title: Cerebellar gene expression profiles of mouse models for Rett Syndrome reveal MeCP2 targets

last: Stanford Microarray Database

summary:
Background  MeCP2, methyl-CpG-binding protein 2, binds to methylated cytosines at CpG dinucleotides, as well as to unmethylated DNA, and affects chromatin condensation. MECP2 mutations in females lead to Rett syndrome, a neurological disorder characterized by developmental stagnation and regression, loss of purposeful hand use and speech, stereotypic hand movements, deceleration of brain growth, autonomic dysfunction and seizures. Most mutations occur de novo during spermatogenesis. Located at Xq28, MECP2 is subject to X inactivation, and affected females are mosaic. Rare hemizygous males suffer from a severe congenital encephalopathy.  Methods  To identify pathways mis-regulated by MeCP2 deficiency, microarray-based global gene expression studies were carried out on cerebellum of Mecp2 mutant mice. We compared transcript levels in mutant/wildtype male sibs of two different MeCP2-deficient mouse models at 2, 4 and 8 weeks of age. Increased transcript levels were evaluated by real-time quantitative RT-PCR. Chromatin immunoprecipitation assays were used to document in vivo MeCP2 binding to promoter regions of candidate target genes.  Results  In the mutants, several hundred genes showed altered expression levels. Twice as many were increased than decreased, and only 27 genes were differentially expressed at more than one time point. The number of misregulated genes was 30% lower in mice with an exon 3 deletion (Mecp2tm1.1Jae) than in mice with a larger deletion (Mecp2tm1.1Bird). Between the mutants, few misregulated genes overlapped at each time point. Real-time quantitative RT-PCR assays validated increased transcript levels for four genes: Irak1, interleukin-1 receptor-associated kinase 1; Fxyd1, phospholemman, associated with Na, K-ATPase; Reln, encoding reelin, an extracellular signaling molecule essential for neuronal lamination and synaptic plasticity; and Gtl2/Meg3, an imprinted maternally expressed non-translated RNA that serves as a host gene for C/D box snoRNAs and microRNAs. Chromatin immunoprecipitation assays documented in vivo MeCP2 binding to promoter regions of Fxyd1, Reln, and Gtl2.  Conclusions  Transcriptional profiling of cerebellum failed to detect significant global changes in Mecp2-mutant mice. Increased transcript levels of Irak1, Fxyd1, Reln, and Gtl2 may contribute to the neuronal dysfunction in MeCP2-deficient mice and individuals with Rett syndrome. Our data provide testable hypotheses for future studies of the regulatory or signaling pathways that these genes act on.
A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out.
Keywords: genetic_modification_design

first: Charandle

last: Jordan


title: Infection with bradyzoites has a diminished impact on host transcript levels relative to tachyzoite infection.

status: Public on Aug 15 2007

city: Stanford

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

summary:
5 arrays per condition (covering 3 biological replicate experiments) were performed on Human Foreskin Fibroblasts (HFFs) at 44 hours post infection.  The four experimental conditions include uninfected "standard", uninfected "stress", tachyzoite-infected "standard+TZ", and bradyzoite-infected "stress+BZ".  Bradyzoite conversion is induced at 4 hours post infection with replacement of standard DMEM+10% FCS with RPMI+1%FCS buffered with 50mM Hepes to pH 8.15.  Approximately 20% of cells are infected and bradyzoite conversion is >90% in these experiments.  These data are normalized using 2-D loess (span factor .4).  The calculations in the manuscript are based on  are log2 ratios of normalized channel 2/channel 1 medians.
A development or differentiation experiment design type assays events associated with development or differentiation or moving through a life cycle. Development applies to organism(s) acquiring a mature state, and differentiation applies to cells acquiring specialized functions.
Developmental Stage: Uninfected (standard or stress medium), or Tachyzoite-infected (standard medium) or Bradyzoite-infected (stress medium)
Keywords: development_or_differentiation_design

overall_design: Complex

first: Ashley

last: Fouts


title: Seasonal bud dormancy progression

status: Public on Aug 24 2007

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

summary:
This study investigated changes in the transcriptome of outdoor grown leafy spurge crown buds as they progress from paradormancy in August and September into endo dormancy in October through to ecodormancy in November and December.
Keywords: Dormancy leafy spurge adventitious-buds

platform_organism:
Manihot esculenta
Euphorbia esula

overall_design: A series of balanced dyeswap rolling circle hybiridizations were used with each year representing s seperate circle and with direction of the circles reversing on alternate years. Note, the Aug-Sep 04 hybridization failed and is missing from the dataset

middle: P

first: James

middle: V

last: Anderson

first: Wun

middle: S

last: Chao


title: Niemann-Pick type C fibroblast analysis

summary:
Primary skin fibroblasts from four Niemann-Pick type C patients homozygous for the I1061T mutation and four control individuals were cultured under identical conditions in DMEM containing 10% fetal bovine serum.  Cells were harvested at 50-70% confluency.      mRNA was isolated with the FastTrack 2.0 mRNA isolation kit according to the manufacturer's instructions (Invitrogen, Carlsbad, CA).  A reference RNA comprised of 10 cell lines was used as the control for each hybridized sample (Stratagene, La Jolla, CA).  Both sample and reference RNAs were amplified using the MessageAmp II aRNA amplification kit (Ambion, Austin, TX).
Set of arrays that are part of repeated experiments
Keywords: Biological Replicate

overall_design:
Biological Replicate
Complex

first: Jon

last: Reddy


title: Frequent occurrence of deletions in primary mediastinal B-cell lymphoma

city: Vancouver

first: Lindsey

last: Kimm

state: British Columbia

address: 675 W10th Ave

department: Cancer Genetics

country: Canada

institute: BC Cancer Research Centre

type: Genome variation profiling by genome tiling array

summary:
Primary mediastinal B-cell lymphoma (PMBCL) is a distinct subtype of diffuse large B-cell lymphoma.  PMBCL has been previously studied with a variety of genomic techniques resulting in frequent detection of chromosomal gains; however, chromosomal losses have been rarely reported.  This finding contrasts many other types of lymphoma, in which deletions are common.  We hypothesize that segmental losses do exist but may have escaped detection by methods used in the previous studies.  Using array comparative genomic hybridization to a tiling-resolution microarray encompassing the entire human genome, PMBCL samples were analyzed for genomic copy number alterations.  Both gains and losses of chromosomal material were detected throughout the genome.  These DNA copy number alterations were confirmed by quantitative real-time PCR.  Recurrent chromosomal losses include a novel event at 1p13.1-p13.2 present in 42% of cases analyzed.   We conclude that losses are present in the PMBCL genome.  Given the similar frequency of losses to that of segmental gains of DNA, they are likely to play an important role in the pathogenesis of PMBCL.
Keywords: array CGH, PMBCL

overall_design: Whole genome tiling path array CGH of 20 PMBCL tumor samples and one cell line was performed against male reference genomic DNA.  Alterations were confirmed via DNA copy number quantitative real-time PCR

middle: R

first: Rolanld

middle: J

last: deLeeuw

first: Kerry

last: Savage

first: Andreas

last: Rosenwald

first: Elias

last: Campo

first: Jan

last: Delabie

first: German

last: Ott

first: Hans-Konrad

last: Muller-Hermelink

first: Elaine

last: Jaffe

first: Lisa

middle: M

last: Rimsza

first: Dennis

middle: D

last: Weisenburger

first: Wing

middle: C

last: Chan

first: Louis

last: Staudt

first: Joseph

last: Conners

first: Randy

last: Gascoyne

first: Wan

middle: L

last: Lam


title: renal ischemia vs sham - 24h

city: Indianapolis

first: David

last: Basile

state: IN

address: 635 Barnhill Drive

department: Cellular & Integrative Physiology

institute: Indiana University

summary:
This experiment was designed to determine alterations in gene expression in rat kidney following ischemia reperfusion injury. Several genes were identified that were significantly up regulated in kidneys at 24 hours following a 45 min ischemic injury.  This group comprises data from 4 different hybridizastion deriving from 4 pairs of animals (1 sham vs 1 ischemic animal) per hybridization
Keywords: disease state

overall_design:
Rat angiogenesis slides were produced with angiogenesis genes printed 6-12 times.  4 pairs of animals were compared with 1 hybridization each to determine ratio of expression in injured vs. sham.

Data analysis were used to first combine data from replicate spots per slide and then to combine data for each genetic element across multiple hybridizations

first: katherine

last: Fredrich

first: Deborah

last: McNew


title: Selenomethionine induced transcriptional programs in human prostate cancer cells.

last: Stanford Microarray Database

summary:
PURPOSE: We determined the effects of selenomethionine, the major organic selenium containing compound found in the diet and the form of selenium being used in the Selenium and Vitamin E Cancer Prevention Trial, on prostate cancer cells. MATERIALS AND METHODS: We assessed global transcript profiles of selenomethionine treated LNCaP using cDNA microarrays and compared them to those of cells treated with methylselenic acid, a direct precursor of methylselenol, which is the active form of selenium in vivo. : After treatment with selenomethionine 2,336 unique genes showed expression changes of at least 1.5-fold in at least 3 time points during 48 hours and 366 unique transcripts differed significantly between selenomethionine and methylselenic acid treated LNCaP. Approximately half of the 76 cell cycle regulated genes affected by selenomethionine were down-regulated and enriched for genes associated with the G2/M phase. Flow cytometry analysis showed that selenomethionine induced G2/M arrest in LNCaP at low concentrations. Selenomethionine also affected expression levels of 35 known androgen responsive genes and 18 of these transcripts showed changes that were the inverse of those seen after androgen stimulation. At high concentrations selenomethionine decreased prostate specific antigen promoter driven luciferase expression. CONCLUSIONS: Selenomethionine modulates transcript levels of genes involved in a number of biological processes, including cell cycle/apoptosis androgen signaling, signal transduction and transcriptional regulation. Although the pathways affected paralleled in many ways those that are modulated by methylselenic acid, distinct differences in transcript patterns and effects on cell cycle regulation suggest that different selenium compounds could exert unique effects in prostate cells.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

overall_design: Computed

first: Hongjuan

last: Zhao


title: Micro-RNAs in Adult Rat Liver are Refractory to Dioxin Treatment

city: Toronto

first: Ivy

last: Moffat

state: Ontario

address: 1 King's College Circle, Medical Science Building Rm.4302

department: Pharmacology

institute: University of Toronto

summary:
Dioxin-like chemicals are well-known for their ability to upregulate expression of numerous genes via the AH receptor (AHR).  However, recent transcriptomic analyses in several laboratories indicate that dioxin-like chemicals or AHR genotype itself also can downregulate levels of mRNAs encoded by numerous genes.  The mechanism responsible for such downregulation is unknown.  We hypothesized that microRNAs (miRNAs), which have emerged as powerful negative regulators of mRNA levels in several systems, might be responsible for mRNA downregulation in dioxin/AHR pathways.  We used the Exiqon miRNA array platform as well as quantitative RT-PCR to measure miRNA levels in dioxin-sensitive Long-Evans (Turku/AB; L-E) rats vs. dioxin-resistant Han/Wistar(Kuopio; H/W) rats. Treatment with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in vivo caused few changes in miRNA levels in rat livers and those changes that were statistically significant were of modest magnitude.  AHR genotype had little effect on hepatic miRNA levels, either in constitutive expression or in response to TCDD – only a few miRNAs differed in expression between between L-E rats (that have wildtype AHR) compared to H/W rats (whose AHR has a large deletion in the transactivation domain).  It is unlikely that mRNA downregulation by dioxins is mediated by miRNAs, nor are miRNAs likely to play a significant role in dioxin toxicity in adult rodent liver.
We conducted a thorough investigation to address the following questions: (1) does AHR genotype itself affect constitutive expression of microRNAs?  (2) does TCDD affect microRNA levels and, if so, is this response dependent on the AHR?  (3) does TCDD affect microRNA levels differently in animals that are sensitive to dioxin toxicity versus those that are dioxin-resistant?  We assessed the in vivo effect of TCDD on microRNA levels in liver at multiple time points after TCDD treatment using microRNA arrays along with quantitative RT-PCR.  The cumulative results of our experiments indicate that downregulation of mRNA levels by dioxins in adult rodent livers is very unlikely to involve microRNAs.
Manuscript Submitted: Moffat ID, Boutros PC, Celius T, Pohjanvirta R & Okey AB. Micro-RNAs in rodent liver are refractory to dioxin treatment. Toxicological Sciences May, 2007.
Keywords: miRNA expression, Time course, response to xenobiotics, genetic modification, comparative genome hybridization

