title: Transcriptional profiling of Campylobacter jejuni wild-type 81-176 and its ciprofloxacin-resistant derivative (P3) in the presence and absence of ciprofloxacin

status: Public on Dec 31 2012

city: Helsinki

first: Heidi

last: Hyytiäinen

address: Agnes Sjöbergin katu 2

department: Dep. of Food Hygiene and Environmental Health

country: Finland

institute: University of Helsinki

summary:
Campylobacter jejuni is one of the most important zoonotic enteric bacterial pathogens able to colonize the gastrointestinal tract of various animals. The number of campylobacteriosis cases has increased worldwide and the particular concern has been the high level of fluoroquinolone resistance observed in C. jejuni isolates.

In this study, we explored the effect of ciprofloxacin in Campylobacter jejuni by gene expression microarray analysis. The comparisons of transcriptional responses were performed in the absence and presence of ciprofloxacin with the wild-type strain 81-176 and its intermediate-resistant variant (P3). The resistant variant contained a single-nucleotide mutation causing amino acid change Asp-90-Asn in the gyrA gene instead of the most common Thr-86-Ile, causing a high-level resistance to ciprofloxacin. After the short-term exposure to a relatively high concentration of ciprofloxacin, the viability of C. jejuni 81-176 wild-type cells remained notably high when compared with other gram-negative bacteria. The general responses of short-term ciprofloxacin exposure were determined from both genetic backgrounds and resulted in the expression variation of genes participating in general cellular processes, e.g. , in carbon and amino-acid metabolism and protein transport.

sample_organism: Campylobacter jejuni subsp. jejuni 81-176

overall_design: Ciprofloxacin effect for gene expression was measured from both genetic backgrounds after 1 hour exposure at the level of 0 and 8 µg/ml ciprofloxacin in MH-broth. For RNA isolation, 5 independent experiments with and without ciprofloxacin were performed, and 4 replicates of each total RNA was applied for the gene expression study.


title: Transcriptional analysis of E. coli whole genome during heat inactivation processes related to industrial cooking

status: Public on Sep 15 2012

city: QUEBEC

first: ANTHONY

last: GUERNEC

state: QUEBEC

address: 2425 RUE DE L'AGRICULTURE

department: ANIMAL SCIENCE

country: Canada

institute: UNIVERSITE LAVAL

summary:
This study was conducted to determine the impact of extreme temperatures, aiming at controlling microorganisms by cooking, on the physiology and the transcriptome of  Escherichia coli.
ABSTRACT: Because the genome of Escherichia coli K12 is well understood, this organism was used as a model to investigate physiological and molecular changes during cell adaptation and survival to cooking temperatures used in the food industry. Bacteria grown at 37°C to stationary phase in Brain Heart Infusion (BHI) broth, were heated at 58°C or 60°C to reach a process lethality value (F) of 2 and 3, or until an internal core temperature of 71°C was reached (control cooking temperature). Both growth recovery and cell membrane integrity were evaluated immediately after heating and a global transcription analysis was performed by using gene expression microarrays. Only cells heated at 58°C F = 2 were still able to grow on liquid or solid BHI after heat treatment. However, their transcriptome did not differ significantly compared to those of bacteria heated at 58°C F = 3 (P-FDR > 0.01) where no growth recovery was observed post treatment. Genome-wide transcriptomic data obtained at 71°C were distinct from the other treatments. Quantification of heat-shock genes expression by real-time PCR revealed that dnaK and groEL mRNA levels were significantly lower at 71°C than at 58°C and 60°C (P < 0.0001). Furthermore, despite of similar cell inactivation but growth on BHI media after heating, 132 and 8 genes were differentially expressed at 71°C when compared to 58°C and 60°C at F = 3 respectively (P-FDR < 0.01). Among them, genes like aroA, citE, glyS, oppB and asd, whose expression was up-regulated at 71°C, may be considered as good biomarkers to determine more accurately the efficiency of heat treatments.

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

overall_design: Bacteria  were submitted to four different heat-treatments. Biological replicates: 5 Controls grown to an optimal temperature of 37°C (and used to prepare a common reference for each array hybridization), 5 Treatment 1 (58°C F = 2), 4 Treatment 2 (58°C F = 3), 4 Treatment 3 (60°C F = 3), 5 Treatment 4 (core temperature of 71°C). Treatment replicates were randomly hybridized on 3 microarray slides Agilent 8x15K (total of 24 array areas). Equal amounts of the labeled control cDNA pool and labeled cDNA from one of the heated groups were mixed and hybridized on each array.

first: Anthony

last: Guernec

first: Philippe

last: Robichaud-Rincon

first: Linda

last: Saucier


title: Histone H3 K56 acetylation in wild-type histone shuffle strain (YBL574)

status: Public on Jul 25 2012

city: Kansas City

first: Swaminathan

last: Venkatesh

state: MO

address: 1000 E 50th Street

country: USA

institute: Stowers Institute for Medical Research

type: Genome binding/occupancy profiling by array

summary: ChIP-on chip assays to measure the change in histone H3 K56 acetylation over the yeast genome in wild-type YBL574 yeast strains compared to H3K36A mutant strains.

overall_design: Two color experiment. Mutant vs WT cells. Biological replicates=3 per IP per cell type.

first: Hua

last: Li

first: Jerry

middle: L

last: Workman


title: Immunoenhancing effects of Montanide adjuvant on recombinant coccidia antigen vaccination against Eimeria spp. and comparative microarray analysis of intestinal lymphocytes

status: Public on Sep 11 2012

city: Beltsville

first: Duk Kyung

last: Kim

state: MD

address: Bldg. 1043, BARC-East

institute: USDA, ARS

summary: This study utilized comparative global gene expression microarray analysis to evaluate the effects of two different Montanide adjuvants, ISA70 and ISA71, in promoting chicken protective immunity following vaccination with profilin, an actin-regulatory protein that is expressed by multiple Eimeria species.

overall_design: Three-condition experiment with reference hybridization design, 1) ISA70 plus profilin immunized chickens vs. profilin alone and 2) ISA71 plus profilin vs. profilin alone, 2 biological replicates with dye-switching, total 4 replicates for each adjuvants

first: Duk

middle: K

first: Hyun

middle: S

last: Lillehoj


title: Histone exchange and histone H4 acetylation in wild-type and SET2 deletion yeast strains

type: Genome binding/occupancy profiling by genome tiling array

summary: ChIP-on chip assays to measure the change in histone exchange or histone acetylation over the yeast genome, in a SET2 deleted strain compared to the wild-type control. ChIP of Flag and Acetylated H4 from wild-type and SET2 deleted cells were normalized to the Myc enrichment.

overall_design: Two color experiment. SET2 deletion vs. WT cells. Biological replicates=3 per IP per cell type.


title: Histone H3 K36 trimethylation in wild-type BY4741 yeast strains

summary: ChIP-on chip assays to measure the change in histone H3 K36 trimethylation over the yeast genome in wild-type yeast strains.

overall_design: Two color experiment.WT cells. Biological replicates=3 per IP per cell type.


title: Histone acetylation in wild-type and SET2 deletion yeast strains

summary: ChIP-on chip assays to measure the change in histone acetylation over the yeast genome, in a SET2 deleted strain compared to the wild-type control. ChIPs of H3K9ac, H3K56ac and H4K12ac  from wild-type and SET2 deleted cells were normalized to the H3 enrichment.


title: Histone H4 acetylation in wild-type, ASF1, SET2 and ASF1 SET2 deletion yeast strains

summary: ChIP-on chip assays to measure the change in histone acetylation over the yeast genome, in  ASF1, SET2 and ASF1 SET2 deletion yeast strains compared to the wild-type control. ChIPs of AcH4 from wild-type, ASF1, SET2 and ASF1 SET2 deletion yeast strains were normalized to the H3 enrichment.

overall_design: Two color experiment. Deletion mutant vs. WT cells. Biological replicates=3 per IP per cell type.


title: Bias in Gene-Set Analysis Applied to High-throughput Methylation Data

status: Public on Jul 13 2012

city: Galway

first: Paul

last: Geeleher

address: University Road

department: Mathematics

country: Ireland

institute: National University of Ireland, Galway

type: Methylation profiling by genome tiling array

summary: Gene set analysis as it is typically applied to genome-wide methylation assays is severely biased as a result of differences in the numbers and sizes of CpG islands associated with different classes of genes. We demonstrate this bias using published data from a study of differential methylation in lung cancer and a data set we generated to study methylation changes in patients with long-standing ulcerative colitis and show that several of the gene sets that appear enriched would also be identified with randomized data. We also report a method to correct the bias. Application of the corrected method to the lung cancer and ulcerative colitis data sets provides novel and potentially interesting biological insights into the role of methylation in cancer development and chronic inflammation.

overall_design: We used Agilent Human CpG Island microarrays to compare methylation patterns in sigmoid colon tissue between five individuals suffering from ulcerative colitis and five healthy age-matched controls.

first: Cathal

last: Seoighe

first: Lori

last: Hartnett

first: Laurance

last: Egan

first: Aaron

last: Golden

first: Raja

middle: A

last: Affendi


title: Isw1 and Chd1 maintain chromatin organization during transcription

first: Michaela

last: Smolle

state: Missouri

summary: ChIP-chip assays to determine the localization of 3xFLAG tagged Ioc4,  Ioc3 & Isw1 in wildtype and set2 yeast.

platform_organism:
Saccharomyces cerevisiae
Saccharomyces cerevisiae S288C

overall_design: Two color experiment. ChIP/Input. Biological replicates=3.

first: Madelaine

last: Gogol


title: CP003: Modulation of glutamine metabolism by the PI3K-PKB/c-akt-FOXO network regulates autophagy

status: Public on Jul 22 2012

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

summary: The PI3K-PKB/c-akt-FOXO signalling network provides a major intracellular hub for regulation of cell proliferation, survival and stress resistance1. Here we report a novel function for FOXO transcription factors in regulating autophagy through modulation of intracellular glutamine levels. To identify novel transcriptional targets of this module we performed an unbiased microarray analysis after conditional activation of the key components PI3K, PKB, FOXO3 and FOXO4. Utilising this global pathway approach we identified glutamine synthetase (GS) as being transcriptionally regulated by PI3K-PKB-FOXO signalling. FOXO-mediated increase in GS expression specifically induced glutamine production independently of cell type, and this was evolutionary conserved. FOXO activation resulted in mTOR inhibition by preventing the translocation of mTOR to lysosomal membranes, which was dependent on GS activity. Increased GS activity resulted in increased autophagosome turnover as measured by LC3 lipidation, p62 degradation, and confocal imaging of LC3, p62, WIPI-1, ULK2 and Atg12. Inhibition of FOXO3-mediated autophagy resulted in increased apoptosis, suggesting that the induction of autophagy by FOXO3-mediated upregulation of GS is important for cellular survival. These findings reveal a novel signalling network that can directly modulate autophagy through regulation of glutamine metabolism.

