title: Sequential changes at differentiation gene promoters as they become active in a stem cell lineage

status: Public on Jul 15 2011

city: Stanford

first: Margaret T.

last: Fuller

address: Beckman Center B300, 279  Campus Drive

department: Departments of Developmental Biology and Genetics

institute: Stanford University School of Medicine

summary:
Transcriptional silencing of terminal differentiation genes by the Polycomb group (PcG) machinery is emerging as a key feature of precursor cells in stem cell lineages. How, then, is this epigenetic silencing reversed for proper cellular differentiation? Here we investigate how the developmental program reverses local PcG action to allow expression of terminal differentiation genes in the Drosophila male germline stem cell lineage. We find that the silenced state, set up in precursor cells, is relieved through developmentally regulated sequential events at promoters once cells commit to spermatocyte differentiation. The programmed events include global down-regulation of PRC2, recruitment of hypophosphorylated RNA Polymerase II (Pol II) to promoters, as well as expression and action of cell-type specific homologs of subunits of TFIID (tTAFs). In addition, action of tMAC, a tissue specific version of the MIP/dREAM complex, is required both for recruitment of tTAFs to target differentiation genes and for proper cell-type specific localization of PRC1 components and tTAFs to the spermatocyte nucleolus. Together, action of the tMAC and tTAF cell-type specific chromatin and transcription machinery leads to loss of
Polycomb and release of Pol II from the promoter of terminal differentiation genes to elongation, allowing robust transcription of the terminal differentiation genes.

overall_design: Total RNA from approximately 200 pairs of fly testes (bam1/bamΔ86; aly2/aly5P; sa1/sa2; y,w) was extracted using TRIzol (Invitrogen, #15596-018, Carlsbad, CA, USA) following the manufacturer's instructions. The genomic DNA was degraded using 2 Units of DNase I (Fermentas, #EN0521, Glen Burnie, MD, USA) at 37°C for 20 minutes. RNA integrity was checked by gel electrophoresis (1% agarose). Approximately 4 μg of total RNA from each biological replicate were used to generate labeling probes to hybridize with the Affymetix GeneChip Drosophila Genome 2.0 Array according to the Affymetrix protocol. Three biological replicates were performed for each genotype. Microarray hybridization was processed at the Core Facility at the Stanford University School of Medicine and the raw data were exported from the Affymetrix Microarray Suite (MAS). The CEL files were used for signal normalization with RMA as part of the limma package from the Bioconductor R packages (http://www.bioconductor.org).

first: Xin

last: Chen

first: Margaret


title: Tuberous sclerosis complex 1 (Tsc1) enforces quiescence of naive T cells to promote immune homeostasis and function

status: Public on Jul 12 2011

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

country: USA

institute: St Jude Children's Research Hospital

summary: The mechanisms that regulate T cell quiescence are poorly understood. We report that tuberous sclerosis complex 1 (Tsc1)   establishes a quiescent program in naïve T cells by controlling cell size, cell cycle entry, and responses to T cell receptor stimulation. Loss of quiescence predisposed Tsc1-deficient T cells to apoptosis that depleted conventional T cells and invariant natural killer T cells. Loss of Tsc1 function dampened in vivo immune responses to bacterial infection. Tsc1-deficient T cells exhibited increased mTORC1 but diminished mTORC2 activities, with mTORC1 activation essential for the disruption of immune homeostasis. Therefore, Tsc1-dependent control of mTOR is crucial in establishing naïve T cell quiescence to facilitate adaptive immune function.

overall_design: Naïve CD4 and CD8 T cells from wild-type and Tsc1-deficient mice (in triplicates each group) were stimulated with or without TCR signaling. RNA was analyzed by microarrays. WT/KO for 0 and 4 hr for CD4 (triplicates), and WT/KO for 0 hr for CD8 (duplicates).

first: K

last: Yang

first: G

last: Neale

first: D

middle: R

last: Green

first: W

last: He

first: H

last: Chi


title: Gene co-expression networks in human brain predict chromatin modifications in alcohol abusers

city: Austin

first: R. Dayne

last: Mayfield

address: 2500 Speedway

institute: University of Texas at Austin

summary: A novel systems approach was applied to transcriptome profiling that included the traditional analysis of differentially expressed genes, gene co-expression networks, cell type - specific transcriptomes and a wide range of gene annotations. By integrating our data with previous findings, we generated the first systems hypothesis of human alcoholism that integrates epigenetic regulation of gene expression with structural and functional alterations in alcoholic brain.

overall_design: Total RNA was extracted from human post-mortem brain and gene expression profiles were compared between alcoholics and matched controls.


title: Interactions between glucocorticoid treatment and cis-regulatory polymorphisms contribute to cellular response phenotypes

status: Public on Aug 18 2011

city: Chicago

first: Joseph

middle: C

last: Maranville

state: IL

address: 920 E. 58th Street

institute: 920 E. 58th Street

summary: Glucocorticoids (GCs) are steroid hormones produced by the human body in response to environmental stressors. Despite their key role as physiological regulators and widely administered pharmaceuticals, little is known about the genetic basis of inter-individual and inter-ethnic variation in GC response. As GC action is mediated by the regulation of gene expression, we profiled transcript abundance and protein secretion in EBV-transformed B lymphocytes from a panel of 114 individuals, including those of both African and European ancestry. Combining these molecular traits with genome-wide genetic data, we found that genotype-treatment interactions at polymorphisms near genes affected GC-regulation of expression for 26 genes and of secretion for IL6. A novel statistical approach revealed that these interactions could be distinguished into distinct types, with some showing genotypic effects only in GC-treated samples and others showing genotypic effects only in control-treated samples, with differing phenotypic and molecular interpretations. The insights into the genetic basis of variation in GC response and the statistical tools for identifying gene-treatment interactions that we provide will aid future efforts to identify genetic predictors of response to this and other treatments.

overall_design: Total RNA was obtained from paired aliquots of lymphoblastoid cell lines (collected as a part of the HapMap project) treated with dexamethasone or vehicle (EtOH) for 8 hours.

first: Francesca

last: Luca

first: Allison

middle: L

last: Richards

first: Xiaoquan

last: Wen

middle: B

last: Witonsky

first: Shaneen

last: Baxter

first: Matthew

last: Stephens

first: Anna

last: Di Rienzo


title: Identification differentially expressed genes upon valproic acid treatment

status: Public on Jul 13 2011

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

country: Germany

institute: Goehte University Frankfurt

summary:
The goal of this study is to define genes that are differentially expressed in Down syndrome leukemic blasts after treatment with valproic acid (VPA)
Here we report the identification gene sets that are downregulated in Down syndrome leukemic cell lines after exposure to valproic acid (VPA)

overall_design: CMK and CMY cells were treated with VPA for 24h and 48h with 1mM or 2mM VPA. Their gene expression profile was compared against the untreated control.

first: Zhe

last: Li

first: Dirk

last: Reinhardt

first: Stuart

last: Orkin


title: Germline PTEN promoter variants affect the expression profile in breast tumors

status: Public on Jul 01 2011

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: Comparison of the tumors PTEN promoter variant carrier and non carrier gene expression profiles.