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: We examined strain differences in miRNA expression independent of TCDD: 19-h vehicle-treated dioxin-resistant H/W AHRH/W/H/W rats (HC19) vs. vehicle- control dioxin-sensitive L-E AHRWT/WT rats (LC19). In the dioxin-sensitive rats we compared miRNA expression levels 3 h (LT3) or 19 h (LT19) post-TCDD treatment vs. LC19.  In the dioxin-resistant rats we compared miRNA levels 3 h (HT3), 19 h (HT19), or 96 h (HT96) post-TCDD treatment vs. HC19.

first: Paul

last: Boutros

first: Trine

last: Celius

first: Jere

last: Lindén

first: Raimo

last: Pohjanvirta

first: Allan

middle: B

last: Okey


title: Early embryoid body differentiation

city: Cardiff

first: Fiona

middle: Catherine

last: Mansergh

state: Wales

address: Museum Avenue

department: Biosciences

country: United Kingdom

institute: Cardiff University

summary:
Embryonic stem (ES) cells, when grown in suspension culture without feeders, spontaneously form round structures known as embryoid bodies. Given the appropriate conditions, these cells can differentiate over time into precursors of all three germ layers. Embryoid bodies, in a disorganized way, mimic early embryonic development to a certain extent and can be used as a synchronously differentiating large scale source of tissue for the study of biological determinants of early differentiation. Embryoid bodies have been used as a source for most early protocols that derive specific differentiated cell types from undifferentiated ES cells, although some protocols, notably those that derive neurons from ES cells, have moved on from EBs as a result of varying replicability and yield. We have decided to look at the transcriptomic profiles of embryoid bodies during the initial stages of embryoid body formation and differentiation, in order to pinpoint novel determinants of key developmental stages.
Keywords: time course

overall_design: We have compared embryoid bodies that have been grown in the presence and absence of LIF, on days 1-4 of differentiation. LIF does not inhibit the development of an outer layer of embryonic endoderm and the maintenance of a core of undifferentiated stem cells in embryoid bodies is continued. The absence of LIF is permissive for differentiation of precursors of all 3 germ layers formed in the embryo proper. We have also included a comparison of differentiating EBs with undifferentiated IMT11 ES cells from which the EBs were derived (Day 0). Arrays were hybridised with experimental sample from Day0-4, and a pooled control derived from equal quantities of Day 1-4 EBs. Fluor switches were carried out. Analysis of the results included comparisons of experimental samples with the pooled control, and also comparisons with each other. The conditions for the growth of the EBs were tightly controlled, we formed EBs of a predetermined size via aggregation of 1000 cells in individual hanging drops, in order to minimize variation. The size was chosen after study of key marker genes of differentiation, which revealed that smaller EBs tended to differentiate too fast and not to express markers of all germ layers, while larger EBs tended to show some signs of cell death and also to maintain increasing numbers of undifferentiating ES cells in the inner core. We chose to use our standard 20% medium serum concentration after studies varying the serum showed less strong growth at early stages, making it difficult to obtain enough sample for the arrays. Concurrent studies with which this one is to be compared (GSE8625, and another to be submitted) also use this serum concentration. Furthermore, preliminary results from a concurrent study of undifferentiated ES cells versus microdissected early embryos has shown that our standard medium recipe gives a good correlation between the transcription profiles of early embryonic compartments and the ES cells themselves. This correlation is not maintained in ES lines grown with feeders, knockout medium and serum replacement (SMH, unpublished data). Since we wish to faithfully mimic early embryonic development as far as possible in these studies, we have therefore proceeded with the ES medium described in the GSM submissions accompanying this entry. We have identified approximately 130 ESTs that showed significant changes as a result of analysis of this timecourse. Following rejection of duplicate genes (the NIA set contains many different clones that represent the same gene in some instances), and ESTs where sequence quality was too poor for primer design, we were left with 101 genes that we tested across 6 biological cDNA sample replicates, 3 from 1000 cell EBs and 3 from 750 cell EBs. Of these, 25 were confirmed as differentially regulated from the -LIF sample set and 12 from the + LIF dataset (9 of these were present in both datasets). 3 genes were expressed only in - LIF samples.

first: Carl

last: Daly

first: Anna

last: Hurley

first: Susan

last: Hunter

first: Martin

last: Evans


title: Micro-RNAs in Adult Long-Evans (Turku/AB) Rat Liver are Refractory to 96 Hours Dioxin Treatment

summary:
Dioxin-like chemicals are well-known for their ability to upregulate expression of numerous genes via the AH receptor (AHR).  However, recent transcriptomic analyses in several laboratories indicate that dioxin-like chemicals or AHR genotype itself also can downregulate levels of mRNAs encoded by numerous genes.  The mechanism responsible for such downregulation is unknown.  We hypothesized that microRNAs (miRNAs), which have emerged as powerful negative regulators of mRNA levels in several systems, might be responsible for mRNA downregulation in dioxin/AHR pathways.  We used the Exiqon miRNA array platform as well as quantitative RT-PCR to measure miRNA levels in dioxin-sensitive Long-Evans (Turku/AB; L-E) rats. Treatment with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) for 96 hr in vivo caused few changes in miRNA levels in rat livers and those changes that were statistically significant were of modest magnitude.
Feed-restricted-control L-E rats were included to ensure that changes in miRNA levels were due to TCDD-treatment per se and not the result of the decreased feed intake which occurs in dioxin-sensitive strains within 96 h after TCDD exposure.
Manuscript Submitted: Moffat ID, Boutros PC, Celius T, Pohjanvirta R & Okey AB. Micro-RNAs in rodent liver are refractory to dioxin treatment. Toxicological Sciences May, 2007.
Keywords: miRNA expression, response to xenobiotics,  feed restriction response

overall_design: A loop design used to profile miRNA levels from dioxin-sensitive L-E AHRWT/WT vehicle-control rats (LC96), those exposed to TCDD for 96 h (LT96), and feed-restricted (LF96) rats.


title: Comparison of apoptosis related gene expression in p7-p14 mouse lenses

status: Public on Aug 11 2007

summary:
Lens development exhibits a seamless progression from embryogenesis through ageing. Lens maturation and growth proceed throughout life; lens fibre cells differentiate from lens epithelial cells at the equator of the lens, migrate inwards at the bow region and mature around pre-existing fibre cells at the centre of the lens. Lens fibre cells lose their nuclei via an apoptosis like mechanism as they mature. We therefore decided to study further the relationship of apoptosis related gene expression during vital stages of lens maturation in the mouse. This is an important question as defects in lens function and/or maturation result in clouding of the lens, or cataract, which can result in considerable visual impairment.
Keywords: development/age comparison

overall_design:
We used manufactured Sigma Panorama mouse apoptosis gene arrays (cat# G1039), in conjunction with RNA extracts from day 7 and day 14 postnatal mice. These stages were chosen because the eyes are closed at day 7, but open on day 14. The postnatal period before day 14 is a period of rapid lens growth, accompanied by lens fibre cell differentiation and organelle loss via apoptosis signalling pathways. Formation of the organelle free zone is complete at day 14 when the eyes open, allowing for clear vision.
4 biological repeats were carried out for day 7, and 3 for day 14 lenses. Each array carries duplicate spots, giving 8 and 6 repeats respectively. Analysis of all day 7 repeats versus all day 14 repeats was carried out by t-test, we also required a fold change of 2. Statistically significant genes were tested by PCR using 3 biological replicates for each stage. We also used the array data to estimate which genes were highly expressed at each stage. We asked that at least one of the spots representing each gene be above background + 2SD in all replicates for a given stage (day7 or day14).

first: Jenny

last: Geatrell

first: Michael

middle: E

last: Boulton

middle: A

last: Wride


title: Micro-RNAs levels in wildtype vs. Ahr-null adult mouse liver constitutively and in response to doxin treatment.

summary:
Dioxin-like chemicals are well-known for their ability to upregulate expression of numerous genes via the AH receptor (AHR).  However, recent transcriptomic analyses in several laboratories indicate that dioxin-like chemicals or AHR genotype itself also can downregulate levels of mRNAs encoded by numerous genes.  The mechanism responsible for such downregulation is unknown.  We hypothesized that microRNAs (miRNAs), which have emerged as powerful negative regulators of mRNA levels in several systems, might be responsible for mRNA downregulation in dioxin/AHR pathways. We conducted a thorough investigation to address the following questions: (1) does AHR genotype itself affect constitutive expression of microRNAs?  (2) does TCDD affect microRNA levels and, if so, is this response dependent on the AHR?  (3) does TCDD affect microRNA levels differently in animals that are sensitive to dioxin toxicity versus those that are dioxin-resistant?
We used the Exiqon miRNA array platform as well as quantitative RT-PCR to measure miRNA levels in wildtype vs. Ahr-null mice. Treatment with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in vivo caused few changes in miRNA levels in mouse livers and those changes that were statistically significant were of modest magnitude.   AHR genotype had little effect on hepatic miRNA levels, either in constitutive expression or in response to TCDD – only a few miRNAs differed in expression between Ahr-null mice compared to mice with wildtype AHR. It is unlikely that mRNA downregulation by dioxins is mediated by miRNAs, nor are miRNAs likely to play a significant role in dioxin toxicity in adult mouse liver.
Manuscript Submitted: Moffat ID, Boutros PC, Celius T, Pohjanvirta R & Okey AB. Micro-RNAs in rodent liver are refractory to dioxin treatment. Toxicological Sciences May, 2007.
Keywords: miRNA expression, gene knockout, response to xenobiotics, genetic modification

overall_design: This was a two-factor, two-level design, the factors being genotype Ahr+/+ (WT) or Ahr-/- (KO) and treatment TCDD-treated (T) or vehicle control (C).   Each total-RNA sample was separately labeled either with a Hy3- or a Hy5-fluorophore (Exiqon).  Hy3- and Hy5-labeled samples were co-hybridized to an array. Dye-reversal was performed to eliminate dye bias. We tested 3 TCDD-treated and 3 control mice in the Ahr-/- groups and 4 TCDD-treated and 4 control mice in the Ahr+/+ groups. Technical replication of 1 TCDD-treated and 1 control mice in the Ahr-/- groups was performed.  A loop design was used.


