title: MSL2 is required for upregulation of male X chromosome but not for expression of autosomal genes

status: Public on Aug 03 2009

city: Detroit

first: Satya

middle: Kiran

last: Koya

state: MI

address: 5047, Gullen Mall

department: Biological Sciences

institute: Wayne State University

summary: Drosophila males double transcription of their single X chromosome to equalize X-linked gene expression with females, which carry two X chromosomes. Increased transcription requires the Male-Specific Lethal (MSL) complex. The MSL2 protein is essential component of the MSL complex. MSL2 is the only protein that is strictly limited to males. MSL2 together with MSL1 forms the core of the MSL complex. The global effect of msl2 mutation on gene expression was measured by microarray analysis. We found that expression of the X chromosome was decreased in msl21 male larvae, supporting the involvement of MSL2 in the up-regulation of X-linked genes. However, there was no change in expression of 4th chromosomal and heterochromatic genes. This finding is broadly comparable to reports of reduced X chromosome expression following msl2 RNAi knockdown in S2 cells. Hence MSL2 is required for up-regulation of male X chromosome where as it is not necessary for normal expression of 4th chromosomal genes and heterochromatic genes in Drosophila melanogaster males.

overall_design: Total RNA was prepared from groups of 50 (or more in case of smaller larvae) third instar larvae by TRIzol (Invitrogen) extraction and purified using the RNeasy kit (Qiagen). Three independent RNA preparations for each genotype served as templates for probe synthesis. Affymetrix Drosophila Genome 2.0 chips were hybridized to these probes (Santa Clara, CA). Affymetrix Gene expression data was background corrected, normalized and summarized into a one expression value per sample and probeset using the RMA (robust multi-array average) algorithm.  Changes in gene expression (log2 fold changes) were determined by comparing the mean RMA expression values in the msl21 sample to the mean RMA expression values in the msl21/+ samples.

middle: K

first: Victoria

middle: H

last: Meller


title: Expression profiling in the Drosophila eye reveals unexpected repression of Notch signaling by the JAK/STAT pathway

status: Public on Aug 01 2009

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

country: France

institute: IARC WHO

summary:
Although the JAK/STAT pathway regulates numerous processes in vertebrates and invertebrates through modulating transcription, its functionally-relevant transcriptional targets remain largely unknown. With one jak and one stat (stat92E), Drosophila provides a powerful system for finding new JAK/STAT target genes. Genome-wide expression profiling on eye discs in which Stat92E is hyperactivated, revealed 584 differentially-regulated genes, including known targets domeless, socs36E and wingless. Other differentially-regulated genes (chinmo, lama, Mo25, Imp-L2, Serrate, Delta) were validated and may represent new Stat92E targets. Genetic experiments revealed that Stat92E cell-autonomously represses Serrate, which encodes a Notch ligand. Loss of Stat92E led to de-repression of Serrate in the dorsal eye, resulting in ectopic Notch signaling and aberrant eye growth there. Thus, our micro-array documents a new Stat92E target gene and a previously-unidentified inhibitory action of Stat92E on Notch signaling. These data suggest that this study will be a useful resource for the identification of additional Stat92E targets.

Identification of the JAK/STAT pathway target genes in the Drosophila eye disc

Keywords: Genotype comparison

overall_design: Gene expression profiles from five biological replicates of eye discs with yw (control) and GMR-upd (overexpressing JAK/STAT ligand unpaired) were compared using genome wide mRNA expression profiling by Affymetrix genechip arrays (Drosophila 2.0) and key targets were validated by clonal analysis, in situ hybridization, immunohistochemical staining and quantitative real-time PCR.

first: Maria

middle: S

last: Flaherty

last: Zavadil

first: Laura

middle: A

last: Ekas

first: Erika

last: Bach


title: Expression data for normal and tumor kidneys

city: Rotterdam

first: Dmitry

last: Zubakov

state: ZH

address: Dr. Molewaterplein, 50

department: FMB

country: Netherlands

institute: Erasmus Medical Centre Rotterdam

summary:
End stage renal disease (ESRD) is associated with hyperplastic-cystic remodelling of the kidneys (ARCD) and increased rate of kidney tumours. Using the Affymetrix oligoarray, we have established the gene expression signature of ESRD/ARCD kidneys and compared to those of normal kidneys and of distinct types of renal tumours.
Keywords: normal and different tumor tissues

overall_design: We analysed several array per specific type of renal tumor and normal kidney tissue

first: Anetta

last: Nagy

first: Gyula

last: Kovacs


title: Goat Model for CML

status: Public on Aug 12 2009

city: Philadelphia

first: Don

last: Baldwin

state: PA

address: 277 John Morgan, 3620 Hamilton Walk

department: Pathology and Lab Medicine

country: USA

institute: University of Pennsylvania

summary: To evaluate the long-term growth potential of BCR-ABL-transduced primitive human hematopoietic cells, lin- cord blood cells containing an MSCV-BCR-ABL-IRES-GFP (BCR-ABL) or control-GFP transgene (MIG) were injected IP into fetal goats at 45-55 days of gestation.  Six transplant goats were born alive.  One was examined three weeks after birth and showed GFP+ cells in the blood, bone marrow (BM), liver, kidney, lung, heart, and both skeletal and smooth muscle.  FISH analysis also showed the liver of this goat contained BCR-ABL-GFP transgenic cells.  The remaining five goats appear normal although, in some, the WBC count is elevated 3- to 5-fold.  GFP+ cells, including cells identifiable by FACS as human CD34+ cells, have been detected in the blood of all these goats.  The presence of BCR-ABL-GFP transgenic cells in the BM and liver was confirmed by FISH analysis, and quantitative real-time PCR analysis of genomic DNA isolated from unpurified BM cells obtained from three of the transplant goats demonstrated 3-5×104 copies of the transgene per microgram of DNA.  Microarray transcript profiling was performed on blood and liver tissues of normal goats, BCR-ABL chimeric goats, MIG chimeric goats, and normal human samples.  RNA for human genes was detected in goats transplanted with cord blood cells but not in normal goats, and the RNA abundance of some genes in BCR-ABL chimeric goat blood was similar to or greater than levels observed in MIG goat blood or normal human samples.  Quantitative RT-PCR confirmed the differential expression of several genes in goats carrying the BCR-ABL vs. control transgene.  These results demonstrate long-term engraftment but slow expansion in a large animal model of primitive human hematopoietic cells transduced with a BCR-ABL fusion gene and transplanted in utero.  This novel xenotransplant goat model should be useful for analyzing the initial phases of development of human CML and for assessing new therapies with potential long-term benefits.

sample_organism:
Homo sapiens
Capra hircus

overall_design: Total RNA was extracted from liver (L) and blood (B) samples of normal goats (ng), humans (hu), chimeric goats engrafted with human cord blood stem cells containing control (mig) vector, and chimeric goats engrafted with CML (bcrabl) vector.  RNA samples were profiled on Affymetrix human U133A GeneChips and examined for differentially expressed genes in CML vs control goats, filtering for signals significantly above background levels observed in normal goat to select for specific human gene expression.

first: Xiaoyan

last: Jiang

first: Fanyi

last: Zeng

first: Mei-Juan

last: Chen

first: Jingbin

last: Yan

first: Zhi

middle: J

last: Gong

first: Yan

middle: P

last: Xiao

first: Hui

last: Qian

first: Yves

last: Chalandon

first: Zhao

middle: R

last: Ren

first: Allen

last: Eaves

first: Connie

first: Shu-Zhen

last: Huang


title: Global expression profiling of Arabidopsis plants overexpressing a member of the DEVIL gene family.

city: Columbia

first: Clayton

middle: T

last: Larue

state: MO

address: 304 Life Sciences Bldg

department: Dept of Biological Sciences

institute: University of Missouri, Columbia

summary:
The DEVIL (DVL) family is a plant-specific family of genes that encode predicted small polypeptides (Wen, et al., 2004; Narita, et al., 2004). Overexpression of DVL family members in Arabidopsis results in pleiotropic developmental phenotypes including shortened stature, rounded rosette leaves, clustered inflorescences, shortened pedicles and horn-like protrusions at the distal end of siliques. Point mutations reveled that a conserved C-terminal domain is required for DVL overexpression phenotypes and is conserved in all family members. Based on the overexpression experiments, DVL family members are suggested to play important roles in plant development.

In an attempt to uncover genes whose transcription was changed in response to DVL overexpression, we designed a microarray-based global profiling experiment. A transgenic Arabidopsis line that carried a GVG construct (glucocorticoid inducible) (Aoyama and Chua, 1997) driving the expression of DVL4 was generated and used in this experiment. This allowed for better identification of primary transcriptional responses to DVL overexpression. Experiments with transgenic lines in which DVL overexpression is driven by a constitutive promoter would add the complexity of secondary transcriptional responses as well. Computational analysis of the datasets generated in this experiment lead to the identification of genes that may be involved in responding to DVL overexpression. Experimentation is currently ongoing to investigate the role these genes play in plant development and the DVL overexpression phenotypes.

overall_design:
To identify genes that are transcriptionally responsive to DVL overexpression, we used microarray analysis to globally profile different transgenic Arabidopsis lines in a Columbia (Col) background. A control line was transformed with the GVG construct, but without a coding sequence inserted in the multiple cloning site. This line was indistinguishable from Col Wt with and without dexamethazone (dex, a steroid that activates transcription of the coding sequence inserted in the GVG vector) treatment or mock treatment. This line is called the empty vector control. A second line was also transformed with the GVG construct containing the DVL4 coding sequence. Without dex treatment or mock treatment, this line was indistinguishable from Col Wt, but displayed a typical DVL overexpression phenotype with dex treatment. This line is called GVG DVL4.