overall_design: Expression profiles of 10 breast cancer patients with PTEN promoter variant and 10 controls matches for histology, ER, PR, T, N, M, Grade, HER2, Ki67, and p53.

first: Tuomas

last: Heikkinen

first: Liisa

middle: M

last: Pelttari

first: Johanna

last: Tommiska

first: Pia

last: Vahteristo

first: Päivi

last: Heikkilä

first: Carl

last: Blomqvist

first: Kristiina

last: Aittomäki

first: Heli

last: Nevalinna


title: Gene transcription signature of obesity in breast cancer

status: Public on Jul 18 2011

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary:
Obesity is thought to contribute to worse disease outcome in breast cancer as a result of increased levels of adipocyte-secreted endocrine factors, insulin, and insulin-like growth factors (IGFs) that accelerate tumor cell proliferation and impair treatment response. We examined the effects of patient obesity on primary breast tumor gene expression, by profiling transcription of a set of tumors for which the patients’ body mass index (BMI) was ascertained. Sample profiles were stratified according to patients’ obesity phenotype defined as normal (BMI <25), overweight (BMI 25-29.9), or obese (BMI>30).  Widespread alterations in gene expression were evident in breast tumors from obese patients as compared to tumors from other patients, allowing us to define an obesity-associated cancer transcriptional signature of 662 genes.

Keywords: two group comparison

overall_design: Primary breast tumor specimens were obtained from patients. Study volunteers completed questionnaires used to define historically normal (BMI<=24.9), overweight (BMI 25-29.9), or obese (BMI>=30) patient categories according to established WHO criteria.

first: Michael

last: Lewis

first: Yvonne

last: Sada


title: Characterization of human breast cancer xenografts

status: Public on Jul 07 2011

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

summary: A bank of human breast tumor xenografts was established by serial passage of primary breast tumor fragments in the cleared mammary fat pads of immuno-compromised NOD-SCID-IL2Rgammac–/– mice. The 15 expression profiles from five different tumors were classified using the ClaNC method [1]. The training data set consisted of 94 samples from Herschkowitz et al. [2]; class labels were based on tumor subtype (Basal-like, Luminal A, Luminal B, Claudin-low, HER2+/ER- and Normal breast-like).  [1] Dabney AR (2005) Classification of microarrays to nearest centroids. Bioinformatics 21:4148-4154.  [2] Herschkowitz JI, et al. (2007) Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors. Genome Biol 8:R76.

overall_design: Total RNA obtained from xenograft tumors from 5 different patients have been profiled in triplicate on the Illumina HT-12 BeadChip platform.

first: Samantha

last: Oakes


title: A Drosophila model for the Zellweger spectrum of peroxisome biogenesis disorders

status: Public on Jul 02 2011

city: Edmonton

first: Fred

middle: David

last: Mast

state: Alberta

address: Medical Sciences Building Room 5-14 Department of Cell Biology University of Alberta

department: Cell Biology

country: Canada

institute: University of Alberta

summary: Human peroxisome biogenesis disorders are lethal genetic disease in which abnormal peroxisome assembly compromises overall peroxisome and cellular function. Peroxisomes are ubiquitous membrane-bound organelles involved in several important biochemical processes, notably lipid metabolism and the use of reactive oxygen species for detoxification. Using cultured cells, we systematically characterized the peroxisome assembly phenotypes associated with dsRNA-mediated knockdown of 14 predicted Drosophila homologs of PEX genes (encoding peroxins; required for peroxisome assembly and linked to peroxisome biogenesis disorders), and confirmed that at least 13 of them are required for normal peroxisome assembly. We also demonstrate the relevance of Drosophila as a genetic model for the early developmental defects associated with the human peroxisome biogenesis disorders. Mutation of the PEX1 gene is the most common cause of peroxisome biogenesis disorders and is one of the causes of the most severe form of the disease, Zellweger syndrome. Inherited mutations in Drosophila Pex1 correlate with reproducible defects during early development. Notably, Pex1 mutant larvae exhibit abnormalities that are analogous to those exhibited by Zellweger syndrome patients, including developmental delay, poor feeding, severe structural abnormalities in the peripheral and central nervous systems, and early death. Finally, microarray analysis defined clusters of genes whose expression varied significantly between wild-type and mutant larvae, implicating peroxisomal function in neuronal development, innate immunity, lipid and protein metabolism, gamete formation, and meiosis.

overall_design: Expression profiles were analyzed in triplicate from whole larvae of wild-type and pex1 homozygous mutant Drosophila.

middle: D

first: Jing

last: Li

first: Maninder

middle: K

last: Virk

first: Sarah

last: Hughes

first: Andrew

middle: J

last: Simmonds

first: Richard

middle: A

last: Rachubinski


title: Expression data from Fine Needle Aspiration (FNA) biopsies from breast cancer patients

first: TAKAYUKI

last: IWAMOTO

address: 1515 Holcombe Blvd

department: Breast medical Oncology

institute: UT MD Anderson

summary:
This is a stage-matched case control study. Cases with clinical diagnosis of  Inflammatory Breast Cancer (IBC) were selected after reviewing all medical records of the 440 FNA samples. IBC was defined as signs of erythema and edema (peau d’orange) involving at least one third of the skin and rapid clinical presentation. Presence of tumor emboli in the dermal lymphatics of the involved skin in the pathology report was not required for inclusion as IBC. Controls were selected to match for T stage, all T4a-c tumors in the data set were included as controls. IBC breast cancer are all T4d breast cancer.
We examined if gene expression differences exist between IBC and stage-matched Non-IBC stratified according to hormone receptor and HER2 status.

overall_design: Pre-treatment FNA from primary tumors were obtained and RNA extracted and hybridized to Affymetrix microarrays according to manufacturer protocol.

first: Lajos

last: Pusztai

first: Naoto

middle: T

last: Ueno

first: Massimo

last: Cristofanilli

first: Takayuki

last: Iwamoto

first: Yuan

last: Qi


title: The effects of Hmgb1 depletion on gene expression in human cells

status: Public on Jun 28 2011

city: Milano

first: Riccardo

middle: Lorenzo

last: Rossi

state: MI

address: Via Trivulzio 10

department: Integrative Biology

country: Italy

institute: Fondazione INGM

summary: High Mobility Group Box 1 (HMGB1) is a highly abundant and evolutionarily conserved non-histone chromatin component with the ability to bind and bend DNA. The protein is involved in fundamental nuclear processes including nucleosome sliding, transcription, replication, V(D)J recombination and DNA transposition. To assess the functional impact of HMGB1 on transcription we performed gene expression profile analyses of HeLa cells stably transfected with an anti-HMGB1 shRNA expressing plasmid or a control plasmid.

overall_design: 2 stable clones: control HeLa, Hmgb1-knocked down HeLa, 3 technical replicates. Hmgb1 knockdown HeLa cells were prepared by stable transfection with the plasmid Hmgb1shRNA-pSuperior.puro or, as a mock control, with the empty vector pSuperior.puro (Invitrogen). Transfection was made starting from 500 thousands (500K) or 5 milions (5mil) cells. Transfected cells were selected with puromycin and single resistant clones were picked, amplified and analyzed for HMGB1 expression by western blot. A clone containing less then 10% of the wt amount of HMGB1 was selected for further experiments. Total RNAs were extracted using Quiagen RNeasy kit  and analyzed on the Illumina BeadsArray platform in 2 technical replica (2 arrays).