title: renal ischemia vs sham - 7d

first: David

last: Basile

summary:
this experiment was designed to determine the effect of ischemia reperfusion on angiogenesis gene expression after 7 days of recovery
Keywords: disease state

overall_design:
rat angiongenesis gene chips were designed.  RNA was compared from kidneys of post-ischemic rats and sham-operated rats.  4 pairs of rats/ 1 hybridization each.

data were first analyzed to combine replicate spot intensities for each hybridization; these normalized ratios were then averaged across each hybridization to determine alteration in gene expression in response to ischemia reperfusion.

first: Katherine

last: Fredrich

last: McNew


title: IAH/VLA VA1 Virus Detection Array Dataset

status: Public on Aug 14 2007

city: Roslin

middle: Bryan

last: Watson

state: Midlothian, EH25 9PS

address: Roslin Biocentre

department: ARK-Genomics

institute: The Roslin Institute

summary:
Data from the IAH/VLA diagnostic pathogen/virus detection microarray.  The array platform for this data is GEO accession GPL5725 (provisional), and consists of 5824 oligos representing over 100 viral families, species and subtypes.  The data set itself consists of 12 arrays, 4 hybridised with RNA from cell cultured foot-and-mouth disease virus (FMDV) type O, 3 hybridised with RNA from FMDV type A, 1 hybridised with RNA from a sheep infected with FMDV type O, and 4 hybridised with cell-cultured Avian Infectious Bronchitis virus (IBV).
Keywords: Virus Detection Microarray

sample_organism:
Infectious bronchitis virus
Foot-and-mouth disease virus A
Foot-and-mouth disease virus O

first: Juliet

last: Dukes

first: Abu-Bakr

last: Abu-Median

last: Britton

first: Donald

last: King


title: Fission yeast Jmj2 reverses histone H3 lysine 4 tri-methylation

city: Austin

first: Matthew

middle: Wayne

last: Vaughn

state: TX

address: 10100 Burnet Rd

department: Texas Advanced Computing Center

institute: University of Texas at Austin

type: Genome binding/occupancy profiling by genome tiling array

summary:
We compared the genomic localization of H3K4me3 in wild type and jmj2- S. pombe.
Keywords: mutant vs wild-type

overall_design: The ChIP-on-chip experiments were implemented as a reference design including a dye reversal. Additional statistical power is added by the fact that the all experimental spots on the array platform are printed in duplicate.

first: Maite

last: Huarte

first: Fei

last: Lan

middle: W

first: Mikel

last: Zaratiegui

first: Robert

last: Martienssen

first: Stephen

last: Buratowski

first: Yang

last: Shi


title: Micro-RNAs in Adult Rat Liver are Refractory to  19 Hours Dioxin Exposure

first: Ivy

last: Moffat

summary:
Dioxin-like chemicals are well-known for their ability to upregulate expression of numerous genes via the AH receptor (AHR).  However, recent transcriptomic analyses in several laboratories indicate that dioxin-like chemicals or AHR genotype itself also can downregulate levels of mRNAs encoded by numerous genes.  The mechanism responsible for such downregulation is unknown.  We hypothesized that microRNAs (miRNAs), which have emerged as powerful negative regulators of mRNA levels in several systems, might be responsible for mRNA downregulation in dioxin/AHR pathways.  We used the Ambion miRNA array platform as well as quantitative RT-PCR to measure miRNA levels in dioxin-sensitive Long-Evans (Turku/AB; L-E) rats vs. dioxin-resistant Han/Wistar(Kuopio; H/W) rats. Treatment with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in vivo caused no significant changes in miRNA levels in rat livers. AHR genotype had no effect on hepatic miRNA levels in response to TCDD – no miRNAs differed in expression between between L-E rats (that have wildtype AHR) compared to H/W rats (whose AHR has a large deletion in the transactivation domain).  It is unlikely that mRNA downregulation by dioxins is mediated by miRNAs, nor are miRNAs likely to play a significant role in dioxin toxicity in adult rodent liver.
Manuscript Submitted: Moffat ID, Boutros PC, Celius T, Pohjanvirta R & Okey AB. Micro-RNAs in rodent liver are refractory to dioxin treatment. Toxicological Sciences May, 2007.
Keywords: miRNA expression, response to xenobiotics, genetic modification, comparative genome hybridization

overall_design: In the dioxin-sensitive L-E rats we compared miRNA expression levels 19 h post-TCDD treatment vs. corn oil vehicle treatment.  In the dioxin-resistant H/W rats we compared miRNA levels 19 h post-TCDD treatment vs.corn oil vehicle treatment.

first: Paul

last: Boutros

first: Trine

last: Celius

first: Jere

last: Lindén

first: Raimo

last: Pohjanvirta

first: Allan

last: Okey


title: Wt-ko_trxB1_Filtered bkg correc transf-norm

status: Public on Aug 09 2007

city: Wageningen

first: L.

middle: Mariela

last: Serrano

address: Nieuwe Kanaal 9A

country: Netherlands

institute: TI Food and Nutrition

summary:
In this experiment we analyzed the impact of the disruption of trxB1in Lactobacillus plantarum at the transcriptome level. Furthermore we studied the effect of 3.5 mM peroxide effect on both Lactobacillus plantarum wild type (strain WCFS1) and a trxB1 mutant (strain NZ7608).
Keywords: mutant analysis of trxB1, hydrogen peroxide stress

overall_design: We ran for each studied culture (wildtype and NZ7608), three independent chemostat cultivations and designed one experiment. The hexagonal hybridization scheme of the experiment was as follows: wt1, trxB1, wt2, wt3_perox, trxB1_perox and wt2_perox. Per array two cDNA labeled targets were hybridized on custom designed L. plantarum WCFS1 11K Agilent oligo microarrays (GEO Acc. Nr. GPL4318) using the Agilent 60-mer oligo microarray processing protocol version 4.1.  In the experiment (6-slides) we compared (1) wild type with trxB1; (2) wild type with wild type with hydrogen peroxide; and (3) wild type with hydrogen peroxide with trxB1 with hydrogen peroxide. The oligo-microarray contained an average of 3 probes per transcript. Dried slides were scanned in the Scan Array Express (PerkinElmer Life Sciences; Packard Bioscience) for both Cy3 and Cy5 at 10 microns and a PMT Gain between 40-50%.  Spot intensity data was normalized and quantified (average intensity) using a customized grid in ImaGene (BioDiscovery, Inc.). Signal intensities of all probes were corrected against background in BioArray Software Environment (BASE) (15). The ratio of each probe (M) was defined as log [cy5 intensity/cy3 intensity] where cy3 is the wild type. Fold change (FC) is defined as 2M. For the statistical analysis we used Linear Models for Microarray Analysis (Limma) (R/limma) (18). In this test we used three variables: mutation, treatment, and interaction. We tested the model taking into consideration the interaction between genotype and treatment. Significant transcripts were defined as transcripts with a False Discovery Rate (FDR) adjusted for the pvalues of less than 0.1%. The statistical test resulted in three sets of data.  One dataset representing the genes affected as a result of the mutation of trxB1 (mutation), another set representing the genes affected due to hydrogen peroxide stress (peroxide) and a third representing the interaction or difference in response towards peroxide between mutant and wild type (interaction).

first: L

first: Douwe

last: Molenaar

first: Bas

last: Teusink

first: Willem

last: de Vos

first: Eddy

last: Smid


title: Effects of fescue toxicosis under chronic heat conditions conditions

city: Columbia

first: Raja

last: Settivari

state: MO

address: 920 E Campus Drive

department: ASRC

institute: University of Missouri

summary:
Rats (n=24) were fed ad libitum diets containing either ground endophyte-free (E-) seed or endophyte–infected (E+) seed for five days at thermoneutrality (21°C) or heat stress (32 C) for 21 days. Rats with intraperitonial transmitters were used with core temperature (Tc) and general activity measured every 5 minutes during the study. At treatment end, the liver was removed, weighed and frozen in liquid nitrogen. RNA was extracted from liver samples, converted to cDNA, and hybridized with the printed oligonucleotide slides. Treatments consisted of four treatment groups, E-TN, E+TN, E-HS, E+HS. E-TN IS control at thermoneutral for 26 days , E+TN toxin fed group at thermoneutral for 26 days; E-HS control at thermoneutral for 5 days and heat treatment for 21 days, E+HS is toxin fed group at thermoneutral for 5 days and heat stress for 21 days.
Keywords: Stress response

overall_design: Rats (n=24) were divided into two groups and fed with either E- or E+ diet for 5 days under TN conditions. At the end of TN period, each group was further subdivided into two groups each. Treatments consisted of four treatment groups, E-TN, E+TN, E-HS, E+HS. E-TN IS control at thermoneutral for 26 days , E+TN toxin fed group at thermoneutral for 26 days; E-HS control at thermoneutral for 5 days and heat treatment for 21 days, E+HS is toxin fed group at thermoneutral for 5 days and heat stress for 21 days.

first: Eric

last: Antoniou

first: Donald

last: Spiers


title: LongSAGE analysis in skeletal muscle at three prenatal stages in lean and obese pig breeds

status: Public on Aug 10 2007

city: Beijing

first: Kui

last: Li

address: 2 West Yuanmingyuan Rd

department: Institute of Animal Science

country: China

institute: Chinese Academy of Agricultural Sciences

summary:
Obese and lean pig breeds showed obvious phenotypic variations and physiological differences in skeletal muscle growth. Prenatal muscle development programs postnatal performance. In this study we initially conducted full transcriptional profiling of prenatal skeletal muscle from Tongcheng pigs (obese) and Landrace pigs (lean) at 33, 65 and 90 days post coitus (dpc), using long serial analysis of gene expression (LongSAGE).  We subsequently sequenced 317,115 LongSAGE tags and identified 1400 and 1201 differentially expressed transcripts that showed eight expression patterns for Tongcheng and Landrace, respectively.  These two breeds had more significant differences in their gene expression profiles at 65 than that at 33 and 90 dpc.  We also identified 532, 653 and 459 transcripts that were differentially expressed at 33, 65 and 90 dpc between the two breeds, respectively. The cellular function of the differentially expressed transcripts that matched annotated genes revealed that each stage had a uniquely altered profile between the two breeds in various functional categories including muscle fiber constitute and contraction, apoptosis, protein synthesis, and signalling transduction. Our results suggest that skeletal muscle development potentially has a greater lag in its growth rate at 33-65 dpc in Tongcheng pigs when compared with their Landrace counterparts.  Our analyses therefore not only will provide valuable resources in the further identification of candidate genes for meat production traits, but also assist in the elucidation of the development of prenatal skeletal muscle in pigs and other vertebrates.
Keywords: comparative transcriptome analysis

overall_design: Three Tongcheng and Landrace sows were mated with the same boar of each corresponding breed, respectively.  The sows were then sacrificed at a commercial slaughterhouse and the uteri containing the embryos were collected immediately.  The longissimus muscle tissues were then rapidly dissected from each of the embryos at 33, 65 and 90 dpc for both the Tongcheng and Landrace pigs.  These samples were snap-frozen in liquid nitrogen and stored at -80°C until further use in the LongSAGE experiments. For the skeletal muscles from the six different samples, that is, Tongcheng (T33, T65 and T90, respectively) and Landrace (L33, L65 and L90, respectively), equal quantities of total RNA from each individual (n=4) were pooled. Six LongSAGE libraries were subsequently generated using I-SAGETM Long kits (Invitrogen, USA) according to the manufacturer’s instructions. Transforming clones were sequenced with the help of an ABI PRIZM 3730 DNA sequencer.

