title: Human respiratory and stool specimens used to detect cardioviruses

status: Public on Sep 17 2008

city: San Francisco

first: Joe

last: DeRisi

department: Biochemistry and Biophysics

institute: University of California, San Francisco

summary:
Cardioviruses are a genus of picornaviruses that cause severe illnesses in rodents, but little is known about the prevalence, diversity, or spectrum of disease of such agents among humans.  We report the identification of a group of human cardioviruses that have been detected and cloned directly from patient specimens (Chiu and DeRisi, et al, PNAS, 2008).  This series includes 9 arrays (both raw and normalized data) used to detect cardioviruses in human respiratory and stool specimens.  The arrays employed here are capable of pan-viral detection (Wang and DeRisi, et al., PNAS, 2002).

Keywords: viral detection, cardiovirus, TMEV, gastroenteritis

overall_design:
The series includes 3 arrays from respiratory samples and 6 arrays from stool samples.  Among the 3 arrays from respiratory sample, 1 array has a signature for an adenovirus, 1 array has a signature for human metapneumovirus, and 1 array has a signature for cardiovirus UC1 (see Chiu and DeRisi, et al., PNAS, in 2008).  All 6 arrays from stool samples are cardiovirus-positive; some show evidence of dual infection with other gastroenteritis viruses (i.e. norovirus, rotavirus, etc.).

Data in Sample records fed to E-Predict (Urisman, et al, Genome Biology, 2005)

E-Predict normalization metrics
Array Normalization: Sum
E-Matrix Normalization: Quadratic
Distance Metric: Pearson Uncentered

first: Charles

middle: Y

last: Chiu

first: Alexander

last: Greninger

first: Don

last: Ganem

first: Joseph


title: Genome-wide inter-primate comparison of gene expression profiles in multiple tissues

city: Chicago

first: Ran

last: Blekhman

state: IL

country: USA

institute: University of Chicago

type: Expression profiling by genome tiling array

summary: Regulatory changes have long been hypothesized to play an important role in primate evolution. To identify adaptive regulatory changes in humans, we performed a genome-wide survey for genes whose regulation evolves under natural selection. To do so, we used a novel multi-species microarray to measure gene expression levels in livers, kidneys, and hearts from six humans, chimpanzees, and rhesus macaques.

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens

overall_design: Using the multi-species microarray, we compared gene expression levels within and between species in three tissues: Livers, Kidneys (cortex) and Heart muscle. For each tissue, we hybridized RNA samples from 6 individuals from each of the three species, and preformed two technical replicates for each sample. The total number of arrays analyzed is therefore 108 (= 3 species X 3 tissues X 6 individuals X 2 technical replicates). Following hybridization, washing, and scanning, raw data was extracted from the images using the NimbleScan software (version 2.4). We performed background correction using the normexp function in limma with an offset of 32, and normalization using an adaptation of the quantile normalization approach.

first: Alicia

last: Oshlack

first: Adrien

middle: E

last: Chabot

first: Gordon

last: Smyth

first: Yoav

last: Gilad


title: Transcriptome profiling of maize anthers using genetic ablation to analyze pre-meiotic and tapetal cell types

status: Public on Sep 16 2008

city: Stanford

first: John

middle: F

last: Fernandes

state: CA

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

summary:
Agilent oligonucleotide arrays were used to profile gene expression in dissected maize anthers of 3 types of male-sterile plants and their fertile siblings at four stages of development: after anther initiation, at the rapid mitotic proliferation stage, pre-meiosis, and meiotic prophase I.  The male-sterile mutants (ms23, msca, and mac1) lack a range of normal cell types resulting from a temporal progression of anther failure.  By combining the data sets from the comparisons between individual sterile and fertile anthers, candidate genes predicted to play important roles during maize anther development were assigned to stages and to likely cell types.

Keywords: anther development, maize, male sterility

overall_design: 3 biological replicates of 3 different male-sterile mutants and their fertile siblings at 4 stages of anther development (36 arrays).  Comparisons were done between male-sterile and fertile sibs at the same development stage.

first: Jiong

last: Ma

first: Virginia

last: Walbot

first: Darren

middle: J

last: Morrow


title: p53-repressed miRNAs are Involved with E2F in a Feed Forward Loop Promoting Proliferation

status: Public on Sep 21 2008

city: Rehovot

first: reut

last: shalgi

address: Weizmann Institute of Science

country: Israel

institute: Weizmann Institute of Science

summary:
miRNA expression profiles of WI38 primary human fibroblasts with an active or inactive p53. Cells were compared under normal untreated conditions (young and proliferating cells), after DNA damage with Doxorubicin, and upon entry into replicative senescence.

Keywords: miRNA, WI-38, p53, GSE56, Senescence, Doxorubicin, Cancer, DNA-damage, fibroblasts.

overall_design:
6 samples of WI38 cells were analyzed on 12 Exiqon miRcurry LNA arrays in biological duplicates (2 different cell culture plates for each experimental condition). The six conditions included:

1. [Con_Young] - Primary Young WI38 cells (passage 20) with a control retroviral vector (pLXSN-NEO). Untreated.

2. [GSE_Young] -Primary Young WI38 cells (passage 20) with a retroviral vector encoding for the p53-inactivating peptide GSE56 (pLXSN-NEO-GSE56).Untreated.

3. [Con_Dox] -Primary Young WI38 cells (passage 20) with a control retroviral vector (pLXSN-NEO). Treated with Doxorubicin (0.2 micrograms/ml) for 24 hours).

4. [GSE_Dox] Primary Young WI38 cells (passage 20) with a retroviral vector encoding for the p53-inactivating peptide GSE56 (pLXSN-NEO-GSE56). Treated with Doxorubicin (0.2 micrograms/ml) for 24 hours).

5. [Con_Old] - Sesescent WI38 cells (passage 30) with a control retroviral vector (pLXSN-NEO). Untreated.

6. [GSE_Old] - Senescent WI38 cells (passage 26) with a retroviral vector encoding for the p53-inactivating peptide GSE56 (pLXSN-NEO-GSE56).Untreated.

RNA was extracted with TRI-Reagent and sent for labeling and hybridization in Exiqon laboratories (In Denamark). Samples were labeled with Cy5. Reference sample (Cy3) was an RNA mix of all samples. Log2 for Ratio(Cy5/Cy3) was used for further analysis.

last: Brosh

first: Reut

last: Shalgi

first: Atar

last: Liran

first: Gilad

last: Landan

first: Katya

last: Korotayev

first: Giang

last: Nguyen

first: Espen

last: Enerly

first: Hilde

last: Johnsen

first: Yosef

last: Buganim

first: Hilla

last: Solomon

first: Ido

last: Goldstein

first: Shalom

last: Madar

first: Naomi

last: Goldfinger

first: Anne-Lise

last: Børresen-Dale

first: Doron

last: Ginsberg

first: Curtis

middle: C

last: Harris

first: Yitzhak

last: Pilpel

first: Moshe

last: Oren

first: Varda

last: Rotter


title: Expression Profiles of Cloned Channel Catfish (Ictalurus punctatus) Lymphoid Cell Lines and a Mixed Lymphocyte Culture

status: Public on Sep 20 2008

city: Silver Spring

first: Sai

middle: P

last: Majji

state: MD

address: 503 Robert Grant Avenue

department: Malaria

institute: Naval Medical Research Center

summary: Clonal channel catfish lymphoid cell lines and mixed lymphocyte cultures (MLC) have proven extremely useful in examining immune responses at the cellular and molecular levels.  To date catfish cell cultures have been biologically and phenotypically characterized using a variety of techniques including reverse transcription PCR (RT-PCR), as well as Northern and Southern Blotting.  To expand the molecular characterization of these cultures, microarray analysis was employed.  Clonal B (3B11), macrophage (42TA), and cytotoxic T cell (TS32.15 and TS32.17) lines and MLC were examined using a cDNA array containing ~ 2500 probes derived from EST libraries prepared from the 42TA macrophage cell line, a MLC, and 5 - 14 day old catfish fry.  Analysis showed that each cell line displayed a unique RNA expression profile that included a variety of immune-related genes.  Pearson correlation analysis indicated that one cytotoxic T cell line clustered with MLC, whereas a second cytotoxic T cell line was more closely associated with B cells and macrophages

overall_design: The microarray experiments were performed as two biological replicates and two technical replicates. In each case, gene expression in one of the three cell lines (TS32.15, TS32.17, and 42TA) or MLCs was compared against gene expression in the cell line 3B11. Biological replicates were performed on samples that were obtained from two different cell stocks that were frozen at different times and after a different number of subcultures. Technical replicates were performed as dye swaps where the dye was swapped between the test and the control cDNA. If a biological replicate was used, the control cell line also was a biological replicate.

first: Venkata

last: Thodima

first: Ana

last: Arnizaut

first: Youping

last: Deng

first: Warren

last: May

first: Donald

last: Sittman

first: Larry

last: Hanson

first: Marvin

last: Cuchens

first: Gregory

last: Chinchar


title: Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

summary: We tested four gene enrichment and complexity reduction target preparation methods for scoring SFPs on the Affymetrix GeneChip 18k Maize Genome Array (Maize GeneChip).  Methylation filtration (MF), Cot filtration (CF), mRNA-derived cRNA, and amplified fragment length polymorphism (AFLP) methods were applied to three diverse maize inbred lines (B73, Mo17, and CML69) with three replications per line (36 Maize GeneChips).    Due to large amounts of repetitive, mobile DNA, the maize genome requires a target preparation method that offers both a high level of gene enrichment and accurate scoring of SFPs. The objectives of this research are (i) to determine which target preparation method (CF, MF, mRNA, or AFLP) optimally  enriches for gene sequences complementary to probe sequences on the Affymetrix GeneChip Maize Genome Array and (ii) to estimate SFP detection power for each target method.    The AFLP technology is covered by patents, and patent applications owned by Keygene N.V. AFLP is a registered trademark of Keygene N.V. GeneChip.     This work was supported in part by U.S. National Science Foundation grant DBI-0321467 and USDA-ARS. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Michael   Gore.  The equivalent experiment is ZM10 at PLEXdb.]

overall_design:
protocol: mRNA - genotype: B73 maize inbred(3-replications)
protocol: mRNA - genotype: Mo17 maize inbred(3-replications)
protocol: mRNA - genotype: CML69 maize inbred(3-replications)
protocol: Cot filtration (CF) - genotype: B73 maize inbred(3-replications)
protocol: Cot filtration (CF) - genotype: Mo17 maize inbred(3-replications)
protocol: Cot filtration (CF) - genotype: CML69 maize inbred(3-replications)
protocol: Methylation filtration (MF) - genotype: B73 maize inbred(3-replications)
protocol: Methylation filtration (MF) - genotype: Mo17 maize inbred(3-replications)
protocol: Methylation filtration (MF) - genotype: CML69 maize inbred(3-replications)
protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: B73 maize inbred(3-replications)
protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: Mo17 maize inbred(3-replications)
protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: CML69 maize inbred(3-replications)

first: Michael

last: Gore


title: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

city: Rishon Le-Zion

first: Igor

middle: Michael

last: Kolotilin

address: Dereh Ha-Macabim

department: Plant sciences

institute: Volcani inst.