first: Barbara

last: Celona

first: Alessandra

last: Agresti

first: Marco

middle: E

last: Bianchi

first: Grazisa

last: Rossetti

first: Massimiliano

last: Pagani


title: Gene expression profile of primary human naive and memory CD4+ T lymphocytes.

status: Public on Jun 26 2011

summary: Gene expression data of primary human naive and memory CD4+T lymphocytes purified from peripheral blood are generated to be analyzed in different ways such as for traditional searching of differentially expressed genes between the two cell subsets or in combination to in-silico data of microRNAs target prediction for microRNAs known to be characteristically expressed in the two cell subsets.

overall_design: Two cell subsets (cell types) FACS purified from peripheral blood of six samples/healthy donors (samples #3,5,6,7,026,065). Naive CD4+ T cells were extracted from all 6 samples and 6 biological replicas were obtained (3N, 5N, 6N, 7N, 026N, 065N), while memory CD4+T cells were extracted from 4 samples and 4 biological replicas were obtained (3m, 5m, 6m, 7m). Both naive and memory replicas from samples 3, 5, 6 and 7 were hybridized onto two beadsarrays each while those from samples 026 and 065 were hybridized on 1 beadsarray each (for a total of 18 beadsarrays used). For analysis purposes naive cells samples 3N, 5N, 6N and 7N can be considered paired with memory samples 3m, 5m, 6m and 7m respectively, since they are obtained from the same blood samples/healthy donors.


title: Genome-wide analysis of gene expression in placentas derived from patients with preeclampsia

status: Public on Jun 24 2011

city: Shenyang

first: Tao

last: Meng

state: Liaoning

address: 155 North Nanjing Street

department: Department of Obstetrics

country: China

institute: The First Affiliated Hospital of China Medical University

summary: The purpose of this study was to perform a comprehensive analysis of gene expression profile in placentas from preeclamptic pregnancies vs normal placentas.

overall_design: Total RNA obtained from placental tissues of patients with normal pregnancies and patients with preeclampsia.

first: Haiying

last: Chen


title: The effect of HES6 silencing on the gene expression profiles of the glioblastoma A172 and LN405 cell lines

status: Public on Jun 30 2011

city: Turku

first: Saija

last: Haapa-Paananen

address: Itäinen Pitkäkatu 4C

department: Medical Biotechnology

institute: VTT Technical Research Centre of Finland

summary: Malignant glioma is the most common type of primary brain tumor diagnosed annually in 16,000 individuals in the United States. We performed a systematic large-scale transcriptomics data mining study of 9,783 Affymetrix samples from the GeneSapiens database in order to identify those genes that are most glioma-specific as compared to other cancers and normal tissues. We searched for genes that are highly expressed in 322 glioblastoma multiforme tissue samples and 66 anaplastic astrocytomas as compared to 425 samples from histologically normal central nervous system. Transcription cofactor HES6 (Hairy and Enhancer of Split 6) emerged as one of the most glioma-specific genes. In immunostaining of a tissue microarray series, HES6 was expressed in 335 (98.8%) out of the 339 clinical glioma samples. Recurrent grade 2 astrocytomas and grade 2-3 oligodendrogliomas showed higher levels of HES6 immunoreactivity than the corresponding primary tumors. Functional studies implied a critical role for HES6 in supporting survival of glioma cells, as evidenced by 60% reduced cancer cell viability and induction of Caspase 3/7 activity after HES6 silencing by RNA interference in A172 and LN405 cells. The biological role and consequences of HES6 silencing and overexpression was explored with genome-wide analyses, which indicated a key role for HES6 in e.g. p53, c-myc, and NF-?B transcriptional networks. We conclude that HES6 has a critical role in sustaining glioma cell growth, survival, migration and possibly angiogenesis. HES6 is a potential therapeutic target and biomarker for glioma.

overall_design: A172 and LN405 cells (240 000 per well on 6-well plates) were transfected for 12-24 h with siHES6 pool, or three individual siRNAs (HES6_1, HES6_2, HES6_3 from Qiagen) or AllStars negative control siRNA (Qiagen) at 30 nM using SiLentFect (Bio-Rad Laboratories, Hercules, CA). One to two biological replicate transfections were performed. LN405 cells were also used for creating stable cell lines by transfecting either pEYFP-C1-mock or pEYFP-HES6 with Fugene6 (Roche) and selecting the positive cells with 600ug/ml of G418 (Sigma). The cells were kept in culture in the presence of 400ug/ml of G418. Total RNA was isolated with RNeasy (Qiagen) or MiRVana? Total RNA Isolation kit (Ambion). RNA quality was evaluated by using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

first: Pekka

last: Kohonen


title: Expression profiling of critically ill influenza and bacterial pneumonia patients, also influenza vaccination recipients

city: Kingswood

first: Grant

last: Parnell

state: NSW

address: Nepean Hospital

department: Nepean Clinical School

institute: University of Sydney

summary: Longitudinal Gene expression profiling of whole blood from critically ill influenza and bacterial pneumonia patients.  In addition before vs 7 days post influenza vaccination volunteer samples are assayed.

overall_design: 3 groups of samples.  First is bacterial pneumonia patients with 6 subjects sampled for up to 5 days.  Second group is severe influenza infection with 4 subjects sampled for up to 5 days.  Third group is influenza vaccination with 18 subjects sampled before and 7 days post vaccination.

middle: P

first: Benjamin

last: Tang


title: Paclitaxel resistant MDA-MB-231 Cells and resensitization with bexarotene treatment

status: Public on Jul 19 2011

city: San Diego

first: Wen

last: Luo

state: CA

address: 6331 Nancy Ridge Drive

institute: Denovo Biopharma

summary:
Acquired drug resistance represents a major challenge in chemo-therapy treatment for various types of cancers.  We have found that the retinoid X receptor–selective agonist bexarotene (LGD1069, Targretin) was efficacious in treating chemo-resistant cancer cells. The goal of this microarray study was to understand the mechanism of bexarotene’s role in overcoming acquired drug resistance using human breast cancer cells MDA-MB-231 as a model system and paclitaxel as model compound.  After MDA-MB-231 cells were repeatedly treated with paclitaxel for 8 cycles with each cycle including a 3-day treatment with 30 nM paclitaxel and followed by a 7-day exposure to control medium, MDA cells resistant to paclitaxel were developed and their growth was no longer inhibited by paclitaxel treatment.  Those MDA cells with acquired drug resistance, when treated with paclitaxel and bexarotene in combination, could regain their sensitivity and their growth were again inhibited.  Therefore, RNA samples from parental MDA-MB-231 cells, paclitaxel-resistant MDA cells treated with vehicle, paclitaxel alone or in combination with bexarotene, were used for perform global gene expression profiling with Affymetrix HG-U133A gene chips.