first: Zhonglin

last: Tang

first: Yong

first: Pin

last: Wan

first: Xiaoping

first: Shuhong

last: Zhao

first: Bang

last: Liu

first: Bin

last: Fan

first: Mengjin

last: Zhu

first: Mei

last: Yu


title: Array-CGH screening of pediatric low-grade astrocytomas (n=66)

city: Heidelberg

first: Stefan

last: Pfister

address: INF 580

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center

summary:
DNA copy-number profiling of 66 astrocytomas of WHO °I or °II
Keywords: Genetic modification

overall_design: Comparison of tumor DNA (tumor) versus control DNA (pool of lymphocyte DNA from 10 healthy donors). Whole-genome screening for DNA copy-number aberrations using array-based comparative genomic hybridization (aCGH). Tumor DNA labeled in Cy3 and control DNA labeled in Cy5.

first: Marc

last: Remke

first: Wiebke

last: Werft

first: Grischa

last: Toedt

first: Peter

last: Lichter


title: Array-CGH screening of supratentorial primitive neuroectodermal tumors (stPNETs)

summary:
DNA copy-number profiling of 10 primary stPNETs
Keywords: Genetic modification

overall_design: Comparison of tumor DNA (stPNET) versus control DNA (pool of lymphocyte DNA from 10 healthy donors). Whole-genome screening for DNA copy-number aberrations using array-based comparative genomic hybridization (aCGH). Tumor DNA labeled in Cy3 and control DNA labeled in Cy5.

first: Frank

last: Mndrzyk

first: Bernhard

last: Radlwimmer


title: Identification of mRNAs that are differentially expressed between serum-stimulated and non-stimulated A. caninum L3

city: Herston

first: Alex

last: Loukas

state: Queensland

address: 300 Herston Rd

department: Division of Infectious Diseases and Immunology

country: Australia

institute: the Queensland Institute of Medical Research

summary:
Third-stage larvae (L3s) of the canine hookworm, Ancylostoma caninum, endure a period of arrested development preceding transmission to a host. Many of the mRNAs up-regulated at this stage are likely to encode proteins that act at the host-parasite interface and facilitate the transition from a free-living to a parasitic larva. The initial phase of the infection of a mammalian host by A. caninum L3s (herein termed “activation”) can be mimicked in vitro by culturing L3s in serum-containing medium. The mRNAs differentially transcribed between activated and non-activated L3s were identified by suppression subtractive hybridisation (SSH). The analysis of these mRNAs on a custom oligonucleotide microarray printed with the SSH ESTs and publicly available A. caninum ESTs (non-subtracted) yielded a total of 602 differentially expressed mRNAs, of which the most highly represented sequences (27) encoded products belonging to the pathogenesis-related protein (PRP) superfamily and different mechanistic classes of proteases. Comparison of these A. caninum mRNAs with those of Caenorhabditis elegans larvae exiting from developmental (dauer) arrest demonstrated unexpectedly large differences with respect to gene ontology profiles. C. elegans L3 exiting developmental arrest up-regulated the expression of collagens and other (mostly intracellular) molecules involved in growth and development. Such mRNAs are virtually absent from activated hookworm larvae, and instead are represented by an inordinately large number of mRNAs encoding extracellular proteins, suggesting that many of the activation-associated hookworm mRNAs are involved in host-parasite interactions. The near absence of mRNAs associated with reproduction, growth and development among activated hookworm L3s probably reflects their ability to further arrest (i.e. undergo hypobiosis) in tissues of non-permissive hosts or in the external environment when conditions for transmission are unfavourable. Although this should not necessarily invalidate C. elegans dauer exit as a model for hookworm activation, it provides substantial information on the limitations of this free-living nematode as a model organism for the transition of nematode larvae from a free-living to a parasitic state.
Keywords: Comparative transcriptomic hybridisation

overall_design: RNA was extracted from two different groups of Ancylostoma caninum L3 that were separated in time and geography (Populations III and IV). From population III, two separate in vitro activation assays were performed. This yielded two sets of RNA from activated worms and two sets of RNA from non-activated worms. Population IV yielded one sample of RNA from activated worms and one sample from non-activated L3. In total, there were three samples of RNA from activated L3 and three from non-activated L3 representing two biological replicates and one technical replicate for activation. For each hybridization, labelled RNA from activated and non-activated L3 (within a biological and technical replicate) were compared. This comparison was also made using the same samples with reciprocal labeling (dye-swap). Lastly, two self-hybridisations were performed. The first compared RNA from Activated A. caninum L3 (population III) that were labelled separately with Cy3 and Cy5. The same self hybridisation was performed for Non-activated A. caninum L3 (population IV). Non-activated A. caninum L3 served as the reference sample for all non-self hybridisations.

first: Bennett

last: Datu

first: Robin

last: Gasser

first: Shivashankar

middle: H

last: Nagaraj

first: Eng

middle: K

last: Ong

last: O'Donoghue

first: Russell

last: McInnes

first: Shoba

last: Ranganathan


title: E. coli TG1/pBS(Kan)Synhox and pBS(Kan) hydrogen production

status: Public on Aug 13 2007

city: College Station

first: Toshinari

last: Maeda

address: 220 Jack E. Brown Building

department: Department of Chemical Engineering

institute: Texas A&M University

summary:
E. coli TG1 with pBS(Kan)Synhox can produce more hydrogen than TG1/pBS(Kan).  To reveal the difference of metabolic activity (gene expression) between these strains in producing hydrogen, the differential gene expression analyses were performed.  All samples cultured in complex medium with fructose containg 5 mM IPTG.
Keywords: hydrogen production

overall_design:
Strains: E. coli TG1/pBS(Kan)Synhox and TG1/pBS(Kan)
Medium: Complex with fructose
Hydrogen producing cells
Time: 6 hour

first: Thomas

last: Wood


title: Human hepatocellular carcinomas validation set

last: Stanford Microarray Database

summary:
A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied.
Keywords: disease_state_design

first: Adam

last: Adler


title: Array CGH analysis of copy number variation identifies 1284 new genes variant in healthy white males

city: Santa Clara

first: Alicia

last: Scheffer

address: 5301 Stevens Creek Blvd.

institute: Agilent Technologies

summary:
The discovery of copy number variation in healthy individuals is far from complete, and due to the resolution of detection systems used, the majority of loci reported so far are relatively large (~65% > 10kb). Applying a two-stage high-resolution array CGH approach to analyse 50 healthy Caucasian males from northern France, we discovered 2208 copy number variants (CNVs) detected by more than one consecutive probe. These clustered into 1469 copy number variant regions (CNVRs), of which 721 are thought to be novel. The majority of these are small (median size 4.4kb) and most have common boundaries, with a coefficient of variation less than 0.1 for 83% of end-points in those observed in multiple samples. Only 6% of the CNVRs analysed showed evidence of both copy number losses and gains at the same site. A further 6089 variants were detected by single probes: 48% of these were observed in more than one individual.
In total, 2570 genes were seen to intersect variants: 1284 in novel loci. Genes involved in differentiation and development were significantly overrepresented, and approximately half the genes identified feature in the OMIM database. The biological importance of many of the genes affected, along with the well-conserved nature of the majority of the copy number variants, suggests they could have important implications for phenotype and, thus, be useful for association studies of complex diseases.
Keywords: comparative genomic hybridization

overall_design:
DNA samples were isolated from peripheral blood of 50 unrelated, apparently healthy white males of northern French origin using Puregene kits (Gentra, USA) and resuspended in Tris -EDTA buffer. For the reference, a particular sample chosen was a north American female of unknown ethnic origin (NA15510), obtained from the Coriell Cell Repository, which has been extensively characterised and has been recommended for use in CNV detection programmes to allow meaningful comparison of data between studies (discussed in Scherer, et al. 2007, Nature Genetics Supplement 39: S7-S15).  Each of the 50 samples was hybridized once, except for one sample 49 for which 4 additional replicates were done. These replicates were done in the reverse polarity, i.e. sample 49 was labeled with Cy3 and NA15510 reference was labeled with Cy5.
Data set has 3 additional control self-self experiments for NA15510 sample. These experiments were used to estimate false positive rate.

last: de Smith

first: Anya

last: Tsalenko

first: Nick

last: Sampas

first: Nazumi

last: Yamada

last: Tsang

first: Amir

last: Ben-Dor

first: Zohar

last: Yakhini

first: Richard

last: Ellis

first: Laurakay

last: Bruhn

first: Stephen

last: Laderman

first: Philippe

last: Froguel

first: Alexandra

last: Blakemore


title: Gene expression profiling identifies distinct subclasses of core binding factor acute myeloid leukemia.