summary: Fruits of transgenic tomato (Solanum lycopersicum) plants engineered with ripening-induced, yeast S-adenosylmethionine decarboxylase (ySAMdc) gene, accumulate the higher polyamines spermidine (Spd) and spermine (Spm) and demonstrate ameliorated phytonutrient content, juice quality, and prolonged vine life. Enhanced nitrogen-carbon interactions were revealed by comprehensive Nuclear Magnetic Resonance (NMR) spectroscopy-based metabolite profiling of the transgenics, suggesting that Spd and Spm are perceived as nitrogenous metabolites by the fruit cells (Mattoo et al., 2006). The recent work by our colleagues identified the effects of Spd/Spm accumulation on various functional classes of tomato genes affected during ripening by probing 1522 ESTs on a custom-made array (Srivastava et al., 2007). In this study we monitored alterations of genome-wide transcriptional patterns in pericarp of Spd/Spm-accumulating tomatoes by means of direct comparison with azygous controls using DNA-microarray technology. Consistent with the ySAMdc expression pattern, very minor transcriptional alterations were detected in mature green developmental stage. For both breaker and red stages, large mutual and unique gene sets displayed altered levels of transcript. Ontological term analysis of up- and down-regulated transcript groups revealed processes in cell metabolism that are regulated by increased levels of Spd/Spm in ripening tomato fruits. These processes mainly involve carbohydrate and amino acids metabolism and protein synthesis. Additionally, transcript levels of representative genes encoding structural enzymes for related biosynthetic pathways show strong relationship to specific metabolites that were identified as regulated in Spd/Spm-accumulating transgenics.

overall_design: Plants of both genotypes were grown in randomized blocks (3 blockes 8-10 plants each). At each of 3 developmental stages (mature green, breaker and pink-red) a single fruit was harvested from a randomly chosen plant of each genotype within each block. In each harvest different plants in each block were taken to represent each genotype. Following harvest, equal pericarp samples were cut from the equator region of each fruit. These samples were pooled according to genotype prior to RNA extraction, allowing equal representation of each block in the final sample. A total of 3 harvests taken from each genotype were eventually analyzed– each harvest representing a biological repeat.

middle: M

first: Ilan

last: Levin


title: Eye imaginal disc development

status: Public on Sep 23 2008

city: Berlin

first: Ansgar

last: Klebes

address: Chausseestr. 117

department: Biology

country: Germany

institute: Humboldt University Berlin

summary: Coordinating cell proliferation and differentiation is essential during organogenesis.  In Drosophila, the photoreceptor, pigment and support cells of the eye are specified in an orchestrated wave as the morphogenetic furrow passes across the eye imaginal disc.  Cells anterior of the furrow are uncommitted to cell type and remain mitotically active, while most cells in the furrow arrest at G1 and adopt specified ommatidial fates.  We used microarray expression analysis to monitor changes in transcription at the furrow and identified genes whose expression correlates with either proliferation or fate specification.

overall_design: This study took advantage of the spatial arrangement of undifferentiated and differentiating cells on either side of the MF in Drosophila melanogaster eye imaginal discs. To identify genes that are important to the undifferentiated state of proliferating eye disc cells, or to cells exiting the mitotic program to differentiate, RNA was isolated from posterior cells and from whole eye discs.  Disc fragments posterior to the MF were obtained by micro-dissection from the w1118 strain that differentiates eyes normally (except for pigmentation).  Whole eye discs were from various mutants that either increase the proportion of differentiating photoreceptor cells (extra R8 phenotype: rough X63 (roX63), and Su(roDom)519 (Chanut et al., 2000) or reduce the proportion of photoreceptor cells due to a stop furrow phenotype (atonal1 (ato1), hedgehog1 (hh1), roughDominant (roDom), and Enhancer(roDom)2033 (E(roDom)2033) (Dokucu et al., 1996; Chanut et al., 2000).  After purification, the RNA populations were processed by linear amplification and hybridized to custom-made DNA glass microarrays.  Hybridization experiments were performed comparing posterior fragments or discs with abnormal numbers of photoreceptors to “normal” discs; a minimum of two independent replicates were made for each of nine different experimental conditions.

first: Thomas

middle: B

last: Kornberg

first: Francoise

last: Chanut


title: Identification of Positional Candidate Genes for Body Weight and Adiposity in Subcongenic Mice

status: Public on Sep 22 2008

city: Davis

first: Kyoungmi

last: Kim

address: One Shields Avenue

department: Rowe Program in Human Genetics

institute: University of California-Davis

summary:
We previously constructed a congenic mouse, B6.S-D2Mit194-D2Mit311 (B6.S-2) with SPRET/Ei donor DNA on distal chromosome 2 in a C57BL/6J background that captured an obesity quantitative trait locus (QTL). Mice homozygous for SPRET/Ei alleles at the donor region had decreased body weight and obesity related phenotypes. The B6.S-2 congenic donor region spanned a minimum of 26 Mb. In this study, we constructed five overlapping subcongenics with smaller SPRET/Ei donor regions to fine map the underlying gene(s). One of the five subcongenic lines derived from the B6.S-2 founding congenic, B6.S-2A, captures most of the body weight and adiposity phenotypes in a donor region with a maximum size of 7.4 Mb. Homozygous SPRET/Ei donor alleles in both the founding congenic and the derived B6.S-2A subcongenic exhibit significant decreases in body weight, multiple fat pad weights with the greatest decrease in mesenteric fat pad weight, and Adiposity Index (total fat pad weight divided by body weight). Interval specific microarray analysis in four tissues for donor region genes from the founding B6.S-2 congenic identified several differentially expressed genes mapping to the B6.S-2A subcongenic donor region, including prohormone convertase 2 (PC2). Quantitative real-time PCR confirmed a modest decrease of PC2 expression in whole brains of mice homozygous for SPRET/Ei donor alleles. Analysis of the relative levels of mRNA for B6 and SPRET/Ei in heterozygous congenic mice showed differentially higher expression of the C57BL/6J allele over the SPRET/Ei allele indicating a cis regulation of differential expression. Using subcongenic mapping, we have successfully narrowed a body weight and obesity QTL interval and identified PC2 as a positional candidate gene.
Keywords: Two strain comparison for gene discovery

overall_design: Two genotypes of B6.S-2 background and congenic strains- for each strain four tissues (whole brain, liver, adipose, muscle) were collected with 3 biological replicates.

first: Sally

last: Chiu

first: Kari

middle: A

last: Hans

first: Ricardo

last: Vedugo

first: Glenda

last: Espinal

first: Craig

middle: H

last: Warden


title: Age-related behaviors have distinct transcriptional profiles in C. elegans

city: Novato

first: Simon

last: Melov

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

summary:
There has been a great deal of interest in identifying potential biomarkers of aging (Butler et al. 2004). Biomarkers of aging would be useful to predict potential vulnerabilities in an individual that may arise well before they are chronologically expected, due to idiosyncratic aging rates that occur between individuals. Prior attempts to identify biomarkers of aging have often relied on the comparisons of long-lived animals to a wild-type control (Dhahbi et al. 2004). However, the effect of interventions in model systems that prolong lifespan (such as single gene mutations, or caloric restriction) can sometimes be difficult to interpret due to the manipulation itself having multiple unforeseen consequences on physiology, unrelated to aging itself (Gems et al. 2002; Partridge & Gems 2006). The search for predictive biomarkers of aging therefore is problematic, and the identification of metrics that can be used to predict either physiological or chronological age would be of great value (Butler et al. 2004). One methodology which has been used to identify biomarkers for numerous pathologies is gene expression profiling. Here, we report whole-genome expression profiles of individual wild-type Caenorhabditis elegans covering the entire wild-type nematode life span. Individual nematodes were scored for either age-related behavioral phenotypes, or survival, and then subsequently associated with their respective gene expression profiles.  This facilitated the identification of transcriptional profiles that were highly associated with either physiological or chronological age. Overall, our approach serves as a paradigm for identifying potential biomarkers of aging in higher organisms that can be repeatedly sampled throughout their lifespan.

The full normalized data set with expression values for all genes of all individual worms at all ages (104 worms/arrays) is available as a 28Mb download as a supplementary file on this page (GSE12290.txt).

Keywords: time couse

overall_design: Time course of aging in C. elegans. 7 ages were assayed, with a minimum of 9 biological replicates per timepoint, and as many as 17 biological replicates. All ages were compared to an independent 4 day old (young) pooled control.


title: Effect of FoxJ1 on expression of cilia genes

status: Public on Sep 15 2008

city: La Jolla

first: Chris

last: Kintner

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute

summary:
Analysis of epithelial explants injected with the intracellular domain of Notch (ICD) to block the formation of multi-ciliate cells, either alone or along with FoxJ1.  FoxJ1 misexpression leads to the induction fo ectopic cilia in Xenopus laevis epithelia. Results show which genes are affected by FoxJ1 during the induction of ectopic cilia.
Ciliated cells that produce a leftward fluid flow have been proposed to mediate left-right patterning in many vertebrate embryos.  These cilia combine features of primary sensory and motile cilia, but how such cilia are specified is unknown.  We address this issue by analyzing the Xenopus and Zebrafish homologs of FoxJ1, a forkhead transcription factor necessary for ciliogenesis in multi-ciliate cells of the mouse.  We show that the cilia that underlie left-right patterning on the Xenopus gastrocoel roof plate (GRP) and Zebrafish Kupffer’s vesicle (KV) are severely shortened or fail to form in FoxJ1 morphants.  We also show that misexpressing XFoxJ1 is sufficient to induce ectopic GRP-like cilia formation in frog embryos.  Microarray analysis indicates that XFoxJ1 induces the formation of cilia by upregulating the expression of motile cilia genes.  These results indicate that FoxJ1 is a critical determinant in specifying cilia used in left-right patterning.

Keywords: Cilia Induction

overall_design: 2-cell stage Xenopus embryos were injected with synthetic mRNA encoding ICD alone or along with FoxJ1.  At stage 9/10 the presumptive ectoderm was cut off the embryo and cultured on a fibronectin coated coverslip.  At stage 22 RNA was harvested from explants and used as the starting material for arrays.

first: Jennifer

middle: L

last: Stubbs

first: Isao

last: Oishi

first: Juan

last: Izpisua-Belmonte


title: The impact of glycerol on the metabolism of Lactobacillus reuteri - Exploratory experiment

city: Amsterdam

first: Douwe

last: Molenaar

address: De Boelelaan 1085

department: Systems Bioinformatics

country: Netherlands

institute: Vrije Universiteit Amsterdam

summary:
Lactobacillus reuteri is a heterofermentative lactic acid bacterium best known for its ability to co-ferment glucose and glycerol. Its genome sequence has recently been deduced enabling the implementation of genome-wide analysis. In this study we developed a dedicated cDNA microarray platform and a genome-scale metabolic network model of L. reuteri and use them to revisit the co-fermentation of glucose and glycerol. The model was used to simulate experimental conditions and to visualize and integrate experimental data in particular the global transcriptional response of L. reuteri to the presence of glycerol. We show how the presence of glycerol affects cell physiology and triggers specific regulatory mechanisms allowing simultaneously a better yield and more efficient biomass formation. Furthermore we were able to predict and demonstrate for this well-studied condition the involvement of previously unsuspected metabolic pathways for instance related to amino acids and vitamins. These could be used as leads in future studies aiming at the increased production of industrially relevant compounds such as vitamin B12 or 1 3- propanediol.