These lines were grown in standard growth chambers with 16hr days to the six rosette leaf stage (vegetative). The plants were then mock treated or dex treated and samples for RNA extraction were collected 10hrs post-treatment. Three different samples were treated and collected: Empty vector control with dex treatment; GVG DVL4 with mock treatment; and GVG DVL4 with dex treatment. All samples were collected as three biological replicates. Affymetrix Arabidopsis ATH1 Genome GeneChips were used for the global analysis. Computational analysis was completed using dChip software (www.dchip.org). The empty vector control with dex treatment can be used to correct for any transcriptional responses due to dex treatment alone.

first: Jiangqi

last: Wen

first: John

middle: C

last: Walker


title: Immune Response of Immature Dendritic Cells after Infection with Human Cytomegalovirus Strain TB40E

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

country: Germany

institute: University Tuebingen

summary: Microarray analysis and quantitative real-time PCR revealed that TB40E infection of DCs led to changes of the gene expression pattern. A variety of pro-inflammatory cytokines and chemokines (CXCL10, CXCL11, CCL5), TLR3 and genes whose products function downstream of the TLR3 signalling pathway (e.g. IFN-α, IFN-β) were significantly upregulated.

overall_design: three mock transfected DC vs. three TB40 transfected DCs

first: Markus

last: Mezger

first: Tobias

last: Kessler

first: Florian

last: Gebhardt

first: Hermann

last: Einsele

first: Juergen

last: Loeffler


title: Genes dominantly expressed in germinating pollen

city: Okazaki

first: Mitsuyasu

last: Hasebe

state: Aichi

address: Nishigounaka 38

country: Japan

institute: National Institute for Basic Biology

summary: In sexual reproduction, a proper communication and cooperation between male and female organs and tissue are essential for male and female gametes to unite. In flowering plants, female sporophytic tissues and gametophyte direct a male pollen tube towards an egg apparatus, which consists of an egg cell and two synergid cells. The cell-cell communication between the pollen tube and the egg apparatus, such as the reception of a signal from the egg apparatus at the pollen tube, makes the tip of pollen tube rapture to release the sperm cell. To isolate male factors involved in the interaction between a pollen tube and an egg apparatus, we focused on receptor-like kinases (RLKs), which are extensively diversified in the flowering plant lineage to comprise a large monophyletic gene family. Approximately 620 members were found in the Arabidopsis thaliana genome. Expression patterns of 558 RLKs were analyzed using an Affymetrix ATH1 microarray of A. thaliana. We focused on two RLKs, ANXUR1 (ANX1) and ANXUR2 (ANX2), and characterized their function. Here we report that pollen tubes of anx1/anx2 ruptured before arriving at the egg apparatus, suggesting that ANX1 and ANX2 are male factors controlling pollen tube behavior with directing rupture at proper timing. Furthermore, ANX1 and ANX2 were the most closely related paralogs to a female factor FERONIA/SIRENE controlling pollen tube behavior expressed in synergid cells. Our finding shows that the coordinated behaviors of female and male reproductive apparatuses are regulated by the sister genes, whose duplication might play a role in the evolution of fertilization system in flowering plants.

overall_design: Arabidopsis thaliana Col-0 was grown at 18°C for 8 hr in the dark and at 22°C for 16 hr in the light. To collect germinated pollen with pollen tubes, opened flowers were touched to cellophane layered on the pollen germination medium containing 13.5% sucrose, 10 mM CaCl2, 0.4 mM boric acid, 1 mM KCl, 0.001% myo-inositol, and 0.6% agarose. The released pollen was incubated at 25°C for 6 hr in the dark. For collection of seedlings, seeds were sown on Murashige-Skoog medium containing 1x Murashige and Skoog Plant Salt Mixture (Wako), 1x Gamborg’s vitamin solution (Wako), 1% sucrose, and 0.8% agar. Seedlings including roots with one or two rosette leaves were collected for RNA extraction. RNA was extracted with Isogene (Nippon Gene), precipitated with LiCl, and further purified with RNeasy. The ATH1 genechip (Affymetrix) was used for expression analysis using 10 µg each of total RNA following the manufacturer's instructions. Array data were processed and analyzed with the GCOS1.2 program (Affymetrix) and Excel 2004 (Microsoft). Hybridization with germinating pollen RNA was duplicated and the results were compared to that with seedling RNA.

first: Saori

last: Miyazaki

first: Takashi

last: Murata

first: Nami

last: Sakurai-Ozato

first: Minoru

last: Kubo

first: Taku

last: Demura

first: Hiroo

last: Fukuda


title: Expression data from lung adenocarcinoma

status: Public on Aug 04 2009

city: Munich

first: Jens

last: Neumann

address: Thalkirchner Straße 36

department: Institute of Pathology

institute: Ludwig-Maximilians-Universität München

summary:
Affymetrix Human Genome U133A platform was used to obtain gene expression profiles of 28 pathologically and clinically well characterized adenocarcinomas of the lung. In addition, EGFR status was determined by fluorescent in situ hybridization and immunohistochemistry.
The classification of the cases using a clustering algorithm applied to the expression data correlated significantly with the histopathological tumor grades. In contrast, no correlation of gene expression data and EGFR status could be detected.

overall_design: In this study we evaluated the gene expression of 28 clinico-pathological well characterized lung adenocarcinomas.


title: roX RNAs are not required for expressional regulation in Drosophila females

first: Ying

last: Kong

address: 5047 Gullen Mall

department: Department of Biological Sciences

summary: roX RNAs are involved in the chromosome-wide gene regulation that occurs during dosage compensation in Drosophila. Dosage compensation equalizes expression of X-linked and autosomal genes. Drosophila males increase transcription two-fold from their single X chromosome. This is mediated by the MSL complex, which is composed of the male-specific lethal (MSL) proteins and two noncoding roX RNAs, roX1 and roX2.  Upon elimination of both roX transcripts, a global decrease of X-linked gene expression is observed in males. Expression of the genes on the entire 4th chromosome also decreased in the absence of both roX transcripts. roX1 RNA also presents in females in the early stages. To investigate the effect of loss of roX transcripts on gene expression in females, gene expression was analyzed by microarrays  in roX1-roX2- female flies. To eliminate inconsistency caused by differences in genetic background, expression of roX1-roX2- females with females of virtually identical genetic background but carrying the [hsp83-roX1+] transgene were compared.  Expression of any chromosome did not change in roX1-roX2- females. It was concluded that roX RNAs only effect in males .

overall_design: Total RNA was prepared from groups of 50 third instar larvae by TRIzol (Invitrogen) extraction and purified using the RNeasy kit (Qiagen). Three independent RNA preparations for each genotype served as templates for probe synthesis. These probes were hybridized to Affymetrix Drosophila Genome 2.0 chips (Santa Clara, CA). Genes were filtered for present/absent calls by a PM-MM (Perfect match-Mismatch) comparison. Affymetrix Gene expression data was background corrected, normalized and summarized into a one expression value per replicate sample and probeset using the RMA (robust multi-array average) algorithm. Changes in gene expression were determined by comparing the mean signal intensities of genes on arrays hybridized with roX1- roX2- (mutant) probes to those hybridized with roX1- roX2-;  [hsp83-roX1+] (control) probes.

first: Victoria

last: Meller


title: Global expression profiling to study the effect of glyphosate herbicide treatment on Arabidopsis thaliana

status: Public on Jul 22 2009

city: Corvallis

first: Malay

last: Das

state: OR

address: 200 SW 35th STreet

department: EEB

institute: National Research Council, US-EPA

summary:
Using whole genome microarray (Affymetrix ATH1) we studied the transcriptional response of Arabidopsis thaliana to glyphosate (Roundup Original) herbicde that inhibits 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) enzyme and thus disrupts aromaticamino acid biosynthesis. Few genes related to defense and secondary metabolism were altered.
Keywords: 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) inhibiting herbicide stress response

overall_design: Surfactant (preference 0.25%) treated plants were used as carrier control group and EC50 concentration of glyphosate was used as the herbicide treatment group. Each of the control and treatment group consisted of 3 biological replicates and each biological replicates comprised leaves from 10 individual plants. RNA was extracted at 24h post treatment to study the transcriptional alterations caused by the herbicide treatment.

last: Mader

first: Jay

last: Reichman

first: Lidia

last: Watrud

first: Thomas

middle: G

last: Pfleeger

first: Anton

last: Schäffner

first: David

middle: M

last: Olszyk


title: Global expression profiling to study the effect of triazolopyrimidine herbicide treatment on Arabidopsis thaliana

summary:
Using whole genome microarray (Affymetrix ATH1) we studied the transcriptional response of Arabidopsis thaliana to triazolopyrimidine (FirstRate) herbicde that inhibits acetolactate synthase (ALS) enzyme and thus disrupts branched chain amino acid biosynthesis. A number of genes related to amino acid, protein metabolism, growth, regulatory networks, respiratory pathways, stress, defense and secondary metabolism were altered.
Keywords: Acetolactate synthase (ALS) inhibiting herbicide stress response

overall_design: Surfactant (preference 0.25%) treated plants were used as carrier control group and EC50 concentration of triazolopyrimidine was used as the herbicide treatment group. Each of the control and treatment group consisted of 3 biological replicates and each biological replicates comprised leaves from 10 individual plants. RNA was extracted at 24h post treatment to study the transcriptional alterations caused by the herbicide treatment.

first: Michael


title: Gene Expression Analysis in Skeletal Muscle from Obese, Diet-Sensitive and Diet-Resistant Women

status: Public on Jul 29 2009

city: RTP

first: Joan

last: Stuart

address: 5 Moore Drive

institute: GSK

summary:
Skeletal muscle (rectus femoris) gene expression was analyzed from diet-resistant and diet-sensitive obese women undergoing clinically supervised weight-loss at a weight management clinic
The goal of the study was to characterize global gene expression profiles in skeletal muscle from obese women, prior to their participation in a clinically supervised, low-calorie diet, weight management program. Following entry into the weight-loss program, subjects can be categorized as being 'diet-sensitive' or 'diet-resistant' depending on the rates of weight loss achieved. In the current study, we selected an equal number of diet-sensitive and diet-resistant subjects for comparative expression profiling

overall_design: Skeletal muscle samples were analyzed from diet-sensitive and diet-resistant women, for a total of 12 samples. There were no replicates.

first: Ruth

last: McPherson

first: Mary

middle: E

last: Harper

first: Robert

last: Dent

first: Sujoy

last: Ghosh


title: Expression data from Arabidopsis pollen and semi in vivo- and in vitro-grown pollen tubes.

status: Public on Jul 28 2009

city: Tucson

first: RAVISHANKAR

last: PALANIVELU

state: AZ

address: 1140 E. South Campus Drive P.O. Box 210036

department: Plant Sciences

institute: University of Arizona

summary:
Pollen tubes extend through pistil tissues and are guided to ovules where they release sperm for fertilization. Although pollen tubes can germinate and elongate in a synthetic medium, their trajectory is random and their growth rates are slower compared to growth in pistil tissues. Furthermore, interaction with the pistil renders pollen tubes competent to respond to guidance cues secreted by specialized cells within the ovule. The molecular basis for this potentiation of the pollen tube by the pistil remains uncharacterized.
We used a surgical procedure to obtain large quantities of uncontaminated pollen tubes that grew through the pistil and defined their transcriptome by microarray analysis. We also characterized the transcriptome of in vitro-grown pollen tubes (for 0.5hours or 4hours) and dessicated mature pollen in Arabidopsis.

overall_design: Pollen and pollen tubes were collected as described in the protocols section for RNA extraction and hybridization on Affymetrix ATH1 Genechip microarrays.