overall_design: conditional activation of foxo3 and foxo4 were followed in a timeseries. Each timepoint consists of 4 independent replicates, labeled with either cy3 or cy5 and put on array against time0 as reference.

first: Kristan

middle: E

last: van der Vos

first: Pernilla

last: Eliasson

first: Tassula

last: Proikas-Cezanne

first: Stephin

last: Vervoort

first: Ruben

last: van Boxtel

first: Marrit

last: Putker

first: Iris

middle: J

last: van Zutphen

first: Mario

last: Mauthe

first: Sebastian

last: Zellmer

first: Cornelieke

last: Pals

first: Liesbeth

last: Verhagen

first: Koen

last: Braat

first: Tobias

middle: B

last: Dansen

first: Frank

middle: C

last: Holstege

first: Rolf

last: Gebhardt

first: Boudewijn

middle: M

last: Burgering

last: Coffer


title: Systematic dissection of roles for chromatin regulators in a yeast stress response

status: Public on Jul 11 2012

city: Jerusalem

first: Nir

last: Friedman

address: Givat Ram

country: Israel

institute: Hebrew University

summary: Packaging of eukaryotic genomes into chromatin has wide-ranging effects on gene transcription. Curiously, it is commonly observed that deletion of a global chromatin regulator affects expression of only a limited subset of genes bound to or modified by the regulator in question. However, in many single-gene studies it has become clear that chromatin regulators often do not affect steady-state transcription, but instead are required for normal transcriptional reprogramming by environmental cues. We therefore have systematically investigated the effects of 83 histone mutants, and 119 deletion mutants, on induction/repression dynamics of 200 transcripts in response to diamide stress in yeast. Importantly, we find that chromatin regulators play far more pronounced roles during gene induction/repression than they do in steady-state expression. Furthermore, by jointly analyzing the substrates (histone mutants) and enzymes (chromatin modifier deletions) we identify specific interactions between histone modifications and their regulators. Combining these functional results with genome-wide mapping of several histone marks in the same time course, we systematically investigated the correspondence between histone modification occurrence and function. We follow up on one pathway, finding that Set1-dependent H3K4 methylation primarily acts as a gene repressor during diamide stress, specifically at genes involved in ribosome biosynthesis. Set1-dependent repression of ribosomal genes occurs via distinct pathways for ribosomal protein genes and ribosomal biogenesis genes, which can be separated based on genetic requirements for repression and based on chromatin changes during gene repression. Together, our dynamic studies provide a rich resource for investigating chromatin regulation, and show that the “activating” mark H3K4me3 functions largely as a repressor in yeast.

overall_design: We set to track how histone modifications change during transcriptional reprogramming. We perfomed a time course experiment following treatment of mid-log growing yeast (BY4741) with diamide. Samples were collected at t=0,4,8,15,30,60 and fixed by crosslinking. We extracted mononucleosomes by MNase digestion and then applied ChIP for selected histone modifications. The IPed material was hybridized to genomic tiling arrays against the input material.

first: Oliver

last: Rando


title: Digitoxin treatment versus control in HEK293 cells

status: Public on May 01 2012

city: Los Angeles

first: Erik

last: Anderson

state: CA

address: 6-567 MRL, 675 Charles E. Young Drive South

department: MBIDP

institute: UCLA

summary: We treated HEK293 cells with the cardiotonic steroid digitoxin to identify alternative splicing changes as compared to DMSO treatment alone.

overall_design: In this set, 6 total samples were analyzed.  There were three biological replicates for each of two conditions: DMSO treatment and Digitoxin treatment.  Arrays were analyzed for gene expression using GeneBase and for alternative splicing using MADS+ and OmniViewer software.

first: Chia-Ho

last: Lin

first: Xinshu

last: Xiao

first: Peter

last: Stoilov

first: Christopher

last: Burge

first: Douglas

last: Black


title: Effect of dietary supplementation with Anethol during Eimeria maxima and Eimeria tenella infection of chickens

status: Public on Oct 02 2012

first: Duk Kyung

last: Kim

summary: This study utilized comparative global gene expression microarray analysis to evaluate the effects of Anethol on intestinal immunity of chicken.

overall_design: Two-condition experiment, Anethol-fed chickens vs. Non-treated control chickens. Biological replicates: 2 control replicates, 2 Anethol-fed replicates with dye-switching.

first: Duk

first: Hyun

last: Lillehoj


title: Co-transcriptional histone acetylation is a consequence of histone exchange

first: Swaminathan

last: Venkatesh

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

overall_design: Refer to individual Series


title: Sex-biased gene expression during head development in a sexually dimorphic stalk-eyed fly

status: Public on Apr 10 2012

city: College Park

first: Gerald

last: Wilkinson

address: Bldg 144, 4094 Campus Dr

department: Biology

institute: University of Maryland

summary: Stalk-eyed flies (family Diopsidae) are a model system for studying sexual selection due to the elongated and sexually dimorphic eye-stalks found in many species. These flies are of additional interest because their X chromosome is derived largely from an autosomal arm in other flies. To identify candidate genes required for development of dimorphic eyestalks and investigate how sex-biased expression arose on the novel X we compared gene expression between males and females using oligonucleotide microarrays and RNA from developing eyestalk tissue or adult heads in the dimorphic diopsid, Teleopsis dalmanni. Microarray analysis revealed sex-biased expression for 26% of 3,748 genes expressed in eye-antennal imaginal discs and concordant sex-biased expression for 86 genes in adult heads. Overall, 415 female-biased and 482 male-biased genes were associated with dimorphic eyestalk development but not differential expression in the adult head.  Functional analysis revealed that male-biased genes are disproportionately associated with growth and mitochondrial function while female-biased genes are associated with cell differentiation and patterning or are novel transcripts.  With regard to chromosomal effects, dosage compensation occurs by elevated expression of X-linked genes in males. Genes with female-biased expression were more common on the X and less common on autosomes than expected, while male-biased genes exhibited no chromosomal pattern.  Rates of protein evolution were lower for female-biased genes but higher for genes that moved on or off the novel X chromosome.  These findings cannot be due to meiotic sex chromosome inactivation or by constraints associated with dosage compensation.  Instead, they could be consistent with sexual conflict in which female-biased genes on the novel X act primarily to reduce eyespan in females while other genes increase eyespan in both sexes. Additional information on sex-biased gene expression in other tissues and related sexually monomorphic species could confirm this interpretation.

overall_design: Two-condition experiment, female vs. male RNA using larval eye discs and adult heads for one species (Teleopsis dalmanni).

first: Richard

middle: H

last: Baker

first: Jackie

middle: D

last: Metheny

first: Philip

last: Johns


title: Expression analysis of D. melanogaster selected for contrasting life histories

status: Public on May 23 2012

city: Urbana

first: Silvia

last: Remolina

state: IL

address: 505 S Goodwin Ave

institute: University of Illinois

summary: Study of transcriptome level changes in Drosophila melanogaster populations with divergent reproduction and lifespan patterns

overall_design: A 120 chip study using mRNA recovered from unmated female fruit flies 35 generations after selection for contrasting life history traits. The study includes samples from five age classes and two tissues of flies derived from three replicated populations.

first: Kimberly

last: Hughes


title: The miRNA-200 family and miRNA-9 exhibit differential expression in primary vs. corresponding metastatic tissue in breast cancer

status: Public on Apr 19 2012

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

country: Sweden

institute: Lund University, Sweden

summary: Global miRNA expression profiling was performed on 47 tumor samples from 14 patients with paired samples from primary breast tumors and corresponding lymph node and distant metastases using LNA-enhanced miRNA microarrays. The identified miRNA expression alterations were validated by real-time PCR, and tissue distribution of the miRNAs was visualized by in situ hybridization

first: Karina

last: Gravgaard

first: Maria

last: Lyng

first: Anne-Vibeke

last: Laenkholm

first: Boye

last: Nielsen

first: Thomas

last: Litman

first: Henrik

last: Ditzel


title: gene expression profiling in CD69 positive blood cells selected from Healthy blood Donors and HTLV-1-infected patients

status: Public on Mar 14 2012

city: LYON

first: Pascale

last: GIRAUDON

address: rue Guillaume Paradin

department: Faculty of Medicine Laennec

country: France

institute: CRNL-U1028 Inserm

summary: The goal of the study was to identify difference in gene expression between activated /CD69+ blood cells selected from HTLV-1-infected patient displaying HAM-TSP disease (HTLV-1-associated myelopathy/tropical spastic paraparesis), compared to healthy blood donor /HD (biological sample providers: Dr. Antoine Gessain, Pasteur Institute Paris and Etablissement Français du Sang)

overall_design: We performed microarray gene expression profiling of Immune cells selected on the marker of early activation, CD69, by the use of MACS beads (Miltenyi Biotec), from 10.106 blood cells of two healthy blood donors and two HAM/TSP patients

first: Pascal

last: Giraudon

first: Michel

last: Varrin-Doyer

first: Joël

last: Lachuer

first: Anne

last: Wierinckx


title: Integrated genome and transcriptome sequencing identifies a novel case of hybrid and aggressive prostate cancer

status: Public on Dec 22 2011

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

institute: Vancouver Prostate Centre

type: Genome variation profiling by genome tiling array

summary: Next generation sequencing is making sequence-based molecular pathology and personalised oncology  viable. We selected an individual initially diagnosed with conventional, but aggressive, prostate  adenocarcinoma and sequenced the genome and transcriptome from primary and metastatic tissues  collected prior to hormone therapy. The histology-pathology and genomic architecture were remarkably  homogeneous, yet it was possible to determine the quadrant of the prostate tumour that likely seeded the  metastatic diaspora. Despite a homogenous cell type, our transcriptome analysis revealed signatures of  both luminal and neuroendocrine cell types. Remarkably, the repertoire of expressed but private gene  fusions, including C15orf21:MYC, recapitulated this biology while the amplification and over expression  of the stem cell gene MSI2 may have contributed to the stable hybrid cellular identity. This hybrid  luminal-neuroendocrine tumour appears to represent a novel and highly aggressive case of prostate cancer  with unique biological features and conceivably a propensity for rapid progression to castrate-resistance.  Overall, this work highlights the importance of integrated analyses of genome, exome and transcriptome  sequences for basic tumour biology, sequence-based molecular pathology, and personalized oncology.

overall_design: 5 samples

first: Alexander

middle: W

last: Wyatt

last: Haegert


title: Gene profile of mid-log phase of SD medium grown Candida albicans rhb1 gene deletion strain

status: Public on Mar 15 2012

city: Hsinchu

first: Yu-Ting

last: Chen

address: No.101, Sec. 2, Guang-Fu Rd.