Keywords: cell type comparison

sample_organism: Limosilactobacillus reuteri subsp. reuteri F275

overall_design: Dye swap

first: Filipe

last: Santos

first: Jeroen

last: Hugenholtz

first: Bas

last: Teusink


title: Donor lung tissues: Control vs. Primary graft dysfunction (PGD)

city: Toronto

first: Masaki

last: Anraku

state: Ontario

address: 101 College Street, TMDT 2-816

department: Surgery

country: Canada

institute: Toronto General Research Institute

summary:
Primary graft dysfunction (PGD) continues to be a major cause of early death after lung transplantation. Moreover, there remains a lack of accurate pre-transplant molecular markers for predicting PGD. To identify distinctive gene expression signatures associated with PGD, we profiled human donor lungs using microarray technology prior to the graft implantation. The genomic profiles of 10 donor lung samples from patients who subsequently developed clinically defined severe PGD were compared with 16 case-matched donor lung samples from those who had a favorable outcome without PGD. Matched factors used were: recipient age (± 10 years), recipient gender, recipient lung disease, and type of transplantation (single or bilateral).
Keywords: Observational case-control study

overall_design: Matched case-control observational study: 10 primary graft dysfunction cases vs 16 Good outcome cases. One replicate per array.

first: Shaf

last: Keshavjee

first: David

last: Kelvin


title: Somatic mosaicism for copy number variation in differentiated human tissues

city: Birmingham

first: Jan

last: Dumanski

state: AL

department: Department of Genetics

institute: University of Alabama at Birmingham

type: Genome variation profiling by genome tiling array

summary:
Genetic variation is responsible for the generation of phenotypic diversity, including susceptibility to disease. Two major types of variation are known: single nucleotide polymorphisms (SNPs) and a more recently discovered structural variation, involving changes in copy number (CNVs) of kilobase- to megabase-sized chromosomal segments. Variation caused by CNVs has exceeded the amount of SNP-based differences expected to exist between two unrelated humans. Furthermore, many CNVs have been associated with disease predisposition. It is unknown whether CNVs arise in somatic cells, but it is, however, generally assumed that normal cells are genetically identical. Here we show that CNVs are frequent in healthy somatic cells of adult humans. We tested 34 tissue samples from three subjects and, having analyzed for each tissue <10-6 of all cells expected in an adult human, we observed at least six CNVs, affecting a single organ or one or more tissues of the same subject. The CNVs ranged from 82-176 kb, often encompassing known genes, potentially affecting gene function. Our results point to a paradigm shift in the genetics of somatic cells and indicate that humans are commonly affected by somatic mosaicism for stochastic CNVs, which occur in a substantial fraction of cells. A considerable number of phenotypes and diseases affecting humans are a consequence of a somatic process. Thus, our conclusions will be important for the delineation of genetic factors behind these phenotypes. Consequently, biobanks should consider sampling multiple tissues in order to better address mosaicism in the studies of somatic disorders. Furthermore, forensic medicine laboratories should be sensitized to the issue of underestimated frequency of somatic CNV mosaicism.
Keywords: copy number variation (CNV), phenotype diversity, somatic cells

overall_design: 31 experiments; each experiment consists of two hybridizations, i.e. regular and dye-swap (62 hybridizations in total); cerebellum from corresponding subject was used as a reference; additionally 12 control self-self hybridizations are included (cerrebellum vs self)

first: Arkadiusz

last: Piotrowski

first: Carl

last: Bruder


title: Porphyromonas gingivalis W50 Heme-excess vs Heme-limitation

status: Public on Nov 19 2008

city: Parkville

first: Helen

last: Mitchell

address: 720 Swanston St

department: School of Dental Science

country: Australia

institute: The University of Melbourne

summary: Transcription profiling of P. gingivalis W50 grown in continuous culture under conditions of heme-excess and heme-limitation.

overall_design: Reference design (using Cy5 labelled genomic DNA as the reference) to compare two conditions: heme-excess vs heme-limitation.  Three samples for each condition, independently grown.

first: Stuart

middle: G

last: Dashper

first: Nada

last: Slakeski

first: Steven

last: Cleal

first: Samantha

last: Byrne

first: Jasmin

last: Lissel

first: Eric

last: Reynolds


title: The impact of glycerol on the metabolism of Lactobacillus reuteri - Main experiment

first: Douwe

last: Molenaar

platform_organism: Limosilactobacillus reuteri subsp. reuteri F275

overall_design: Loop design


title: Phytoplankton community composition and gene expression involved in carbon and nitrogen assimilation

status: Public on Sep 12 2008

city: Princeton

first: Bess

last: Ward

state: NJ

address: Guyot Hall

department: Geosciences

institute: Princeton University

summary:
A functional gene microarray was developed and used to investigate phytoplankton community composition and gene expression in the English Channel.  Genes encoding the CO2 fixation enzyme RuBisCO (rbcL) and the nitrate assimilation enzyme nitrate reductase (NR) representing several major groups of phytoplankton were included as oligonucleotide probes on the 'phytoarray'.   Five major groups of eukaryotic phytoplankton that possess the Type 1D rbcL gene were detected, both in terms of presence (DNA) and activity (rbcL gene expression).  Changes in relative signal intensity among the Type 1D rbcL probes indicated a shift from diatom dominance in the spring bloom to dominance by haptophytes and flagellates later in the summer.  Because of the limitations of a smaller database, NR probes detected fewer groups, but due to the greater diversity among known NR sequences, NR probes provided higher phylogenetic resolution than did rbcL probes, and identified two uncultivated diatom phylotypes as the most abundant (DNA) and active (NR gene expression) in field samples.  Unidentified chlorophytes and the diatom Phaeodactylum tricornutum were detected at both the DNA and cDNA (gene expression) levels.   The reproducibility of the array was evaluated in several ways and future directions for further improvement of probe development and sensitivity are outlined.  The phytoarray provides a relatively high resolution, high throughput approach to assessing phytoplankton community composition in marine environments.

Keywords: seawater natural assemblages, functional gene expression

sample_organism:
unidentified
uncultured organism

platform_organism:
Phaeodactylum tricornutum
Dunaliella tertiolecta
Chlamydomonas reinhardtii
Pseudochlorella pringsheimii
Asterionellopsis glacialis
Cylindrocystis sp. UTEX 1925
uncultured eukaryote
uncultured Chlorophyta
Haptophyta environmental samples

overall_design: Two functional genes, nitrate reductase and RuBisCO, 4 - 8 replicate features per array

first: B


title: Expression Profiles of Planarain Stem Cells and their Immediate Division Progeny

city: Salt Lake City

first: Alejandro

last: Sánchez Alvarado

state: UT

department: Neurobiology and Anatomy

institute: University of Utah School of Medicine

summary: Throughout adulthood, the replacement of cells lost to physiological turnover or injury in planarians is sustained by the proliferation and differentiation of adult stem cells known as neoblasts.  Because neoblasts are the only known mitotic cells in asexual planarians, they can be efficiently eliminated by irradiation without significantly affecting post-mitotic differentiated cells.  We uncovered a cohort of transcripts specific to the stem cells and their division progeny by defining the expression profiles of wild type and irradiated animals at different time points after irradiation.

overall_design: RNA from wild type animals, or from animals 24 hours or seven days after exposure to radiation, were compared to a common reference.

first: George

middle: T

last: Eisenhoffer

first: Hara

last: Kang


title: Endogenous shRNAs, siRNAs, and Other Microprocessor-independent, Dicer-dependent Small RNAs in Mouse ES Cells

status: Public on Sep 10 2008

city: San Francisco

first: James

middle: Graham

last: Ruby

address: 1700 4th Street QB3 s404

department: Biochemistry

institute: UCSF

type: Non-coding RNA profiling by high throughput sequencing

summary: Canonical microRNAs (miRNAs) require two processing steps: the first by the Microprocessor, a complex of DGCR8 and Drosha, and the second by Dicer. dgcr8delta/delta mouse embryonic stem cells (mESCs) have less severe phenotypes than dicer1delta/delta mESCs, suggesting a physiological role for Microprocessor-independent, Dicer-dependent small RNAs.  To identify these small RNAs with unusual biogenesis, we performed high-throughput sequencing from wild type, dgcr8delta/delta, and dicer1delta/delta mESCs.  Several of the DGCR8-independent, Dicer-dependent RNAs were non-canonical miRNAs. These derived from mirtrons and a newly identified subclass of miRNA precursors, which appears to be the endogenous counterpart of short hairpin RNAs (shRNAs).  Our analyses also revealed endogenous siRNAs resulting from Dicer cleavage of long hairpins, the vast majority of which originated from one genomic locus with tandem, inverted short interspersed nuclear elements (SINEs). Our results extend the known diversity of mammalian small-RNA generating pathways and show that mammalian siRNAs exist in tissues outside of oocytes.

overall_design:
Small RNAs were sequenced from wt, dgcr8(-), and dicer(-) mouse ES cells and the frequencies of small RNA types compared between the three.  This record includes Illumina-platform-generated datasets from all three samples and 454-platform-generated datasets from wt and dgcr8(-) samples.

[raw data files are unavailable]

first: Joshua

last: Babiarz

first: J

first: Yangming

last: Wang

first: David

last: Bartel

first: Robert

last: Blelloch


title: Gene expression profile for ectopic vs. eutopic endometrium

status: Public on Sep 13 2008

city: Paris

first: Bruno

last: Borghese

address: 24, rue du Faubourg Saint-Jacques

department: Genetics and Development

country: France

institute: Institut Cochin

summary:
Endometriosis is a common gynecological disorder characterized by pain and infertility, where the lesions disseminate everywhere in the body with a preference for the pelvis. In that, it could be regarded as a “benign metastatic disease”, since its issue is not fatal. However, the molecular bases of this intriguing clinical condition are not well known. The objective of this study is to characterize the transcriptome differences between eutopic vs ectopic endometrium with a special interest in pathways involved in cancerogenesis. We performed two hybridizations in technical replicate on highly specific long oligonucleotides microarrays (NimbleGen™), with cDNA prepared from 6-patients pools, where the same patient provided both eutopic and ectopic endometrium (endometriomas). In order to confirm the expression microarrays data, qRT-PCR validation was performed on 12 individuals for 20 genes. Over 8,000 transcripts were significantly modified (more than twice) in the lesions corresponding to 5,600 down- or up-regulated genes. These were clustered through DAVID Bioinformatics Resources into 55 functional groups. The data are presented in a detailed and visual way on 24 KEGG pathways implemented with induction ratios for each differentially expressed gene. An outstanding control of the cell cycle and a very specific modulation of the HOX genes were observed and provide some new evidence on why endometriosis only very rarely degenerates into cancer. The study constitutes a noteworthy update of gene profiling in endometriosis, by delivering the most complete and reliable list of dysregulated genes to date.