first: Yuan

last: Qin

first: Mark

last: Johnson

first: Ravishankar

last: Palanivelu


title: Global expression profiling to study the effect of imidazolinone herbicide treatment on Arabidopsis thaliana

summary:
Using whole genome microarray (Affymetrix ATH1) we studied the transcriptional response of Arabidopsis thaliana to imidazolinone (Arsenal) herbicde that inhibits acetolactate synthase (ALS) enzyme and thus disrupts branched chain amino acid biosynthesis. A number of genes related to amino acid, protein metabolism, growth, regulatory networks, respiratory pathways, stress, defense and secondary metabolism were altered.
Keywords: Acetolactate synthase (ALS) inhibiting herbicide stress response

overall_design: Surfactant (preference 0.25%) treated plants were used as carrier control group and EC50 concentration of imidazolinone was used as the herbicide treatment group. Each of the control and treatment group consisted of 3 biological replicates and each biological replicates comprised leaves from 10 individual plants. RNA was extracted at 24h post treatment to study the transcriptional alterations caused by the herbicide treatment.


title: Global expression profiling to study the effect of sulfometuron methyl herbicide treatment on Arabidopsis thaliana

summary:
Using whole genome microarray (Affymetrix ATH1) we studied the transcriptional response of Arabidopsis thaliana to sulfometuron methyl (oust XP) herbicde that inhibits acetolactate synthase (ALS) enzyme and thus disrupts branmched chain amino acid biosynthesis. A number of genes related to amino acid, protein metabolism, growth, regulatory networks, respiratory pathways, stress, defense and secondary metabolism were altered.
Keywords: Acetolactate synthase (ALS) inhibiting herbicide stress response

overall_design: Surfectant (preference 0.25%) treated plants were used as carrier control group and EC50 concentration of sulfometuron was used as the herbicide treatment group. Each of the control and treatment group consisted of 3 biological replicates and each biological replicates comprised leaves from 10 individual plants. RNA was extracted at 24h post treatment to study the transcriptional alterations caused by the herbicide treatment.


title: Global expression profiling to study the effect of primisulfuron herbicide treatment on Arabidopsis thaliana

summary:
Using whole genome microarray (Affymetrix ATH1) we studied the transcriptional response of Arabidopsis thaliana to primisulfuron (Beacon) herbicde that inhibits acetolactate synthase (ALS) enzyme and thus disrupts branmched chain amino acid biosynthesis. A number of genes related to amino acid, protein metabolism, growth, regulatory networks, respiratory pathways, stress, defense and secondary metabolism were altered.
Keywords: Acetolactate synthase (ALS) inhibiting herbicide stress response

overall_design: Surfectant (preference 0.25%) treated plants were used as carrier control group and EC50 concentration of primisulfuron was used as the herbicide treatment group. Each of the control and treatment group consisted of 3 biological replicates and each biological replicates comprised leaves from 10 individual plants. RNA was extracted at 24h post treatment to study the transcriptional alterations caused by the herbicide treatment.


title: Gene Expression Profiles of Germinal Center B Cells

status: Public on Jul 31 2009

city: Los Angeles

first: Joseph

middle: Gerard

last: Hacia

state: CA

address: 2250 Alcazar Street, IGM 261

department: Biochemistry and Molecular Biology

institute: University of Southern California

summary: We report the gene expression profiles of germinal center B cells obtained by FACS analyses of normal human lymph nodes.

overall_design: We used FACS analyses to isolate germinal center B cells from 3 different individuals with one individual sampled twice. The overall goal was simply to identify genes that are highly expressed or silent in these purified cell populations.

first: Xiaoming

last: Wang

first: Uttam

last: Sinha


title: Affymetrix HG-U133A gene expression profiles of 39 human breast cancer cell lines

status: Public on Jul 13 2009

first: Antoinette

last: Hollestelle

address: Dr. Molenwaterplein 50

department: Medical Oncology

institute: Erasmus University Medical Center

summary: Microarrays were used to detail the global programme of gene expression underlying breast cancer cell lines. We identified two main groups of luminal-type and basal-type breast cancer cell lines by unsupervised Pearson correlation of breast cancer cell lines and intrinsic subtyping. Supervised analysis on spindle versus non-spindle breast cancer cell lines identified a spindle cell signature of 1,144 genes identifying all spindle, basal-type, E-cadherin methylated breast cancer cell lines.

overall_design: Breast cancer cell lines were grown to optimal cell densities for RNA extraction and hybridization on Affymetrix microarrays.

first: Mieke

last: Schutte


title: Heterologous microarrays for the study of drought stress in Musa

status: Public on Jul 04 2009

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

type:
Expression profiling by array
Other

summary: 'Systems-wide' approaches such as microarray RNA-profiling are ideally suited to the study of the complex, overlapping responses of plants to biotic and abiotic stresses. However, commercial microarrays are only available for a limited number of plant species and development costs are so substantial as to be prohibitive for most research groups. Here, we evaluate the use of cross-hybridisation to Affymetrix oligonucleotide GeneChip microarrays to profile the response of the banana (Musa sp.) leaf transcriptome to drought stress using a genomic DNA (gDNA)-based probe-selection strategy to improve the efficiency of detection of differentially expressed Musa transcripts.

platform_organism:
Arabidopsis thaliana
Oryza sativa

overall_design: GeneChip analyses were performed to profile the response of the banana (Musa sp.) leaf transcriptome to drought stress using a genomic DNA (gDNA)-based probe-selection strategy to improve the efficiency of detection of differentially expressed Musa transcripts.

middle: W

last: Davey

first: Neil

last: Graham

first: Bartel

last: Vanholme

first: Rony

last: Swennen

first: Sean

last: May

first: Johan

last: Keulemans


title: Cell Adhesion Molecule 1 (CADM1): A Novel Risk Factor for Venous Thrombosis

status: Public on Jul 15 2009

city: Minneapolis

middle: P.

last: Hebbel

state: MN

address: MMC 480, 420 Delaware St. SE

department: Medicine

institute: University of Minnesota

summary:
Protein C (PC) deficiency increases the risk of venous thrombosis (VT) among members of Kindred Vermont II, but fails to fully account for the inheritance pattern. A genome scan of the pedigree supported the presence of a prothrombotic gene on chromosome 11q23 with weaker support on chromosomes 10p12 and 18p11.2-q11.
Preliminary data from Affimetrix microarray expression analysis of Blood Outgrowth Endothelial Cells of 3 members of Kindred Vermont II compared to a well established normal control group indicated that IgsF4 was decreased in patients versus controls. In addition, both statistical and pathway analysis results suggested that these genes are associated protein C.  Further studies indicated that Cell Adhesion Molecule 1 (CADM1), a member of the IgsF4 superfamily, may be associated with VT.

overall_design: We obtained BOEC (blood outgrowth endothelial cells) from 3 female kindred subjects (ages 56, 61, and 74) with Protein C Deficiency. We also performed microarray analysis on BOEC from 27 normal subjects of diverse ages.

first: Liming

last: Milbauer

first: Peng

last: Wei

first: Judy

last: Enenstein

first: Edwin

last: Bovill


title: Gene-expression profiles of non-tumor-reactive CD8+ T cells

status: Public on Jun 15 2009

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary:
Non-tumor-reactive T cells are characterized by the inabilitzy to lyse autologous tumor cells, low to intermediate avidity TCRs and lack of NY-ESO-1 peptide tetramer binding. However most strikingly, non-tumor-reactive T cells are characterized by a molecular program associated with ‘division arrest anergy’ with elevated expression of the inhibitory molecule p27kip1. This is accompanied by elevated expression of inhibitory molecules and reduced levels of transcription factors involved in T cell activation. Frequency analysis of the inhibited T cell population using the established molecular fingerprint as a novel biomarker might be applied for cancer vaccine development and optimization.
Keywords: cell type comparison

overall_design: Genome-wide transcriptional changes in human non-tumor-reactive CD8+ T cell clones from NY-ESO-1 expressin tumor patients after peptide vaccination using Affymetrix HGU133A arrays.

first: Marc

last: Beyer

middle: L


title: Gene expression profiling of CD4+ and CD8+ T-cells from gene therapy treated ADA patients and from healthy controls

city: Milan

first: Alessandro

last: Aiuti

address: via olgettina 58

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET)

summary:
Gene transfer into HSCs by gammaretroviral vectors (RV) is an effective treatment for inherited blood disorders, although potentially limited by the risk of insertional mutagenesis. We evaluated the genomic impact of RV integration in T-lymphocytes from adenosine deaminase (ADA)-Severe combined immunodeficiency (SCID) patients 10 to 30 months after infusion of autologous, genetically-corrected CD34+ cells. Expression profiling on ex vivo T-cell bulk population revealed no difference with respect to healthy controls. To assess the effect of vector integration on gene expression at the single cell level, primary T-cell clones were isolated from two patients. T-cell clones harboured either one or two vector copies per cell and displayed partial to full correction of ADA expression, purine metabolism and TCR-driven functions. Analysis of retroviral integration sites (RIS) indicated a high diversity in T-cell origin, consistent with the polyclonal TCR-Vbeta repertoire. Quantitative transcript analysis of 120 genes within a 200kb-window around RIS showed modest (2.8- to 5.2-fold) disregulation of 5.8% genes in 18.6% of the T-cell clones compared to controls. Nonetheless, affected clones maintained a stable phenotype and normal functions in vitro. These results confirm that RV-mediated gene transfer for ADA-SCID is safe, and provide crucial information for the development of future gene therapy protocols.

Global gene expression profiling was performed on CD4+ and CD8+ T-cell subsets purified ex vivo from three ADA-SCID patients at different times after gene therapy. The microarray analysis showed a substantial overlap with the expression patterns of T-cells from controls, indicating the absence of gross abnormalities in the development and function of T-cells derived from genetically corrected hematopoietic stem/progenitor cells.

overall_design: Transcript profiling was carried out in CD4+ and CD8+ T-cells purified with immunomagnetic beads (Miltenyi Biotec, Germany) from the peripheral blood lymphocytes of ADA-SCID patients (Pt1, 3 and 4) 10-30 months after autologous transplantation with genetically corrected CD34+ cells. At the indicated time points, the percentage of vector-positive T-cells by qPCR was >75%. Transcript profiles were determined using the Affymetrix HG-U133A microarray and compared to those of age-matched healthy controls (n=4; C1, C2, C3, C4).

first: Barbara

last: Cassani

first: Eugenio

last: Montini

first: Giulietta

last: Maruggi

last: Ambrosi

first: Massimiliano

last: Mirolo

first: Silvia

last: Selleri

first: Erika

last: Biral

first: Ilaria

last: Frugnoli

first: Vivian

last: Hernandez-Trujillo

first: Clelia

last: DiSerio

first: MariaGrazia

last: Roncarolo

first: Luigi

last: Naldini

first: Fulvio

last: Mavilio


title: Uncovering the Arabidopsis thaliana nectary transcriptome: nectary and reference tissues

city: Duluth

first: Clay

last: Carter

address: 1035 Kirby Dr

department: Biology

institute: University of Minnesota Duluth

summary:
Many flowering plants attract pollinators by offering a reward of floral nectar. Remarkably, the molecular events involved in the development of nectaries, the organs that produce nectar, as well as the synthesis and secretion of nectar itself, are poorly understood. Indeed, to date, no genes have been shown to directly affect the de novo production or quality of floral nectar. To address this gap in knowledge, the ATH1 Affymetrix GeneChip array was used to systematically investigate the Arabidopsis nectary transcriptome to identify genes and pathways potentially involved in nectar production. In this study, we identified a large number of genes differentially expressed between secretory lateral nectaries and non-secretory median nectary tissues, as well as between mature lateral nectaries (post-anthessis) and immature lateral nectary tissue (pre-anthesis).