department: Institute of Molecular and Cellular Biology

country: Taiwan

institute: National Tsing Hua University, Taiwan

summary: Candida albicans is an opportunistic pathogenic yeast that is commensally found in variety of host niches. Rhb1 serves as an positive regulator of Tor1 kinase which is the central component of the TOR signaling in controlling several virulence factors. Here, we used microarray to determined changes in transcript profile while the cell lacks the RHB1 gene.

overall_design: 10 array generated by six batchs of individual experiment (from cell isolation to culture); each included one flask of wild type culture (SC5314) and one flask of rhb1∆ (CCT-D1)mutant culture.

first: Yu

middle: T

first: Pei

last: Tsai

first: Wen

middle: P

last: Hsieh

first: Chung

middle: Y

last: Lan


title: High-throughput sequencing of small RNAs in Volvox carteri

status: Public on Sep 30 2011

city: Udine

first: Emanuele

last: De Paoli

state: UDINE

address: via delle Scienze 206

department: Agricultural, Food, Environmental and Animal Sciences

country: Italy

institute: University of Udine

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from cultures of Volvox carteri  (in control, phosphate starvation and sulphate starvation conditions). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study.

overall_design: Small RNA libraries were derived from cultures of Volvox carteri in control, phosphate starvation and sulphate starvation conditions. Total RNA was isolated using the TriReagent (Molecular Research Center), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.

first: Monica

last: Accerbi

first: Pamela

last: Green

first: Blake

last: Meyers


title: Effect of dietary supplementation with Curcuma longa (turmeric) during Eimeria maxima and Eimeria tenella infection of chickens

status: Public on May 08 2012

first: Duk Kyung

last: Kim

summary: This study utilized comparative global gene expression microarray analysis to evaluate the effects of curcumin on intestinal immunity of chicken.

overall_design: Two-condition experiment, Curcumin-fed chickens vs. Non-treated control chickens. Biological replicates: 2 control replicates, 2 Curcumin-fed replicates with dye-switching.

first: Duk

first: Hyun

last: Lillehoj


title: Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing

status: Public on May 09 2012

city: Beijing

first: Tianzuo

last: Wang

address: No.20 Nanxincun, Xiangshan

department: State Key Laboratory of Vegetation and Environmental Change

country: China

institute: Institute of Botany, the Chinese Academy of Sciences

summary: Two hundreds eighty three and 293 known miRNAs were identified from the control and drought stress libraries, respectively. In addition, 253 potential candidate miRNAs were identified, and among them 48 novel miRNAs/ novel members of known miRNA families whose complementary miRNAs were also detected. Both high-throughput sequencing and RT-qPCR confirmed that 22 members of 4 miRNA families were up-regulated and 10 members of 6 miRNA families were down-regulated in response to drought stress. Among the 48 novel miRNAs, 24 miRNAs were responsive to drought stress with 21 and 3 miRNAs being up- and down-regulated, respectively. The known and predicted targets of these miRNAs in response to drought stress are involved in diverse cellular processes in plants, such as development, transcription, protein degradation, detoxification, nutrient status and cross adaptation.

overall_design: To identify miRNAs in response to drought stress in M. truncatula, control and drought stress shoots were used to construct small RNA libraries, respectively. The date from Solexa sequencer (Illumina) was compared to identify miRNAs in response to drought stress.

first: Wenhao

last: Zhang


title: Comparative Genome Hybridization between Candida albicans and Candida dubliniensis and their derivatives

status: Public on Dec 31 2010

city: Bangalore

first: Kaustuv

last: Sanyal

state: Karnataka

address: Jakkur

department: Molecular Biology and Genetics Unit

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research

summary: Total genomic DNAs of J118, CdUM4b, the pseudotetraploid hybrid  strain HBT1 and the progeny hybrid strain HBP1 were isolated. In an attempt to determine the number of copies of individual chromosomes, we used comparative genome hybridization (CGH) analysis using specially designed whole genome microarrays representing C. albicans and C. dubliniensis genomes. The arrays contained 60 mer probes that fell in three categories either C. albicans specific or C. dubliniensis specific or common to both. The specific probes were expected to work as internal controls when hybridized to parental genomic DNA alone. The arrays were individually hybridized to Cy3-labeled genomic DNA from either of C. albicans (J118), C. dubliniensis (CdUM4b) parents or the somatic psudotetraploid hybrid strain, HBT1 and the pseudodiploid progeny hybrid HBP1. After experimentally determining species-specific probes and common probes, the ratios of intensity on the HBT1 hybrid array to those of either of the parents were calculated. The copy number was determined for the entire chromosomes by comparing individual probe intensities from the pseudotetraploid to either diploid parent genome DNA intensities.

sample_organism:
Candida albicans
Candida dubliniensis
Candida albicans x Candida dubliniensis

platform_organism:
Candida albicans
Candida dubliniensis

overall_design: Agilent one-color CGH experiment,Organism: Human ,Agilent-24598 Genotypic designed C.albicans and C. dubliniensis Cross Species CGH Microarray 4x180k  , Labeling kit:  Agilent Genomic DNA labeling Kit (Part Number: 5190-0453)

first: Uttara

last: Chakraborty

first: Pallavi

last: Kakade

first: Aiyaz

last: Mohamed

first: Raja

last: Mugasimangalam

first: Parag

last: Sadhale


title: human leukemia cell line K562 offspring acquring imatinib resistance(K562-r) : Control vs. Drug treated

status: Public on Dec 30 2010

city: Shanghai

first: wentao

last: yang

address: chong qing nan lu #225

department: Institute of Health Science

institute: Shanghai Institute for Biological Sciences,China Academy of Science

summary: Transcriptional profiling of K562-r comparing control untreated human leukemia cells with human leukemia cells treated with AMN107 and ATO individually or combined.Four timepoints included are 3h,12h,24h,48h, covering the whole time window of K562-r cells responsing to the drug treatment.At the combination of 1.5uM ATO and 8uM AMN107, K562-r cells have the most significant coordinated effects (the apoptosis rate at 72h was 56.41% compared to 12.23% in ATO alone and 29.8% in AMN107 alone.). We studied gene expression series in K562-r cells with or without drug treatments by cDNA microarray analysis. Many genes involved in endoplasmic reticulum (ER) stress signaling, including ATF3, DDIT3, HERPUD1, HSPA5, XBP1 and TXNDC12, were highly up-regulated within 12 h of co-treatment, suggesting that the combination of ATO with AMN107 induced an ER stress response leading to apoptosis later on. Other ER-stress markers like the JNK pathway, which bridges the ER-stress and apoptosis, have been activated. Knock down the initiator of JNK partially alleviate the effects of apoptosis (p<0.05). Co-administering AMN107 and arsenic trioxide, inducing apoptosis via the ER-stress, indicates a novel therapy alternative for the imatinib induced secondary resistance.

overall_design: 17-condition experiment, untreated K562-r vs. Drug-treated K562-r cells, including 4 time points, for each point the untreated and 1.5uM ATO treated,8uM AMN107 treated and both 1.5uM ATO and 8uM AMN107 treated, independently grown and harvested. One replicate per array. Untreated K562-r_0h used to counteracting the background.

first: Yuan

last: Xia

first: Yanzhi

last: Du

first: Ying

last: Chen

first: Bin

last: Hu


title: Sub1 and RPA associate with RNA Polymerase II at different stages of transcription

status: Public on Sep 27 2011

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation St.

institute: UMass Medical School

summary: Single stranded DNA binding proteins play many roles in nucleic acid metabolism, but their importance during transcription remains unclear. Quantitative proteomic analysis of RNA polymerase II (RNApII) pre-initiation complexes (PICs) identified Sub1 and the Replication Protein A complex (RPA), both of which bind single-stranded DNA (ssDNA).  Sub1, homolog of mammalian coactivator PC4, exhibits strong genetic interactions with factors necessary for promoter melting. Sub1 localizes near the transcription bubble in vitro and binds to promoters in vivo dependent upon PIC assembly. In contrast, RPA localizes to transcribed regions of active genes, strongly correlated with transcribing RNApII but independently of replication.  RFA1 interacts genetically with transcription elongation factor genes.  Interestingly, RPA levels increase at active promoters in cells carrying a Sub1 deletion or ssDNA binding mutant, suggesting competition for a common binding site. We propose that Sub1 and RPA interact with the non-template strand of RNApII complexes during initiation and elongation, respectively.

overall_design:
Chip-chip from wt and sub1D cells with Rfa1
Chromatin immunoprecipitation (ChIP) of Rfa1 in wt and sub1D yeast demonstrated that Rfa1 localization correlates with RNA Polymerase II and is increased at some transcription start sites when Sub1 has been deleted.
Comparison of Rfa1 localization in wt vs sub1D yeast

first: Timothy

last: Sikorski

first: John

last: Holik

first: Steve

last: Buratowski


title: Differential Gene Expression Profiles in Broiler Chickens with Gangrenous Dermatitis (GD)

status: Public on Oct 27 2010

first: Duk Kyung

last: Kim

summary: This study utilized comparative global gene expression microarray analysis of GD-affected and clinically healthy chickens from a recent GD outbreak to glean insights into the molecular and cellular changes associated with this disease process.

overall_design: Two-condition experiment, GD-affected vs. Healthy chickens. Biological replicates: 2 control replicates, 2 GD-infected replicates with dye-switching.

first: Duk-Kyung

first: Hyun

last: Lillehoj


title: Investigation of differential expression: Differentiating cells vs Salmonella infected cells (t6)

status: Public on Mar 10 2010

city: Cologne

first: Ludwig

last: Eichinger

address: Joseph-Stelzmann-Strasse 52

country: Germany

institute: Institute for Biochemistry 1

summary: Dictyostelium discoideum is a professional phagocyte and it uses phagocytosis as a way to get food. However, there are a number of bacteria that subvert this professional phagocyte. In this study we investigated whether Salmonella typhimurium is also pathogenic for D. discoideum.

overall_design: AX2 cells were grown in a 1000-fold excess of E.Coli B/r in Soerensen phosphate buffer under shaking. Cells were washed and resuspended at a concentration of 2 x 10^6 per ml with a 1000-fold excess of S. typhimurium or in phosphate buffer. After 0, 3, 6, 9 and 12 hours, cells were washed free of bacteria and total RNA was extracted. RNA from the 3 and 6 hour time points was used for DNA microarray analysis.


title: Analysis of testicular transcriptome changes in the presence of Y-chromosomal microdeletions

status: Public on May 01 2010

city: 20246 Hamburg

first: Andrej-Nikolai

last: Spiess

address: Martinistr. 52

department: Andrology

institute: University Hospital Hamburg-Eppendorf

summary:
We investigated the transcriptional changes in human testis in the presence of AZFc/AZFb+c microdeletions. As one encounters a dominating 'germ cell effect' in this pursuit, testicular biopsies were pre-selected by clustering based on similar quantitative germ cell composition.
Statistical testing was employed to filter genes that are influenced by the 'deletion effect' using the selected subset of biopsies, thereby obtaining several hundered genes that may be involved in YCMD-induced spermatogenic impairment.