Keywords: Gene expression microarrays

first: Françoise

last: Mondon

first: Thérèse-Marie

last: Mignot

first: Daniel

last: Vaiman

first: Charles

last: Chapron


title: Gene expression profiling of constitutively competent comR and proQ mutants and RNase R (rnr) mutant of L. pneumophila

status: Public on Sep 18 2008

city: New York

first: Xavier

last: Charpentier

state: NY

address: 701 West 168th Street Rm 1216

department: Microbiology

institute: Columbia University

summary:
Bacterial competence is a genetically programmed process that  is triggered as a response to environmental stimuli. DNA uptake from the extracellular milieu by competence requires the expression of a complex machinery composed of a competence pseudopilus and a DNA translocase. In L. pneumophila, it has been reported that microaerophilic conditions and genetic alteration of the competence repressors ComR and ProQ result in competence. We have analyzed the gene expression profiles of the proQ and comR mutants using the L. pneumophila Philadelphia-1 microarray. Many competence genes were found to be induced in the comR and proQ mutants and represent a defined,  regulon. The gene expression profiling of the proQ and comR mutants was  part of a study aimed at understanding the function of the processive 3'-5' exoribonuclease RNase R (rnr gene) in L. pneumophila. We found that the gene expression profile of the rnr mutant shares similarities with the gene expression profiles of the comR and proQ mutants and that loss of the exoribonuclease activity of RNase R was sufficient to induce competence development.

RNase R is a processive 3'-5' exoribonuclease with a high degree of conservation in prokaryotes. Although some bacteria possess additional hydrolytic 3´-5-exoribonucleases such as RNase II, RNase R was found to be the only one predicted in the Legionella pneumophila genome. This provided a unique opportunity to study the role of RNase R in the absence of an additional RNase with similar enzymatic activity. We investigated the role of RNase R in the biology of Legionella pneumophila under various conditions and performed gene expression profiling using microarrays. At optimal growth temperature, loss of RNase R had no major consequence on bacterial growth and had a moderate impact on normal gene regulation. However, at lower temperatures loss of RNase R has a significant impact on bacterial growth and resulted in the accumulation of structured RNA degradation products. Concurrently, gene regulation was affected and specifically resulted in increased expression of the competence regulon. Loss of the exoribonuclease activity of RNase R was sufficient to induce competence development, a genetically-programmed process normally triggered as a response to environmental stimuli. Temperature-dependent expression of competence genes in the rnr mutant was found to be independent of the previously identified competence regulators comR and ProQ.

platform_organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

overall_design:
comR: Three test samples and three reference samples were analyzed. The test sample being the strain KS79, a comR mutant of L. pneumophila strain JR32 which is used as a reference.

proQ: Three test samples and three reference samples were analyzed. The test sample being the strain LELA3825, a proQ mutant of L. pneumophila strain JR32 which is used as a reference.

rnr: Six test samples and six reference samples grown at 30°C or 37°C were analyzed. The test sample being the strain LELA559, a rnr mutant of L. pneumophila strain JR32 which is used as a reference.

first: Sebastien

last: Faucher

first: Sergey

last: Kalachikov

first: Howard

last: Shuman


title: Comparison between Borrelia burgdorferi wild type strain and cognate rpoS, rpoN and rrp2 mutants

status: Public on Sep 09 2008

city: Dallas

first: zhiming

last: ouyang

state: TX

address: 6000 Harry Hines Blvd

department: Department of Microbiology

institute: UT Southwestern Medical Center

summary:
The RpoN-RpoS alternative sigma factor pathway is essential for key adaptive responses by Borrelia burgdorferi, particularly those involved in the infection of a mammalian host.  A putative response regulator, Rrp2, ostensibly is required for activation of the RpoN-dependent transcription of rpoS.  However, questions remain regarding the extent to which the three major constituents of this pathway (Rrp2, RpoN, and RpoS) act interdependently.  To assess the functional interplay between Rrp2, RpoN, and RpoS, we employed microarray analyses to compare gene expression levels in rrp2, rpoN, or rpoS mutants of parental strain 297.  We identified 98 genes that were similarly regulated by Rrp2, RpoN and RpoS, and an additional 47 genes were determined to be likely regulated by this pathway.  The substantial overlap between genes regulated by RpoS and RpoN provides compelling evidence that these two alternative sigma factors form a congruous pathway and that RpoN regulates B. burgdorferi gene expression through RpoS.  Although several known B. burgdorferi virulence determinants were regulated by the RpoN-RpoS pathway, a defined function has yet to be ascribed to most of the genes substantially regulated by Rrp2, RpoN and RpoS, therefore providing additional avenues for future research into the genetic determinants contributing to virulence expression by B. burgdorferi.
Keywords: gene profiling

overall_design:
297 (wt) vs rpoS mutant: 6 slides, 12 hybridizations (including dyeswaps), three biological replicates

297 (wt) vs rpoN mutant: 5 slides, 10 hybridizations (including dyeswaps), three biological replicates

297 (wt) vs rrp2 mutant: 6 slides, 12 hybridizations (including dyeswaps), three biological replicates

5A18 (wt) vs XY424.3 (rrp2 mutant): 5 slides, 10 hybridizations (including dyeswaps), three biological replicates
297 (wt) vs rpoS mutant: 6 slides, 12 hybridizations (including dyeswaps), three biological replicates

297 (wt) vs rpoN mutant: 5 slides, 10 hybridizations (including dyeswaps), three biological replicates

297 (wt) vs rrp2 mutant: 6 slides, 12 hybridizations (including dyeswaps), three biological replicates

5A18 (wt) vs XY424.3 (rrp2 mutant): 5 slides, 10 hybridizations (including dyeswaps), three biological replicates

first: Michael

middle: V

last: Norgard

first: Xiaofeng

last: Yang

first: Zhiming

last: Ouyang

first: Jon

middle: S

last: Blevins

first: Bethany

middle: K

last: Boardman

first: Ming

last: He

first: Haijun

last: Xu

first: Dalai

last: Yan

first: Xiujuan

last: Pang


title: MN1 or MN1-TEL in the promonocytic cell line U937

city: Rotterdam

first: Magda

last: Meester

address: Dr. Molewaterplein 40

department: Pathology

institute: Erasmus Medical Center

summary:
Expression profiling of U937 derived cell lines with induced expression of MN1or MN1-TEL in combination with all-trans retinoic acid (ATRA)
Keywords: expression profiling

overall_design: Two similar experiments (A and B, biological duplicates) were performed. Hybridization includes dye swaps. See experimental_design.jpg (below) for detailed setup of the study. In short, different time points after induction of MN1 or MN1-TEL were compared to uninduced samples. The effects of all-trans retinoic acid (ATRA) were also investigated

last: Meester-Smoor

first: MJF

middle: W

last: Janssen

first: Ellen

last: Zwarthoff


title: Transcription analysis of E. coli processed at persistent and decreasing glucose limitation in a fed-batch cultivation

city: Stuttgart

first: Karin

last: Lemuth

address: Allmandring 31

institute: Universität Stuttgart

summary:
A time series of whole-genome transcription profiling of E. coli K-12 W3110 was performed to study the dynamic physiological response of E. coli K-12 W3110 to limited carbon conditions. cDNA from eight time intervals after glucose limitation, representing different stages of glucose depletion, along with cDNA of an unrestricted growth were hybridized to whole-genome microarrays of E. coli K-12. Glucose concentrations were gradually reduced in a fed-batch cultivation process with constant feeding rate in a bioreactor.
Major focus was put on the dynamic changes in the transcription level of genes involved in the central carbon metabolism (glycolysis, pentose phosphate pathway, TCA cycle and glyoxylate shunt), high-affinity glucose transport systems, movement, growth, and stress response.
In total, 40 microarrays were hybridized. The data were statistically analysed using the software R (R, 2005) and the Limma package included (Smyth, 2005). The data were normalized “print-tip-loess”. “Multiple hypothesis testing” correction was performed with the method of Benjamini and Hochberg (Benjamini and Hochberg, 1995), which controls the “false discovery rate” (fdr). Genes were regarded as differentially expressed when the “adjusted p values” were < 0.05, therefore nominally controlling the expected fdr to less than 0.05.
The reproducibility of dye swap experiments as well as biological replicates was estimated by calculating “Pearson’s correlation coefficients”. A high correlation was observed for the dye swap pairs (with averaged Pearson’s correlation coefficients of 0.89 ± 0.06 for the reference samples and of 0.87 ± 0.08 for the different points of time) as well as for biological replicates (with averaged Pearson’s correlation coefficients of 0.86 ± 0.04 for the red channel (Cy5) and 0.80 ± 0.09 for the green channel (Cy3)).

Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc B 57, 289-300.

Smyth, G.K. (2005). Limma: Linear models for microarray data. In Bioinformatics and Computational Biology Solutions using R and Bioconductor, R. Gentleman, Carrey, V., Dudoit, S., Irizzary, I., Huber, W., ed. (New York, Springer), pp. 397-420.

R (2005). R: A language and environment for statistical computing. (R Development Core Team).

Supplementary files:

Data_table_A: TabelleA_Signifikante.txt
Description:
Data table with coefficients of the linear model for every gene which was differentially expressed for at least one point in time according to the reference sample. The statistical analysis was performed as described in Series section (GSE10307) based on the normalized log2(test/ref) ratios in the Sample records' VALUE columns.

Data_table_B1: Tabelle_B1; /E. coli/, unlimited growth via glucose limitation (glucose concentration < 0.05 gL-1)
Data_table_B2: Tabelle_B2; /E. coli/, unlimited growth via glucose limitation, acetate concentration = 0.35 gL-1
Data_table_B3: Tabelle_B3; /E. coli/, unlimited growth via glucose limitation, 30 min after depletion of extracellular acetate
Data_table_B4: Tabelle_B4; /E. coli/, unlimited growth via glucose limitation, 50 min after depletion of extracellular acetate
Data_table_B5: Tabelle_B5; /E. coli/, unlimited growth via glucose limitation, 110 min after depletion of extracellular acetate
Data_table_B6: Tabelle_B6; /E. coli/, unlimited growth via glucose limitation, 170 min after depletion of extracellular acetate
Data_table_B7: Tabelle_B7; /E. coli/, unlimited growth via glucose limitation, 230 min after depletion of extracellular acetate
Data_table_B8: Tabelle_B8; /E. coli/, unlimited growth via glucose limitation, 350 min after depletion of extracellular acetate
Description:
Data_tables_B1-B8 report statistical values (A: average intensity value (1/2log2(test*ref)); M: average expression value (log2(test/ref)), t and P.value ('adjusted P.value')) for every point in time (studied conditions are described above for the corresponding table). Every differentially expressed gene of the corresponding point in time according to the reference sample is listed. Genes were regarded as differentially expressed when their 'adjusted P.values' were < 0.05, therefore nominally controlling the expected fdr to less than 0.05. The data are based on maximal three biological replicates (three independent fed-batch cultivations).