To identify genes that are specifically upregulated in nectary tissues, and therefore may contribute to nectar production, we compared individual nectary samples (ILN, MLN & MMN) with 51 non-nectary reference tissues (downloaded .cel files from other studies).  270 genes were identified as being significantly upregulated in nectaries.  The expression patterns for multiple genes were also confirmed via RT-PCR.

The co-normalized RMA expression data (i.e., our own 8 nectary samples and 51 samples downloaded from GEO) are available as a supplementary file at the foot of this record.

overall_design:
Three different types of RNA samples were prepared from Arabidopsis thaliana ecotype Columbia-0 nectaries: mature lateral nectaries (MLN; Stage 14-15 flowers), immature lateral nectaries (ILN, Stage 11-12 flowers), and mature median nectaries (MMN, Stage 14-15 flowers) [developmental stages defined by (Smyth et al., 1990)]. MLN are secretory tissues, whereas, ILN and MMN are pre-secretory and nonsecretory tissues, respectively. All nectary tissues were separately dissected by hand from the flowers of primary inflorescences of ca. 30-35 day-old plants.  All plants were grown in soil with a 16h light/8h dark light regimen. Due to the small size of nectaries, dissections took place over several days from 4-8 hours after dawn (h.a.d.).

The gene expression dataset obtained by our laboratory was enriched with third party expression data (i.e., 51 GEO Samples: GSM131510..GSM131660).  The final gene expression dataset includes 59 hybridizations.

first: Brian

last: Kram

first: Wayne

last: Xu


title: Comparison of VEGF versus EGF gene expression in HUVEC

status: Public on Jun 30 2009

city: Vienna

first: Bernhard

last: Schweighofer

address: Lazarettgasse 14

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

summary:
Angiogenesis is defined as the formation of new capillaries by sprouting from preexisting vessels. It is mainly triggered by vascular endothelial growth factor (VEGF) and occurs in the adult primarily in wound healing processes or in pathologic tumor vessel growth. To identify genes specifically triggered by VEGF and involved in the process of angiogenesis, we utilized Affymetrix microarrays hybridized with cRNA of human umbilical vein endothelial cells (HUVEC) stimulated with either the main trigger of angiogenesis, VEGF or a more general mitogenic growth factor, EGF.
This was done under the assumption that, in comparison to EGF, VEGF would induce an additional set of genes not solely required for cell division but necessary for angiogenesis. The obtained data revealed that in HUVEC VEGF induces a large repertoire of genes, the majority of which are not or significantly less induced by EGF.
Keywords: time course

overall_design: HUVEC, quiescent by maintaining dense cultures in complete medium for four days without change of medium were stimulted with 100ng of VEGF or 50ng of EGF for 30, 60, 150 and 360 minutes and total RNA was isolated using Trizol.

first: Martin

last: Bilban

first: Erhard

last: Hofer


title: Uncovering the Arabidopsis thaliana nectary transcriptome

summary: Many flowering plants attract pollinators by offering a reward of floral nectar. Remarkably, the molecular events involved in the development of nectaries, the organs that produce nectar, as well as the synthesis and secretion of nectar itself, are poorly understood. Indeed, to date, no genes have been shown to directly affect the de novo production or quality of floral nectar. To address this gap in knowledge, the ATH1 Affymetrix GeneChip array was used to systematically investigate the Arabidopsis nectary transcriptome to identify genes and pathways potentially involved in nectar production. In this study, we identified a large number of genes differentially expressed between secretory lateral nectaries and non-secretory median nectary tissues, as well as between mature lateral nectaries (post-anthessis) and immature lateral nectary tissue (pre-anthesis).

overall_design: Three different types of RNA samples were prepared from Arabidopsis thaliana ecotype Columbia-0 nectaries: mature lateral nectaries (MLN; Stage 14-15 flowers), immature lateral nectaries (ILN, Stage 11-12 flowers), and mature median nectaries (MMN, Stage 14-15 flowers) [developmental stages defined by (Smyth et al., 1990)]. MLN are secretory tissues, whereas, ILN and MMN are pre-secretory and nonsecretory tissues, respectively. All nectary tissues were separately dissected by hand from the flowers of primary inflorescences of ca. 30-35 day-old plants.  All plants were grown in soil with a 16h light/8h dark light regimen. Due to the small size of nectaries, dissections took place over several days from 4-8 hours after dawn (h.a.d.).


title: Candidate genes for the recurrence of glioblastoma multiforme identified by microarray

city: Roma

first: Nathalie

last: Saulnier

address: Largo Francesco Vito,1

institute: Università Cattolica del Sacro Cuore di Roma

summary:
Background: Glioblastoma multiforme (GBM) is the most aggressive and most lethal primary malignant brain tumor, correlated with survival rates of less than one year from the time of diagnosis. Current surgical procedure attempts to remove the bulk of the tumor mass, whereas GBM frequently recurs within 1-3cm from the primary tumor resection site. Molecular mechanisms involved in the recurrence of the tumor are still poorly understood. The aim of the study was to define the molecular signature of GBM surrounding white matter (WM) in order to better understand the molecular mechanisms involved with tumor relapse.
Material & Methods: Human GBM tumor bulk and surrounding tissue (1-3cm from the border of the tumor) were obtained from five patients who underwent total tumour resection, while normal white matter was harvested from patients who underwent surgical procedure for nonmalignant pathologies. Samples were processed for hybridization on the Affymetrix Human U133A arrays and data were examined with the GeneSpring analysis software.
Results: Gene expression analysis of the samples was done in 2 independent steps. First, molecular profiling comparison of GBM surrounding WM and normal WM resulted in 59 genes differentially expressed between both tissues. Among these, numerous genes expressed by mature neural cells were down-regulated in GBM surrounding WM, while gene products supporting invasion were overexpressed. Moreover, KLRC1, a specific natural killer receptor naturally involved in the activation of antitumoral cells was drastically repressed in GBM surrounding WM, suggesting that the antitumoral immune surveillance is compromised in this tissue.
Second, we focused our study on genes specifically regulated in GBM periphery respectively to GBM core. The highest up-regulated gene in GBM surrounding tissue encodes for DTX4, a regulator of NOTCH signalling pathway described for its key role in maintaining neural progenitors in an uncommitted state.
Conclusion: This study revealed unique molecular characteristics of GBM surrounding tissue, showing the dysregulation of genes involved in immune surveillance along with genes associated to stemness maintenance. All together, these data may help to understand the molecular mechanisms associated with GBM recurrence

overall_design: This study attempted to define the molecular characteristics of the GBM surrounding tissue. To this end, GBM tumor samples were obtained from 5 patients who underwent total tumor resection. Surrounding tumor mass tissue was retrieved in all cases from not infiltrated white matter sited at 2 cm from the macroscopic tumor border. Furthermore, control white matter biopsies were harvested from patients operated on for deep intracerebral cavernomas. Each sample was hybridized onto Affymetrix human U133 arrays. For each patient, tumor core sample and surrounding tissue were harvested and are identified with the same suffix number. In 2 cases, (patients 3 and 4), two tumor peripheral tissue samples were harvested and are identified with the same number followed by "R" (replicate).

first: Pasquale

last: de Bonis

first: Barbara

last: Pettorini

first: Giovanni

last: Sabatino

first: Antonio

last: Gasbarrini

first: Annunziato

last: Mangiola


status: Public on Jun 23 2009

city: Little Rock

first: Ying

last: Su

state: AR

address: 1120 Marshall St. South Campus

department: physiology

institute: UAMS

summary: A Krüppel-like factor 9 (Klf9) regulated network in HEC-1-A endometrial carcinoma cells encompassing adhesion proteins, steroid- and menstrual cycle-regulated proteins of the uterine endometrium, novel membrane proteins, and nuclear receptors

overall_design: The 4S and 9S sub-lines were derived from the original human HEC-1-A endometrial carcinoma cell line and contain a stably transfected expression plasmid encoding full-length Krüppel-like factor 9 (KLF9), whereas the 2AS and 3AS sub-lines contain a stably transfected plasmid encoding an antisense (AS) RNA to KLF9. All cell lines were derived concurrently. The ‘sense’ (S) and ‘antisense’ (AS) cell lines differ in relative levels of KLF9 protein and activity, with sense greater than antisense, respectively. For the present work, the 4S and 2AS sub-lines were propagated to near confluence. The 9S and 3AS sub-lines were propagated on a different occasion than for the 4S and 2AS cell lines.RNA preparationRNA was harvested using TRIzol reagent. Two replicate cRNA targets were generated from each HEC-1-A sub-line RNA preparation; all eight targets were made and sized at the same time.

first: Frank

last: Simmen

first: Rijin

last: Xiao

first: Rosalia


title: Differentially expressed genes among cells constituting an in vitro human lung carcinogenesis system

status: Public on Jul 16 2009

city: Houston

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

summary: Genes differentially expressed among cells constituting an in vitro human lung carcinogenesis model consisting of normal, immortalized, transformed and tumorigenic bronchial epithelial cells were identified. The differentially expressed genes were then analyzed to determine their relevance to the gene expression patterns of clinical non-small cell lung cancer (NSCLC) samples as well as the clinical outcome of patients with this disease.

overall_design: Total RNA was extracted from two different replicate culture dishes for each cell line. Differentially expresed genes between the tumorigenic 1170-I lung epithelial cells and the NHBE normal cells that also displayed gradual modulation in expression across the entire in vitro model were determined. The differentially expressed genes were further analyzed by functional pathways analysis and integrated (as gene signatures) with gene expression data of human NSCLC clinical samples obtained from published datasets.

first: Ludovic

last: Lacroix

first: Carmen

last: Behrens

first: Luisa

last: Solis

first: Xuemin

last: Gu

first: Jack

last: Lee

first: Eiji

last: Tahara

first: Dafna

last: Lotan

first: Waun

last: Hong

first: Ignacio

middle: I

last: Wistuba

first: Reuben


title: Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots.

status: Public on Jun 09 2009

city: Ithaca

first: Ji-Young

state: NY

address: Tower Rd.

institute: Boyce Thompson Institute

summary: Understanding how the expression of transcription factor (TF) genes is modulated is essential for reconstructing gene regulatory networks. There is increasing evidence that sequences other than upstream noncoding can contribute to modulating gene expression, but how frequently they do so remains unclear. Here, we investigated the regulation of TFs expressed in a tissue-enriched manner in Arabidopsis roots. For 61 TFs, we created GFP reporter constructs driven by each TF's upstream noncoding sequence (including the 5'UTR) fused to the GFP reporter gene alone or together with the TF's coding sequence. We compared the visually detectable GFP patterns with endogenous mRNA expression patterns, as defined by a genome-wide microarray root expression map.

overall_design: To obtain a comprehensive non-overlapping root expression map which would be compared with promoter GFP fusion lines by imaging, we identified three cell type specific GFP marker lines and profiled transcripts in selected cell types using a cell sorting-microarray technique.

first: Jean

last: Wang

first: Philip

last: Benfey


title: Expression data from precisely staged blastula wild-type and haploid Drosophila embryos

status: Public on Jun 02 2009

city: Princeton

last: Lu

state: NJ

address: Washington Rd

department: Molecular biology

institute: Princeton University

summary:
In most embryos, the mid-blastula transition is a complex process featuring maternal RNA degradation, cell cycle pause, zygotic transcriptional activation and morphological changes. The nucleocytoplasmic (N/C) ratio has been proposed to control the multiple events at MBT. To understand the global transcriptional response to the changes of the N/C ratio, we profiled wild type and haploid embryos using cDNA microarrays at three developmental stages.