overall_design: A set of 34 biopsies was used from which 26 samples remained after pre-selection. Transcriptional changes of the control and YCMD groups were analyzed for hypospermatogenesis, meiotic arrest and Sertoli-cell only syndrome

first: Heike

last: Cappallo-Obermann

first: Kathrein

last: von Kopylow

first: Wolfgang

last: Schulze


title: Investigation of differential expression: Differentiating cells vs Salmonella infected cells (t3)


title: Differential Expression upon infection with Salmonella typhimurium (t1)

overall_design:
AX2 cells were grown in a 1000-fold excess of E.Coli B/r in Soerensen phosphate buffer under shaking. Cell were washed and resuspended at a concentration of 2 x 10^6 per ml with a 1000-fold excess of either S. typhimurium or E.Coli B/r in Soerensen phosphate buffer. After 0, 1, 2 and 3 hours cells were washed free of bacteria and total RNA was extracted for DNA microarray analysis.
For each timepoint three samples were taken and the experiment was done twice so that we had six samples for each timepoint (e.g. S1, S2, S3 and S1', S2', S3' ).


title: Coeevolution of a transcriptional network by compensatory trans and cis mutations

status: Public on Sep 17 2010

city: La Jolla

first: Dwight

last: Kuo

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

summary: Transcriptional networks have been shown to evolve very rapidly, prompting questions as to how such changes arise and are tolerated. Recent comparisons of transcriptional networks across species have implicated variations in the cis-acting DNA sequences near genes as the main cause of divergence. What is less clear is how these changes interact with trans-acting changes occurring elsewhere in the genetic circuit. Here, we report the discovery of a system of compensatory trans and cis mutations in the yeast AP-1 transcriptional network that allows for conserved transcriptional regulation despite continued genetic change. We pinpoint a single species, the fungal pathogen Candida glabrata, in which a trans mutation has occurred very recently in a single AP-1 family member distinguishing it from its Saccharomyces ortholog. Comparison of chromatin immunoprecipitation profiles between Candida and Saccharomyces shows that, despite their different DNA binding domains, the AP-1 orthologs regulate a conserved block of genes. This conservation is enabled by concomitant changes in the cis-regulatory motifs upstream of each gene. Thus, both trans and cis mutations have perturbed the yeast AP-1 regulatory system in such a way as to compensate for one another. This demonstrates an example of “co-evolution” between a DNA-binding transcription factor and its cis-regulatory site, reminiscent of the co-evolution of protein binding partners.

sample_organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

overall_design: 3 Experiments were performed. Three replicates CgAp1-TAP was ChIPped under MMS treatment (GSM397447..GSM397449), two replicates each of ScYap1R79K and ScYap4K252R (GSM594724..GSM594727), were ChIPped under MMS treatment.


title: Implications of transcriptomics, proteomics and metabolomics analysis of maize seeds for food safety

status: Public on Dec 31 2009

city: Wageningen

first: Jeroen

last: van Dijk

address: Bornsesteeg 45

institute: RIKILT, institute of food safety

summary: In this study we used non-targeted molecular profiling to provide insight into the extent of variation in the maize transcriptome, proteome and metabolome by analyzing replicas of two genetically modified and one isogenic maize genotype.

overall_design: Three white maize lines,  the transgenic commercial Bt hybrid line DKC78-15 Bt (event MON810 from Monsanto), the transgenic commercial Roundup Ready (RR) line DKC78-35R (event NK603 from Monsanto) and its respective control line CRN 3505 (conventional from Monsanto) were grown in three consecutive years, and in two or three different locations in South Africa.

first: Henriek

middle: G

last: Beenen

first: Esther

last: Kok

first: Eugenia

last: Barros


title: Time course of Saccharomyces cerevisiae Exposed to Arsenic under Phosphate Limited Conditions

city: Seoul

first: Joo Myung

last: Ahn

address: Anam-dong, Seongbuk-gu

department: Life Science and Biotechnology

country: South Korea

institute: Korea University

summary:
Arsenic is known as a human carcinogen that easily be exposed by the living organisms through environment and food consumption. The arsenic is transport into the cells via phosphate transporters due to its structural similarity with phosphate in both prokaryotes and eukaryotes.
We here evaluated and analyzed the toxicogenomic impacts of arsenate and the role of different phosphate concentrations on arsenic toxicity. Our results showed that arsenic uncoupled phosphate levels which eventually affected the growth rate of yeast cells. Analysis of arsenate levels in the medium over 4 to 10 h of its exposure clearly showed that arsenate was easily taken up by the cells in phosphate limited condition.

overall_design: 2 μM Arsenate under 100uM and 1 mM phosphate condition experiments with three time intervals (4, 8, and 10 hour).

first: Joo-Myung

first: Chun-Nu

last: Geng

first: Man

last: Gu


title: Transcriptomic analysis of maize developing earshoot, B73 X Mo17 hybrid

status: Public on Jan 14 2010

first: Stephen

middle: Patrick

last: Moose

address: 1201 W Gregory

department: Crop Sciences

institute: University of Illinois at Urbana-Champaign

summary: Maize earshoot is a metabolic sink espcially related to nitrogen metabolism. Studies on the transcriptomic and metabolic changes occuring in earshoot can provide interesting answers about the nitrogen metabolic potential of the maize variety under study. B73 X Mo17 is a model maize hybrid. Developing earshoots from this genotype grown at nitrogen-deficient and nitrogen-sufficient conditions were sampled, processed and analyzed through microarray technology.

overall_design: B73 X Mo17 hybrid_developing earshoot microarray data: Technical replicates, no biological replicates

first: Jayanand

last: Boddu


title: Differential Expression upon infection with Salmonella typhimurium (t3)


title: Differential Expression upon infection with Salmonella typhimurium (t0)


title: Differential Expression upon infection with Salmonella typhimurium (t2)


title: Genotype changes in 8DAP leaf

status: Public on Dec 11 2009

summary:
Genotype dependent gene expression changes in the leaves of Illinois protein lines at 8 days after pollination (DAP).
Illinois protein lines (IPL) comprise lines known as Illinois high protein (IHP), Illinois low protein (ILP), Illinois reverse-low protein (IRLP) and Illinois reverse-high protein (IRHP) lines.
These lines represent over a century old experiment containing lines that represent various levels of nitrogen metabolism potential as a function of their grain protein concentration.
Microarray experiment was conducted using 8 DAP leaves from the above mentioned four IPLs.

Keywords: Genotype response

overall_design: Technical replicates, dye swaps, technical replicates of dye swaps, no biological replicates

first: Han

last: Zhao


title: Transcriptomic analysis of maize developing earshoot, IBMRIL X IHP1 hybrid

status: Public on Feb 04 2010

summary:
Maize earshoot is a metabolic sink espcially related to nitrogen metabolism. Studies on the transcriptomic and metabolic changes occuring in earshoot can provide interesting answers about the nitrogen metabolic potential of the maize variety under study. Intermated B73 X Mo17 recombinant inbred lines (IBMRIL) belong to a predominantly used mapping population. Illinois high protein (IHP) line is a metabolic extreme with respect to nitrogen mebolism with around 30% seed protein. Developing earshoots from this genotype grown at nitrogen-deficient and nitrogen-sufficient conditions were sampled, processed and analyzed through microarray technology. IBMRIL population was crossed to IHP to find the allelic interaction related to nitrogen metabolism. Microarray experiment was conducted using the developing earshoots from IBMRIL X IHP1 lines that deffered in their grain yield significantly.

Keywords: Yield response


title: Carolina_Gastritis_DU_GC_series

status: Public on Sep 25 2009

city: Seattle

first: Nina

middle: Reda

last: Salama

state: WA

address: 1100 Fairview Ave. N

department: Division of Human Biology

institute: Fred Hutchinson Cancer Research Center

summary:
Array CGH of Mexican patient strains from Javier Torres laboratory analyzed by Carolina Romo. Patients have a range of pathologies form gastritis to ulcer to cancer. Multiple strains were isolated from each patient and all those giving distinct RAPD patterns were profiled against a reference sample of 26695/J99 genomic DNA. For each array 0.25-1 micrograms of genomic DNA of a test strains was labeled with Cy5 and 0.5 micrograms of an equimolar mix of 26695 and J99 genomic DNA was labeled with Cy3.
A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc.
Individual: Patient from whom the strain was isolated (#)
Disease State: Disease of patient from whom the strain was isolated
Replicate: strain isolate (within patient) (#)

Keywords: clinical_history_design

sample_organism:
Helicobacter pylori
Helicobacter pylori 26695
Helicobacter pylori J99

overall_design: Computed


title: UVB-induced persistent activation of cellular pathways revealed by a loop-designed microarray approach

status: Public on Apr 10 2009

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

institute: nthu

summary:
Ultraviolet B (UVB) irradiation has strong biological effects and modulates the expression of many genes. However, the major biological themes affected by UVB remain poorly understood. This work employs a loop-designed microarray approach and applies a log linear model along with multiple hypotheses testing to identify differentially regulated genes at 4, 8, 16, or 24 hours following UVB irradiation. The most prominent biological themes in lists of differentially regulated gene sets were extracted by functional enrichment analysis using DAVID bioinformatics resources 2007. By this approach, we identify that genes that participate in two prime cellular processes – the ribosome pathway and the oxidative phosphorylation pathway - are persistently activated over a period of 24 hours following UVB irradiation. Microarray results were further verified by both mitochondrial activity assay and real-time PCR analysis. These data suggest that the persistent activation of ribosome and oxidative phosphorylation pathways may have a key role in UVB-induced cellular responses. For the first time, the specific cellular pathways that respond to UVB irradiation consistently and persistently can be delineated confidently using a loop-designed microarray approach and functional bioinformatics analysis. The results of this study offer further insight into UVB-induced stress responses.
Keywords: UVB, cDNA microarray, loop design, KEGG pathway

overall_design: We used a loop design in this study, cDNA microarray experiment consisted of eight RNA samples, including UVB-treated samples and their corresponding controls of 4 time points after UVB irradiation.

first: Kun-Yu

first: Tsai-Jiuan

last: Weng

first: Wun-Yi

last: Shu

first: Chi-Shiun

last: Chiang

first: Min-Lung

last: Tsai

first: Yu-Ling

last: Hsieh

first: Cheng-Wei

first: Ian

last: Hsu

first: Chin-Lung

last: Huang

first: Hua-Kuo

last: Lin


title: Genetic factors that respond to N in maize leaf tissue

summary:
Genotype and nitrogen-dosage effect on maize leaves collected at V8 leaf stage
B73 is a model maize genotype while Illinois high protein line (IHP) is a metabolic extreme selected for higher grain protein concentration. It is a well known fact that the leaves serve as source and earshoot as a sink.
Microarray analysis of V8 leaf collected from B73 and IHP genotypes grown at vairable nitrogen applications.