RT-PCR_results_7genes.txt and RT-PCR_protocol.PDF
Keywords: Time course, stress response

sample_organism: Escherichia coli str. K-12 substr. W3110

overall_design:
Hybridization involved the hybridization of a common reference (unlimited growth, batch phase) on all arrays together with each sample of interest. This allowed the direct comparison of the transcripts of a time series taken during fed-batch cultivation with the unlimited reference sample. All samples were taken in duplicates and the experiments were performed as dye swap experiments.
The first four samples of the time series (T1 - T4) were taken from three individual fed-batch cultivations (three biological replicates), the subsequent four samples (T5 - T8) were taken only from two individual fed-batch cultivations. On each array, the genes were spotted in duplicates. Therefore, twelve replicates (duplicates on dye swaps for three cultivations) were analyzed for T1 – T4 and eight replicates (duplicates on dye swaps for two cultivations) were analyzed for T5 – T8.

first: Timo

last: Hardiman

first: Stefan

last: Winter

last: Lange

first: Rolf

middle: D

last: Schmid

first: Matthias

last: Reuss

first: Martin

last: Siemann-Herzberg


title: Colonic tissues from an acute TNBS-induced colitis model in SJL mice.

status: Public on Sep 08 2008

first: Antonie

last: Zwiers

address: Van der Boechorststraat 7

department: MCBI

institute: Vrije Universiteit Medical Center

summary:
Experimental colitis is often used as a model for the inflammatory bowel diseases, ulcerative colitis and Crohn’s disease. Results identify the inflammatory processes during acute colitis in affected tissues from TNBS-treated susceptible 5-7 week old SJL mice.

Keywords: Disease state analysis

overall_design: Two-condition experiment, Treated vs Non-treated. Biological replicates: 4 treated, 4 non-treated. One replicate per array.

first: Tineke

middle: C

last: van der Pouw Kraan


title: Genome wide profiling of H3K9me2 in Arabidopsis thaliana

status: Public on Sep 11 2008

city: Los Angeles

first: Steve

middle: E

last: Jacobsen

address: 621 Charles E. Young Dr. South

department: Molecular Cell and Developmental Biology

institute: University of California, Los Angeles

type: Genome binding/occupancy profiling by genome tiling array

summary: The objective of the study is to profile histone H3 lysine nine di-methylation (H3K9me2) in Arabidopsis thaliana and to correlate it with DNA methylation.

overall_design:
We constructed a high-resolution genome-wide map of H3K9me2 methylation by using native chromatin immunoprecipitation coupled with HD2 whole genome Nimblegen microarrays.
Three replicas were performed for the native ChIP. As a control, one replica of ChIP isolated from crosslinked tissue was used.

first: Xiaoyu

last: Zhang

first: Matteo

last: Pellegrini

first: Xinmin

first: Luke

last: Dannenberg

first: Leo

last: Iniquez

first: Heather

last: Holster

first: Yana

last: Bernatavichute


title: A Functional Survey of Light-Responsive Genes Using A Rice NSF45K Microarray

status: Public on Sep 07 2008

city: Rockville

first: Jia

last: Liu

address: 9712 Medical Center Drive

institute: Plant Genomics

summary:
We performed expression profiling experiments on two-week old rice leaf tissues grown in light and dark condition with the rice 47k array. Four biological replicates and a dye-swap were used. To generate more consistent results on light vs dark response in rice, biological replicates were prepared from 4 different varieties such as Kitaake, Nipponbare, Tapei309 and IR24 because individual genetic background can affect to expression profile (Townsend et al., 2003). Gene expression was assayed by probing the microarray with pooled Cy3 and Cy5 labeled cDNAs derived from 0.5-1.0ug high quality mRNA prepared from leaf samples.
Keywords: Direct comparison

overall_design: 16 hybs total

first: K

last: Jung


title: Gene expression and intragenic polymorphism in a Populus trichocarpa and Populus deltoides pseudo-backcross pedigree

status: Public on Sep 06 2008

city: Gainesville

first: Matias

last: Kirst

state: FL

institute: University of Florida

summary:
A microarray analysis of whole-genome gene expression and single feature polymorphism in a (Populus trichocarpa X Populus deltoides) X Populus deltoides pseudo-backcross pedigree.  Genetic variation in gene expression was quantified for 55,793 predicted gene models based on a single probe per gene.  Concurrently, sequence-level polymorphism was analyzed based on dedicated probes identified in a pilot study comprised of the two parent genotypes (GPL7169).  Resultant data contributed to a high density genetic map and to analysis of the genetic architecture of gene expression in Populus.

Keywords: Genetic analysis of gene expression and polymorphism, eQTL

overall_design: Data include one biological replicate of 178 segregating pseudobackcross progeny analyzed for gene expression (GE) using one probe per gene for 55793 independent gene models (probes E_POPLARSxxxxxPxxxxx) and single feature sequence polymorphism (SFP) using one probe per gene for 12084 independent gene models (probes G_POPLARSxxxxxPxxxxx).  GE and SFP probes were selected from 6-7 probes per gene previously tested in a pilot study of the two parent trees of the cross (Populus deltoides X Populus trichocarpa).


title: msn2/4 mutant 3 hour exposure to zymolyase

city: Madrid

first: Javier

last: Arroyo

state: Madrid

address: Plaza Ramon y Cajal S/N

department: Microbiologia II

country: Spain

institute: Facultad de Farmacia (UCM)

summary:
We did transcription profiling on the effect of msn2 msn4 deletion, genes involved in several stress process
Keywords: cell wall stress response

overall_design: S. cerevisiae (msn2/4 mutant) was grown on YEPD. For Zymolyase experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with 5units/ml Zymolyase 100T. Cells were collected at 3 hours of growth, frozen at -80 °C and processed for RNA extraction. The total RNA from one culture was analyzed, and, in addition, for this sample two different hybridizations were performed, including fluorochrome swapping in order to minimize transcriptional changes due to technical variability. This therefore corresponded to two DNA microarrays analyzed.

first: Raul

last: Garcia

first: Clara

last: Bermejo

first: Jose

last: Rodriguez-Peña

first: Cesar

last: Nombela


title: Screen of oligonucleotides for microarray transcriptome analysis of Populus deltoides and P. trichocarpa

summary: The purpose of this study was to evaluate a set of 6-7 long oligonucleotide probes developed based on the sequence of the Populus trichocarpa genome, that are optimal for gene expression analysis of P. deltoides and a hybrid of P. deltoides and P. trichocarpa. To evaluate these probes, multiple tissues (differentiating xyle, leaf and whole-root) of a pure P. deltoides and a hybrid (P. deltoides X P. trichocarpa) were transcript profiled for identification of one or more probes that are not biased towards one or the other genotype.

sample_organism:
Populus trichocarpa x Populus deltoides
Populus deltoides

overall_design: Three vegetative tissues (root, leaf and xylem) harvested from two biological replicates from each genotypes of Populus deltoides (genotype D124) and a Populus hybrid (P. deltoides X P. trichocarpa, genotype 52-225) were hybridized separately to microarrays in a single-dye experiment.

first: Derek

last: Drost

first: Evandro

last: Novaes


title: rlm1 mutant 3 hour exposure to zymolyase

summary:
We did transcription profiling on the effect of rlm1 deletion, gene involved in cell wall stress response
Keywords: cell wall stress response

overall_design: S. cerevisiae (rlm1 mutant) was grown on YEPD. For Zymolyase experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with 5units/ml Zymolyase 100T. Cells were collected at 3 hours of growth, frozen at -80 °C and processed for RNA extraction. The total RNA from two different cultures was analyzed, and, in addition, for each sample two different hybridizations were performed, including fluorochrome swapping in order to minimize transcriptional changes due to technical variability. This therefore corresponded to four DNA microarrays analyzed for each condition.


title: hog1 mutant 3 hour exposure to zymolyase

summary:
We did transcription profiling on the effect of hog1 deletion, gene involved in cell osmotic stress and cell wall stress response
Keywords: cell wall stress response

overall_design: S. cerevisiae (hog1 mutant) was grown on YEPD. For Zymolyase experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with 5units/ml Zymolyase 100T. Cells were collected at 3 hours of growth, frozen at -80 °C and processed for RNA extraction. The total RNA from two different cultures was analyzed, and, in addition, for each sample two different hybridizations were performed, including fluorochrome swapping in order to minimize transcriptional changes due to technical variability. This therefore corresponded to four DNA microarrays analyzed for each condition.


title: Genetic heterogeneity versus molecular analysis of prion susceptibility in neuroblasma N2a sublines

first: Marc-Henri

last: Stern

address: 26 rue d'Ulm

department: Research Dept

institute: INSERM/Curie Institute

summary: The neuroblastoma-derived cell line N2a is permissive to certain prion strains but resistant sublines unable to accumulate the pathological proteinase-K resistant form of the prion protein can be isolated. We compared for gene expression and phenotypes different N2a sublines that were susceptible or resistant to the 22L prion strain. Karyotypes and comparative genomic hybridization arrays revealed chromosomal imbalances but did not demonstrate a characteristic profile of genomic alterations linked to prion susceptibility. Likewise, we showed that this phenotype was not dependent on the binding of PrPres, the expression of the prion protein gene, or on its primary sequence. We completed this analysis by looking using real-time quantitative PCR at the expression of a set of genes encoding proteins linked to prion biology. None of the candidates could account by itself for the infection phenotype, nevertheless sublines had distinct transcriptional profiles. Taken together, our results do not support a role for specific genomic abnormalities and possible candidate proteins in N2a prion susceptibility. They also reveal genetic heterogeneity among the sublines and serve as a guidance for further investigation into the molecular mechanisms of prion infection.

overall_design: In a first approach, CGHa profiles were established for the parental cell line N2apcl, a sensitive (G9) and a resistant (F1) sublines, as compared to A/HeJ mouse strain normal DNA. To allow a more precise description of the differences between N2apcl and six of its derived sub-lines (58, D11, F1, G9, R4, R10), N2apcl DNA was used as reference DNA in a series of CGHa experiments, avoiding the potential copy number polymorphisms between the cell lines and A/HeJ murine DNAs.