Keywords: time course and different genotype

overall_design: For the diploid transcriptional profile, we prepared cDNA from hand selected wild-type embryos at cycle 13 interphase (15min after the nuclear division of cycle 12) and at early and late cycle 14 interphase (15min and 40 min after the nuclear division of cycle 13), respectively. For the haploid, cDNA was prepared from cycle 14 embryos  (15min after the nuclear division of cycle 13) and early and late cycle 15 embryos (15min and 40 minutes after the nuclear division of cycle 14). The collection was designed in this way so that each cell cycle stage of the diploid has a counterpart stage with matched  N/C ratio in the haploid (e.g. cycle 13 in the diploid has the same N/C ratio as cycle 14 in the haploid). In all experiments, the cell cycle progression was monitored by the Histone-GFP pattern. Triplicates of about 50 embryos each with right age were collected for each time point.

first: Eric

last: Wieschaus


title: Expression data from liver of obese (with or without type 2 diabetes) and lean human subjects.

status: Public on Jun 01 2009

city: Boston

first: Mary Elizabeth

last: Patti

state: MA

address: 1 Joslin Place

department: Research Division

institute: Joslin Diabetes Center

summary: Hepatic lipid accumulation is an important complication of obesity linked to risk for type 2 diabetes. To identify novel transcriptional changes in human liver which could contribute to hepatic lipid accumulation and associated insulin resistance and type 2 diabetes (DM2), we evaluated gene expression and gene set enrichment in surgical liver biopsies from 13 obese (9 with DM2) and 5 control subjects, obtained in the fasting state at the time of elective abdominal surgery for obesity or cholecystectomy. RNA was isolated for cRNA preparation and hybridized to Affymetrix U133A microarrays.

overall_design: Human liver samples were obtained from 5 lean control subjects undergoing elective cholecystectomy and 13 obese subjects (with or without Type 2 diabetes) undergoing gastric bypass surgery.  Subjects with diabetes were classified as either well-controlled or poorly-controlled.

first: Jussi

last: Pihlajamäki

first: Joshua

last: Schroeder

first: Edward

last: Mun

first: Allison

middle: B

last: Goldfine

first: Mary-Elizabeth


title: Gene Expression Profiles of Pregnant and Non-pregnant Whole Blood

status: Public on Jun 10 2009

city: Hong Kong

first: Yuk Ming

middle: Dennis

last: Lo

address: The Prince of Wales Hospital

department: Department of Chemical Pathology

country: China

institute: The Chinese University of Hong Kong

summary: Comparison of gene expression profiles in whole blood collected from pregnant and non-pregnant females.

overall_design: Peripheral whole blood samples from 5 third trimester pregnant females and 5 non-pregnant females were collected. The gene expression profiles of the two groups were compared using Affymetrix HG-U133A and HG-U133B array sets.

first: Macy

last: Heung

first: Shengnan

last: Jin

first: Nancy

last: Tsui

first: Chunming

last: Ding

first: Tak

middle: Y

last: Leung

first: Tze

middle: K

last: Lau

first: Rossa

last: Chiu

first: Yuk


title: Transcript profiling in LTR mutants

city: Planegg

first: Michael

last: Scharfenberg

state: Bayern

address: Großhaderner Str. 2-4

department: Botanik I

institute: LMU München

summary: STN7-dependent phosphorylation of an as yet unknown thylakoid protein triggers the signaling events associated with the  long-term acclimatory response (LTR). The LTR-associated signaling events regulate the expression of photosynthesis-related genes on the post-transcriptional level (nucleus), as indicated by transcript profiling in LTR mutants.

overall_design: 5 µg of total RNA of two to three biological replicates of the different pools (10 plants each pool) of rosette leaves of 4-week-old Col-0, Wassilewskija, stn7-1, psad1-1, stn7-1 psad1-1, psae1-3 and stn7-1 psae1-3 plants was processed and hybridized to a GeneChip Arabidopsis ATH1 Genome Array using the One-Cycle Target Labeling and Control Reagents according to the manufacturer’s instructions (Affymetrix); psad1 (2 replicates) psad1 stn7 (3 replicates) Col-0 (3 replicates) Ws (2 replicates) psae (2 replicates) psae stn7 (2 replicates) stn7 (3 replicates)

first: Paolo

last: Pesaresi

first: Dario

last: Leister


title: Arabidopsis thaliana gene expression changes upon treatment with green peach aphid saliva

first: Georg

last: Jander

address: 1 Tower Rd

institute: Boyce Thompson Institute for Plant Research

summary: Myzus persicae (green peach aphid) feeding on Arabidopsis thaliana induces a defense response, quantified as reduced aphid progeny production, in infested leaves but not in other parts of the plant. Similarly, infiltration of aphid saliva into Arabidopsis leaves causes only a local increase in aphid resistance. Further characterization of the defense-eliciting salivary components indicates that Arabidopsis recognizes a proteinaceous elicitor with a size between 3 to 10 kD. Genetic analysis using well-characterized Arabidopsis mutant shows that saliva-induced resistance against M. persicae is independent of the known defense signaling pathways involving salicylic acid, jasmonate, and ethylene. Among 78 Arabidopsis genes that were induced by aphid saliva infiltration, 52 had been identified previously as aphid-induced, but few are responsive to the well-known plant defense signaling molecules salicylic acid and jasmonate. Quantitative PCR analysis confirms expression of saliva-induced genes. In particular, expression of a set of O-methyltransferases, which may be involved in the synthesis of aphid-repellent glucosinolates, was significantly up-regulated by both M. persicae feeding and treatment with aphid saliva. However, this did not correlate with increased production of 4-methoxyindol-3-ylmethylglucosinolate, suggesting that aphid salivary components trigger an Arabidopsis defense response that is independent of this aphid-deterrent glucosinolate.

overall_design: 3 biological replicates (control and treatment). Total number of samples: 6.

first: Martin

last: de Vos


title: Transcriptome comparison of Col-0, se-1, ago1-27 and se-1 35S::MIR156 in Arabidopsis thaliana.

status: Public on Jun 12 2009

city: Tuebingen

first: Jiawei

last: Wang

address: Spemannstr 37-39

institute: Max Planck Institute for Developmental Biology

summary: Microarray analysis of wild type plants and plants with reduced (ago1-27 and se-1) or increased miR156 levels (se-1 p35S:MIR156). Shoot apices were dissected from 20-day-old, short-day grown plants.

overall_design: Plants are grown in short day for 20 days. Total RNAs from shoot apex are extracted by RNeasy Plant Mini kit (Qiagen). The probes are labeled with MessageAmp-Biotin Enhanced, single round aRNA amplification kit from Ambion and hybridized to Affy ATH1 array. Each genotype has two replicates.

first: Detlef

last: Weigel


title: CD2 distinguishes two subsets of human plasmacytoid  dendritic cells with distinct phenotype and functions

status: Public on May 21 2009

city: Dallas

first: Damien

last: Chaussabel

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

summary: Plasmacytoid dendritic cells (pDCs) are key regulators of anti-viral immunity. They rapidly secrete IFN-alpha and cross-present viral antigens thereby launching adaptive immunity. Here we show that activated human pDCs inhibit replication of cancer cells, and kill them in a contact dependent fashion. Expression of CD2 distinguishes two pDC subsets with distinct phenotype and function. Both subsets secrete IFN-alpha and express Granzyme B and TRAIL. CD2high pDCs uniquely express lysozyme and can be found in tonsils and in tumors. Both subsets launch recall T cell response. However, CD2high pDCs secrete higher levels of IL12 p40, express higher levels of co-stimulatory molecule CD80 and are more efficient in triggering proliferation of naïve allogeneic T cells. Thus, human blood pDCs are composed of subsets with specific phenotype and functions.

overall_design: pDC subsets were isolated from two different donors. They were analyzed in two independent experiments.


title: Differences Between Follicular Lymphoma With and Without Translocation t(14;18)

status: Public on Jun 03 2009

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

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

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

summary: Follicular lymphoma (FL) is genetically characterized by the presence of the t(14;18)(q32;q21) chromosomal translocation in approximately 90% of cases. In contrast to FL carrying the t(14;18), their t(14;18)-negative counterparts are less well studied regarding their immunohistochemical, genetic, molecular and clinical features. Within a previously published series of 184 FL grade 1-3A with available gene expression data, we identified 17 FL lacking the t(14;18). Comparative genomic hybridization and high resolution SNP array profiling demonstrated that gains/amplifications of the BCL2 gene locus in 18q were restricted to the t(14;18)-positive FL subgroup. A comparison of gene expression profiles revealed an enrichment of germinal center B-cell associated signatures in t(14;18)-positive FL, whereas activated B-cell like, NFƒÛB, proliferation and bystander cell signatures were enriched in t(14;18)-negative FL. These findings were confirmed by immunohistochemistry in an independent validation series of 84 FL, in which 32% of t(14;18)-negative FL showed weak or absent CD10 expression and 91% an increased Ki67 proliferation rate. Although overall survival did not differ between FL with and without t(14;18), our findings suggest distinct molecular features of t(14;18)-negative FL.

overall_design: Fresh-frozen tumor-biopsy specimens were obtained from 184 untreated patients who had received a diagnosis of follicular lymphoma. RNA was extracted from the biopsy specimens and was examined for gene expression with the use of Affymetrix U133A and U133B microarrays.


title: Differential gene expression in peripheral blood CD2+ leukocytes from PATH particpants

status: Public on May 26 2009

city: Los Angeles

first: Steve

last: Cole

address: 11-934 Factor Bldg, UCLA

institute: UCLA School of Medicine

summary:
Gene expression profiling was carried out on peripheral blood CD2+ leukocytes from 29 children with asthma.  The primary research question is whether gene expression differs in individuals from high socioeconomic status environments vs low socioeconomic status environments.
Keywords: Risk prediction


title: Genetical toxicogenomics of lead treatment

city: Birmingham

first: Grier

last: Page

state: AL

institute: University of Alabama at Birmingham

summary:
75 Diosophilia Roo lines, recominant inbred lines, were raised to adulthood either on conventional diet or diet supplemented with lead acetate. Whole flies were used for RNA extraction. RNA was run on Dros Genome 2 arrays. Each line also genotyped for 88 markers
Control food consisted of standard cornmeal, agar, sugar, yeast, and 250 microM NaAc (Ashburner 1989). Lead-contaminated food consisted of standard food plus 250 microM PbAc (lead exposure at this concentration has been shown to affect locomotion in adults (Hirsch et al. 2003)).