Keywords: Drug Treatment

overall_design: MDA-MB-231 cells were exposed to regimens on a 10-day cycle:  a 3-day treatment with 30 nM paclitaxel and followed by a 7-day exposure to control medium.  Paclitaxel resistant MDA-MB-231 cells (MDA-PR) were established within 8 cycles of such treatment (80 days).  These MDA-PR cells were then treated with vehicle control, paclitaxel along, or the combination of  30 nM paclitaxel ( 3 days on and 7 days off) and 1 µM Targretin (10 days on) in a new 10-day cycle for 3 months. Thus, there are four treatment groups, parent MDA cells, MDA-PR, MDA-PR treated with paclitaxel, MDA-PR treated with paclitaxel and bexarotene, and each group had four biological replicates.

first: Thomas

middle: W

last: Hermann

first: Jenifer

last: Sanders


title: Expression data from control and high sugar-fed third instar Drosophila larvae

status: Public on Jun 21 2011

city: Saint Louis

middle: John

last: Baranski

state: MO

address: 660 S. Euclid Ave. Box 8127

institute: Washington University School of Medicine

summary:
Chronic high sugar feeding induces obesity, hyperglycemia, and insulin resistance in flies and mammals. To gain insight into the mechanisms underlying this response, we profiled gene expression in chronically high sugar fed, wandering (post-prandial) third instar wild type larvae (L3). These data were compared to control-fed larvae as well as those (mid-L3) actively feeding for twelve hours on both diets.
We used microarrays to detail the response of Drosophila larvae to high sugar-induced insulin resistance.

overall_design: Male Canton-S third instar larvae were fed control (0.15M) or high (1M) sucrose and selected for RNA extraction and hybridization on Affymetrix microarrays. Wandering L3 were selected as those in the top half of the vial with partial blue guts to confirm that they had stopped eating the (blue) food. Mid-L3 were selected as L2, aged overnight until early L3, then transferred to fresh control or high sucrose food for 12 more hours before selection.

first: Laura

last: Musselman


title: Drosophila Staged follicles

status: Public on Jun 09 2011

city: Iowa City

first: Tina

last: Tootle

state: IA

address: 51 Newton Rd, 1-500BSB

department: Anatomy and Cell Biology

institute: University of Iowa

summary:
Gene expression analysis of yw follicles at S9/10a, S10B, S12, and S14; Gene expression analysis of pxt mutant follicles (f01000 and EY03052) at S10B, S12, S14
Drosophila ovarian follicles complete development using a spatially and temporally controlled maturation process in which they resume meiosis and secrete a multi-layered, protective eggshell before undergoing arrest and/or ovulation. Microarray analysis revealed more than 150 genes that are expressed in a stage-specific manner during the last 24 hours of follicle development. These include all 30 previously known eggshell genes, as well as 19 new candidate chorion genes and 100 other genes likely to participate in maturation. Mutations in pxt, encoding a putative Drosophila cyclooxygenase, cause many transcripts to begin expression prematurely, and are associated with eggshell defects. Somatic activity of Pxt is required, as RNAi knockdown of pxt in the follicle cells recapitulates both the temporal expression and eggshell defects. One of the temporally regulated genes, cyp18a1, which encodes a cytochromome P450 protein mediating ecdysone turnover, is downregulated in pxt mutant follicles, and cyp18a1 mutation itself alters eggshell gene expression. These studies further define the molecular program of Drosophila follicle maturation and support the idea that it is coordinated by lipid and steroid hormonal signals.

overall_design: minimum of 2 replicates per stage and genotype. yw=control follicles. pxt=mutant follicles.

first: Allan

last: Spradling


title: Identification of DNA Methylation Markers for Lineage Commitment of in vitro Hepatogenesis [mRNA profiling]

status: Public on Jun 10 2011

city: Daejeon

first: Mirang

last: Kim

address: 52 Eoeun-dong

department: human genome center

country: South Korea

institute: KRIBB

summary: Hepatocytes that have differentiated from human embryonic stem cells have great potential for the treatment of liver disease as well as for drug testing. Moreover, in vitro hepatogenesis is a powerful model system for studying the molecular mechanisms underlying liver development. DNA methylation is an important epigenetic mechanism that influences differential gene expression during embryonic development. We profiled gene expression and DNA methylation of three cell states of in vitro hepatogenesis—human embryonic stem cells, endoderm progenitors, and mature hepatocytes—using microarray analysis. Among 525 state-specific expressed genes, 67 showed significant negative correlation between gene expression and DNA methylation. State-specific expression and methylation of target genes were validated by quantitative reverse transcription–PCR and pyrosequencing, respectively. To elucidate genome-scale methylation changes beyond the promoter, we also performed high-throughput sequencing of methylated DNA captured by MBD2 protein [see SRA link below]. We found dynamic methylation changes in intergenic regions of the human genome during differentiation. Conclusion: This study provides valuable methylation markers for the lineage commitment of in vitro hepatogenesis and should help elucidate the molecular mechanisms underlying stem cell differentiation and liver development.

overall_design: ES, EP, and MH expression assays were run in quadruplicate. RNA isolated from the cell line at the indicated time points was used for gene expression analysis using the Human-6 Whole-Genome Expression BeadChip (Illumina, San Diego, CA), which generates expression profiles for more than 46,000 human transcripts. Biotin-labeled cRNA was produced using a linear amplification kit (Ambion, Austin, TX) using 300 ng of quality-checked total RNA as input. Chip hybridizations, washing, Cy3-streptavidin staining, and scanning were performed on a BeadArray Reader (Illumina) platform using reagents and following protocols supplied by the manufacturer. The detection score was used to determine expression

first: Yong-Sung


title: Effect of emtine treatment on RNA expression  and stablization of RNA otherwise degraded by NMD pathway in head and neck cell lines

status: Public on Jun 08 2011

city: Los Angeles

first: Sanjai

last: Sharma

department: Hematology Oncology

institute: UCLA West LA VA Medical Center

summary: The data shows the effect of NMD inhbition on cell  lines  and the change in RNA transcripts. The data also shows comparison of non-transformed cells (tert kert) to a Head and Neck tumorigenic cell line SCC12.

overall_design: Cell lines were treated with emetine at 100 microgm /ml for 8 hours and RNA isolated and analyzed by Affymetrix HG-U133A chip for change in RNA expression.


title: Gene Expression Patterns in Peripheral Blood Mononuclear Cells Associated with Asthma Exacerbation Attack

status: Public on Jul 14 2011

city: Cambridge

first: Andrew

last: Hill

state: MA

address: 300 Technology Square

department: Research Business Technology

institute: Pfizer

summary: A large, prospective, non-interventional study was designed to study gene expression changes in peripheral blood mononuclear cells (PBMCs) associated with asthma exacerbations over the course of a year. PBMC samples were collected from subjects at the time of the study visits defined as 1) Quiet: during stable disease at 3 month intervals, 2) Exacerbation: during a 14 day period of deteriorating asthma and 3) Follow-up: within 14 days after cessation of an exacerbation. Gene expression levels during stable asthma, exacerbation, and two weeks after an exacerbation were compared.