Keywords: Genotype and N-treatment response

first: Jeff

last: Church


title: Salmonella infected Dictyostelium discoideum

first: Ludwig

last: Eichinger

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

overall_design: Refer to individual Series


title: Transcriptome analysis of 16 DAP seeds of Illinois protein lines.

first: Stephen

summary:
Illinois protein lines (IPL) comprise lines known as Illinois high protein (IHP), Illinois low protein (ILP), Illinois reverse-low protein (IRLP) and Illinois reverse-high protein (IRHP) lines.
These lines represent over a century old experiment containing lines that represent various levels of nitrogen metabolism potential as a function of their grain protein concentration.
Microarray experiment was conducted using 16 DAP seeds from the above mentioned four IPLs.

Keywords: Genotype response


title: Emory_Pediatric_Strains_1

status: Public on Nov 05 2009

summary:
Array CGH analysis of Helicobacter pylori strains isolated from a North American cohort of symptomatic pediatric patients.

Keywords: genotyping_design

overall_design:
A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's.

Patients enrolled under Benjamin Gold's Emory IRB protocol. Initial strain isolation from antral biopsies performed at Emory and culture sweeps sent to FHCRC (Seattle) for analysis. Single colony isolates (4) from each patient antral biopsy were isolated and profiled using RAPD. A single clone of each RAPD type detected in each patient (1-2) were analyzed on duplicate arrays. For analysis 500 ng of genomic DNA of each test strain was labeled with Cy5 and 500 ng of genomic DNA of a reference sample (equimolar mix of 26695 and J99) was labeled with Cy3. Strains identified as Em-patient#-clone#.


title: Signature gene expression profiles for cytokinesis mutants in the budding yeast Saccharomyces cerevisiae

status: Public on May 21 2009

city: San Juan

first: José

middle: R

last: Rodríguez-Medina

state: PR

department: Biochemistry

institute: University of Puerto Rico Medical Sciences Campus

summary: During cytokinesis in the budding yeast Saccharomyces cerevisiae, contraction of the cytokinetic ring and primary septum synthesis by chitin synthase II (Chs2p) are coupled processes.  Myosin II (Myo1p), is involved in the actomyosin ring formation, required for proper cytokinesis, while Chs2p is responsible for the chitin primary septum formation which is necessary to stabilize the cytokinetic ring during its contraction. Morphological phenotypes of myo1∆ and chs2∆ mutants are therefore similar particularly in that both are unable to complete normal cytokinesis. A comparison between the global mRNA transcription profiles of myo1∆ and chs2∆ strains was conducted using oligonucleotide microarrays to establish if these cytokinesis mutants exhibited similar mRNA expression patterns and signature profiles were later generated from gene set enrichment analysis (GSEA). Genetic experiments were conducted to further test predictions based on the GSEA results. As reported previously in myo1∆ strains, a significant number of protein biosynthesis and RNA processing genes that may be attributed to regulation by cell integrity pathway(s) were also down-regulated in the chs2∆ strain. Genes coding for proteins involved in autophagy were coordinately upregulated only in the chs2∆ strain yet an ATG9 genetic knockout that completely blocks autophagy was viable in chs2∆ and myo1∆ genetic backgrounds.. However, the chs2∆ strain was significantly more susceptible to lysis by B-1,3-glucanase than myo1∆ and fks1 control strains. We interpret this result to indicate that these two cytokinesis mutant strains possess different cell wall properties. This interpretation was further supported by the observation that Slt2p hyperphosphorylation was detected in the chs2∆ strain yet expression of SLT2 was not required for cell viability. We conclude that in contrast to myo1∆ strains, chs2∆ strains do not activate the cell integrity pathway.

overall_design: All the experiments were performed using Saccharomyces cerevisiae wild type and chs2 strains. Five biological replicates were performed for this experiment.  YFR23 is a chs2::KANMX4 strain generated by homologous recombination in the parental haploid wild type strain, MGD-353-46D using a PCR based method. Cultures were grown overnight at 26ºC to an optical density between 0.5-0.8 (OD600) in complete synthetic media (CSM, 2% glucose, 1X Nitrogen base) or histidine dropout media (CSM-HIS-) with continuous shaking at 200 rpm. Total RNA was extracted from 4 X 10^7 cells derived from triplicate biological replicate cultures of strains MGD343-56D and YFR23 using the RNeasy Mini Kit for isolation of total RNA following manufacturer’s instructions. RNA concentrations were determined by measuring absorbance at 260nm using a Nanodrop spectrophotometer (Nanodrop Technologies). The purity and integrity of the RNA was monitored using an Agilent Bioanalyzer (Agilent Technologies) following manufacturer’s instructions. 1.0 ug of total RNA from each sample was amplified using the Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies). The amplified cRNA was labeled with 10mM Cyanine 5-CTP (Cy5) or Cyanine 3-CTP (Cy3) (Perkin Elmer Life Sciences). Labeled cRNA’s were purified with Qiagen RNeasy mini spin columns and dye incorporation was monitored on an Agilent Bioanalyzer. Hybridization of Cy5 and Cy3 labeled cRNA’s were performed using Yeast Oligo Microarray slides and hybridization kit from Agilent Technologies in 1012AG hybridization chambers (Sheldon Manufacturing) at 60ºC for 17 hours. Slides were washed at high stringency and scanned with a VersArray Chip Reader system (BioRad, Hercules, CA) at a resolution of 5um with detector sensitivity values between 704-800 and laser power at 85%. Scanned images were transferred to the Imagene 3.0 software (Biodiscovery) for further analysis to locate spots, adjust the appropriate grid, and obtain the Cy3 and Cy5 TIFF files. The microarrays raw data generated with Imagene 3.0 were analyzed using Limma software (Bioconductor Package 1.7). The data was prepared for analysis by correcting for background intensity. The individual data sets were normalized using the locally weighted linear regression (Lowess) within each array. After normalization, the difference between the experimental and control signal was calculated, replicates were combined, and their averages were calculated. The fold change in gene expression was calculated by 2^(M), where M is the log2-fold change after background correction and normalization. An Empirical Bayes Statistics for differential expression analysis (eBayes statistics) was performed by Limma. Genes with a p-value ≤ 0.01 were established as a cutoff for differential expression. In addition, a false discovery rate (FDR) test was performed by Limma program.

first: Jose

middle: F

last: Rodriguez-Quinones

last: Rodriguez-Medina


title: Transcriptional responses of Saccharomyces cerevisiae to carbon and nitrogen deprivation

status: Public on Feb 02 2009

city: Princeton

first: Patrick

last: Bradley

state: NJ

address: 119 Lewis Thomas Labs

department: Molecular Biology

institute: Princeton University

summary: Metabolite concentrations can regulate gene expression, which can in turn regulate metabolic activity. The extent to which functionally related transcripts and metabolites show similar patterns of concentration changes, however, remains unestablished.  We have therefore measured and analyzed the metabolomic (previously published in Brauer et al., PMID 17159141) and transcriptional responses (presented here) of Saccharomyces cerevisiae to carbon and nitrogen starvation.

overall_design: The transcriptomes of filter cultures of FY4 (a prototrophic, Mata derivative of S288C presented by Winston et al., PMID 7762301) were sampled during exponential growth in minimal media and at 10, 30, 60, 120, 240, and 480 minutes following a switch to media lacking ammonium (nitrogen starvation) or D-glucose (carbon starvation).  Transcriptional profiles were measured using an Agilent Yeast Oligo Microarray (V2), with the zero timepoint (i.e. exponential growth) as the reference sample.  This yielded 2 time-courses of 6 time-points each.  Further information is available in the accompanying manuscript.

first: Matthew

last: Brauer

first: Joshua

last: Rabinowitz

first: Olga

last: Troyanskaya


title: UV-B Effects on the IBM Recombinant Inbred Population

status: Public on Feb 18 2009

city: Rockville

first: Jia

last: Liu

address: 9712 Medical Center Drive

institute: Plant Genomics

summary:
All plants used in this study were derived from the IBM 94 (Lee, Sharopova et al. 2002) mapping population and names used in the MIAME information correspond to Stapleton laboratory names.  A conversion table identifying the official IBM names is presented below. Maize IBM94 seed was supplied by the Maize Coop and increased at the field nursery in Clayton, NC.  For sowing, twelve seeds were placed in six-pack pots filled with sterilized vermiculite.  Flats filled with 36 pots were placed in the greenhouse at the University of North Carolina Wilmington with solar illumination and daily watering until the majority of the plants were at the three-leaf stage (8 days).  These growth conditions are similar to those used for previous inbred comparisons (Blum, Casati et al. 2004).  Glass does not transmit UV-B, therefore, the plants received none of this radiation unless treated as part of the experimental design. For treatment, one set of flats with a six-pot of each line was moved onto irradiation benches with UV313 bulbs (Q-Panel Lab Products, Cleveland, OH USA) mounted 30 cm above the bench and covered with cellulose diacetate (US Plastics, Lima OH, USA).  These plants received UV-B at a rate of 0.024 Wm-2, as previously described (Blum et al., 2004) for two hours (11 AM to 1PM) in August 2004.  Control plants were placed under UV313 bulbs that were covered with plastic (MylarD, US Plastics, Lima, OH, USA) to block all UV-B radiation.  Immediately following irradiation plants were removed from irradiation benches, and both control and experimental groups were allowed to recover for 3 h in the greenhouse.  Three hours of recovery allows time for post-transcriptional regulation (such as RNA processing and small RNA cleavage) so that we are measuring the steady-state level of mRNA for each gene.  Plants were irradiated centered on solar noon to maximize the amount of sunlight reaching the plants.  Following recovery, the second and third seedling leaves of each of the control and experimental plants were harvested and immediately frozen in liquid nitrogen.  The second and third replicate sets of plants were irradiated and harvested on succeeding days. Plant tissue batches used for RNA preparation were later used to verify genotypes. Genomic DNA was prepared from crushed tissue samples and PCR products from eleven SSR primers were scored by comparison to parental B73 and Mo17 PCR product sizes.  The eleven SSR primers were chosen using and algorithm designed by T. Hudson, Dept. of Computer Science, UNCW; the algorithm allows rapid selection of a minimal combination of markers that will distinguish each IBM94 genotype.   Total RNA was extracted from frozen tissue using Trizol (Invitrogen Co., Carlsbad, CA).  After extraction, RNA was shipped on dry ice to the University of Arizona.  Target labeling via RNA amplification and hybridization were in accordance to standard protocols posted on the Maize Microarray Project website (http://www.maizearray.org/maize_protocols.shtml ).  Briefly, the target labeling protocol utilizes the Ambion Message Amp II kit to produce cRNA which is indirectly labeled using a dye coupling reaction.  All arrays are prehybridized in 1% BSA, 5X SSC, 0.1% SDS.  The resulting labeled cRNA (3 ug/slide) is hybridized to the arrays using a 50% formamide, 5X SSC, 0.1% SDS hybridization buffer at 42 C overnight and the arrays are washed using a series of high stringency washes.    Official IBM ID Stapleton Laboratory ID Mo005 M2 Mo014 M7 Mo016 M9 Mo017 M10 Mo021 M11 Mo033 M22 Mo034 M23 Mo045 M29 Mo057 M36 Mo060 M38 Mo067 M43 Mo077 M47 Mo265 M51 Mo267 M53 Mo317 M69 Mo325 M73 Mo341 M77 Mo344 M78 Mo352 M81 Mo355 M83 Mo364 M86 Mo365 M87 Mo368 M88 Mo369 M89 Mo383 M55(akaM93)
Keywords: Reference design

overall_design: 108 hybs total

first: Ann

last: Stapleton


title: Genome-wide analysis of gene expression profiles during the kernel development of maize (Zea mays L.)