Keywords: genetical genomic

overall_design: 75 RI lines each line treated and untreated with lead acetate

first: Page

last: Grier P


title: Effects of Nipped-B and Rad21 sister chromatid cohesin proteins on gene expression in Drosophila ML-DmBG3 cells

status: Public on May 19 2009

city: Saint Louis

first: Dale

last: Dorsett

address: 1100 South Grand Boulevard

institute: Saint Louis University School of Medicine

summary:
Effects of Nipped-B and Rad21 sister chromatid cohesin proteins on gene expression data in ML-DmBG3 cells derived from Drosophila melanogaster larval central nervous system
We examined the effects of Nipped-B and Rad21 knockdown on gene expression in BG3 cells using microarrays that measure over 18,700 transcripts to (a) determine if the effects of cohesion on E(spl)-C and invected-engrailed expression are unique, (b) look for effects of cohesin on regulators of E(spl)-C and engrailed, and (c) obtain a comprehensive view of the effects of cohesin on gene expression.

overall_design:
Effects of cohesin knockdown on E(spl)-C and invected-engrailed transcription vary over time, so we used two independent samples for three days after RNAi treatment, one four day and one six day sample for both Nipped-B and Rad21 knockdown, and mock RNAi controls for each time point.

For RNAi treatment, cells were plated at 5x106 cells per 3 cm well. Media was replaced with 1 ml of Express Five SFM (Invitrogen) with 1% FCS, and 10 micrograms per ml insulin. The indicated amount of dsRNA was added per well. Media was adjusted to 3 ml and 10% FCS with Schneider’s media after 2 hrs. Cells were replated as needed. Templates for dsRNA synthesis were made by PCR from cDNA templates using primers with T7 promoters (see supplementary file linked below). Equal amounts of two dsRNAs against each target were used.

first: Akbar

last: Siddiqui


title: Bladder Cancer 40 Cell Lines

status: Public on Aug 26 2009

city: Charlottesville

first: Jae

last: Lee

state: VA

department: Public Health Sciences

institute: University of Virginia

summary:
40 bladder cancer cell lines were profiled with their genome-wide gene expression patterns using Affymetrix HG-U133A chips.
Keywords: bladder cancer cell line expression profiling

overall_design: Total RNA sample of each of the 40 cell lines was obtained before the treatment of any anticancer compound.

first: Dan

last: Theodorescu


title: Iron-deficiency-induced changes in wild type, ubc13A and cucumber CsUBC13 overexpressed Arabidopsis roots

status: Public on Jul 07 2009

city: Taipei

first: Wolfgang

last: Schmidt

address: No. 128, Sec 2, Academia Rd, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

summary: CsUBC13 was identified via proteomics from iron starvation treated Cucumber root. ubc13A is an ABRC seed stock (CS51269). CS851269 was purchased from ABRC and confirmed as homozygous Atubc13A knock-out T-DNA mutant. We generated transgenic arabidopsis with ectopic expression of CsUBC13 gene under control of the cauliflower 35S promotor. Both genotypes and Col-0 were used to investigate the transcriptional response to Iron (Fe) deficiency.

overall_design: Wild type Col-0, ubc13A and transgenic overexpressor OE were grown under normal and iron-deficiency conditions. Roots were collected with 3 biological replicates.

first: Wenfeng

last: Li

first: Chungwen

last: Lin


title: Genes regulated by hepatocyte growth factor as targets to sensitize ovarian cancer cells to cisplatin

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

summary: Advanced ovarian cancers are initially responsive to chemotherapy with platinum drugs but develop drug resistance in most cases. We showed recently that hepatocyte growth factor (HGF) enhances death of human ovarian cancer cell lines treated with cisplatin (CDDP) and that this effect is mediated by the p38 mitogen-activated protein kinase. In this work, we integrated genome-wide expression profiling, in silico data survey, and functional assays to identify transcripts regulated in SK-OV-3 ovarian cancer cells made more responsive to CDDP by HGF. Using oligonucleotide microarrays, we found that HGF pretreatment changes the transcriptional response to CDDP. Quantitative reverse transcription-PCR not only validated all the 15 most differentially expressed genes but also confirmed that they were primarily modulated by the combined treatment with HGF and CDDP and reversed by suppressing p38 mitogen-activated protein kinase activity. Among the differentially expressed genes, we focused functional analysis on two regulatory subunits of the protein phosphatase 2A, which were down-modulated by HGF plus CDDP. Decrease of each subunit by RNA interference made ovarian cancer cells more responsive to CDDP, mimicking the effect of HGF. In conclusion, we show that HGF and CDDP modulate transcription in ovarian cancer cells and that this transcriptional response is involved in apoptosis regulation. We also provide the proof-of-concept that the identified genes might be targeted to either increase the efficacy of chemotherapeutics or revert chemotherapy resistance.

overall_design:
Two of the time-course experiments, done independently
(TR5 and TR7), were analyzed.
time 0 (h0)
time 6 hours (h6)
time 12 hours (h12)
time 24 hours (h24)
with (hgf1) and without addition of HGF (hgf0)

first: Martina

last: Olivero

first: Tina

last: Ruggiero

first: Silvia

last: Saviozzi

first: Andrea

last: Rasola

first: Nadia

last: Coltella

first: Stefania

last: Crispi

first: Ferdinando

last: Di Cunto

first: MariaFlavia

last: Di Renzo


status: Public on May 16 2009

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

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

summary:
A SNP microarray and FISH-based procedure to detect allelic imbalances in multiple myeloma: an integrated genomics approach reveals a wide dosage effect on gene and microRNA expression

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Effects of heat, anoxia, and combined heat-anoxia treatments

status: Public on May 30 2009

city: San Giuliano Terme

first: Pierdomenico

last: Perata

state: Pisa

address: Via Guidiccioni 8-10

department: Institute of Life Sciences

institute: Sant'Anna School of Advanced Studies

summary: Anoxia induces several heat shock proteins and a heat pre-treatment can acclimatize Arabidopsis seedlings to a subsequent anoxic treatment.  In this work we analyzed the response of Arabidopsis seedlings to anoxia, heat and a combined heat+anoxia stress. A significant overlapping between the anoxic and heat shock responses has been observed by whole-genome microarray analysis.

overall_design:
We treated Arabidopsis seedling, 4-days old, dark germinated with:
-Control (23°C, dark, liquid Murashige-Skoog medium containing 30mM sucrose).
-Heat-treated (38°C for 90 minutes, dark, liquid Murashige-Skoog medium containing 30mM sucrose).
-Anoxia-treated (23°C,  under anoxia for 6h, dark, liquid Murashige-Skoog medium containing 30mM sucrose).
-combined heat+Anoxia-treatment (23°C,  treated at 38°C for 90 min and thereafter under anoxia for 6h, dark, liquid Murashige-Skoog medium containing 30mM sucrose).

Two biological replicates for each condition.

first: Valeria

last: Banti

first: Fabrizio

last: Maffessoni

first: Elena

last: Loreti

first: Amedeo

last: Alpi


title: Global gene expression pattern of human brain neuronal (SH-SY5Y) cell lines exposed to sarin (GB).

status: Public on May 11 2009

city: Augusta

first: Pachiappan

last: Arjunan

state: Georgia

address: 1120 15th ST, Laney walker Blvd,

department: Anatomy, Unit on Retinal Vascular Neurobiology, BMB

institute: NUS, NIH, GRU

summary:
Total RNA was isolated from sarin (GB) treated (n = 6 flasks) untreated (control n = 6) neuronal (SH-SY5Y) cell lines using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). (Biological Replicates for each time points).
Keywords: Time-course

overall_design: Global gene expression pattern of human neuronal (SH-SY5Y) cell lines exposed to sarin (GB) at various time points.

first: Manikandan

last: Jayapal

first: Gopalakrishnakone

last: Ponnampalam


title: Gene expression in benzene-exposed workers

city: Berkeley

first: Cliona

last: McHale

address: 384 Li Ka Shing Center

department: School of Public Health

institute: University of California Berkeley

summary:
The effect of benzene exposure on peripheral blood mononuclear cell (PBMC) gene expression was examined in a population of shoe-factory workers with well-characterized occupational exposures to benzene.
We compared data from two microarray platforms (Illumina and Affymetrix).
Keywords: occupational exposure

overall_design: Eight workers exposed to benzene and eight unexposed controls who were frequency-matched to these subjects on the basis of age and gender were analyzed. Affymetrix and Illumina arrays.  Illumina: Group A - control, Group B - benzene.


title: Hybrids assimilate organ-specific metastasis gene signatures from both parental cells

status: Public on May 06 2009

city: Princeton

first: Yibin

last: Kang

address: LTL 254, Washington Road

department: Molecular Biology

institute: Princeton University

summary:
Spontaneous cell fusion of MDA-MB-231 bone-metastatic subline Bm (i.e., SCP2) and lung metastatic subline Lm (i.e., LM2) gave rise to hybrid lines BLm-FACS or BLm-DRUG, as well as its single clones (#8, #12, #18). The hybrids acquired the metastasis tropisms from both parental cells. Expression profiles of the parental cells, the hybrids and several previously characterized MDA-MB-231 metastatic derivatives were compared. Hierarchical clustering showed the hybrids assimilated the organ-specific metastasis gene signatures from both parental cells.