overall_design: This series of samples comprises of peripheral blood mononuclear cells (PBMCs) collected  during the following study visits (a) quiet (N=394 samples from 118 subjects), (b) exacerbation (N=166 samples from 118 subjects) and (c) follow-up (N=125 samples from 102 subjects)

first: Unnur

middle: S

last: Bjornsdottir

first: Stephen

last: Holgate

first: Charlotte

last: McKee

first: Cristina

last: Csimma

first: Amy

last: Weaver

first: Holly

last: Legault

first: Clayton

middle: G

last: Small

first: Renee

last: Ramsey

first: Debra

last: Ellis

first: Conor

last: Burke

first: Philip

last: Thompson

first: Peter

middle: H

last: Howarth

last: Wardlaw

last: Bardin

first: David

middle: I

last: Bernstein

first: Louis

last: Irving

first: Geoffrey

last: Chupp

first: George

last: Bensch

first: Gregory

first: Jon

last: Stahlman

first: Monroe

last: Karetszky

first: James

last: Baker

first: Rachel

last: Miller

first: Brad

last: Goodman

first: Donald

last: Raible

first: Samuel

last: Goldman

first: Douglas

first: John

last: Ryan

last: Dorner

first: Padmalatha

last: Reddy

first: Frederick

last: Immermann

first: Margot

last: O'Toole


status: Public on Jun 07 2011

city: Memphis

first: David

last: Finkelstein

address: 332 N. Lauderdale St.

institute: St Jude Children's Research Hospital

summary: Upon antigen stimulation, the bioenergetic demands of T cells increase dramatically over the resting state. Although a role for the metabolic switch to glycolysis has been suggested to support increased anabolic activities and facilitate T cell growth and proliferation, whether cellular metabolism controls T cell lineage choices remains poorly understood. Here we report that the glycolytic pathway is actively regulated during the differentiation of inflammatory TH17 and Foxp3-expressing regulatory T cells (Treg), and controls cell fate determination. TH17 but not Treg-inducing conditions resulted in strong upregulation of the glycolytic activity and induction of glycolytic enzymes. Blocking glycolysis inhibited TH17 development while promoting Treg cell generation. Moreover, the transcription factor hypoxia-inducible factor 1a (HIF1a) was selectively expressed in TH17 cells and its induction required signaling through mTOR, a central regulator of cellular metabolism. HIF1a-dependent transcriptional program was important for mediating glycolytic activity, thereby contributing to the lineage choices between TH17 and Treg cells. Lack of HIF1a resulted in diminished TH17 development but enhanced Treg differentiation, and protected mice from autoimmune CNS inflammation. Our studies demonstrate that HIF1a-dependent glycolytic pathway orchestrates a metabolic checkpoint for the differentiation of TH17 and Treg cells.

overall_design: Naïve CD4 T cells from wild-type and HIF1a-deficient mice (in triplicates each group) were differentiated under TH17 conditions for 2.5 days, and RNA was analyzed by microarrays.

first: Lewis

middle: Z

last: Shi

first: Ruoning

last: Wang

first: Gonghua

last: Huang

first: Peter

last: Vogel

last: Neale

middle: R

last: Green

first: Hongbo

last: Chi


title: RNA profiles of total RNA and Ago2-immunoprecipitated RNA

status: Public on Jun 01 2011

city: Boston

first: Tatsuya

last: Kobayashi

address: 50 Blossom Street, Thier 1101

department: Endocrine Unit

institute: Massachusetts General Hospital

summary:
Compared gene enrichment in Ago2-RNA immunopreciptant between wildtype and Mir140-null chondrocytes
Identified Mir140 targets that are most exclusively regulated by Mir140

overall_design: Biological duplicate.  Total RNA and Ago2-immunoprecipitated RNA were prepared from the same primary chondrocyte culture.  Chondrocytes were isolated from newborn mouse rib and cultured overnight in 10%FCS-containing medium.  Total RNA and Ago2-immunoprecipitated RNA were amplified using Ovation pico, and subjected to microarray analysis (HT-mouse 430 PM).  Two sets of experiments (two samples from wildtype mice for total RNA and Ago2 immunoprecipitated RNA, and two samples from Mir140-null mice for total RNA and Ago2 immunoprecipitated RNA) were performed (a total of 8 chips)


title: GPM6B regulates osteoblast differentiation and induction of mineralization by controlling cytoskeleton and matrix vesicle release.

city: Rotterdam

first: Jeroen

last: van de Peppel

address: 's Gravendijkwal 230

country: Netherlands

institute: ErasmusMC

summary: Analysis of GPM6B silenced osteogenic hMSC at gene expression level.  Analysis is showing significant changes in genes involved in cytoskeleton organization and biogenesis. Immunocytochemistry confirms changed distribution of actin filaments and change in shape and in size of focal adhesions upon GPM6B silencing. Moreover, we demonstrated that production and release of ALP-positive matrix vesicles (MVs) was reduced. In conclusion, we identified GPM6B as a novel regulator of osteoblast differentiation and bone formation and thereby demonstrating the significance of cytoskeleton organization for MV production and eventual mineralization.

overall_design: Total RNA obtained from osteogenic hMSC, 7days after shRNAi lenti viral transductions with 3 different GPM6B silencing constructs (sh1, sh2, sh3) compared to 3 different controls (shC:non-silencing shRNA, tGFP: tGFP control vector and Mock: mock transduced cells)

first: Ksenija

last: Drabek

first: Marco

last: Eijken

first: Johannes

last: van Leeuwen


title: Human lung CD8+ T cells compared with paired non-naive peripheral blood CD8+ T cells

status: Public on Jun 20 2011

city: Amsterdam

first: Berber

last: Piet

address: Meibergdreef 9

department: Experimental Immunology

institute: Academic Medical Centre

summary: It is unknown whether human lung T cells recirculate or belong to a distinct tissue-specific population. This issue is important for understanding their role in protection against viral infection and their contribution to pathophysiology of lung diseases such as chronic obstructive pulmonary disease. By comparing transcriptional profiles of blood and lung CD8+ T cells, we aimed to reveal specific traits of lung CD8+ T cells.

overall_design: A total of 12 samples was analyzed: 10 patient samples (including 1 technical replicate) and 2 reference samples (including 1 technical replicate). Per patient (in total 3 patients), 3 paired samples were analyzed. These samples were non-naive peripheral blood CD8+ T cells (CD45R0+CD3+CD8+ T cells), memory-type lung CD8+ T cells (CD45R0+CD27+CD3+CD8+ T cells) and effector-type lung CD8+ T cells (CD45R0+CD27-CD3+CD8+ T cells). The reference population consisted of a mix of naive peripheral blood CD8+ T cells from 5 healthy donors.

first: Perry

last: Moerland

first: René

last: Jonkers

last: van Lier


title: Gene expression in response to genetic and chemical perturbations of chromatin structure

status: Public on Jun 03 2011

city: West Lafayette

first: Karen

last: Hudson

state: IN

address: 915 West State Street

department: Crop Production and Pest Control

institute: USDA-ARS

summary: Microarray expression profiling was used to identify genes expressed misexpressed in wild-type Arabidopsis seedlings treated with 5-aza-2’ deoxyctidine (5AC) or trichostatin A (TSA), and in decrease in dna methylation1 (ddm1) mutant seedlings.

overall_design: 10 day-old Arabidopsis seedlings (ecotype Ws) were grown in 0.5X MS media (containing 1% sucrose) at 21 C in continuous white light.  Media (including 5AC and TSA) were refreshed after 5 days of growth.  RNA was extracted using the Qiagen Plant RNeasy kit. Three biological replicates for each treatment and genotype were used.