status: Public on Apr 09 2008

first: Guoying

last: Wang

address: Zhongguancun Nandajie 12

department: Institute of Crop Sciences

institute: Chinese Academy of Agricultural Sciences

summary:
Maize kernel is an important source of food, feed and industrial raw materials. The illustration of the molecular mechanisms of maize kernel development will be helpful for the manipulation of maize improvements. Although a great many researches based on molecular biology and gecetics have greatly increased our understanding on the kernel development, many of the mechanisms controlling this important process remain elusive. In current study, a microarray with approximately 58,000 probes was used to study the dynamic gene expression during kernel development from the fertilization to physiological maturity. Samples from two consecutive time-points were paired and labeled using different fluorescent dyes (Cy3 and Cy5) and hybridized in the same array. Hybridization of slides was performed according to the manufacturer’s instructions (http://www.maizearray.org/). The hybridized slides were scanned by a Genepix 4000B (Axon, USA). A loop design was applied for running the microarray. Two replicates of each pair of samples were carried out to test both the reproducibility and quality of the chip hybridizations. By comparing six consecutive time-points, namely 1, 5, 10, 15, 25 and 35 days after pollination (DAP), 3,445 differentially expressed genes were identified. These genes were then grouped into 10 clusters showing specific expression patterns using a K-means clustering algorithm. An investigation of function and expression patterns of genes expanded our understanding of the regulation mechanism underlying the important developmental processes, cell division and kernel filling. The differential expression of genes involved in plant hormone signaling pathways suggested that phytohormone might play a critical role in the kernel developmental process. Moreover, regulation of some transcription factors and protein kinases might be involved in the whole developmental process.
Keywords: Time course, development

overall_design: To obtain the global gene expression profile during maize kernel development, a microarray with approximately 58,000 probes was used. The maize inbred line X178 was planted on the field. Each plant was self-pollinated by hand. The ears were harvested from healthy plants at 1, 5, 10, 15, 25 and 35 days after pollination (DAP), respectively. In order to increase the consistency & uniformity of the isolated kernels, the upper half and about one sixth of ears from the bottom were cut and discarded, the kernels were isolated from the rest part of the ears. Samples at each time-point were collected from at least thirty ears and pooled to represent the line characteristics of X178. Two sub-samples for replication in the microarray analysis were randomly drawn. Samples from two consecutive time-points were paired and labeled using different fluorescent dyes (Cy3 and Cy5) and hybridized in the same array. A loop design was applied for running the microarray. Two replicates of each pair of samples were carried out to test both the reproducibility and quality of the chip hybridizations.


title: Adaptation to hydrogen peroxide

status: Public on Apr 23 2009

first: Ryan

last: Kelley

address: 9500 Gilman Drive

department: Bioinformatics

summary: Adaptation to hydrogen peroxide in Saccharomyces cerevisiae is profiled with expression arrays. Adaptation describes the process in which a mild dose of toxin (in this case, hydrogen peroxide) is able to protect against a later acute dose. Here, we study two adaptive protocols (0.1 mM H2O2 and 0.1 + 0.4 mM H2O2) and one acute protocol (0.4 mM H2O2) to identify processes uniquely involved in adaptation. Predictions from these studies are validated in expression profiling of deletion mutants of the transcription factors Yap1, Mga2, and Rox1.

overall_design:
Three different treatment protocols were studied.
  Pretreatment - 0.1 mM H2O2 for 45 minutes.
  Adapted - 0.1 mM H2O2 for 45 minutes, followed by 0.4 mM H2O2 for 1 hour.
  Acute - 0.4 mM H2O2 for 1 hour.
Each treatment protocol was examined with 4x biological replicates, with the dye orientation reversed in two of the replicates (no technical replicates). The effect of the pretreatment protocol (0.1 mM H2O2) was also studied in three transcription factor deletion mutants (Yap1, Mga2, and Rox1) with the same number/orientation of biological replicates.

first: Trey

last: Ideker


title: Differential gene expression analysis of maize leaf at heading stage in response to water-deficit stress

status: Public on Feb 25 2008

city: jinan

first: juren

last: zhang

address: shanda nanlv 27

institute: shandong university

summary:
Periods of soil water deficit could occur at any time during the crop season, but maize is particularly sensitive to water stress around flowering time. At this time the stress usually causes remarkable yield loss. Heading time, which is just before tassel flowering, is one of the most important stages that maize productivity would be affected severely if plants encounter water stress. The whole-genomic gene expression changes of maize plants in response to water deficit stress at this stage have not been studied. The present work utilized an Arizona Maize Oligonucleotide Array Version 1.9，which was consisted of A and B slides carrying with a total of 57,452 maize 70-mer oligonucleotides, was used to monitor gene expression profile changes in maize leaves subjected to 1 day and 7 days water-deficit stress respectively at the heading stage.
Keywords: stress response

overall_design: Maize (Zea mays L.) inbred line DH4866 was used in this study. Plants grew in flowerpots containing field soil under natural conditions. When the tassel spread out of the uppermost leaf, some plants were treated with drought stress for 7 days, and others were left under normal-watered conditions as control. In the period of the stress, the middle part of the top fully expanded leaves of the plants under water stress treatment and the control were taken to measure the leaf osmotic potential at different times by the Fiske® Micro-Osmometer (FISKE® ASSOCIATES, USA). And the stressed plants were watered every day to maintain a similar water-deficiency state by adjusting water supply, according to the osmotic potential of the fully expended leaf of the plants measured at 8:00 am each day. During the stress, the leaf osmotic potential of the stressed plants was hold to -0.4 to -0.5 Mpa, while the osmotic potential was -0.2 to -0.25 Mpa in the leaves of the control plants. And there were visible signs of water deficiency such as leaf rolling during the daytime, though at night the rolled leaves spread out. Maize plants were stress-treated at the beginning of heading stage. After 7 days of water deficiency by withholding water, the plants began to enter the flowering stage. The maize flag leaves were harvested after 24h (1d) and 168h （7d） of stress treatment, frozen in liquid nitrogen immediately and stored at -80℃ for further analysis. Unstressed plants as controls were harvested at the same time as the stressed plants. One sample consisted of the leaves from three independent plants under the same condition. Total RNA was isolated as McCarty (1986) described from the frozen samples. For each sample, 100ug of total RNA was transcribed into cDNA and fluorescently labeled with Cy3 and Cy5 dyes using the SuperScript indirect cDNA labeling system (INVITROGEN, USA) according to the manufacturer’s instructions. The Cy3 and Cy5 labels were swapped between sample and control cDNA to minimize any possible impact of inequalities in DNA incorporation and photobleaching of the fluorescent dyes. Hybridizations were performed according to the protocols at the website of the Maize Oligonucleotide Array Project. Two technical replicates (dye-swap experiments) for each biological sample from two independent treatments were performed.

first: Guidong

last: Yue

first: Yunlong

last: Zhuang

first: Zhaoxia

last: Li

first: Li

last: Sun

first: Juren

last: Zhang


title: Integrating Large-Scale Functional Genomic Data to Dissect the Complexity of Yeast Regulatory Networks

status: Public on Jun 15 2008

first: Erin

middle: N

last: Smith

address: 110 Carl Icahn Labs

department: Ecology and Evolutionary Biology

summary:
A major goal of biology is the construction of networks that predict complex system behavior.  We combine multiple types of molecular data, including genotypic, expression, transcription factor binding site (TFBS), and protein-protein interaction (PPI) data previously generated from a number of yeast experiments in order to reconstruct causal gene networks.  Networks based on different types of data are compared using metrics devised to assess the predictive power of a network.  A network reconstructed by integrating genotypic, TFBS and PPI data is shown to be the most predictive. This network is used to predict causal regulators responsible for hot spots of gene expression activity in a segregating yeast population.  The network is also shown to elucidate the mechanisms by which causal regulators give rise to larger-scale changes in gene expression activity.  Predictions are prospectively validated to provide direct experimental evidence that predictive networks can be constructed by integrating multiple, appropriate data types.
Keywords: allele replacement

overall_design: Allele replacement strains were created in two backgrounds: BY (BY4724 and BY4742), and RM11-1a, and compared to the parental type (BY4716 and RM11-1a). BY7g, BY9g, BY11g are BY4716, while RM7g, RM9g, and RM11g are RM11-1a. YAD350 is a MKT1 D30G replacement strain in BY4742 background. YLK804 is a SAL1-RM allele in BY4724 and YLK806 is a SAL1-BY allele in RM11-1a. All strains were grown in YNB + 2% glucose, with leucine, lysine, and uracil. YAD350 was also grown with histidine.

first: Jun

last: Zhu

first: Bin

first: Becky

last: Drees

first: Rachel

last: Brem

first: Leonid

last: Kruglyak

first: Roger

last: Bumgarner

first: Eric

last: Schadt


title: De-regulation of maize C4 photosynthetic development in a mesophyll cell defective mutant: Bundle sheath and Mesophyll

status: Public on Feb 01 2008

city: Ithaca

first: Thomas

middle: P.