Keywords: Cell type comparison

overall_design: Twenty-six cell lines were analyzed, including the parental line MDA-MB-231; cell fusion partner lines Bm and Lm; self-fused lines BBm and LLm; hetero-fused lines BLm-FACS, BLM-DRUG and clones BLm-DRUG-8, -12 and -18; strongly bone-metastatic lines 1833, SCP14, SCP20, SCP25 and SCP46; strongly lung-metastatic lines 3481, 4142, 4173, 4175 and 4180; and weakly metastatic lines SCP3, SCP4, SCP6, SCP28, SCP32 and SCP43. Single sample for each line.

first: Xin

last: Lu


title: Flg22 regulates MAP kinase 6 interaction with an ethylene response factor substrate via ethylene

status: Public on May 15 2009

city: Halle

first: Tino

last: Unthan

address: Weinberg

department: stress and developmental biology

institute: Leibniz Institue of Plant Biochemistry (IPB)

summary:
Despite their importance, plant MAP kinase targets are still poorly elucidated. Here, the specific in vivo interaction of an ethylene response factor (ERF104) with the Arabidopsis MAP kinase, MPK6, is shown by fluorescence resonance energy transfer. The interaction, which is lost within minutes after treatment with the flagellin-derived flg22 peptide, is dependent on both MPK6 kinase activity and rapid ethylene signaling initiated downstream of MPK6 activation. ERF104 is an MPK6 substrate and phosphorylation site mutations affected its stability. ERF104 activates promoters with GCC elements. This was evident from microarray data of overexpressing transgenic plants, where promoters of up regulated genes contain GCC motifs and chromatin immunoprecipitation showing ERF104 association with PDF1.2 promoter. The ERF104 overexpressor did not affect biotrophic bacteria proliferation but was more susceptible to necrotrophic Botrytis cinerea. Microarray performed with erf104 or mpk6 revealed only a limited number of flg22-induced genes that require these elements - possibly as a
result of functional redundancies. Thus, ERF104 phosphorylation by MPK6, in concert with ethylene signaling induced by pathogen-derived molecules, modulates defense in Arabidopsis.

overall_design:
Leaves of six week old Col-0, erf104, mpk6 and 35S::ERF104 plants were infiltrated with 1µM Flg22 or water and harvested four hours later. Total RNA was isolated and processed according to the Affymetrix protocol for biotin-labelled cRNA and hybridized to the Affymetrix ATH1 chip. The data
was analyzed with Genespring GX 7.3.1 software (Agilent) with the following parameters: Filter on Flags for present or marginal in 50% of all considered experiments, Filter for reliable differentially expressed genes based on volcano plot (one way ANOVA p-value <0.05 and >3-fold change in expression). For the flg22 experiments, analysis for each genotype was separately performed and a composite list of flg22-regulated genes compiled – with the aim of including genes that may be differentially regulated in the genotype. Global expression profile was visualized by k-means clustering and condition tree (Genespring).

first: Gerit

last: Bethke

first: Justin

last: Lee

first: Dierk

last: Scheel


title: Expression data from effects of Ganoderma lucidum polysaccharides F3 on human monocytic leukemia cell line THP-1

status: Public on May 08 2009

first: Hsueh-Fen

last: Juan

address: No. 1, Sec. 4, Roosevelt Road

department: Institute of Molecular and Cellular Biology

institute: National Taiwan University

summary: In order to identify patterns of gene expression associated with biological effects in THP-1 cells induced by F3, we performed a transcriptomic analysis on the THP-1 control and F3-treated THP-1 cells by oligonucleotide microarray

overall_design: 10^7 cells/mL concentrations of THP-1 cells were seeded in 100 mm dish and incubated overnight. After that, cells were treated with F3 at a final concentration of 30 ug/mL. After incubated for 6 and 24 hours, the cell pellets were collected by centrifugation at 250g for 5 min, correspondingly. Controlled samples of un-induced cells were treated in the same way with the same amount of medium.

first: Jia-Wei

last: Hsu

first: Hsuan-Cheng

last: Huang

first: Shui-Tein

last: Chen

first: Chi-Huey

last: Wong


title: Influence of anti-CD25 mAb on the transcriptome of activated PBMC

status: Public on May 02 2009

city: Munich

first: Guenther

middle: HS

last: Richter

address: Parzivalstr. 16

department: Pediatrics & Children's Cancer Research Center

institute: Klinikum rechts der Isar, TU-Muenchen

summary: CD25 monoclonal antibody binding to the alpha-chain of the Interleukin-2 (IL-2) receptor, blocks high affinity IL-2 binding thereby preventing complete T cell activation and being of ample importance in transplantation medicine and potentially the treatment of autoimmune disease. However, CD25 antibodies do not only block T cell activation but also prevent activation induced cell death (AICD) attributing a dual function to IL-2. In this study, the modulation of the genomic expression profile of human peripheral blood mononuclear cells (PBMC) with therapeutic concentrations of humanized anti-CD25 mAb was investigated. PBMC were stimulated with CD3 antibody OKT-3 together with recombinant IL-2 in the absence or presence of anti-CD25 mAb. RNA was extracted and subjected to microarray analysis on U133A microarrays (Affymetrix). The expression profile revealed the up-regulation of 62 genes and down-regulation of 38 genes by anti-CD25 mAb, respectively.

overall_design: Peripheral blood mononuclear cells (PBMC) were stimulated for 8 or 16 hrs with 100 ng/ml OKT-3 together with 100 U/ml recombinant human interleukin-2 (rhIL-2) in the absence or presence of 30 µg/ml anti-CD25 antibody. RNA from cells under such treatment was isolated with Trizol and subjected to microarray analysis onto human U133A microarray following the Affymetrix protocol.

first: Günther

middle: H

first: Andreas

last: Mollweide

first: Stefan

last: Burdach


title: Kasumi-1 AML1-ETO knockdown samples

status: Public on May 01 2009

city: Boston

first: Kimberly

last: Stegmaier

address: Harvard Medical School

department: Department of Pediatric Oncology

institute: Dana-Farber Cancer Institute and Children’s Hospital Boston

summary:
Kasumi-1 AML cells that were transfected in triplicate with AML1-ETO or luciferase siRNA constructs by either Amaxa nucleofection or Biorad siLentFect and incubated for 96 hours.
Microarrays used to discover an AML1-ETO signature for a GE-HTS screen to identify AML1-ETO modulators.

overall_design: Kasumi-1 AML cells incubated for 96 hours after they were transfected in triplicate with AML1-ETO or luciferase siRNA constructs by either Amaxa nucleofection or Biorad siLentFect along with three control samples not transfected with a construct.

first: Steven

last: Corsello

first: Giovanni

last: Roti

first: Kenneth

middle: N

last: Ross


title: AML1-ETO induction and knockdown

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


title: Genes that mediate breast cancer metastasis to the brain

city: New York

first: Paula

middle: D

last: Bos

address: 1275 York Avenue

department: Cancer Biology

institute: Memorial Sloan Kettering Cancer Institute

summary:
Brain metastasis is one of the most feared complications of cancer and the most common intracranial malignancy in adults. Its underlying mechanisms remain unknown.
From breast cancer patients with metastatic disease we isolated cell populations that aggressively colonize the brain. Transcriptomic analysis of these cells yielded overlapping gene sets whose expression is selectively associated with brain metastasis.
The expression of seventeen of these genes in primary breast tumors is associated with brain relapse in breast cancer patients. Some of these genes are also associated with metastasis to lung but not to liver, bone or lymph nodes, providing a molecular basis for the long-observed clinical link between brain and lung metastasis. Among the functionally validated brain metastasis genes, the cyclooxygenase COX-2, the EGFR ligand HB-EGF, and the brain-specific α2-6 sialyltransferase ST6GALNAC5 mediate cancer cell passage through the blood-brain barrier. Other brain metastasis genes encode inflammatory factors and brain-specific proteolytic regulators, suggesting a multifaceted program for breast cancer colonization of the brain.

overall_design: Two different breast cancer cell lines, MDA-MB-231 and freshly isolated pleural effusion CN34 were used in this study. The MDA-MB-231 group contains three biological replicates of the parental, unselected population, and 4 brain metastatic isolates. CN34 contains 2 biological replicates of the parental, unselected population,  and 4 brain metastatic isolates. In each case, the parental population was compared to the brain metastatic isolates to identify gene expression changes associated with the brain metastatic phenotype.

first: Joan

last: Massague


title: Transcriptional response of human cells to the absence of mitochondrial DNA

city: Kansas City

first: Norman

last: Pavelka

state: MO

address: 1000 E. 50th Street

institute: Stowers Institute for Medical Research

summary:
Mitochondrial biogenesis is under the control of two different genetic systems: the nuclear genome (nDNA) and the mitochondrial genome (mtDNA). mtDNA is a circular genome of 16.6 kb encoding 13 of the approximately 90 subunits that form the respiratory chain, the remaining ones being encoded by the nuclear genome (nDNA). Eukaryotic cells are able to monitor and respond to changes in mitochondrial function through alterations in nuclear gene expression, a phenomenon first defined in yeast and known as retrograde regulation. With this experiment we aimed to identify the set of nuclear genes that significantly change their expression level in response to depletion of mtDNA.

Keywords: case-control

overall_design: We used Affymetrix HG-U133A GeneChips to study the transcriptome of two human cell lines, 143BTK- and A549, which had been entirely depleted of mtDNA (rho0 cells), and compared it with the corresponding undepleted parental cells (rho+ cells). Three independent biological replicates were analyzed for each cell line and treatment group.

first: Rossana

last: Mineri

first: Erika

last: Fernandez-Vizarra

first: Paola

last: Ricciardi-Castagnoli

first: Massimo

last: Zeviani

first: Valeria

last: Tiranti


title: Distinct Mechanisms Underlying Tolerance to Intermittent and Constant Hypoxia in Drosophila melanogaster

status: Public on Apr 30 2009

city: La Jolla

first: Dan

last: Zhou

address: CMG 103, 9500 Gilman Drive, MC0735

department: Pediatrics

institute: University of California, San Diego, School of Medicine

summary:
Background: Constant hypoxia (CH) and intermittent hypoxia (IH) occur during several pathological conditions such as asthma and obstructive sleep apnea.  Our research is focused on understanding the molecular mechanisms that lead to injury or adaptation to hypoxic stress using Drosophila as a model system.   Our current genome-wide study is designed to investigate gene expression changes and identify protective mechanism(s) in D. melanogaster after exposure to severe (1% O2) intermittent or constant hypoxia.
Methodology/Principal Findings: Our microarray analysis has identified multiple gene families that are up- or down-regulated in response to acute CH or IH.  We observed distinct responses to IH and CH in gene expression that varied in the number of genes and type of gene families. We then studied the role of candidate genes (up-or down-regulated) in hypoxia tolerance (adult survival) for longer periods (CH-7 days, IH-10 days) under severe CH or IH. Heat shock proteins up-regulation (specifically Hsp23 and Hsp70) led to a significant increase in adult survival (as compared to controls) of P-element lines during CH. In contrast, during IH treatment the up-regulation of Mdr49 and l(2)08717 genes (P-element lines) provided survival advantage over controls. This suggests that the increased transcript levels following treatment with either paradigm play an important role in tolerance to severe hypoxia. Furthermore, by over-expressing Hsp70 in specific tissues, we found that up-regulation of Hsp70 in heart and brain play critical role in tolerance to CH in flies.
Conclusions/Significance: We observed that the gene expression response to IH or CH is specific and paradigm-dependent. We have identified several genes Hsp23, Hsp70, CG1600, l(2)08717 and Mdr49 that play an important role in hypoxia tolerance whether it is in CH or IH. These data provide further clues about the mechanisms by which IH or CH lead to cell injury and morbidity or adaptation and survival.