first: Stephanie

last: Chasseigneaux

first: Manuela

last: Pastore

first: Janice

last: Britton-Davidian

first: Elodie

last: Manie

first: Jacques

last: Callebert

first: Josette

last: Catalan

first: Danielle

last: Casanova

first: Maxime

last: Belondrade

first: Monique

last: Provansal

first: Yonghua

first: Alexander

last: Burkle

first: Jean-Louis

last: Laplanche

first: Nicolas

last: Sevenet

first: Sylvain

last: Lehmann


title: The pilus retraction protein PilT has a global influence on the transcriptome of Neisseria gonorrhoeae

status: Public on Sep 01 2008

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: The ATPase protein PilT mediates retraction of type IV pili.  We performed microarrays comparing the transcription profile of the Neisseria gonorrhoeae wild-type strain MS11 and its isogenic pilT mutant. 63 open reading frames were found to be differentially regulated in the pilT mutant. Most interestingly, a loss of function mutation in pilT leads to an upregulation of pilE, which encodes the pilus subunit protein.

overall_design:
Ngo arrays were generated as custom 8x15 K microarrays (Agilent Technologies) covering all open reading frames (ORFs) from N. gonorrhoeae strain FA1090 (accession number AE004969) supplemented with all ORFs from the gonoccoccal genetic island of strain MS11 (accession number AY803022) by 6 specific 60-mer oligonucleotides per gene on average.
Microarray analysis was performed as dual-color hybridization with dye-reversal color-swaps as technical replicates for Cy-dye specific effect compensation and three independent biological replicates.
Microarray features were extracted with the FE 9.5.3.1 software from Agilent Technologies using the GE2-v4_95_Feb07 protocol with default settings.
Data were loaded into Resolver (Rosetta Biosoftware) using the MAGE-ML loader and analyzed for differential gene expression. Ratio profiles were combined into ratio experiments and regulated genes were identified with a threshold of 1.75 fold-change and anti-correlation of the color-swapped dye reversals, rendering the analysis highly stringent and robust with P values <0.0001 of the results.

first: Alexandra

last: Friedrich


title: Livers from lean or fat muscle lines fed low or high lipid diets

city: saint-pée sur nivelle

first: catherine

last: kolditz

address: quartier Ibarron

institute: INRA

summary:
We used fish from two divergent lines of rainbow trout, selected for low or high muscle fat content (respectively L and F lines) and fed two different diets, containing either 10% (LE diet) or 23% (HE diet) lipids. For more details about experimental fish and diets, see Kolditz et al.,Am J Physiol Regul Integr Comp Physiol 294: R1154–R1164, 2008.   There are 4 experimental conditions: L-LE, L-HE, F-LE and F-HE. This experiment contain the data derived from the hybridization of the RNA extracted from individual liver of these fish.    for each membrane, spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

Keywords: Nutritional genomics, response to divergent selection for muscle fattening, liver metabolism, rainbow trout

overall_design: 32 samples

first: Catherine

last: Kolditz

first: Gilles

last: Paboeuf

first: Maiena

last: Borthaire

first: Diane

last: Esquerré

first: Magali

last: San Cristobal

first: Florence

last: Lefèvre

first: Françoise

last: Médale


title: Variations in stress sensitivity and genomic expression in diverse S. cerevisiae strains (gene expression)

status: Public on Sep 05 2008

city: Madison

first: Audrey

middle: P.

last: Gasch

state: WI

address: 425-g Henry Mall

department: Laboratory of Genetics

institute: University of Wisconsin Madison

summary:
Gene expression variation was measured in 17 non-laboratory strains compared to the sequenced S288c lab strain
Keywords: Gene expression comparisons in different yeast strains

overall_design: Each strain was grown in at least biological triplicate to log phase in rich (YPD) medium.  Extracted total RNA was compared to that collected from the diploid S288C strain, DBY8268 (ura3-52/ura3-delta, ho/ho, GAL2/GAL2)

first: Daniel

middle: J

last: Kvitek

first: Jessica

last: Will

middle: P


title: Organogenic nodule formation from internodes of Humulus lupulus

city: Lisboa

first: Ana

middle: Margarida

last: Fortes

address: Campus da FCUL

department: Plant Biology

country: Portugal

summary:
Transcriptional profiling of hop samples throughout in vitro culture on medium with sucrose and hormones IAA and BAP

Study of gene expression involved in stress response during in vitro culture and in organogenic nodule formation

Hop (Humulus lupulus L.) is an economically important plant forming organogenic nodules which can be used for genetic transformation and micropropagation. We are interested in the mechanisms underlying reprogramming of cells through stress and hormone treatments.

To investigate the spatio-temporal sequence of events that underlies competence acquisition for organogenesis three main stages were selected: (i) internodes at the time of excision from the parent plant (T0); (ii) internodes grown for 15 days on culture medium in which several prenodular structures are formed inside the calli (T15d); and (iii) nodule forming tissue after 28 days of culture (T28d). Additionally a control was included corresponding to 28 days of culture without hormones, lacking nodule formation and plantlet regeneration abilities, in order to identify genes specifically involved in morphogenesis (T28dWH).
Organogenic nodule formation is a morphogenic process that shares features with somatic embryogenesis though in the former no shoot/root pole is established and plantlet regeneration can occur from different peripheral regions of nodules. Previous studies have shown that the organogenesis-determining period (when cells are determined to form nodules) occurs in between 15 and 25 days of culture corresponding to prenodular and first nodular stages. When nodules are fully developed they are surrounded by layers of elongated, highly vacuolated cells that may degenerate when nodules start differentiating plantlets. Plantlet regeneration from organogenic nodules can be observed after 45 days of culture. However, organogenic nodules after 28 days of culture are already determined to undergo plantlet regeneration, since they no longer require exogenous supply of hormones. Explants cultured in medium without hormones can develop incipient prenodular structures with vascular tissue but not nodules, thus lacking morphogenic potential.

Keywords: Plant development, Time course

overall_design:
3 time points: 3 Biological replicates and 1 technical replicate (1 dye-swap). 1 control at beginning of culture and 1 control wihout hormones. One replicate per array.
Each clone printed twice in the same sub-grid

middle: M

first: Filipa

last: Santos

first: Bartolomeu

last: Acioli-Santos

first: Maria

last: Pais


title: slt2 mutant 3 hour exposure to zymolyase

first: Javier

last: Arroyo

summary:
We did transcription profiling on the effect of slt2 deletion, gene involved in cell wall stress response
Keywords: cell wall stress response

overall_design: S. cerevisiae (slt2 mutant) was grown on YEPD. For Zymolyase experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with 5units/ml Zymolyase 100T. Cells were collected at 3 hours of growth, frozen at -80 °C and processed for RNA extraction. The total RNA from two different cultures was analyzed, and, in addition, for each sample two different hybridizations were performed, including fluorochrome swapping in order to minimize transcriptional changes due to technical variability. This therefore corresponded to four DNA microarrays analyzed for each condition.

first: Raul

last: Garcia

first: Clara

last: Bermejo

first: Jose

last: Rodriguez-Peña

first: Cesar

last: Nombela


title: Saccharomyces cerevisiae response to various stressors

first: David

middle: B

last: Berry

address: 3456 Genetics Biotech. Building

institute: University of Wisconsin: Madison

summary:
Samples GSM206658-GSM206693:
Acquired Stress resistance in S. cerevisiae: NaCl primary and H2O2 secondary
Transcriptional timecourses of yeast cells exposed to 0.7M NaCl alone, 0.5mM H2O2 alone, or 0.5mM H2O2 following 0.7M NaCl, all compared to an unstressed sample.  Repeated using msn2∆ strain.

Samples GSM291156-GSM291196:
Transcriptional response to stress in strains lacking MSN2  and/or MSN4
Transcriptional timecourses of yeast cells (WT, msn2∆, msn4∆, or msn2∆msn4∆) exposed to 0.7M NaCl for 45 minutes or 30-37˚C Heat Shift for 15 min compared to an unstressed sample of the same strain.

Keywords: Stress Response

overall_design:
Samples GSM206658-GSM206693: 2 condition timecourses; stressed cells vs unstressed cells; 2 biological replicates for the WT arrays, 1 biological replicate for the msn2∆ arrays; 1 replicate per array; samples were taken every 15 minutes for NaCl arrays and every 10 minutes for H2O2 arrays

Samples GSM291156-GSM291196: 1 condition timecourses; stressed cells vs unstressed cells; 5-6 biological replicates for the WT arrays, 5 biological replicate for the msn2∆ arrays; 1 replicate per array; samples were taken at 45 minutes for NaCl arrays and at 15 minutes for Heat Shock arrays

NOTE: Supplementary GPR files (GSM206663 and GSM291161) are identical. The normalization and the processing are almost identical, however, the submitter used a different cutoff internally for data that have been accepted or rejected between the two datasets.


title: Microarray analysis of vegetative phase change in maize

city: Ames

first: Patrick

middle: S.

last: Schnable

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

summary:
Vegetative phase change is the developmental transition from the juvenile phase to the adult phase during which a plant becomes competent for sexual reproduction.  Gain of ability to flower is often accompanied by changes in patterns of differentiation in newly forming vegetative organs.  In maize, juvenile leaves differ from adult leaves in morphology, anatomy, and cell wall composition.  Whereas the normal sequence of juvenile followed by adult is repeated with every sexual generation, this sequence can be altered in maize by the isolation and culture of the shoot apex from an adult phase plant; an “adult” meristem so treated reverts to forming juvenile vegetative organs.  To investigate the molecular differences between the juvenile and adult phases in maize comparisons among two juvenile samples, leaf 4 and culture-derived leaf 3 or 4, and an adult sample (leaf 9) were made using cDNA microarrays.  All samples were leaf primordia at plastochron 6.  A gene was scored as “phase specific” if it was up- (or down-) regulated in both juvenile samples compared to the adult sample with at least a twofold-change in gene expression at P-value less than or equal to 0.005. Some 221 ESTs up-regulated in juvenile and 28 ESTs up-regulated in adult were identified.  Altered patterns of expression of selected ESTs in the phase change mutants Tp2, d1 and gl15 further confirmed these genes as being phase-specific and allowed us to position these genes in the known genetic hierarchy regulating phase change.
Keywords: Transcript profiling among seed-derived juvenile leaf 4 and adult leaf 9 and culture-rejuvenated leaf 3 or 4 in maize

overall_design: To identify juvenile or adult specific ESTs, total RNA from leaf primordia at plastochron 6 (P6) was isolated from leaves 4 (L4) and 9 (L9) from seed-derived plants and leaf 3 or 4 (RL3/4) from culture-derived plants.  For each of six biological replications, each of the three pairwise comparisons of P6-staged leaf primordia from L4, L9 and RL3/4 was made on one slide.  With six biological replications and three slides per replication (L4 vs. L9, L9 vs. RL3/4, RL3/4 vs. L4), this replicated loop design used a total of 18 slides.  To ensure dye balance, each of the 18 target samples was measured once with Cy3 labeling and once with Cy5 labeling.