last: Brutnell

state: NY

address: Cornell University

institute: Boyce Thompson Institute for Plant Research

summary:
During Zea mays (maize) C4 differentiation, mesophyll (M) and bundle sheath (BS) cells accumulate distinct sets of photosynthetic enzymes, with very low photosystem II (PSII) content in BS chloroplasts. Consequently, there is little linear electron transport in the BS and ATP is generated by cyclic electron flow. In contrast, M thylakoids are very similar to those of C3 plants and produce the ATP and NADPH that drive metabolic activities. Regulation of this differentiation process is poorly understood but involves expression and coordination of nuclear and plastid genomes. Here, we identify a recessive allele of the maize Hcf136 homologue that in Arabidopsis thaliana functions as a PSII stability or assembly factor located in the thylakoid lumen. Proteome analysis of the thylakoids and electron microscopy reveal that Zm hcf136 lacks PSII complexes and grana thylakoids in M chloroplasts, consistent with the previously defined Arabidopsis function. Interestingly, hcf136 is also defective in processing the full-length psbB-psbT-psbH-petB-petD polycistron specifically in M chloroplasts. To determine whether the loss of PSII in M cells affects C4 differentiation, we performed cell-type specific transcript analysis of hcf136 and wild-type seedlings. The results indicate that M and BS cells respond uniquely to the loss of PSII, with little overlap in gene expression changes between data sets. These results are discussed in the context of signals that may drive differential gene expression in C4 photosynthesis.
Keywords: cell type comparison

overall_design:
To explore the disruption of PSII activity on gene expression, transcript profiles from separated M and BS cells were examined using two-label microarray analysis. Total RNA was isolated from the second leaves of mutant and wild-type silbings. Six biological replicates were used to compare wild-type and mutant transcript profiles in separate M and BS experiments. To maximize biological replication, different seedling pools were used for each of the 12 hybridizations. Microarray experiments and analyses were performed using the Genisphere MPX900 kit and the Maize Array Consortium oligonucleotide platform (GPL5439; GPL5440). Feature intensity values were log-transformed and corrected for local background signal, and a LOWESS procedure (Dudoit et al., 2002) was used to normalize between channels. Features with either low or saturating signal intensity were discarded from further analysis. High expression filtering was less stringent to avoid elimination of previously characterized, high abundance, C4 cell-specific transcripts. After filtering, features that were not assigned an MZ number by the Maize Array Consortium were discarded from further analysis. The moderated t-test (Smyth, 2004) using the R package limma was applied to identify differentially expressed genes. The p-values for each test (gene) were converted to q-values for false discovery rate analysis as described by Storey et al. (2004).

To avoid confounding treatment effects associated with direct comparisons of M and BS transcriptomes (Sawers et al., 2007),  comparisons were only made using the same cell type across the hcf136 and wild-type sibling genotypes.
Bundle sheath (BS) Samples: GSM245063-GSM245164
Mesophyll (M) Samples: GSM245165 - GSM245206

first: Sarah

last: Covshoff

first: Wojciech

last: Majeran

first: Peng

last: Liu

first: Judith

last: Kolkman

first: Klaas

last: van Wijk


title: Gene expression profiling and array CGH in Ewing's sarcoma

status: Public on Nov 15 2007

city: MAJADAHONDA

first: Javier

last: Alonso

state: MADRID

address: CTRA. MAJADAHONDA-POZUELO KM 2

department: AREA DE GENÉTICA HUMANA

country: Spain

institute: INSTITUTO DE SALUD CARLOS III - IIER

summary:
According to array-CGH data tumors were segregated in two different groups: one genomic stable and other genomic unstable. The genomic unstable group showed a statistically significant shorter overall survival ans was more refractory to chemotherapy.
Gene expression profile revealed that genes related with chromosome segregation, DNA repair pathways and cell cycle control were upregulated in the genomic unstable group
Keywords: Tumor comparison

overall_design: We have carried out a high-resolution genomic DNA analysis and expression profiling on 25 Ewing sarcoma tumors in an attempt to characterize the genomic aberrations occurring in these tumors and determine their association with gene expression profiles and clinical outcome

first: J

last: Carrillo


title: Regulation by the homologous Ace2 and Swi5 factors of Saccharomyces cerevisiae

status: Public on May 13 2008

city: SALT LAKE CITY

first: David

last: Stillman

state: UT

address: 15 N. Medical Drive East, Room 2100

department: Pathology

institute: University of Utah

summary:
The homologous Ace2 and Swi5 transcription factors of Saccharomyces cerevisiae have identical DNA-binding domains, and both are cell cycle regulated. There are common target genes, as well as genes activated only by Ace2 and other genes activated only by Swi5.
Keywords: genetic modification

overall_design: RNA was isolated from four strains: wild type, ace2 gene deletion, swi5 gene deletion, and the ace2 swi5 double gene deletion. RNAs from the three mutant strains were compared to wild type RNA in a microarray hybridization experiment.

first: Warren

last: Voth

first: Yaxin

last: Yu

first: Shinya

last: Takahata

first: Kelsi

middle: L

last: Kretschmann

first: Jason

last: Lieb

first: Rebecca

last: Parker

first: Brett

last: Milash

middle: J


title: Transcriptomic analysis of maize developing earshoot from tropical maize hybrid genotypes native to Nigeria

city: Urbana

first: Stephen

last: Moose

summary:
Tropical maize genotypes are well known for their traits of late flowering and higher biomass. Carbon/Nitrogen balance in these genotypes is significantly different from temperate genotypes. Microarray analysis of gene expression
changes occuring in developing earshoots was done and results were compared with the temperate genotype microarray analysis, previously conducted. A low yielding variety was used as a reference against three high yielding varities.

Keywords: Genotype response

first: Abe

last: Ayodeji


title: CodeLink Expression Data from primary prostate tumor and prostate tumor metastases

status: Public on Feb 20 2007

city: Houston

first: Federico

middle: Alberto

last: Monzon

state: TX

address: 6565 Fannin St, MS205

institute: The Methodist Hospital

summary:
Prostate cancer is characterized by heterogeneity in the clinical course that often does not to correlate with morphologic features of the tumor. Metastasis reflects the most adverse outcome of prostate cancer, and to date there are no reliable morphologic features or serum biomarkers that can reliably predict which patients are at higher risk of developing metastatic disease. Understanding the differences in the biology of metastatic and organ confined primary tumors is essential for developing new prognostic markers and therapeutic targets. Using Affymetrix oligonucleotide arrays, we analyzed gene expression profiles of 24 androgen-ablation resistant metastatic samples obtained from 4 patients and a previously published dataset of 64 primary prostate tumor samples. Differential gene expression was analyzed after removing potentially uninformative stromal genes, addressing the differences in cellular content between primary and metastatic tumors. The metastatic samples are highly heterogeneous in expression; however, differential expression analysis shows that 415 genes are upregulated and 364 genes are downregulated at least 2 fold in every patient with metastasis. The expression profile of metastatic samples reveals changes in expression of a unique set of genes representing both the androgen ablation related pathways and other metastasis related gene networks such as cell adhesion, bone remodeling and cell cycle. The differentially expressed genes include metabolic enzymes, transcription factors such as Forkhead Box M1 (FoxM1) and cell adhesion molecules such as Osteopontin (SPP1). We hypothesize that these genes have a role in the biology of metastatic disease and that they represent potential therapeutic targets for prostate cancer.
Keywords: disease state analysis

first: Uma

last: Chandran

first: Changqing

last: Ma

first: Rajiv

last: Dhir

first: Michelle

last: Bisceglia

first: Maureen

last: Lyons-Weiler

first: Wenjing

last: Liang

first: George

last: Michalopoulos

first: Michael

last: Becich

middle: A


title: Effects of aneuploidy on cellular physiology and cell division in haploid yeast.

status: Public on May 17 2007

first: Maitreya

middle: J.

last: Dunham

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

summary:
Aneuploidy is a condition frequently found in tumor cells but how it affects cellular physiology is not known. We have characterized one aspect of aneuploidy, the gain of extra chromosomes. We created a collection of haploid yeast strains that each bear an extra copy of one or more of almost all of the yeast chromosomes.  Their characterization revealed that aneuploid strains share a number of phenotypes, including defects in cell cycle progression, increased glucose uptake and increased sensitivity to conditions interfering with protein synthesis and protein folding. These phenotypes were observed only in strains carrying additional yeast genes indicating that they reflect the consequences of additional transcription and translation as well as the resulting imbalances in cellular protein composition. We conclude that aneuploidy causes not only a proliferative disadvantage but also a set of phenotypes that is independent of the identity of the individual extra chromosomes.
Keywords: CGH, gene expression

overall_design: This series of microarrays compares yeast strains carrying extra chromosomes to wt yeast with normal chromosome content.  Both DNA/CGH and gene expression comparisons were done, as noted.  In some experiments, biological replicates were performed as noted.  Reference wt nucleic acid was most commonly labeled with Cy3.  Experiments labeled as "swap" have the wt reference nucleic acid labeled with Cy5, and ratio values for these experiments are reported as Cy3/Cy5.

first: Eduardo

middle: M

last: Torres

first: Tanya

last: Sokolsky

first: Cheryl

last: Tucker

first: Leon

last: Chan

first: Monica

last: Boselli

first: Angelika

last: Amon


title: Global Mapping of Transposon Location

status: Public on Nov 15 2006

summary:
Transposable genetic elements are ubiquitous, yet their presence or  absence at any given position within a genome can vary between  individual cells, tissues, or strains. Transposable elements have  profound impacts on host genomes by altering gene expression,  assisting in genomic rearrangements, causing insertional mutations,  and serving as sources of phenotypic variation. Characterizing a  genome?s full complement of transposons requires whole genome  sequencing, precluding simple studies of the impact of transposition  on interindividual variation. Here, we describe a global mapping  approach for identifying transposon locations in any genome, using a  combination of transposon-specific DNA extraction and microarray- based comparative hybridization analysis. We use this approach to map  the repertoire of endogenous transposons in different laboratory  strains of Saccharomyces cerevisiae and demonstrate that transposons  are a source of extensive genomic variation. We also apply this  method to mapping bacterial transposon insertion sites in a yeast  genomic library. This unique whole genome view of transposon location  will facilitate our exploration of transposon dynamics, as well as  defining bases for individual differences and adaptive potential.
Keywords: transposon mapping

overall_design: Experiments are comparisons between extracted DNA, either two DNAs extracted with the same probes, or the same DNA extracted with different probes.

first: Abram

last: Gabriel

first: Johannes

last: Dapprich

first: Mark

last: Kunkel

first: David

last: Gresham

first: Stephen

middle: C

last: Pratt


title: Global Patterns of Gene Expression Associated with Vulnerability and Resilience to Social Defeat

status: Public on Sep 01 2007

city: Dallas

first: guanghua

last: xiao

address: 5323 Harry Hines Blvd

department: Psychiatry

institute: University of Texas Southwestern Medical Center

summary:
While stressful life events are an important cause of psychopathology such as Post-Traumatic Stress Disorder (PTSD) and Major Depressive Disorder (MDD), most individuals exposed to chronic stress remain psychologically unperturbed. The molecular mechanisms such variations in stress resilience remain to be explored. Utilizing a mouse social defeat paradigm as a model for chronic social stress exposure, we segregated socially defeated c57bl/6J mice into Susceptible and Unsusceptible groups based on scores of social avoidance, and these groups differ along multiple behavioral and physiological domains. To explore neuroplastic changes within the mesolimbic dopamine circuit that may explain variations in susceptibility, we examined global patterns of gene expression within the VTA (ventral tegmental area) and the NAc (nucleus accumbens). Tissue punches of NAc and VTA were obtained from either non-defeated control, Susceptible and Unsusceptible mice approximately 48 hours after the cessation of social defeat stress. Data from Illumina sentrix gene expression microarrays revealed three main findings: (1) the total number of genes significantly up or downregulated was considerably higher within the NAc, (2) the Unsusceptible phenotype was associated with the regulation of a much higher number of genes, and (3) as compared to the NAc, the VTA displayed far fewer genes that were identically regulated in both Susceptible and Unsusceptible groups. Taken together, these data strongly suggest that the VTA is an important substrate for transcriptional changes that can be correlated with variations in Susceptibility. In addition, they suggest that changes in anxiety (found in both Susceptible and Unsusceptible groups) versus changes in reward behavior (found only in Susceptilbe mice) can be explained by gene expression changes within the mesolimbic dopamine circuit.
Keywords: neural stress response

overall_design:
This microarray experiment involved 18 arrays that were run simultaneously. The experimental design can be captured in factorial format.