title: Age-related change of callus formation capability in Arabidopsis hypocotyls

status: Public on Jun 19 2011

city: Changhua

first: Shih-Feng

last: Fu

state: Changhua

address: No.1 Jin-De Road

department: Biology

country: Taiwan

institute: National Changhua University of Education

summary:
Transcriptional profiling of age-related change of callus formation capability in Arabidopsis hypocotyls
Organogenesis in vitro consists of many aspects such as phytohormone perception, dedifferentiation of differentiated cell to acquire organogenic competence, and re-entry of quiescent cells into cell cycle.  In this study, we established an in vitro experimental system to study the age-dependent callus formation capacity in Arabidopsis.  Interestingly, mature (35- to 38-day-old) hypocotyl explants exhibited better callus-forming potential than that of juvenile (7- to 10-day-old), determined by callus growth rates.  To explore genome-wide expression changes underlying the phenomenon of age-dependent callus formation, a transcriptome-based analysis was performed.  Gene expression profiling indicated that age-dependent callus formation capacity was associated with changes in phytohormone (auxins, cytokinins, abscisic acid, brassinosteroids and gibberellins) homeostasis, epigenetic mechanism and the cell cycle regulation.  Besides, we identified two groups of genes involved in age-dependent callus formation capacity: (1) positive regulatory and (2) negative regulatory categories, i.e. genes that were significantly up- or down-regulated during callus formation derived from mature explants, respectively. One gene encoding DNA-binding protein (VARIANT IN METHYLATION 1, VIM1) belonging to the positive regulatory category was selected for functional analysis and assessment of age-dependent callus formation capacity.  Indeed, vim1 reduced the efficiency of callus formation in mature explants, but not in juvenile.  The result suggests that VIM1 plays an important role in regulating age-dependent callus formation capacity.  Taken together, the investigation will help to better understand the molecular regulatory mechanism of age-dependent callus formation.

overall_design: Comparison of young and mature Arabidopsis hypocotyls either with or without auxin treatment for 1 day

first: Chi-Chien

last: Chen

first: Chung-Yi

last: Lin

first: Wan-Chen

first: Hao-Jen


title: Proteolytic inactivation of the autoinhibitory prodomain is essential for the pro-tumorigenic function of membrane type-1 matrix metalloproteinase (MT1-MMP)

city: La Jolla

first: Andrei

last: Chernov

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

summary: Invasive cancers employ pericellular proteolysis to breach the extracellular matrix and basement membrane barriers and invade the surrounding tissue. Pro-invasive, pro-tumorigenic MT1-MMP is the primary mediator of proteolytic events on the cancer cell surface. Cellular MT1-MMP is synthesized as a latent zymogen. The latency of MT1-MMP is maintained by its N-terminal inhibitory prodomain. Our study reveals a critical mechanism underlying the activation pathway and subsequent execution of the tumor-promoting function of MT1-MMP. Evidence suggests that the prodomain undergoes intradomain cleavage at the PGD↓L50 cleavage site followed by the release of the degraded prodomain by furin cleavage of the R108RKR111↓Y112 site. These events, only if combined, cause the activation of MT1-MMP. The significance of these molecular events to the pro-tumorigenic function of MT1-MMP in malignancy remained, however, unidentified. To identify the functional importance of the PGD↓L50 intradomain cleavage in the activation and tumorigenic program of MT1-MMP, our current studies employed the cells which expressed the wild-type prodomain-based fluorescent biosensor and the mutant biosensor with the inactivated PGD↓L50 cleavage site (L50D mutant) and also the cells with the enforced expression the wild-type and mutant MT1-MMP. Using cell-based tests and orthotopic breast cancer xenografts in mice, we demonstrated that the intradomain cleavage of the PGD↓L50 sequence of the prodomain is essential for the pro-tumorigenic function of MT1-MMP. Our study contributes to the growing consensus for the design of selective, precisely focused MT1-MMP inhibitors in cancer.

overall_design: Analysis of global gene expression in orthotopic tumor and cultured breast cancer cells expressing wild-type and mutant Mt1-MMP forms

first: Vladislav

last: Golubkov

first: Alex

last: Strongin


title: Differential effects of progesterone and medroxyprogesterone acetate on normal breast cells

status: Public on May 30 2011

city: Torino

first: Daniela

last: Cimino

state: Torino

address: Via Nizza 52

department: Oncological Science

institute: Molecular Biotechnology Center

summary: Comparison between the effects of progesterone (P4) and medroxyprogesterone acetate (MPA) combined to estradiol (E2) on gene expression in normal breast cells to provide insight on their possible different impact on breast cancer risk in vivo.

overall_design: Total RNA obtained from cultures of normal human breast epithelial cells (HBE) under E2, E2+MPA and E2+P4 six hour treatments, compared to untreated HBE cells

first: Aurélie

last: Courtin


title: Comparison of root transcriptomes in Arabidopsis thaliana plants supplied with different forms of inorganic nitrogen

status: Public on May 28 2011

city: San Marcos

first: Matthew

last: Escobar

address: 333 S. Twin Oaks Valley Rd.

department: Biological Sciences

institute: California State University San Marcos

summary:
Plants aquire nitrogen from the soil, most commonly in the form of either nitrate or ammonium. Unlike ammonium, nitrate must be reduced (with NADH and ferredoxin as electron donors) prior to assimilation. Thus, nitrate nutrition imposes a substantially greater energetic cost than ammonium nutrition. Our goal was to compare the transcriptomes of nitrate-supplied and ammonium-supplied plants, with a particular interest in characterizing the differences in redox metabolism elicited by different forms of inorganic nitrogen.
We used microarrays to compare the short-term transcriptional response to either nitrogen supply or ammonium supply in Arabidopsis roots. Genes upregulated or downregulated by nitrate only, ammonium only, or both ammonium and nitrate were identified and analyzed.

overall_design: Arabidopsis thaliana (Col-0) plants were grown hydroponically until they reached growth stage 5.10. They were then transferred to a nitrogen-free medium for 26 hr and then supplied with 1 mM nitrate or 1 mM ammonium. RNA isolation (and subsequent microarray analysis) was performed on root tissue isolated just before nitrogen supply (time 0) and at 1.5 hr and 8 hr after nitrogen supply (1.5 hr nitrate, 8 hr nitrate, 1.5 hr ammonium, 8 hr ammonium).

first: Kurt

last: Patterson


title: Expression profiling of MCF10A cells in 2D and 3D culture

city: Nashville

first: David

last: Simpson

address: Suite 4140 Medical Research Building III

institute: Vanderbilt University Medical Center

summary:
In these microarray experiments, we characterize the gene expression of mammary epithelial cells (MCF10A cells) grown in either a traditional monolayer cell culture setting (2D) or on Matrigel, which induces single MCF10A cells to form organized acinar structures (3D). Morphogenesis of mammary epithelial cells into organized acinar structures in vitro is accompanied by widespread changes in gene expression patterns, including a substantial decrease in expression of Myc.
The purpose of this study was to analyze the impact of morphogenesis and organization on gene expression with respect to changes in overall gene expression and Myc target gene expression.