title: ATF2 knockout in papillomas

city: Bethesda

first: Sean

last: Davis

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

summary:
RNA was prepared from papilomas of 2-3 mice (2 for WT and 3 for Knockout) and this was pooled to perform the array. Each pooled sample was run in triplicates.   The mice were treated once with DMBA, followed by TPA application for 30 wks. These mice are mixed background of FVB and C57bl6 and the age when they got the papillomas was about 9 months.
Keywords: Genetic modification

first: Ze'ev

last: Ronai

first: Anindita

last: Bhoumik

first: Paul

last: Meltzer


title: L. lactis ΔlmrCD and cholate-adapted L. lactis ΔlmrCDR

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

summary:
Transcriptome profiling of a L. lactis strain lacking the MDR transporter genes lmrCD and the same strain adapted to cholate was performed. As compared to the parental strain, the cholate-adapted strain showed 124 genes that were significantly differentially expressed more than 1.8-fold . These genes could be grouped into four major functional classes: i.e., genes involved in (i) cell envelope biogenesis;  (ii) stress response and molecular chaperones; (iii) general metabolism and house-keeping function; and (iv) the chromosomally embedded sex-factor.
Keywords: Mutant versus wild type comparison, stress response, cholate

platform_organism: Lactococcus cremoris subsp. cremoris MG1363

overall_design:
1. WT1 L. lactis ΔlmrCD (labeled with Cy3)

2. WT2 L. lactis ΔlmrCD (labeled with Cy5)

3. WT4 L. lactis ΔlmrCD (labeled with Cy3)

4. WT5 L. lactis ΔlmrCD (labeled with Cy5)

5. M1 L. lactis ΔlmrCD(R) (labeled with Cy5)

6. M2 L. lactis ΔlmrCD(R)(labeled with Cy3)

7. M4 L. lactis ΔlmrCD(R) (labeled with Cy5)

8. M5 L. lactis ΔlmrCD(R) (labeled with Cy3)

Hybridization schema:

1+5 (Slide 176631)

3+7 (Slide 176632)

2+8 (Slide 176633)

4+6 (Slide 176634)


title: eQTL mapping in Lake Whitefish Species Pairs.

city: Québec

first: Nicolas

last: Derome

state: QC

address: Av de la médecine

department: Biologie

institute: Université LAVAL

summary:
Mapping of expression quantitative trait loci (eQTL) is a powerful means for elucidating the genetic architecture of gene regulation. Yet, eQTL mapping has not been applied towards investigating the regulation architecture of genes involved in the process of population divergence, ultimately leading to speciation events. Here, we conducted an eQTL mapping experiment to compare the genetic architecture of transcript regulation in adaptive traits differentiating the recently evolved limnetic (dwarf) and benthic (normal) species pairs of lake whitefish. The eQTL were mapped in three data sets derived from a F1 hybrid-dwarf backcrossed family: the entire set of 66 genotyped individuals, and the two sexes treated separately. We identified strikingly more eQTL in the female dataset (174), compared to both male (54) and combined (33) data sets. The majority of these genes were not differentially expressed between male and female progeny of the backcross family, thus providing evidence for a strong pleiotropic sex-linked effect in transcriptomic regulation. The subtelomeric region of a linkage group segregating in females encompassed more than 50% of all eQTL, which exhibited the most pronounced additive effects. We also conducted a direct comparison of transcriptomic profiles between pure dwarf and normal progeny reared in controlled conditions. We detected 34 differentially expressed transcripts associated with eQTL segregating only in sex-specific data-sets, and mostly belonging to functional groups that differentiate dwarf and normal whitefish in natural populations. Therefore, these eQTL are not related to inter-individual variation, but instead to the adaptive and historical genetic divergence between dwarf and normal whitefish. This study exemplifies how the integration of genetic and transcriptomic data offers a strong means for dissecting the functional genomic response to selection by separating mapping family specific effects from genetic factors under selection, potentially involved in the phenotypic divergence of natural populations.
Keywords: eQTL mapping

overall_design:
Dissected white muscle tissue (250-350 mg) was sampled for 76 individuals from the hybrid x dwarf backcross mapping family. We used a loop design (YANG and SPEED 2002; CHURCHILL 2002) to maximize the number of sampled meioses. Each of 76 samples was technically replicated on two distinct slides, while performing dye swapping (Cy3 and Alexa) to estimate the dye intensity variation bias. After correcting for local background, raw intensity values were both log2 transformed and normalized using the regional LOWESS method implemented in the R/MANOVA software (KERR et al. 2000).
The design file used for the maanova analysis is linked below as a supplementary file.

first: Bérénice

last: Bougas

last: Rogers

first: Andrew

middle: A

last: Whiteley

first: Aurélie

last: Labbe

first: Jérôme

last: Laroche

first: Louis

last: Bernatchez


title: TL2 14028s M9+arabinose (3 passages) LibM9 vs Lib0 Exp.2

city: Irvine

first: Michael

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

summary:
Salmonella typhimurium 14028s Transposon library recovered after three consecutive rounds of growth to late log phase in M9 minimal medium (arabinose 0.4%) at 37°C with aeration, compared to an expansion of the initial library selected on Luria agar plates + kanamycin (50ug/ml), O/N at 37°C
Keywords: Transposon tag analysis

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: 2 biological replicates analysed after arbitrarily primed sampling (Klenow, DOPR degenerate primer) + specific PCR amplification (Taq DNA Pol) + T7 in vitro transcription (AmpliScribe T7) + RT labeling (Cy3) + hybridization, compared to identically processed standard library (Cy5)

first: Carlos

last: Santiviago

first: Brian

last: Ahmer

first: Steffen

last: Porwollik

first: Yipeng

last: Wang

first: Nabil

last: Arrach

first: Pui

last: Cheng

first: Yakhya

last: Dieye

first: Jenee

middle: N

last: Smith

first: Jessica

middle: L

last: Dyszel


title: TL2 14028s invA::cam IP BALBc mouse LibS invA vs Lib0 invA Mice

summary:
Salmonella typhimurium 14028s invA::cam Transposon library recovered from spleen 2 days after IP passage of 2.2 x 10^6 through BALB/c mouse, compared to the initial Transposon library grown in LB broth (kanamycin 50ug/ml), O/N at 37°C with aeration
Keywords: Transposon tag analysis

overall_design: 6 biological replicates analysed after arbitrarily primed sampling (Klenow, DOPR degenerate primer) + specific PCR amplification (Taq DNA Pol) + T7 in vitro transcription (AmpliScribe T7) + RT labeling (Cy3) + hybridization, compared to identically processed standard library (Cy5)


title: Mature B cell versus Plasma Cell Gene Expression

middle: M.

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

summary:
Comparing the gene expression of primary human B cell populations using human Lymphochip cDNA spotted arrays. Primary samples (Cy5) were compared to a reference pool of polyA+ RNA (Cy3).
Keywords: cell type comparison design

overall_design: PolyA+ RNA was extracted from primary B cell populations (Cy5) and compared to a reference pool of polyA+ RNA (Cy3) on human Lymphochip cDNA spotted arrays. Each population was labelled and hybridized in duplicate.


title: Wild type 3 hour exposure to zymolyase

first: Javier

last: Arroyo

summary:
We did transcription profiling on the effect of Zymolyase in Saccharomyces cerevisiae using strains BY4741 (wild type). Yeast cells exposed to Zymolyase in YPD growth medium show a significant induction of cell wall compensatory mechanism.
Keywords: cell wall stress response

overall_design: S. cerevisiae was grown on YEPD. For Zymolyase experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with 5units/ml Zymolyase 100T. Cells were collected at 3 hours of growth, frozen at -80 °C and processed for RNA extraction. The total RNA from two different cultures was analyzed, and, in addition, for each sample two different hybridizations were performed, including fluorochrome swapping in order to minimize transcriptional changes due to technical variability. This therefore corresponded to four DNA microarrays analyzed for each condition.

first: Raul

last: Garcia

first: Clara

last: Bermejo

first: Jose

last: Rodriguez-Peña

first: Cesar

last: Nombela


title: Gene Expression of the Geobacter sulfurreducens omcB mutant (GSU_2737) grown with soluble iron as an electron acceptor

first: Chun-Hua

last: Wan

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

institute: The J. Craig Venter Institute

summary:
Previous studies demonstrated that an outer membrane c-type cytochrome, OmcB (GSU_2737), was involved in Fe(III) reduction in Geobacter sulfurreducens. An OmcB-deficient mutant was greatly impaired in its ability to reduce both soluble and insoluble Fe(III). Reintroducing omcB restored the capacity for Fe(III) reduction at a level proportional to the level of OmcB production. Here, we report that the OmcB-deficient mutant gradually adapted to grow on soluble Fe(III) but not insoluble Fe(III). The adapted OmcB-deficient mutant reduced soluble Fe(III) at a rate comparable to that of the wild type, but the cell yield of the mutant was only ca. 60% of that of the wild type under steady-state culturing conditions. Analysis of proteins and transcript levels demonstrated that expression of several membrane-associated cytochromes was higher in the adapted mutant than in the wild type. Further comparison of transcript levels during steady-state growth on Fe(III) citrate with a whole-genome DNA microarray revealed a significant shift in gene expression in an apparent attempt to adapt metabolism to the impaired electron transport to Fe(III). These results demonstrate that, although there are many other membrane-bound c-type cytochromes in G. sulfurreducens, increased expression of these cytochromes cannot completely compensate for the loss of OmcB. The concept that outer membrane cytochromes are promiscuous reductases that are interchangeable in function appears to be incorrect. Furthermore, the results indicate that there may be different mechanisms for electron transfer to soluble Fe(III) and insoluble Fe(III) oxides in G. sulfurreducens, which emphasizes the importance of studying electron transport to the environmentally relevant Fe(III) oxides. (From Leang C, Adams LA, Chin KJ, Nevin KP, Methé BA, Webster J, Sharma ML, Lovley DR. Adaptation to disruption of the electron transfer pathway for Fe(III) reduction in Geobacter sulfurreducens. J Bacteriol. 2005 Sep;187(17):5918-26.)
Keywords: Geobacter, gene expression, genetic modification

overall_design: RNA was extracted and used for hybridizations from two identically treated chemostat cultures (biological replicates) of both the wild type and the adapted OmcB-deficient mutant of Geobacter sulfurreducens. A two-color hybridization strategy was used to produce a total of eleven technical replicates (hybridizations) from two biological replicates as follows. Six technical replicates were completed from the first biological replicate of which three of the technical replicates were in the opposite or “flip dye” configuration and five technical replicates were produced from the second biological replicate of which two were “flip dyes”

first: B

last: Methe

first: C

last: Leang

first: D

middle: R

last: Lovley

first: L

last: Adams

first: K

last: Chin

last: Nevin

first: M

last: Sharma


title: Primary B Cells acute activation

first: Louis

summary:
To identify early activation genes in primary human B cells.
Keywords: time series design

overall_design: Primary B cells (Cy5) are compared to a reference pool of RNA (Cy3) over a time course of stimulation with anti-Ig. Two independent unstimulated samples were analyzed.