overall_design: Expression profiles were determined by expression arrays in Drosophila melanogaster following acute constant or intermittent hypoxia. Three groups of samples were included in this analysis (3 x control, 3x CH treated and 3 x IH treated samples).

first: Priti

last: Azad

first: Erilynn

last: Russo

first: Gabriel

middle: G

last: Haddad


title: Expression data from human breast tumors and their paired normal tissues

status: Public on Apr 28 2009

city: Kuala Lumpur

first: Ivyna

middle: PN

last: Bong

state: Kuala Lumpur

address: Jalan Pahang

department: Cancer Research Centre

country: Malaysia

institute: Institute for Medical Research

summary:
Microarray is widely used to monitor gene expression changes in breast cancer. The transcriptomic changes in breast cancer is commonly occured during the transition of normal cells to cancerous cells. This is the first study on gene expression profiling of multi ethnic of Malaysian breast cancer patients (Malays, Chinese and Indian). We aim to identify differentially expressed genes between tumors and normal tissues. We have identified a set of 33 significant differentially expressed genes in the tumor vs. normal group at p<0.001.
We study the gene expression patterns of 43 breast tumors and their paired normal control by using Affymetrix genechip U133A.  We have identified a set of 33 significant differentially expressed genes in the tumor vs. normal group at p<0.001.

overall_design: Total RNAs were extracted from breast cancer and normal tissues. Samples were processed and hybridized on the chip for 16 hours. At the end of the study, we obtained a total of 86 set of gene expression data, which were from 43 tumors and 43 normal tissues. The gene expression were then compared between the tumor and normal groups.

first: Pau

last: Ni

first: Zubaidah

last: Zakaria

first: Rohaizak

last: Muhammad

first: Norlia

last: Abdullah

first: Naqiyah

last: Ibrahim

first: Nor

last: Emran

first: Sharifah

last: Hussain


title: Nuclear and Extranuclear Pathway Inputs in the Regulation of Global Gene Expression by Estrogen Receptors

status: Public on Apr 18 2009

city: Urbana

first: Zeynep

last: Madak Erdogan

state: IL

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

summary:
Whereas estrogens exert their effects by binding to nuclear estrogen receptors and directly altering target gene transcription, they can also initiate extranuclear signaling through activation of kinase cascades.
We have investigated the impact of estrogen-mediated extranuclear initiated pathways on global gene expression by using estrpgen-dendrimer conjugates.

Keywords: ligand treatment

overall_design: MCF-7 human breast adenocarcinoma cells were treated with empty dendrimer control, E2, or Estrogen Dendrimer Conjugate (EDC) for 4 hours, and cDNA microarray analyses were carried out using Affymetrix HG-U133A GeneChips

middle: M

last: Erdogan

first: Benita

last: Katzenellenbogen


title: Gene expression of Peg-interferon alfa-2b plus ribavirin in hepatitis C patients during the first 10 weeks of treatment

status: Public on Apr 21 2009

city: Bloomington

first: Milton

middle: W

last: Taylor

state: IN

address: 343 Jordan Hall

department: Biology

institute: Indiana University

summary:
Study of PBMC gene expression during the first 10 weeks of therapy with Pegylated-interferon-alfa2b (PegIntronTM) and ribavirin (administered by weight) in HCV patients.
This study compared the kinetics of gene expression during the first 10 weeks of therapy with Pegylated-interferon-alfa2b (PegIntronTM) and ribavirin (administered by weight) in HCV patients with the recently completed Virahep C study (9999) in which Peginterferon-alfa2a and ribavirin was administered. RNA was isolated from peripheral blood monocytes from twenty treatment-naïve patients just before treatment (day 0,) and at days 3, 6, 10, 13, 27, 42 and 70 days after treatment. Gene expression at each time was compared to that of day 0 using Affymetrix DNA-micro-arrays. Focusing upon genes that changed at least 1.5-fold and p<0.001, the numbers were high at day 3 (300 probes) and 10 (255) but dropped at days 6 (128) and 13 (142) but were steady at later time points. A large number of genes continued to be up regulated throughout the trial period. A second group of genes, including CXCL10, chemokine receptor 1, TRAIL, IL1 R  and genes associated with complement and lipid metabolism, were transiently induced. CDKN1C (cyclin kinase inhibitor 1) was induced early but repressed at later times. Genes induced at later times were mostly related to blood chemistry and oxygen transport. Genes down regulated were related to ribosomal proteins and eukaryotic translation complexes. By week 10, 50% of the patients demonstrated a positive response to therapy. Conclusions: The response to pegintron/ribavirin was similar to that reported for Pegasys/ribavirin, although the extent of gene induction was less. No differences were found between patients responding to treatment or non-responders during this period.  Our data suggest that more than once a week dosing might be desirable early on during treatment.
Keywords: Time Course, gene expression

overall_design: Time course, 20 individuals, samples taken before first treatment (day 0) and days 3, 6, 10, 13, 27, 42 and 70.

first: Takuma

last: Tsukahara

first: Jeanette

last: McClintick

first: Howard

middle: J

last: Edenberg

first: Paul

last: Kwo


title: Early-induced genes of human regulatory CD4+CD25hi Treg and CD4+CD25- Th cells

status: Public on Apr 20 2009

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary:
Goals and objectives of this study: to identify genes preferentially induced in human CD4+CD25hi Treg cells following T-cell activation with potential role for stabililization & maintenance of the regulatory program.

Keywords: T-cell receptor stimulation, gene-regulation, comparative gene expression profiling

overall_design: Homo sapiens CD4+CD25- and CD4+CD25hi T cells were sorted from healthy individual donors and analyzed ex vivo (non-activated) or 1 day following T-cell receptor activation using anti-CD3/IL2 and anti-CD3/-CD28/IL2 (activated), respectively.

first: R

first: M

last: Probst-Kepper


title: Expression data from colorectal cancers

status: Public on May 04 2009

city: Potsdam

first: Bernd

last: Hinzmann

address: Voltaireweg 4b

department: Molecular Profiling

institute: Signature Diagnostics AG

summary:
Wiskott-Aldrich syndrome (WAS) predisposes patients to leukemia and lymphoma. WAS is caused by mutations in the protein WASP which impair its interaction with the WIPF1 protein. Here, we aim to identify a module of WIPF1-coexpressed genes and to assess its use as a prognostic signature for colorectal cancer, glioma, and breast cancer patients. Two public colorectal cancer microarray data sets were used for discovery and validation of the WIPF1 co-expression module. Based on expression of the WIPF1 signature, we classified more than 400 additional tumors with microarray data from our own experiments or from publicly available data sets according to their WIPF1 signature expression. This allowed us to separate patient populations for colorectal cancers, breast cancers, and gliomas for which clinical characteristics like survival times and times to relapse were analyzed. Groups of colorectal cancer, breast cancer, and glioma patients with low expression of the WIPF1 co-expression module generally had a favorable prognosis. In addition, the majority of WIPF1 signature genes are individually correlated with disease outcome in different studies. Literature gene network analysis revealed that among WIPF1 co-expressed genes known direct transcriptional targets of c-myc, ESR1 and p53 are enriched. The mean expression profile of WIPF1 signature genes is correlated with the profile of a proliferation signature. The WIPF1 signature is the first microarray-based prognostic expression signature primarily developed for colorectal cancer that is instrumental in other tumor types: low expression of the WIPF1 module is associated with better prognosis.
We used microarrays for the  validation of a WIPF1 co-expression module which was developed on two publically available datasets.

Keywords: disease state analysis

overall_design: For the generation of our own microarray data set, 62 CRC patients undergoing elective standard oncological resection at the Department of General, Vascular and Thoracic Surgery, Campus Benjamin Franklin, Charité, were prospectively recruited.

first: Eike

last: Staub

first: Joern

last: Groene

first: Maya

last: Heinze

first: Detlev

last: Mennerich

first: Stefan

last: Roepcke

first: Irina

last: Klaman

first: Esmeralda

last: Castanos-Velez

first: Christian

last: Pilarsky

first: Benno

last: Mann

first: Thomas

last: Brümmendorf

first: Birgit

last: Weber

first: Heinz

last: Buhr

first: André

last: Rosenthal


title: PRC2 in Ewing tumors

status: Public on Apr 29 2009

city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

summary: We found the PRC2 component EZH2 to be upregulated by the pathognomonic fusion oncogene EWS-FLI1 in Ewing tumors and mesenchymal stem cells (Richter GH et al., Proc Natl Acad Sci U S A. 2009;106:5324-9). Downregulation of EZH2 by RNA interference in Ewing tumor cell lines suppressed oncogenic transformation in vitro and in vivo. These data suggest that EZH2 might play a central role in Ewing Tumor pathology.

overall_design: RNA from tumor samples was isolated with Trizol and subjected to microarray analysis using HG_U133A microarrays following the Affymetrix protocol. Ewing tumors vs. neuroblastoma controls

first: Günther

last: Richter

middle: S

middle: E

last: Burdach


title: Early phosphate-deficiency induced signal changes in Arabidopsis roots

status: Public on Apr 14 2009

city: Taipei

first: Wolfgang

last: Schmidt

address: No. 128, Sec 2, Academia Rd, Nankang

department: Institute of Plant and Microbial Biology

institute: Academia Sinica

summary: A mutant previously isolated from a screen of EMS-mutagenized Arabidopsis lines, per1, showed normal root hair development under control conditions but displayed an inhibited root hair elongation phenotype upon Pi deficiency. Additionally, the per1 mutant exhibited a pleiotropic phenotype under control conditions, resembling Pi-deficient plants in several aspects. Under Pi deficiency, the accumulation of Pi and iron was increased in the mutant when compared to the wild-type. Inhibition of root hair elongation upon growth on low Pi media was reverted by treatment with the Pi analog phosphite, suggesting that the mutant phenotype is not the result of a defect in Pi sensing. Reciprocal grafting experiments revealed that the mutant rootstock is sufficient to cause the phenotype. Transcriptional profiling of per1 and wild-type plants subjected to short-term Pi starvation revealed genes that may be important for the signaling of Pi deficiency. We conclude that UBP14 function is crucial for adapting root development to the prevailing local availability of phosphate.

overall_design: Col-0 and per1 mutant plants were grown under control conditions or subjected to phosphate starvation for 10 h


title: Metastases of breast cancer (U133A)

city: Houston

first: Xiang

last: Zhang

address: One Baylor Plaza, BCM600

department: Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

summary:
Comparisons among breast cancer metastases at different organs revealed distinct microenvironments as characterized by cytokine content.
Such microenvironment distinction might be important to dictate how the cancer cells adapt to survival before they successfully colonize.

Keywords: Disease state analyses

overall_design: 58 breast cancer metastases from different organs were  profiled and compared by the expression level of over 400 cytokines. 36 samples were incuded in this series. 22 others as well as 7 of these 36 were profiled on U133plus2 platforms and included in series GSE14017.

first: Joan

last: Massague