overall_design: MCF10A cells were cultured in 2D for either 2 or 5 days (3 biological replicates each) or in 3D for 8 or 16 days (3 or 5 biological replicates, respectively)

first: William

last: Tansey

first: Zhongming

last: Zhao

first: Siyuan

last: Zheng

first: Min

last: Yu

first: Senthil

last: Muthuswamy


title: Expression data from human CD34+ HPC subpopulations isolated from umbilical cord blood (Haddad et al. Blood 104:3918, 2004)

status: Public on May 25 2011

city: Paris

first: Marc

last: Delord

address: Hopital Saint-Louis, 1 avenue Claude Vellefaux

department: Recherche clinique

country: France

institute: Centre hospitalier de Versailles

summary:
We used microarrays to analyze the gene expression profile of CD34+CD45RA+CD7+, CD34+CD45RA+CD10+CD19- and CD34+CD45+CD7-CD10-CD19- HPCs isolated from umbilical cord blood
CD34+CD45RA+CD7+(CD10-) and CD34+CD45RA+CD10+(CD7-CD19-) HPCs correspond respectively to prothymocytes and early pre-proB precursors. CD34+CD45RA+CD7-CD10-CD19- HPCs  correspond to lympho-granulo-macrophagic precursors

overall_design: The corresponding populations were sorted from total CD34+ HPCs isolated from 2 or 3 individual donors

first: Bruno

last: CANQUE


title: Effects of SAA treatment on global gene expression in THP-1 derived macrophages

status: Public on May 11 2011

city: Singapore

first: Koon Yeow

last: Leow

address: 21 Lower Kent Ridge Road

country: Singapore

institute: NUS

summary: The effect of SAA1 treatment on global gene expression in THP-1 macrophages was studied. The study determined the gene expression upon wild-type SAA1 treatment, variant SAA1 treatment (p.Gly72Asp) and in untreated THP-1 macrophages. SAA1 treatment of macrophages induces the expression of genes involved in inflammation, angiogenesis, phagocytosis and tissue remodeling which are important in the pathogenesis of chronic inflammatory diseases such as atherosclerosis and rheumatoid arthritis.

overall_design: THP-1 macrophages were treated with SAA1 for either 8 hours or 24 hours. RNA were then extracted and the gene expression pattern was compared between (i) wild-type SAA1 vs untreated (ii) variant SAA1 vs wild-type SAA1 at both 8 hr and 24 hr.

first: Koon

middle: Y

first: Wilson

last: Goh


title: JMJD1B target gene screening :JMJD1B is the H3K9 demethylase involved in transcriptional activation of Lmo2 in leukemia

city: seoul

first: jiyoung

last: kim

address: Heusokdong

institute: Chung-Ang University

summary: A genome-wide analysis identified a subset of JMJD1B target genes including leukemic oncogene lmo2

overall_design: Total RNA obtained from isolated JMJD1B knock down stable cell in K562 cells compared to sh-CTL control stable cells.

first: Ji-Young

last: Kim

first: Sang-Beom

last: Seo


title: Classical Hodgkin lymphoma shows epigenetic features of an abortive plasma cellular differentiation: expression of Hodgkin vs. B-cell lines

status: Public on May 05 2011

city: Berlin

first: Volkhard

last: Seitz

address: Hindenburgdamm 30

department: Institute of Pathology

institute: Charité Universitätsmedizin

summary:
Background
Epigenetic changes are involved in the extinction of the B-cell gene expression program of classical Hodgkin lymphoma. However, little is known regarding epigenetic similarities between classical Hodgkin lymphoma and plasma cell myeloma cells, both of which share an extinction of the gene expression program of mature B-cells.

Design and methods
Global histone H3 acetylation patterns were determined in cell lines derived from classical Hodgkin lymphoma, plasma cell myeloma and B-cell lymphoma by chromatin immunoprecipitation and subsequent hybridization onto promoter tiling arrays. H3K27 trimethylation was analyzed by chromatin immunoprecipitation and real-time DNA-PCR for selected genes. Epigenetic modifications were compared to gene expression data.

Results
B-cell characteristic genes were hypoacetylated in classical Hodgkin lymphoma and plasma cell myeloma cell lines, as demonstrated by comparison of their histone H3 acetylation patterns to those of B-cell lines. However, the number of genes jointly hyperacetylated and expressed in classical Hodgkin lymphoma and plasma cell myeloma cell lines, such as IFR4/MUM1 and RYBP, is limited. Moreover, H3K27 trimethylation for selected B-cell characteristic genes revealed that this additional epigenetic silencing is much more prevalent in classical Hodgkin lymphoma as compared to plasma cell myeloma.

Conclusion
Our epigenetic data support the view that classical Hodgkin lymphoma is characterized by an abortive plasma cell differentiation with a down-regulation of B-cell characteristic genes but without activation of most plasma cell typical genes.

overall_design:
Gene expression analysis of Hodgkin lymphoma (cHL) and B-cell lines:
Microarray data for three Hodgkin lymphoma cell lines (KM-H2, L1236, L428) and the B-cell line Namalwa that were published previously by our group (GEO accession GSE8388) were analyzed together with newly generated data for the B-cell lines SU-DHL4 and SU-DHL6. For all cell lines, RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).  Microarrays were normalized using RMA, and differential expression was calculated using moderated t-test.  The gene expression profiles of the cell lines were generated in duplicates.

first: Philippe

last: Thomas

first: Karin

last: Zimmermann

first: Ulrike

last: Paul

first: Anke

last: Ehlers

first: Maria

last: Joosten

first: Lora

last: Dimitrova

first: Dido

last: Lenze

last: Sommerfeld

first: Elisabeth

last: Oker

first: Ulf

last: Leser

first: Harald

last: Stein

first: Michael

last: Hummel


title: Classical Hodgkin lymphoma shows epigenetic features of an abortive plasma cellular differentiation: expression of A/T-treated vs. untreated B-cell lines

overall_design:
Combined 5-aza-dC/TSA (A/T) treatment:
The diffuse large B-cell lymphoma (DLBCL)-derived cell lines SU-DHL4, SU-DHL6 and HT and the Burkitt lymphoma-derived cell lines Daudi, Namalwa and Raji were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA. RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A). Microarrays were normalized using RMA and differential expression was calculated using moderated t-test. The gene expression profiles of the untreated and treated cell lines (with the exception of HT) were generated in duplicates. Microarray data (CEL files) for AZA/TSA-treated BL-derived cell lines Raji, Daudi and Namalwa were previously published (GEO accession GSE8388).


title: Gene expression data of sensitive, Docetaxel resistant and Paclitaxel resistant MDA-MB-231 Cells

status: Public on Apr 22 2011

city: Washington DC

first: Nesrin

last: Rechache

state: Washington DC

address: W401 Research Building  Georgetown University Medical Center  3970 Reservoir Rd NW

institute: Georgetown University

summary:
The taxanes, namely Paclitaxel and Docetaxel, are important and widely used cancer chemotherapy drugs in the treatment of invasive and metastatic human breast cancer.  Although treatment with the taxanes is beneficial to many patients, drug-responsive tumors in patients with metastatic breast cancer often display resistance to these drugs, either initially or over time following the continued administration of chemotherapy drugs.  To investigate the patterns of cross-resistance with the taxane drugs and to identify potential mechanisms of resistance, we generated a series of MDA-MB-231 taxane resistant cell lines.
We then used microarrays to determine gene expression differences between sensitive, Docetaxel and Paclitaxel resistant MDA-MB-231 cells.