title: Gene expression during biotrophic growth

city: Karlsruhe

first: Jörg

middle: Thomas

last: Kämper

address: Hertzstrasse 16, Geb. 06.40

department: Department for Applied Biosciences

institute: Karlsruhe Institute of Technology

summary:
Comparison between Ustilago maydis cells grown in axenic culture and U. maydis cells from plant tumors.
Keywords: developmental stages

overall_design: U. maydis FB1 cells were grown in axenic culture; corn plants were infected with a mixture of strains FB1 and FB2, and tumors were harvested 13 days post infection. SAmples were taken from two biological replicates each.

first: Miroslav

last: Vranes

first: Mario

last: Scherer


title: TL2 14028s IP BALBc mouse LibB vs Lib0 Mice

first: Michael

last: McClelland

summary:
Salmonella typhimurium 14028s Transposon library recovered from spleen after IP passage of 2x10^6 through BALB/c mouse, compared to the initial Transposon library grown in LB broth (kanamycin 50ug/ml), O/N at 37°C with aeration
Keywords: Transposon tag analysis

overall_design: 7 biological replicates analysed after arbitrarily primed sampling (DOPR) + specific PCR amplification + T7 in vitro transcription + RT labeling (Cy3) + hybridization, compared to identically processed standard library (Cy5)


title: Gene expression profiling of human monocytes and monocyte-derived-macrophages

status: Public on Aug 31 2008

city: Paris

first: Francois

last: Cambien

state: France

address: 91 Bd de l'Hôpital

department: Cardiovascular Genomics

institute: INSERM

summary:
In this study we analyzed the gene expression profiles of human monocytes and monocyte-dervied-macrophages.
Keywords: Gene expression profiling

overall_design:
Blood samples were obtained from 86 patients with symptoms of acute coronary syndrome who had undergone coronary angiography at the department of cardiology of the Pitié-Salpêtrière Hospital, Paris and who had on stenosis > 50 % diagnosed in at least one major coronary artery.
48 monocyte and 48 macrophage samples (38 pools of 2 samples and 10 individual samples for each type of RNA) were hybridized to the RNG/MRC platform.

first: Seraya

last: Maouche

first: Tiphaine

last: Godefroy

first: Odette

last: Poirier

first: Robert

last: Olaso

first: Ivo

last: Gut

first: Jean-Phillipe

last: Collet

first: Gilles

last: Montalescot

first: François


title: Rhesus macaque rhadinovirus (RRV) gene expression in vivo

status: Public on Aug 29 2008

city: Beaverton

first: Scott

middle: William

last: Wong

state: OR

address: 505 NW 185th Avenue

department: Vaccine and Gene Therapy Institute

institute: Oregon Health & Science University

summary: Viral gene expression profiling in a rhesus macaque rhadinovirus positive B cell lymphoma obtained from a rhesus macaque experimentally infected with simian immunodeficiency virus and rhesus macaque rhadinovirus strain 17577. The experiment identified two viral open reading frames (ORFs) that were expressed in the lymphoma. Expression of these viral ORFs were confirmed by reverse transcriptase-PCR.

overall_design: The design of the experiment was to identify viral ORFs expressed in virus infected tissue that possessed abnormal cellular features. In this case, we obtained a B cell lymphoma from an animal experimentally inoculated with SIV and RRV. This one sample was utilized as our experimental sample and we utilized CD20+ B cells from six different rhesus macaques sero-negative for RRV exposure as negative controls. To provide ratio data (experimental sample/negative control), the negative control contained a small percentage of tumor derived RNA. There were no biological replicates as only one single tumor sample was analyzed; however, technical replicates (four) were performed and the samples were averaged to derive the values to define the ratios.

middle: W

last: Searles

first: Beata

middle: U

last: Orzechowska

middle: F

last: Powers

first: Jerald

last: Sprague

first: He

last: Li

first: Bonnie

last: Yen

middle: K

last: Axthelm


title: CWRU_Colon_Cancer

city: Redwood City

first: Jordan

last: Hiller

address: 1400 Seaport Blvd.

institute: PDL BioPharma

summary:
CWRU_Colon_Cancer
Keywords: other


title: Ovarian cancer cell line study

city: London

first: Ken

last: Choi

address: 46 Cleveland Street

department: Gynaecological Oncology

country: United Kingdom

institute: University College London

summary: An ovarian cancer cell line study to identify possible trends between chromosomal aberrations depicted from CGH microarray profiling with expression profiling. CGH microarray profiles of a panel of ovarian cancer cell lines will be analysed and 10 cell lines with chromosomal aberrations of recurrent regions (with the strongest trend) will be taken forward for further expression array analysis to identify candidate genes. CGH microarray analyses will restrict the regions of aberrations with high resolution and accurracy, combined with expression array analysis to pinpoint candidate genes that will relate to the amplified and deleted regions. Identified candidates will allow the better understanding of mechanisms and specific pathways involved in ovarian cancer development.

overall_design: A collection of 31 cell lines in the laboratory will be used. CGH microarray profile analyses will be carried for all, a selection process will be used to separate the groups such as the subtypes of the cell line. An analysis program will be used to depict recurrent regions and 10 cell lines will be taken forward for further expression array analysis to identify candidate genes.

first: James

last: Morris

first: Dimitra

last: Dafou

first: Christopher

last: Jones

first: Simon

last: Gayther


title: U937 cells: differentiating vs. undifferentiated

city: Chicago

first: Elizaveta

middle: V

last: Benevolenskaya

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

summary:
Gene-expression changes in U937 cells undergoing monocytic differentiation with TPA treatment
Keywords: differentiation treatment

overall_design: The promonocytic U937 cell line was maintained at 37C in RPMI 1640 medium (Mediatech) supplemented with 10% fetalclone (HyClone) under a 5% CO2, 95% air atmosphere. U937 cells were differentiated by the addition to the growth medium 100 nM 12-O-tetradeconoyl-phorbol 13-acetate (TPA) (Sigma).Three condition experiment, treated with TPA for two different time points (27 and 96 hrs) vs. untreated. Biological replicates: independently grown, treated and harvested


title: Sessile serrated adenomas and conventional adenomas of the colon

status: Public on Aug 27 2008

city: Adelaide

first: maria

last: caruso

state: SA

address: Frome Road

institute: SA Pathology

summary:
Sessile serrated adenomas are now recognized as precursor lesions of a substantial subset of colorectal cancers arising via a so-called “serrated pathway”. However, their biological markers remain to be defined. The aim of our study was to identify differentially expressed genes in sessile serrated adenomas, hyperplastic polyps and tubular adenomas. Gene expression analysis demonstrated molecular differences between polyp types. Further studies using QRT-PCR on Cathepsin E demonstrated a significantly (p< 0.05) higher expression in sessile serrated adenomas as compared to both other polyp types. Trefoil Factor 1, showed the same trend of expression for sessile serrated adenomas as compared to hyperplastic polyps, and was significantly higher in both polyps compared to tubular adenomas. Immunohistochemistry for both proteins demonstrated strong cytoplasmic staining of abnormal crypts in all sessile serrated adenomas while staining in tubular adenomas and hyperplastic polyps was weak and focal. BRAF and KRAS mutation analysis were employed to further validate polyp discrimination. The findings demonstrated the positive association of the BRAF mutation, V600E, with sessile serrated adenomas and KRAS mutations with tubular adenomas (P<0.05). This study demonstrates CTSE and TFF1 over-expression in sessile serrated adenomas compared to both hyperplastic polyps and tubular adenomas.
Keywords: colonic polyp tissue comparison, linear modelling, SSA

overall_design: Microarray analysis was performed on 13 SSAs and 11 TAs. SSAs were from 4 males and 9 females (mean age of 75) and TAs were from 5 males and 6 females (mean age of 72). Samples were directly hybridised to each other (SSA versus TA) or to a pooled normal control (SSA versus control). A linear model (Smyth 2004) was fitted to the data bringing together the three contrasts: SSA versus control, TA versus control and SSA versus TA. Human OligoLibrary (Compugen Human Oligo Library (v1) containing 18861 60-mer oligonucleotides, representing approximately 16,000 unique genes) by the Adelaide Microarray Centre (Australia) was used. Slides were scanned using a GenePix 3000B scanner (Axon Instruments, Sunnydale, CA), and the Spot package (CSIRO, Australia) was used to identify spots and estimate fore- and background intensities (using a morphological opening background estimator) (Yang, Buckley et al. 2001; Ritchie 2004). Data analysis was performed in R (www.r-project.org) using the Limma package of Bioconductor (Gentleman, Carey et al. 2004; Smyth 2004). Loess print tip method was used to correct for dye-bias and intensity within each group of adjacent spots printed by one pin (Yang, Dudoit et al. 2002). Linear modelling was performed with the Limma package of Bioconductor (Smyth 2004).

first: Maria

last: Caruso

last: Moore

first: Gregory

middle: J

last: Goodall

first: Michelle

last: Thomas

first: Stuart

last: Phillis

first: Anna

last: Tyskin

first: Glenice

last: Cheetham

first: Nancy

last: Lerda

first: Hiroyiki

last: Takahashi

first: Andrew

last: Ruszkiewicz


title: Sall4 ChIP-chip in mouse ES cell line W4 using NimbleGen MM8 RefSeq Promoter array (2.5kb)

city: Las Vegas

first: Yupo

last: Ma

state: NV

address: 1 Breakthrough Way

institute: Nevada Cancer Institute

summary:
Embryonic stem cells have potential utility in regenerative medicine due to their pluripotent characteristics. Sall4, a zinc-finger transcription factor, is expressed very early in embryonic development with Oct4 and Nanog, two well characterized pluripotency regulators. Sall4 plays an important role in governing the fate of stem cells through transcriptional regulation of both Oct4 and Nanog. Using chromatin immunoprecipitation coupled to microarray hybridization (ChIP on Chip), we have mapped global gene targets of Sall4 unveiling possible regulation of broad ES cell functions. Approximately 5,000 genes were identified that were bound by the Sall4 protein and many of these have major functions in developmental and regulatory pathways.  Sall4 bound more than six times as many annotated genes within promoter regions as Oct4 and twice as many as Nanog. Immunoprecipitation revealed a heterotrimeric protein complex between Sall4, Oct4, and Nanog, consistent with binding site co-occupancies.  Further, Sall4 bound many genes that are regulated in part by the chromatin-based epigenetic events mediated by polycomb-repressive complexes and bivalent domains. This suggests that Sall4 plays a central and diverse role in regulating stem cell pluripotency during early embryonic development that involves integration of transcriptional and epigenetic control processes.
Keywords: ChIP-chip

overall_design: We used ChIP-chip to map global promoter bound by Sall4, a zinc finger transcription factor.  Growing evidence has suggested that Sall4 plays a vital role in ES cell pluripotency maintenance.  Evidence for this includes its recent use as a marker for somatic cell reprogramming, in a genetic signature for ES cells, and evidence that Sall4 enhances reprogramming.  These recent findings and two previously described interactions with Oct4 and Nanog strongly support the role of Sall4 in ES cells.  This hypothesis was furthered here as we show that Sall4 plays important roles through transcriptional regulation of vital ES cell genes.

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