summary:
Core binding factor (CBF) leukemias, characterized by either inv(16)/t(16;16) or t(8;21), constitute acute myeloid leukemia (AML) subgroups with favorable prognosis. However, there exists substantial biological and clinical heterogeneity within these cytogenetic groups, which is not fully reflected by the current classification system. To improve the molecular characterization we profiled gene expression in a large series (n=93) of AML patients with CBF leukemia [inv(16) n=55, t(8;21) n=38]. By unsupervised hierarchical clustering we were able to define a subgroup of CBF cases (n=35) characterized by shorter overall survival times (P=0.03). While there was no obvious correlation with fusion gene transcript levels, FLT3 tyrosine kinase domain, KIT, and NRAS mutations, the newly defined inv(16)/t(8;21)-subgroup was associated with elevated white blood cell counts and FLT3 internal tandem duplications (P=0.011 and P=0.026, respectively). Supervised analyses of gene expression suggested alternative cooperating pathways leading to transformation. In the ?favorable? CBF leukemias anti-apoptotic mechanisms and deregulated mTOR-signaling, and in the newly defined ?unfavorable? subgroup aberrant MAPKinase-signaling and chemotherapy-resistance mechanisms might play a role. While the leukemogenic relevance of these signatures remains to be validated, their existence nevertheless supports a prognostically relevant biological basis for the heterogeneity observed in CBF leukemia.
A reference experiement design type is where all samples are compared to a common reference.
Keywords: reference_design

overall_design: Using regression correlation

first: Lars

last: Bullinger


title: AP2 transcription factors regulate expression of CRABPII in hormone responsive breast carcinoma

summary:
BACKGROUND: The AP2 transcription factor family is a set of developmentally regulated, retinoic acid (RA) inducible genes, which regulate expression of estrogen receptor-alpha (ERalpha) in breast carcinoma. We hypothesized that AP2 factors regulate a set of genes characteristic of the hormone responsive breast cancer phenotype. To better understand the role of AP2 factors in hormone responsive breast cancer, we sought to identify AP2-target genes in breast epithelial cells. MATERIALS AND METHODS: Overexpression of AP2 factors was achieved in human mammary epithelial cells (HMECs) using adenoviral vectors. AP2 target genes were identified by comparative hybridization to cDNA microarrays containing 30,000 human genes. Expression patterns were confirmed by Northern and Western blot and by elimination of AP2 using siRNA. Potential regulatory elements in promoters of target genes were identified by DNase I hypersensitive site mapping. : Comparative cDNA microarray hybridization identified a set of genes induced by overexpression of AP2alpha and AP2gamma in HMECs. The up-regulation of cellular retinoic acid-binding protein 2 (CRABPII), EST-1, and ECM1 was induced by overexpression of AP2alpha, AP2gamma, or a chimeric AP2 factor in which the activation domain of AP2alpha was replaced by the activation domain of herpesvirus VP16. Interestingly, hormone unresponsive MDA-MB-231 cells were resistant to CRABPII induction by any of the AP2 factors. Elimination of AP2gamma in MCF7 cells resulted in a significant reduction in CRABPII expression. AP2alpha induced DNase I hypersensitive sites in the promoter of the CRABPII gene at -5000 bp, which corresponds to the site of action of RAR/RXR factors. CONCLUSIONS: AP2 factors regulate CRABPII expression in HMECs and breast cancer cells and accounts for the associated expression of ERalpha and CRABPII in hormone responsive breast cancer. Because CRABPII mediates growth suppressive effects of RA in breast cancer, the data suggest that AP2 factors have the ability to mediate RA responsiveness through the regulation of CRABP II expression.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Computed

first: Charles

last: Perou


title: Expression differences between worker(female) and drone(male) honey bee antennae

city: Urbana

first: Hugh

last: Robertson

state: IL

address: 505 S. Goodwin Ave.

department: Entomology

institute: University of Illinois at Urbana-Champaign

summary:
We have identified a honeybee (Apis mellifera) odorant receptor (Or) for the queen substance 9-oxo-2-decenoic acid (9-ODA) from four candidate sex pheromone odorant receptors from the honeybee genome based on their biased expression in drone antennae.
Keywords: Tissue Comparison

overall_design:
Oligonucleotides (70-mer sense-strand) were designed using ArrayOligoSelector3.5 software (43, http://sourceforge.net) using default settings and the Apis mellifera genome (Assemby 2) for the following conceptual cDNA categories: 168 odorant receptors; 49 cytochrome p450s; 19 odorant binding proteins; 17 tetraspanins; 10 gustatory receptors; 10 carboxyl esterases; 7 glutathione S transferases; 6 chemosensory proteins (sensory appendage proteins); 5 lipocalins; 5 visual and non-visual opsins; 4 alpha-arrestins; 4 arrestins; 3 G-protein alpha subunits; 1 Pinocchio ortholog (a Drosophila melanogaster sensory-related protein); 1 sensory neuron membrane protein, and 4 housekeeping genes (cytoplasmic actin, EF1alpha, ribosomal protein 49, ribosomal protein S3), for a total of 313 genes.

ArrayControl sense 70-mer oligonucleotides (Ambion) were printed as negative control spots.

Four microarray hybridizations (replicates) were performed using mature drone antennal total RNA versus worker antennal total RNA with an even dye swap.  Each total RNA pool was derived from an independent collection of 50 sets of antennae.

first: Kevin

last: Wanner

first: Kimberly

last: Walden


title: cdt1-Characterization of the AtCDT1a and AtCDT1b by RNAi

city: Evry

first: Frederique

last: Bitton

address: 2 rue Gaston Cremieux

country: France

institute: INRA

summary:
rs04-06_cdt1 - cdt1 - CDT1 is a protein of the pre-replication complex, and accumulates during the G1-S transition, thus play a major role in S-phase entry - Comparison of 3 independant RNAi lines
Keywords: normal vs rnai mutant comparaison

overall_design: 3 dye-swap - CATMA arrays

first: Jean-Pierre

middle: P

last: Renou

first: Catherine-

last: Bergounioux

first: Marie-Laure

last: Martin-Magniette


title: Array CGH after human challenge

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

institute: Stanford Microarray Database (SMD)

summary:
Array CGH of H. pylori strain BCS100 after challenge to a new host (patients and experiment described in Graham et al., 2004, Gut, 53:1235-1243). Genomic DNA (500 ng) from the ouput from singel colony isolates obtained 15 or 90 days post innoculation were labeled with Cy5 (red) and cohybridized with 500 ng of genomic DNA from the innoculating strain BCS100 labeled with Cy3 (green).
A reference experiement design type is where all samples are compared to a common reference.
Keywords: reference_design

first: Nina

last: Salama


title: Array CGH of Mexican Patient Isolates and BCS100 Strain

summary:
Array CGH of human H. pylori isolates from natrually infected Mexican patients and BCS-100 strain used for experimental infection of humans which is labeled as OVX-34 in this sample set(Graham et al., 2004, Gut, 53:1235-1243). Each Mexican isolate has a three digit number indicating the patient, a letter indicating biopsy site location and number indicating single colony clone number. Patient 249,259 and 251 are adults and patient 291,293,612 and 653 are children. Multiple single clonies were isolated from 2-4 gastric biopsy sites (a- antrum, c-corpus, f- fundus, i-incisura angularis). Genomic DNA prepared from each experimental strain (500 ng) was labeled with Cy5 (red channel) and co-hybridized with an equimolar mixture of genomic DNA from the reference strains 26659 and J99 (500 ng).
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set


title: The effects of Yariv-reagent on barley aleurone GA signaling

city: Tokyo

first: kiyoshi

last: mashiguchi

address: 1-1-1 Yayoi, Bunkyo-ku

country: Japan

institute: University of Tokyo

summary:
Microarray analysis was performed to know how many gibberellin (GA)-responsive genes are inhibited by beta-Yariv reagent, a specific binder of plant arabinogalactan-proteins.  cRNAs were prepared from mRNAs isolated from aleurone protoplasts that were treated with GA, GA plus beta-Yariv reagent, or mock (DMSO)-treated for 24 hours, and were subjected to microarray analysis. The analysis was performed twice using target cRNAs prepared independently.
Keywords: repeat sample

overall_design: 2 control (DMSO), 2 gibberellin and 2 gibberellin plus beta-Yariv reagent-treated biological replicates were analyzed at 24 h.

first: Kiyoshi

last: Mashiguchi

first: Eriko

last: Urakami

first: Morifumi

last: Hasegawa

first: Kazutsuka

last: Sanmiya

first: Ichiro

last: Matsumoto

first: Isomaro

last: Yamaguchi

first: Tadao

last: Asami

first: Yoshihito

last: Suzuki


title: mutant axel-4 seedlings

summary:
A mutant screen was conducted in Arabidopsis that was based on deregulated expression of auxin-responsive transgenes. Two different tightly regulated (i.e., very low expression in the absence of auxin treatment and very high expression after exogenous auxin treatment) auxin-responsive promoters were used to drive the expression of both a ?-glucuronidase (GUS) reporter gene and a hygromycin phosphotransferase (HPH)?selectable marker gene. This screen yielded several mutants, and five of the mutations (axe1-1 to axe1-5) mapped to the same locus on chromosome 5. A map-based cloning approach was used to locate the axe1 mutations in an Arabidopsis RPD3-like histone deacetylase gene, referred to as HDA6. The axe1 mutant plants displayed increased expression of the GUS and HPH transgenes in the absence of auxin treatment and increased auxin-inducible expression of the transgenes compared with nonmutant control plants. None of a variety of endogenous, natural auxin-inducible genes in the mutant plants were upregulated like the transgenes, however. Results of treatment with the DNA methylation inhibitor 5-aza-2'-deoxycytidine suggest that the axe1 mutations affect transgene silencing; however, histone deacetylase inhibitors had no affect on transgene silencing in mutant or control plants. The specific effect of AtHDA6 mutations on the auxin-responsive transgenes implicates this RPD3-like histone deacetylase as playing a role in transgene silencing. Furthermore, the effect of AtHDA6 on transgene silencing may be independent of its histone deacetylase activity.
A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
Keywords: replicate_design

first: Tom

last: Guilfoyle


title: Transcriptional profiles induced by either androgen depletion or androgen receptor knockdown

summary:
Although the vital role of the androgen receptor (AR) has been well demonstrated in primary prostate cancers, its role in the androgen-insensitive prostate cancers still remains unclear. Here, we used a small hairpin RNA approach to directly assess AR activity in prostate cancer cells. Reduction of AR expression in the two androgen-sensitive prostate cancer cell lines, LNCaP and LAPC4, significantly decreased AR-mediated transcription and cell growth. Intriguingly, in two androgen-insensitive prostate cell lines, LNCaP-C42B4 and CWR22Rv1, knockdown of AR expression showed a more pronounced effect on AR-induced transcription and cell growth than androgen depletion. Using cDNA microarrays, we also compared the transcriptional profiles induced by either androgen depletion or AR knockdown. Although a significant number of transcripts appear to be regulated by both androgen depletion and AR knockdown, we observed a subset of transcripts affected only by androgen depletion but not by AR knockdown, and vice versa. Finally, we demonstrated a direct role for AR in promoting tumor formation and growth in a xenograft model. Taken together, our results elucidate an important role for the AR in androgen-insensitive prostate cancer cells, and suggest that AR can be used as a therapeutic target for androgen-insensitive prostate cancers.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Hongjuan

last: Zhao


title: Cell wide response to air exposure in Desulfovibrio vulgaris Hildenborough

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:
We investigated the effects of air exposure on Desulfovibrio vulgaris Hildenborough using microarrays.
Keywords: stress response, time course

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: Comparison of cells treated with air to untreated cells at 0,10,30,120,240 min.


