in liquid nitrogen after 24, 36, 48, 72, 120 and 168 hpi. For each time point roots from 15 to 20 living plants or 21 to 36 autoclaved plants were pooled.

first: Alga

last: Zuccaro

first: Stefanie

last: Pfiffi

first: Dagmar

last: Biedenkopf

first: Birgit

last: Samans

first: Karl-Heinz

last: Kogel


title: Changes in gene expression during cold exposure in Drosophila montana and D. virilis

city: Jyväskylä

first: Laura

last: Vesala

address: Survontie 9

department: Department of Biological and Environmental Science

institute: University of Jyväskylä

summary: We utilized a candidate gene approach using custom microarray constructed for our study species Drosophila montana and D. virilis to identify genes with modulated expression patterns under low temperature conditions. The flies were exposed to four different treatments (+5°C for 6 days, 0°C for 1 hour, two periods of recovery after cold stress and a control treatment). The aim of the study was to identify potential cold-responsive genes and to investigate differences in gene expression between the species. Microarray analysis revealed altogether 31 out of 219 genes on the array to show expression changes during different stages of cold stress. Among the potential stress tolerance genes detected earlier in D. melanogaster, hsr-omega was upregulated in both species during cold acclimation, expression changes in other genes being treatment- and species specific. Our microarray study clearly showed that different stages of cold response elicit changes at least in genes involved in heat shock response, circadian rhythm and metabolism.

sample_organism:
Drosophila virilis
Drosophila montana

platform_organism:
Drosophila virilis
Drosophila montana

overall_design: Cold- induced gene expression was investigated comparing four different treatments to the control treatment: 1) Cold acclimation: 14 days in control conditions, then 6 days at +5°C 2) Cold hardening: 20 days in control conditions, then1 hour at 0°C  3) 15-min recovery from chill coma: the 20-day-old flies were exposed to -6°C for 16 hours, after which they were let to recover for 15 minutes 4) 1-hour recovery from chill coma:  the 20-day-old flies were exposed to -6°C for 16 hours, after which they were let to recover for 1 hour. In control treatment flies were kept for 20 days at 19°C. All the flies were 20-days old at the time of sample collection, and the light:dark cycle was 22 hours of light and 2 hours of dark. Because of the limited space on the array plate, the recovery samples were collected only for D. montana. All the samples were collected 5-6 hours after the lights had been turned on in the chamber and the flies were immediately immersed in liquid nitrogen, after which they were stored at -84ºC. Three pools of ten flies were collected from each treatment group.

first: Tiina

middle: S

last: Salminen

first: Asta

last: Laiho

first: Anneli

last: Hoikkala

first: Maaria

last: Kankare


title: Liver hyperplasia; Gadd45beta-null mouse (C57Bl/6 background)

city: Scarsdale

first: Joseph

last: Locker

address: Pathology

institute: Albert Einstein College of Medicine

summary:
Four experimental groups each for wild-type and Gadd45beta-null (5 - 7 months old); (1) Untreated mice, and (2 - 4) treatment with TCPOBOP for 3, 6, or 12 hr
2 - 4 replicates for each experimental group;

overall_design:
Two color arrays; RNA from treated livers, red; pooled normal liver RNA, green.
Each experimental condition was studied with 2 - 4 replicates, each from separate mice. The experimental RNA was cohybridized with RNA pooled from several normal livers. Data are the ratios of treated to normal hybridization.

first: Jianmin

last: Tian


title: Zebrafish embryos exposed to the model hedgehog pathway inhibitor cyclopamine, as well as to the potential hedghog pathway disrupters SANT-2 and GANT-61.

city: Leipzig

first: Wibke

last: Busch

address: Permoser Str. 15

department: Bioanalytical Ecotoxicology

institute: UFZ Helmholtz Centre for Environmental Research

summary: The hedgehog (Hh) signaling pathway is important for various developmental processes during embryogenesis and for homeostasis of adult tissue in vertebrates. Aberrant signaling results in severe birth defects and malignancies, respectively. The small molecules SANT-2 and GANT-61 were identified as potential Hh-pathway inhibitors in a reporter gene assay (Shh-light II cells). We aimed to analyze the effects of these compounds on the gene expression level in zebrafish embryos in comparison with the well known Hh-pathway inhibitor cyclopamine.

overall_design: Zebrafish embryos were treated with Ethanol (0,1%) (control), 10 µM Cyclopamine (C), 10 µM SANT-2 (S), and 10 µM GANT-61 (G), for 24 h (0.5 - 24 hpf), respectively; all in 5 independent replicates with 100 zebrafish embryos per treatment. Total RNA was extracted and processed as recommended by Agilent. One color arrays were used and data is given as normalized log2 of the gprocessed signals.

first: Anita

last: Büttner

first: Nils

last: Klüver

first: Stefan

last: Scholz


title: Developmental trajectories of gene expression reveal candidates for diapause termination, a key life history transition in the apple maggot fly, Rhagoletis pomonella

city: Gainesville

first: Greg

last: Ragland

state: FL

department: Entomology and Nematology

institute: University of Florida

summary: Gene expression microarray experiment comparing differential expression across a developmental and metabolic trajectory of diapause termination.

overall_design:
Six phenotypes representing 6 developmental time points, four replicate individuals for each phenotype, four competitve hybridizations for each of six phenotypic comparisons. Each individual was hybridized up to 3 times, each in a separate phenotypic comparison.

Phenotypes:
24Fridge = early diapause (24 hours after transfer from fridge to 24C)
LateDia =  late diapause (2 weeks after transfer from fridge to 24C)
Break24 = 24 hours after initial metabolic rate increase
Break48 = 48 hours after initial metabolic rate increase
Plat = in the metabolic rate plateau
PostPlat = in the final, exponential phase of metabolic rate increase

first: Gregory

middle: J

first: Scott

last: Egan

first: Jeffrey

last: Feder

first: Stewart

middle: H

last: Berlocher

first: Daniel

last: Hahn