3 behavioral groups: Control (C), Susceptible (S) and Unsusceptible (U)
2 anatomical structures: VTA and NAc
3 biological replicates for each condition

Each biological replicate consisted of tissue pooled from four animals. Biological replicates within each condition (e.g., Unsusceptible NAc) displayed comparable avoidance scores. Data analysis and conclusions were derived from pairwise comparisons of C Vs. S and C Vs. U.

first: William

last: Renthal

first: Danielle

last: Graham

first: Quincey

last: LaPlant

first: Eric

last: Nestler


title: Transcriptome response to gcr1 deletion in raffinose, galactose, and glucose

status: Public on Nov 27 2006

city: Hattiesburg

first: Kellie

last: Barbara

state: MS

address: 118 College Dr. #5018

department: Biological Sciences

institute: Univ. of Southern MS

summary:
This experiment compares transcriptomic response of yeast cells to the deletion of Gcr1 to isogenic wild type strains, grown in YEP(3%)R at 23C.  The goal was to identify misregulated target genes and analyze the functional classifications of those targets.
Keywords: cell type comparison

overall_design: This experiment included biological replicates as well as technical dye-swap replicates of each biological sample.


title: Washington Human Monocyte Macrophage Profiles

status: Public on Jan 10 2007

middle: K

last: Pritchard

address: 815 Mercer Street Rm.  418

summary:
In order to study the gene expression profiles of monocyte and macrophages, we collected three type of cells and performed pair-wised comparison. It includes human peripheral blood monocyte (MONO), human peripheral blood monocyte derived macrophages treated with M-CSF (MACRO)and primary alveolar macrophages (BAL). All the experiments are performed comparing two of the three cell types from the same person (total 4 persons). Totally we got three set of microarray data, MONO/MACRO, MONO/BAL and MACRO/BAL with 4 biological replicates.
Keywords: cell_type_comparison_design

overall_design: See summary

first: Jiangning

last: Li


title: Role of Histone Ubiquitylation and Deubiquitylation as Determined by the Analysis of an HTB1_K123R S. cerevisiae Strain

status: Public on Jan 19 2007

city: London

first: Christopher

last: Brandl

state: Ontario

address: 1151 Richmond St.

institute: University of Western Ontario

summary:
In Saccharomyces cerevisiae histone H2B is ubiquitylated at lysine 123. The SAGA complex component, Ubp8, is one of two proteases that remove this ubiquitin moiety. We analyzed gene expression in a strain containing a variant of histone H2B with lysine 123 converted to arginine to address the mechanisms by which ubiquitylation and deubiquitylation of histone H2B affects gene expression. We show that changes in gene expression observed upon deletion of ubp8 are suppressed by htb1K123R. This provides genetic evidence that Ubp8 alters gene expression through deubiquitylation of histone H2B. Second, microarray analyses of the htb1K123R strain show that loss of histone ubiquitylation results in a two-fold or greater change in expression of ~1.5% of the protein coding genes with greater than two-thirds increasing. For genes in which ubiquitylation represses expression, ubiquitylation principally acts through its effects on histone methylation. In contrast, decreased expression of the CWP1 gene was not paralleled by deletions of the methyltransferase components Swd3, Set2 or Dot1 and is thus likely independent of methylation. Finally, by comparing gene expression changes in the htb1K123R strain with those in a strain deleted for rad6, we conclude that lysine 123 affects transcription primarily because of its being a site of ubiquitylation.
Keywords: yeast, histone ubiquitylation, Ubp8, gene expression, genetic modification, histone H2B

overall_design: Two dye-swapped, biological replicate experiments were performed for yeast strains CY1272(Htb1_K123R;htb2_delta0), BY10809(ubp8_delta0) and CY1383(Htb1_K123R;htb2_delta0;ubp8_delta0) with reference to BY4742(wt).  Three biological replicates, including one dye-swap experiment, were performed comparing CY1272(Htb1_K123R;htb2_delta0) to BY13026(htb2_delta0).

first: Ana

middle: I

last: Mutiu

last: Hoke

first: Julie

last: Genereaux

first: Gaoyang

last: Liang


title: Human decidual NK cells

status: Public on Jun 28 2006

city: Jerusalem

first: Ofer

last: Mandelboim

department: The Lautenberg Center for General and Tumor Immunology

institute: The Hebrew University of Jerusalem

summary:
Microarray analysis was performed on highly purified human CD56brightCD16- decidual NK  cells pooled from healthy 1st trimester elective terminations. Experiment was performed to find out about genes expressed in this subset.
Keywords: Genes transcribed in cells studied

overall_design: Total cellular RNA from dNK subset was pooled and subjected to clean up protocol with RNeasy mini kits (Qiagen), according to the manufacturer’s specifications.  First and second strand cDNA was prepared from RNA template, and the cDNA was subjected to in vitro transcription in the presence of biotinylated nucleoside triphosphates. The biotinylated cRNA was fragmented to uniform sizes (~100nt). CodeLinkTM Uniset Human 20K I Bioarrays (Amersham Biosceinces) were hybridized with each prepared cRNA target in duplicates and stained with Cy5-streptavidin and subsequently washed according to manufacturer’s instructions, and then scanned on an Axon GenePix 4000B scanner.


title: Genomic and genetic characterization of rice Cen3 reveals evolutionary remnants of a complex centromere (small RNA data)

status: Public on May 26 2006

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary:
The centromere is the chromosomal site for assembly of the kinetochore where spindle fibers attach during cell division.  In most muticellular eukaryotes, centromeres are composed of long tracks of satellite repeats that are recalcitrant to sequencing and fine scale genetic mapping.  Here we report the genomic and genetic characterization of the complete centromere of rice chromosome 3.  Using a DNA fiber-fluorescence in situ hybridization approach, we demonstrated that the centromere of chromosome 3 (Cen3) contains ~414 kb of the centromeric satellite repeat CentO.  Cen3 includes a ~1,851-kb domain associated with CENH3, the centromere-specific histone H3 variant.  This CENH3-associated chromatin domain is embedded within a 3,083-kb region that lacks genetic recombination.  We detected several active genes within the CENH3-binding domain based on a comprehensive annotation and a survey for matches with mRNA signatures.  However, the gene density in the CENH3-binding domain is significantly lower than in the pericentromeric domains.  In contrast, the CENH3-binding domain contains a higher percentage of repetitive DNA sequences than the pericentromeric regions.  These results suggest that Cen3 is in the process of evolving from a genic region toward an accumulation of satellite repeats and transposable elements that is more characteristic of centromeres in most complex eukaryotic species.
Keywords: MPSS, small RNA, rice, centromere, Cen3, chromosome 3

overall_design: MPSS was performed to sequence small RNAs that derived from inflorescence and seedling.  The method for the MPSS sequencing of small RNAs are described in the paper associated with this dataset (Lu et al., 2005).


title: Expression data of testis biopsies obtained from men with spermatogenic impairment

status: Public on Oct 13 2006

city: 20246 Hamburg

first: Andrej-Nikolai

last: Spiess

address: Martinistr. 52

department: Andrology

institute: University Hospital Hamburg-Eppendorf

summary:
Testicular biopsies were extracted surgically from men presenting with different states of spermatogenic impairments. The biopsies were scored histologically according to the Johnsen score system and microarrray technology was applied in order to correlate the gene expression pattern with the morphological categorization.
Keywords: disease state analysis

overall_design: Testicular biopsies were extracted surgically and fixed in RNAlater. Total RNA was extracted by GITC-method and post-purified using RNeasy columns. Arrays were hybridized overnight with 10 ug of Biotin-11-UTP-labeled cRNA, stringency washed and stained with Cy5-Streptavidin.

first: Caroline

last: Feig

first: Wolfgang

last: Schulze

first: Christiane

last: Kirchhoff

first: Heike

last: Capallo-Obermann


title: Anaerobic NO-exposed Chemostat Comparison of Wt & norR mutant Responses

status: Public on Sep 01 2006

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

country: United Kingdom

institute: University of Sheffield

summary:
Escherichia coli strains MG1655 and an isogenic norR::Tn5 mutant were grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture
(chemostat) conditions. Cells were grown in defined media containing 54 mM glycerol as the sole and limiting source of energy and carbon. The working volume
was 1 litre, and the dilution rate 0.1 h-1. In order to establish anaerobic growth, nitrogen was sparged through the chemostat medium prior to inoculation
and throughout the course of the experiment at a rate of 0.2 l/min. No dissolved oxygen was detectable using the OxyProbe. Sodium fumarate was added at a
final concentration of 50 mM to act as a terminal electron acceptor. Cells were grown as above to steady-state, At steady-state, NOC-5 and NOC-7 were added to the chemostat culture and to the nutrient feed at a final concentration of 10 uM of each. Samples were taken after a period of 5 min exposure to NOC for subsequent analysis using microarrays. Cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.
Equal quantities of RNA from Wild type and norR::Tn5 cultures were labelled using nucleotide analogues of dCTP containing either Cy3 or Cy5 fluorescent dyes. The average signal intensity and local background correction were obtained using a commercially available software package from Biodiscovery, Inc (Imagene, version 4.0 and GeneSight, version 3.5). The mean values from each channel were log2 transformed and normalised using the Lowess method to remove intensity-dependent effects in the log2(ratios) values. The Cy3/Cy5 fluorescent ratios were calculated from the normalized values
Keywords: Mutant Comparison, stress response, nitric oxide, NorR, chemostat, continuous culture

overall_design:
Each strain was grown twice in seperate chemostat runs, exposed to NO.
Samples were hybridised as WT vs NorR::Tn5 and each hybridisation had a corresponding dye-swap performed.

first: Steven

middle: T

last: Pullan

first: Jeffrey

last: Green