title: New molecular phenotypes in the dst mutants of Arabidopsis revealed by DNA microarray analysis

summary:
In this study, DNA microarray analysis was used to expand our understanding of the dst1 mutant of Arabidopsis. The dst (downstream) mutants were isolated originally as specifically increasing the steady state level and the half-life of DST-containing transcripts. As such, they offer a unique opportunity to study rapid sequence-specific mRNA decay pathways in eukaryotes. These mutants show a threefold to fourfold increase in mRNA abundance for two transgenes and an endogenous gene, all containing DST elements, when examined by RNA gel blot analysis; however, they show no visible aberrant phenotype. Here, we use DNA microarrays to identify genes with altered expression levels in dst1 compared with the parental plants. In addition to verifying the increase in the transgene mRNA levels, which were used to isolate these mutants, we were able to identify new genes with altered mRNA abundance in dst1. RNA gel blot analysis confirmed the microarray data for all genes tested and also was used to catalog the first molecular differences in gene expression between the dst1 and dst2 mutants. These differences revealed previously unknown molecular phenotypes for the dst mutants that will be helpful in future analyses. Cluster analysis of genes altered in dst1 revealed new coexpression patterns that prompt new hypotheses regarding the nature of the dst1 mutation and a possible role of the DST-mediated mRNA decay pathway in plants.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Pam

last: Green


title: Aluminum-inducible genes

summary:
Aluminum (Al) toxicity, which is caused by the solubilization of Al3  in acid soils resulting in inhibition of root growth and nutrient/water acquisition, is a serious limitation to crop production, because up to one-half of the world?s potentially arable land is acidic. To date, however, no Al tolerance genes have yet been cloned. The physiological mechanisms of tolerance are somewhat better understood; the major documented mechanism involves the Al-activated release of Al-binding organic acids from the root tip, preventing uptake into the primary site of toxicity. In this study, a quantitative trait loci analysis of Al tolerance in Arabidopsis was conducted, which also correlated Al tolerance quantitative trait locus (QTL) with physiological mechanisms of tolerance. The analysis identified two major loci, which explain approximately 40% of the variance in Al tolerance observed among recombinant inbred lines derived from Landsberg erecta (sensitive) and Columbia (tolerant). We characterized the mechanism by which tolerance is achieved, and we found that the two QTL cosegregate with an Al-activated release of malate from Arabidopsis roots. Although only two of the QTL have been identified, malate release explains nearly all (95%) of the variation in Al tolerance in this population. Al tolerance in Landsberg erecta   Columbia is more complex genetically than physiologically, in that a number of genes underlie a single physiological mechanism involving root malate release. These findings have set the stage for the subsequent cloning of the genes responsible for the Al tolerance QTL, and a genomics-based cloning strategy and initial progress on this are also discussed.
A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
Keywords: replicate_design

first: Leon

last: Kochian


title: ASFV array analysis

summary:
African swine fever virus (ASFV) produces a fatal acute hemorrhagic fever in domesticated pigs that potentially is a worldwide economic threat. Using an expressed sequence tag (EST) library-based antisense method of random gene inactivation and a phenotypic screen for limitation of ASFV replication in cultured human cells, we identified six host genes whose cellular functions are required by ASFV. These included three loci, BAT3 (HLA-B-associated transcript 3), C1qTNF (C1q and tumor necrosis factor-related protein 6), and TOM40 (translocase of outer mitochondrial membrane 40), for which antisense expression from a tetracycline-regulated promoter resulted in reversible inhibition of ASFV production by >99%. The effects of antisense transcription of the BAT3 EST and also of expression in the sense orientation of this EST, which encodes amino acid residues 450 to 518 of the mature BAT3 protein, were investigated more extensively. Sense expression of the BAT3 peptide, which appears to reversibly interfere with BAT3 function by a dominant negative mechanism, resulted in decreased synthesis of viral DNA and proteins early after ASFV infection, altered transcription of apoptosis-related genes as determined by cDNA microarray analysis, and increased cellular sensitivity to staurosporine-induced apoptosis. Antisense transcription of BAT3 reduced ASFV production without affecting abundance of the virus macromolecules we assayed. Our results, which demonstrate the utility of EST-based functional screens for the detection of host genes exploited by pathogenic viruses, reveal a novel collection of cellular genes previously not known to be required for ASFV infection.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Annie

last: Chang


title: Pax5-deficient progenitor cell tumors vs wt pro-B-cells

status: Public on Aug 08 2007

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohr-Gasse 7

country: Austria

institute: Research Institute of Molecular Pathology

summary:
Comparison of the RNA-expression pattern of Pax5-deficient progenitor-cell tumors with wild-type pro-B-cells
Keywords: Genetic modification

overall_design: Two-condition experiment. Pax5-deficient progenitor tumor cells versus wildtype -/- pro-B cells. Biological replicates: 3 wild-type samples, 3 tumor cell-samples

first: Cesar

last: Cobaleda


title: Role of IdeR in Iron-Dependent Gene Expression, Iron Metabolism, and Oxidative Stress Response

first: SMD

last: Staff

summary:
The mycobacterial IdeR protein is a metal-dependent regulator of the DtxR (diphtheria toxin repressor) family. In the presence of iron, it binds to a specific DNA sequence in the promoter regions of the genes that it regulates, thus controlling their transcription. In this study, we provide evidence that ideR is an essential gene in Mycobacterium tuberculosis. ideR cannot normally be disrupted in this mycobacterium in the absence of a second functional copy of the gene. However, a rare ideR mutant was obtained in which the lethal effects of ideR inactivation were alleviated by a second-site suppressor mutation and which exhibited restricted iron assimilation capacity. Studies of this strain and a derivative in which IdeR expression was restored allowed us to identify phenotypic effects resulting from ideR inactivation. Using DNA microarrays, the iron-dependent transcriptional profiles of the wild-type, ideR mutant, and ideR complemented mutant strains were analyzed, and the genes regulated by iron and IdeR were identified. These genes encode a variety of proteins, including putative transporters, proteins involved in siderophore synthesis and iron storage, members of the PE/PPE family, a membrane protein involved in virulence, transcriptional regulators, and enzymes involved in lipid metabolism.
Keywords: strain or line design, genetic modification design, comparative genome hybridization design and stimulus or stress design

overall_design: 18 samples were analyzed. The quality controls were biological replicate and technical replicate

first: G

last: Rodriguez

first: M

middle: I

last: Voskuil


title: GSI, Human T-ALL

status: Public on Aug 06 2007

city: Rahway

first: Olivia

last: Fong

state: NJ

department: Molecular Profiling

institute: Merck & Co.

summary:
The NOTCH signaling cascade, which is deregulated in T-cell acute lymphoblastic leukemia (T-ALL) and many other human cancers, offers an attractive target for molecular therapy.  One approach employs gamma-secretase inhibitors (GSIs) to suppress production of the intracellular form of NOTCH (NICD), leading to cell growth arrest and apoptosis. Here we show that missense mutations or homozygous deletion of FBW7, which encodes a ubiquitin ligase that targets the NICD for destruction, mediate constitutive NICD expression. FBW7 mutations target key arginine residues needed for binding to the NICD. Although the mutant forms of Fbw7 still bind to MYC, they do not target MYC for degradation, suggesting that stabilization of both NICD and MYC may contribute to transformation in leukemias with mutations in FBW7. Leukemias with FBW7 mutations are resistant to the growth suppressive and apoptotic effects of the MRK-003 GSI. In some resistant lines that express the NICD, this resistance is accompanied by sustained mRNA levels of the NOTCH target DELTEX1 as well as MYC mRNA and protein, implying that residual NICD activity due to the mutant FBW7 can contribute to GSI resistance.
Keywords: T-ALL, gamma-secretase, GSI, cell line comparison, FBW7 mutation

overall_design: Total RNA isolated from cultured cells was used to make fluorescently labeled cRNA that was hybridized to DNA oligonucleotide. Briefly, 4 µg of total RNA was used to synthesize dsDNA through reverse transcription. cRNA was produced by in vitro transcription and labeled postsynthetically with Cy3 or Cy5. Two populations of labeled cRNA, a reference population and an experimental population, were compared with each other by competitive hybridization to microarrays. Two hybridizations were done with each cRNA sample pair using a fluorescent dye reversal strategy. Human microarrays contained oligonucleotide probes corresponding to approximately 21,000 genes. All oligonucleotide probes on the microarrays were synthesized in situ with inkjet technology (Agilent Technologies, Palo Alto, CA). After hybridization, arrays were scanned and fluorescence intensities for each probe were recorded. Ratios of transcript abundance (experimental to control) were obtained following normalization and correction of the array intensity data. Gene expression data analysis was done with the Rosetta Resolver gene expression analysis software (version 6.0, Rosetta Biosoftware, Seattle, WA).

first: Jennifer

last: O'Neil

first: Jonathan

last: Grim

first: Peter

last: Strack

first: Sudhir

last: Rao

first: Deanne

last: Tibbitts

first: Christopher

last: Winter

first: James

last: Hardwick

first: Markus

last: Welcker

first: Jules

last: Meijerink

first: Rob

last: Pieters

first: Guilio

last: Draetta

first: Rosalie

last: Sears

first: Bruce

last: Clurman

first: A.

middle: T

last: Look


title: Array-based comparative genomic hybridization analysis of primary neuroblastoma

city: Chiba

first: Akira

last: Nakagawara

address: 666-2 Nitona, Chuoh-ku

institute: Chiba Cancer Center Research Institute

summary:
We conducted microarray-based comparative genomic hybridization (array-CGH) with a DNA chip carrying 2,464 BAC clones to examine genomic aberrations of 236 neuroblastomas (112 sporadic and 124 mass screening-detected). In paralell, gene-expression profiling was also performed by using in-house cDNA microarrays.
Keywords: Comparative genomic hybridization

overall_design: A UCSF BAC array carrying 2,464 clones, which covers the whole human genome at roughly 1.2-Mb resolution, was used. The 500-ng aliquots of tumors and reference DNAs were labeled by random priming with each Cy3-dCTP and Cy5-dCTP (Amersham Pharmacia, Piscataway, NJ). Hybridization was performed as previously reported [Pinkel D, et al. Nat Genet 1998;20:207-11.]. UCSF Spot and UCSF Sproc programs to analyze values for spotted clones [Jain AN, et al. Genome Res 2002;12:325-32.] were used.


title: Role of the extracytoplasmic-function sigma Factor sigmaH in Mycobacterium tuberculosis global gene expression

status: Public on Aug 04 2007

first: SMD

last: Staff

summary:
Like other bacterial species, Mycobacterium tuberculosis has multiple sigma (s) factors encoded in its genome. In previously published work, we and others have shown that mutations in some of these transcriptional activators render M. tuberculosis sensitive to various environmental stresses and, in some cases, cause attenuated virulence phenotypes. In this paper, we characterize a M. tuberculosis mutant lacking the ECF s factor sigma-H. This mutant was more sensitive than the wild type to heat shock and to various oxidative stresses, but did not show decreased ability to grow inside macrophages. Using quantitative reverse transcription-PCR and microarray technology, we have started to define the sigma-H regulon and its involvement in the global regulation of the response to heat shock and the thiol-specific oxidizing agent diamide. We identified 48 genes whose expression increased after exposure of M. tuberculosis to diamide; out of these, 39 were not induced in the sigH mutant, showing their direct or indirect dependence on sigma-H. Some of these genes encode proteins whose predicted function is related to thiol metabolism, such as thioredoxin, thioredoxin reductase and enzymes involved in cysteine and molybdopterine biosynthesis. Other genes under sigma-H control encode transcriptional regulators such as sigB, sigE, and sigH itself.
Keywords: comparative genome hybridization design and genetic modification design

overall_design: 15 samples were analyzed. The quality controls were biological replicate and technical replicate

first: R

last: Manganelli

first: M

last: Voskuil


title: The Mycobacterium tuberculosis ECF sigma Factor sE: role in global gene expression and survival in macrophages

status: Public on Aug 03 2007

summary:
In previously published work, we identified three Mycobacterium tuberculosis sigma (s) factor genes responding to heat shock (sigB, sigE and sigH ). Two of them (sigB and sigE ) also responded to SDS exposure. As these responses to stress suggested that the s factors encoded by these genes could be involved in pathogenicity, we are studying their role in physiology and virulence. In this work, we characterize a sigE mutant of M. tuberculosis H37Rv. The sigE mutant strain was more sensitive than the wild-type strain to heat shock, SDS and various oxidative stresses. It was also defective in the ability to grow inside both human and murine unactivated macrophages and was more sensitive than the wild-type strain to the killing activity of activated murine macrophages. Using microarray technology and quantitative reverse transcriptionÐpolymerase chain reaction (RTÐPCR), we started to define the sigmaE regulon of M. tuberculosis and its involvement in the global regulation of the stress induced by SDS. We showed the requirement for a functional sigE gene for full expression of sigB and for its induction after SDS exposure but not after heat shock. We also identified several genes that are no longer induced when sigmaE is absent. These genes encode proteins belonging to different classes including transcriptional regulators, enzymes involved in fatty acid degradation and classical heat shock proteins.
Keywords: genetic modification design and comparative genome hybridization design

overall_design: 15 samples were analyzed. The quality controls were biological replicate and  technical replicate


title: Spike-in at 0.25pmol with 18 replicates

city: Singapore

first: Bing

last: Lim

state: Singapore

address: 60 Biopolis Street

department: Stem Cell and Developmental Biology

country: Singapore

institute: GIS

summary:
We have conducted a study to determine which DNA microarray analysis method for identification of differential expression works best with a varying number of replicates, in particular, when the number of replicates is small. Using spiked-in mRNA with two-channel microarrays, as well as simulated data generated /in silico/, we measured the efficacy of five gene identification methods, namely /t/-test, Significance Analysis of Microarrays (SAM), median log ratio, median fold change and Wilcoxon ranksum test. By comparing the receiver operating characteristic (ROC) curves as well as the ranking accuracy versus sample size plots, our results show that the simple median methods (median log ratio and median fold change) are more accurate and robust than the other statistical methods in identifying differential gene expression, especially when the number of sample replicates is small.
Keywords: Spike-in

overall_design: In this study, total mRNA was extracted from mouse hybridoma CRL1606 cells and divided equally into two samples. These two samples are essentially the same, but will be referred to as ‘Sample R’ and ‘Sample G’ for the sake of explanation. From self-hybridization results, 200 random genes were selected ensuring uniform representation of the whole intensity range to avoid expression intensity-biased spikes. mRNA that correspond to these 200 genes were obtained from in-vitro transcription, as described above.  RNA gel electrophoresis was performed on selected samples and quantified by a spectrometer (Genequant Pro RNA/DNA calculator, Amersham Biosciences). Due to inefficiency in in-vitro transcription, 31 of 200 genes were dropped. A total of 169 genes were used eventually. To create artificial differential expression, one group with 78 transcripts was mixed with Sample G and labelled with Cy3 whilst the other group with 91 transcripts was mixed with sample R and labelled with Cy5.  Since mRNA from Sample R and Sample G are the same, the only ‘truly’ differentially expressed genes should be those that were spiked in. The in vitro transcripts were spiked-in with 18 array replicates with a concentration of 0.25 pmol.

first: Ying-Leong

last: Chan

first: Teng-Ting

middle: M

last: Nissom

first: Ming

last: Zhan

first: Mahendra

middle: S

first: He

last: Yang


title: Transcriptome analysis of zebrafish yquem/urod mutant

city: Norman

first: Han

last: Wang

state: OK

address: 101 David L. Boren Boulevard

department: Zoology/Stephenson Research and Technology Center

institute: University of Oklahoma

summary:
Zebeafish yquem harbors a mutation in the gene encoding uroporphyrinogen decarboxylase (UROD), the fifth enzyme in heme biosynthesis, and was established  as a vertebrate model for human hepatoerythropoietic porphyria (HEP). In an effort to investigate the unknown aspects of UROD deficiency pathogenesis, we used a 14,000-oligonucleotide-gene microarray to determine differentially expressed genes in yquem/urod (-/-) and wild type control zebrafish larvae.
Keywords: zebrafish, Danio rerio, wild-type yquem, urod, porphyria

overall_design: RNA was isolated from pools of approximately 50 wild-type and from approximately 50 homozygous yquem/urod mutant zebrafish at 56, 72, 84 and 86 hours post-fertilization (hpf). One set of larvae were used for each time point. RNA from each replicate at each time point was separately reverse transcribed and labeled by direct incorporation with dUTP-Cy3 prior to hybridization to microarrays printed with zebrafish 50-mer oligonucleotide library (MWG/Ocimum) to identify genes affected in development in organisms with this mutation.

first: Qingchun

last: Zhou

first: Jason

last: Kesinger

first: Chad

last: Norris

first: Cammi

last: Vladez


title: Gene expression analysis in 13 patients with mitochondrial ATP synthase deficiency (MitoArray)

status: Public on Aug 02 2007

city: Prague

first: Viktor

last: Stranecky

address: Ke Karlovu 2

department: 1st Faculty of Medicine

country: Czech Republic

institute: Charles University

summary:
Defects of mitochondrial functions lead in humans to vast array of usually multisystemic pathologies and several hundreds of diseases resulting from various defects of mitochondria biogenesis and maintenance, defects of respiratory chain complexes (OXPHOS) or defects of individual mitochondrial proteins are known. To strengthen diagnostic work-up for various mitopathies we designed focused oligonucleotide microarray which allows expression profiling of 1632 human mitochondria related genes and tested its performance in analysis of genetically heterogeneous group of 13 patients with biochemically proven ATP synthase deficiency. Gene expression data analysis allowed classification of patients into several distinct groups, provided information on subgroup and patient specific gene expression profiles, defined candidate disease causing genes and gave basic information on pathogenic mechanisms associated with ATP synthase deficiency.
Keywords: ATP synthase, mitochondrial biogenesis, ROS, gene expression, microarray, human

overall_design: Two-condition experiment, patients vs. controls cells. Biological replicates: 9 control, 13 patients, independently grown and harvested. Two replicates per array.

first: Alena

last: Čížková

last: Stránecký

first: Stanislav

last: Kmoch


title: Comparative expression analysis between CRP (TTHA1437) deletion mutant and wild-type of T. thermophilus HB8

status: Public on Aug 05 2007

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

department: SPring-8 Center

institute: RIKEN Harima Institute

summary:
We observed the expression profile of the total mRNA of crp (TTHA1437) deletion mutant of Thermus thermophilus HB8 strain grown in a rich (TT) medium at 70oC compared with that of wild type.
Keywords: cell type comparison

overall_design: Three wild-type and mutant T. thermophilus HB8 strains were each pre-cultured at 70oC for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH.  The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70oC.  Cells were collected after 6 h and 8 h, and then crude RNA was extracted.  In order to compare mRNA expression in the crp (TTHA1437) deletion mutant with that of wild type, the expression of each mRNA at each time point was analyzed on a GeneChip as described under Sample Description Sheet of each sample in this website.

first: Satoshi

last: Kira

first: Noriko

last: Nakagawa

first: Aiko

last: Kashihara

first: Seiki

last: Kuramitsu

first: Shigeyuki

last: Yokoyama


title: SAGE and MPSS libraries from activated CD4+ T cell clone 29

city: Oxford

first: Edward

middle: J

last: Evans

state: Oxfordshire

address: HIU, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital

department: Nuffield Dept. Clinical Medicine

institute: University of Oxford

type:
Expression profiling by SAGE
Expression profiling by MPSS

summary:
SAGE and MPSS libraries were produced from the same RNA sample extracted from an activated CD4+ T cell clone in order to compare the ability of these techniques to indentify the full range of genes expressed in a single cell type.
Keywords: Technical comparison of tag-based technologies SAGE and MPSS

overall_design: One very large LongSAGE library (~500,000 tags) and three separate MPSS libraries were produced from a single RNA sample. Tags were linked to the human genome sequence and to the Ensembl database of known human genes in order to determine how many transcripts had been identified in the cell by each technique.  Despite its much smaller library size, SAGE identified many more transcripts in the sample than MPSS.  Because SAGE libraries may include many erroneous tags, we consider just tags from known genes and still SAGE identified more transcripts in the sample than all three MPSS libraries combined.

first: Lawrence

last: Hene

first: Vattipally

last: Sreenu

first: Mai

last: Vuong

first: Hussain

last: Abidi

first: Julian

last: Sutton

first: Sarah

middle: L

last: Rowland-Jones

first: Simon

last: Davis


title: Comparison of undifferentiated ES cell lines HM1, IMT11, SHBL6.3

city: Cardiff

first: Fiona

middle: Catherine

last: Mansergh

address: Museum Avenue

institute: Cardiff University

summary:
3 different ES cell lines were compared in order to determine whether there are significant expression profile differences between ES cell lines, or whether the constraints of maintaining pluripotency in culture force a similar expression profile on cell lines derived from disparate sources. Our results indicate that the latter is more likely. We identified 21 genes that were significantly differentially regulated, either on comparison with the pooled control, or on direct comparison of individual ES cell line data from different slides. Using semi-quantitative RT-PCR on 3 separate isolates from each cell line, we have confirmed 4 of these genes as consistently differentially regulated, Hprt, and 3 others. We would conclude therefore that different ES cell lines at the same passage number in identical culture conditions show very similar expression profiles.
Keywords: cell type comparison

overall_design: Cardiff University Array Facility NIA 15K slides were used in conjunction with 3 different RNA isolates from each of the ES cell lines. A pooled control was assembled using equal quantities of cells from each cell line, RNA was extracted and labelled, for use on every slide. Fluor switches were carried out, and 12 replicates were used for each cell line (3 biological replicates). The ES cell lines were each derived from different sources; IMT11 cells are derived from 129 strain mice. HM1 cells are also derived from 129 mice, but are missing a functional copy of Hprt. SHBl6.3 cells are derived from the less permissive C57Bl6/J mouse strain. Data were analysed as described in the GSM submissions.

middle: C

first: Anna

last: Hurley

first: Susan

last: Hunter

first: Martin


title: Array-CGH screening of medulloblastoma

status: Public on Aug 01 2007

city: Heidelberg

first: Stefan

last: Pfister

address: INF 580

institute: German Cancer Research Center

summary:
DNA copy-number profiling of 80 primary medulloblastomas of different histologies
Keywords: Genetic modification

overall_design: Comparison of tumor DNA (medulloblastoma) versus control DNA (pool of lymphocyte DNA from 10 healthy donors). Whole-genome screening for DNA copy-number aberrations using array-based comparative genomic hybridization (aCGH). Tumor DNA labeled in Cy3 and control DNA labeled in Cy5.

first: Axel

last: Benner

first: Grischa

last: Toedt

first: Bernhard

last: Radlwimmer

first: Peter

last: Lichter


title: Gene expression analysis of mouse testis after treatment with histone deacetylase inhibitor TSA

city: Giessen

first: Hamid

last: Hossain

address: Gaffky Str. 20

department: University of Giessen

institute: Institute for Medical Microbiology

summary:
Trichostatin A (TSA) is one of the most potent reversible histone deacetylase (HDAC) inhibitors. In male mice, subcutaneous application of TSA is followed by infertility due to apoptosis of pachytene spermatocytes. To get more insight into the mechanisms underlying this phenomenon, we performed a genome-wide expression analysis of murine testes after TSA treatment. The whole genome transcriptome analysis revealed 507 significantly regulated genes. Validation by real-time quantitative PCR confirmed the expression of 7 from 9 genes tested (78%).
Keywords: time course

overall_design: TSA was resolved in dimethylsulfoxide and PBS. 15 animals were divided into 5 groups each containing 3 mice. Group 1 received only the carrier and were sacrificed after 10h (control). Groups 2 - 5 received 60ug/day/mouse TSA applied by one subcutaneous injection and were sacrificed after 2.5h (group 2), 5h (group 3), 7.5h (group 4) and 10h (group 5).Total RNA was extracted from frozen tissue of 3 animals per group. The variability between animals in each group was minor, as demonstrated by the histological and immunohistochemical stainings. Therefore, the material from each group was pooled. cRNA of each group was hybridized in duplicate (technical replicates). In total, 10 bioarrays (2 arrays per group) were processed in parallel.

first: Irina

last: Fenic

first: Felix

last: Thierer


title: Resting and activating NK cells_gene signatures

city: omaha

first: Javeed

last: Iqbal

state: NE

address: 40th street

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

summary:
Genome-wide transcriptional profiling was used to identify gene expression signatures and pathways in resting and IL2 activated NK cell isolated from peripheral blood of healthy donors
Keywords: Time series_NK cells gene profile

overall_design: The aim of the study was to investigate the activation of human NK cells by IL2 through analyzing the global gene expression at different time points (0, 2, 8 and 24 hours) after culture with the cytokine IL2 at 100 IU/ml. NK cells with the CD56+/CD16+ and CD3- phenotype were negatively selected by immunomagnetic beads and re-examined by flow-cytometry to ensure greater than 90% purity (Figure1). Equivalent amount of total RNA from NK cells derived from 3 or 4 different donors for each time point was pooled, amplified and labeled before duplicate hybridizations was performed on spotted (pre-synthesized oligonucleotide) microarrays.

first: Karen

last: Dybkaer

first: Guimei

last: Zhou

first: Huimin

last: Geng

first: Li

last: Xiao

first: Alexander

last: Schmitz

first: Francesco

last: d’Amore

first: Wing

last: Chan


title: Functional coordination of alternative splicing in the mammalian central nervous system

city: Toronto

first: Qun

last: Pan

address: 160 College St.

institute: University of Toronto

summary:
Using a quantitative alternative splicing (AS) microarray platform, we have identified a large number of widely-expressed mouse genes containing single or coordinated-pairs of alternative exons that are spliced in a tissue-regulated fashion. The majority of these AS events display differential regulation in central nervous system (CNS) tissues. Approximately half of the corresponding genes have neural-specific functions and operate in common processes and interconnected pathways. Differential regulation of AS in the CNS tissues correlates strongly with a set of mostly new motifs that are predominantly located in the intron and constitutive exon sequences neighboring CNS-regulated alternative exons. Different subsets of these motifs are correlated with either increased inclusion or increased exclusion of alternative exons in CNS-tissues, relative to the other profiled tissues.
Keywords: Alternative splicing

overall_design: Hybridizations were performed in duplicate with fluor reversal: that is, each mRNA sample was examined in duplicate, once in the Cy3 channel and once in the Cy5 channel, on separate arrays. Each array was hybridized with two samples simultaneously, each from an individual tissue.

first: Matthew

last: Fagnani

first: Yoseph

last: Barash

first: Joanna

last: Ip

first: Christine

last: Misquitta

first: Arneet

last: Saltzman

first: Ofer

last: Shai

first: Leo

last: Lee

first: Aviad

last: Rozenhek

first: Naveed

last: Mohammad

first: Sandrine

last: Willaime-Morawek

first: Tomas

last: Babak

first: Wen

last: Zhang

first: Timothy

middle: R

last: Hughes

first: Derek

last: van der Kooy

first: Brendan

last: Frey

first: Benjamin

last: Blencowe


title: Gene expression profile in labouring and non-labouring human placenta near term

city: Tromsø

first: Ruth

middle: Hracky

last: Paulssen

address: MH-Bygget Breivika

department: Institute of Clinical Medicine

country: Norway

institute: Universitetet i Tromsø

summary:
Sample and RNA preparation:
The series is composed of seventeen hybridizations for analysis of differentially expressed genes in placenta tissues from women after vaginal delivery (labouring) and after elective caesarean section (non-labouring). Total RNA extraction was performed by using the MagNa Pure Compact RNA Isolation Kit (Roche Applied Science).
Labeling and hybridization:
Total RNA was reverse transcribed and labeled with Cy3-attached dendrimer using the Genisphere 3DNA HS kit (Genisphere) as described in the manufacturer’s protocol. Hybridizations were carried out with a TECAN HS4800 instrument using the foramamide-based hybridization buffer from Genisphere containing 5% dextran sulphate and 0.5 microgram COT1 DNA/microgram RNA at 37°C for 23 hours. 3DNA dendrimer hybridizations were carried out in formamide-based hybridization buffer alone. Post-hybridization washes were carried out at room temperature with 2xSSC for 1 min, 0.2% SDS/2xSSC for 1 min and finally with0.2xSSC for 30 sec.
Scanning, image analysis and data processing:
The microarrays were scanned on an AXON 4000B scanner and images were quantified using GenePix pro 6.0 software. The background estimates were calculated using the morphological opening method. Spots that displayed a signal-to-noise ratio of less than 3 or that were significantly saturated (more than 20 % saturation among foreground pixels) were filtered out. The median was used as the averaging measure of the foreground pixels.  After quality control, genes that were present in less than 50 % of the arrays were filtered out. Normalization was carried out using lowess normalization Sample labelling was balanced across the groups, presumably attenuating any dye-effect. For the purpose of finding differentially expressed genes empirical Bayes analysis, using the LIMMA package was applied. The data were analysed using a two-component linear model. The prior guess of the number of D.E genes was set to 0.01. Multiple testing was accounted for by estimating the false discovery rate. We applied the Benjamini-Hochberg procedure, as well as Storeys less conservative Q-value procedure was applied. In none of the cases were any genes significant at a reasonable (15-20% FDR) level. In summary, a 2.5-fold change in expression of any gene that was present on ≥ 8 arrays was considered significant, if the difference in fluorescence intensity between two groups reached a p-value of < 0.01.

Keywords: Tissue samples of placenta from women after vaginal delivery (labouring) and after elective caesarean section (non-labouring)

overall_design:
Samples from the placenta of 17 women who  had elective sectio(non-labouring) were hybridised together on the same array with placenta samples from women who had vaginal delivery (labouring). This resulted in 17 direct comparisons on 17 arrays.

To reduce the dye-bias, every second array had a reversed labeling orientation.

first: Vasilis

last: Sitras

first: Halvor

last: Grønaas

first: Ase

last: Vårtun

first: Ganesh

last: Acharya


title: Integrated genome-wide analysis of gene dosage and gene expression in Non Small Cell Lung Cancer

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

summary:
Understanding the molecular events in non-small cell lung cancer (NSCLC) is essential to improve early diagnosis and treatment for this disease. We examined the effect of chromosomal copy number changes on gene expression in resected NSCLC patients. We identified a deletion on 14q32.2-33 as a common alteration in NSCLC (44%), which significantly influenced gene expression for HSP90AA1, residing on 14q32. This deletion was correlated with better overall and recurrence free survival (P=0.008 and P=0.004, respectively) and survival was also longer in patients whose tumors had low expression levels of HSP90AA1. We extended the analysis to an independent validation set of 140 resected NSCLC patients, and confirmed low HSP90AA1 expression to be significantly related with overall survival and recurrence free survival (P=0.003 and P=0.007, respectively). In vitro treatment with an HSP90 inhibitor had potent antiproliferative activity in NSCLC cell lines. We suggest that targeting HSP90 will have clinical impact for NSCLC patients.
Keywords: Array CGH gene expression integration

overall_design: Array CGH and gene expression arrays (data available via array express accession: 0000) were performed on 32 radically resected tumor samples from stage I and II NSCLC patients. An integrative analysis tool ACE-it was applied to determine whether chromosomal copy number affects gene expression.

first: Marielle

last: GallegosRuiz

first: Karijn

last: Floor

first: Paul

last: Roepman

first: Jose

middle: A

last: Rodriguez

first: Gerrit

last: Meijer

first: Wolter

last: Mooi

first: Ewa

last: Jassem

first: Jacek

last: Niklinski

first: Thomas

last: Muley

first: Nico

last: van Zandwijk

first: Egbert

middle: F

last: Smit

first: Kristin

last: Beebe

first: Len

last: Neckers

first: Bauke

last: Ylstra

first: Giuseppe

last: Giaccone


title: Regulation of the Mycobacterium tuberculosishypoxic response gene encoding alpha-crystallin

city: Stanford

first: SMD

last: Staff

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
Unlike many pathogens that are overtly toxic to their hosts, the primary virulence determinant of Mycobacterium tuberculosis appears to be its ability to persist for years or decades within humans in a clinically latent state. Since early in the 20th century latency has been linked to hypoxic conditions within the host, but the response of M. tuberculosis to a hypoxic signal remains poorly characterized. The M. tuberculosis alpha-crystallin (acr) gene is powerfully and rapidly induced at reduced oxygen tensions, providing us with a means to identify regulators of the hypoxic response. Using a whole genome microarray, we identified >100 genes whose expression is rapidly altered by defined hypoxic conditions. Numerous genes involved in biosynthesis and aerobic metabolism are repressed, whereas a high proportion of the induced genes have no known function. Among the induced genes is an apparent operon that includes the putative two-component response regulator pair Rv3133cy Rv3132c. When we interrupted expression of this operon by targeted disruption of the upstream gene Rv3134c, the hypoxic regulation of acr was eliminated. These results suggest a possible role for Rv3132cy3133cy3134c in mycobacterial latency.
Keywords: comparative genome hybridization design and stimulus or stress design

overall_design: Six samples were analyzed. The quality controls were biological replicate and  technical replicate

first: D

last: Sherman

first: M

last: Voskuil