overall_design: RNA isolated from three independent passages of sensitive, Docetaxel and Paclitaxel resistant cell lines and purified using the Qiagen RNeasy Mini Kit.  Total RNA was processed and hybridized to Affymetrix Genechip HU133A arrays.

first: Alan

last: Zwart


title: Classical Hodgkin lymphoma shows epigenetic features of an abortive plasma cellular differentiation

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Perturbation of the Akt/Gsk3-beta signaling pathway is common to Drosophila expressing expanded untranslated CAG, CUG and AUUCU repeat RNAs

status: Public on Apr 28 2011

city: Brisbane

first: Gareth

last: Price

state: Queensland

address: Carmody Road

institute: Queensland Facility for Advanced Bioinformatics

summary: Recent evidence supports a role for RNA as a common pathogenic agent in both the  “polyglutamine” and “untranslated” dominant expanded repeat disorders. One feature of all  repeat sequences currently associated with disease is their predicted ability to form a hairpin  secondary structure at the RNA level. In order to investigate mechanisms by which hairpin forming  repeat RNAs could induce neurodegeneration, we have looked for alterations in gene  transcripts as hallmarks of the cellular response to toxic hairpin repeat RNAs. Three disease associated  repeat sequences - CAG, CUG and AUUCU - were specifically expressed in the  neurons of Drosophila and resultant common, early, transcriptional changes assessed by  microarray analyses. Transcripts that encode several components of the Akt/Gsk3-β signalling  pathway were altered as a consequence of expression of these repeat RNAs, indicating that  this pathway is a component of the neuronal response to these pathogenic RNAs and may  represent an important common therapeutic target in this class of diseases.

overall_design: The heads from newly eclosed Male Drosophila were used for RNA extraction and profiling on Affymetrix Drosophile Genome 2.0 microarrays. Twenty samples were analysed, representing control and experimental lines. Two independently derived control lines were used in each exeriment, totaling 4 samples. The tri-nucleotide repeats (CAG, CUG, CAA) were represented by three independently derived two transgene insertion lines each in one experiment and two independent four transgene insertion lines each in a second experiment, totaling 15 samples. A single four transgene insertion line was analysed for AUUCU. Candidates were selected from the pool of transcripts which showed a ‘present’ call in either all independent lines for a particular repeat sequence, or in all samples for the elav- GAL4/+ control in that experiment. Where possible, T-tests were performed on raw values to determine samples that showed a significant difference with a P-value < 0.05.

first: Clare

middle: L

last: van Eyk

first: Loiuse

middle: V

last: O'Keefe

first: Kynan

last: Lawlor

first: Saumya

last: Samaraweera

first: Catherine

last: McLeod

first: Deon

last: Venter

first: Robert

last: Richards


title: Penfield: Understanding the affect of maternal environment on seed dormancy

status: Public on Apr 21 2011

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

summary:
Maternal environment is an important regultor of seed dormancy, but the mechanisms underlying the process are poorly understood. We have found that genes in the circadian clock control dormancy, in part through their regulation of the canonical photoperiod pathway known from research into flowering time control. In this experiment we compare the affects of altering seed maturation temperature or maternal photoperiod on dry seed transcriptomes, and the photoperiod-insenstive ft-1 mutant to wt type Ler. In this way we are identifying gene expression programmes which result from the seed's response to maternal environmental experience.

Keywords: Expression profilling by array

overall_design: 12 samples were used in this experiment

first: Steven

last: Penfield


title: Gene expression during SMC cord morphogenesis

status: Public on Apr 17 2011

city: London

first: J. Geoffrey

last: Pickering

state: ON

address: 100 Perth Drive

institute: Robarts Research Institute

summary: SMCs must undergo specialzed patterning during blood vessel stabilization. We used microarray analysis to identify differentially expressed genes as smooth muscle cells were induced to assemble into a network of elongated cords.

overall_design: Two time points (Day 0 and Day 8) and three biological replicates for each, using Affymetrix HGU133A and HGU133B arrays for each sample.

first: J

first: Matthew

middle: J

last: Frontini


title: The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma

status: Public on May 19 2011

city: New York

first: Yupu

last: Liang

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

type: Genome variation profiling by genome tiling array

first: Marc

last: Ladanyi

last: Bott


title: COPD-Specific Gene Expression Signatures of Alveolar Macrophages as well as Peripheral Blood Monocytes Overlap and Correlate with Lung Function

status: Public on Apr 18 2011

city: Debrecen

first: Szilard

last: Poliska

address: Egyetem ter 1.

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

summary:
Rationale: Chronic Obstructive Pulmonary Disease (COPD) is considered a chronic inflammatory disease characterized by progressive airflow limitation and also has significant extrapulmonary (systemic) effects that lead to comorbid conditions. Very little is known about the pathomechanism of the disease.

Objectives: Among inflammatory cell types, alveolar macrophages appear to have a key role in initiating and/or sustaining disease progression. These cells are derived from peripheral monocytes. Identification of disease and cell type specific gene expression profiles can be revealing and also practically useful in order to diagnose and characterize disease progression and the effect of drug treatment.

Methods: We used Affymetrix microarrays to obtain gene expression data of alveolar macrophages and circulating monocytes of COPD and healthy control patients. The microarray results were confirmed by quantitative real-time polymerase chain reaction in multiple patient collections.

Measurements and Main Results: We have identified gene sets specifically associated with COPD in alveolar macrophages and also in monocytes. Immune function, responses to stimuli, and cell death related genes appear to be impacted in both cell types. Remarkably, there is an overlapping gene set between the two cell types.

Conclusions: Taken together, our data show that COPD-specific gene signatures can be identified and validated, and that the disease also affects peripheral monocytes. Moreover, monocytes and alveolar macrophages carry overlapping gene expression signatures. Our findings further support the notion that altered responsiveness to stimuli is the key characteristic of alveolar macrophages and also of their precursors, peripheral monocytes.

overall_design:
Brochoalveolar lavage fluid samples were collected from of COPD and healthy control patients. Alveolar macrophages were isolated using Percoll gradient centrifugation, isolated using CD14+ magnetic beads, and total RNA was extracted using Qiagen RNeasy Kit. The monocyte samples represent a pool of RNA from 5 patients. Total RNA was labeled with biotin and individual samples were hybridized to Affymetrix HG U133A GeneChips.

Affymetrix data files were analyzed using GeneSpring 7.3 software. Using a non-parametric statistical test, we compared the gene expression patterns of the COPD and the healthy control patients and identified a set a genes that showed differential expression between the two groups.

first: Eszter

last: Csanky

first: Attila

last: Szanto

first: Istvan

last: Szatmari

first: Lajos

last: Szeles

first: Balazs

last: Dezso

first: Beata

last: Scholtz

first: Iain

last: Kilty

first: Laszlo

last: Takacs

last: Nagy

first: Janos

last: Podani

first: Bertalan

last: Mesko


title: Differential gene expression profiles induced by Hoechst dyes

status: Public on Apr 16 2011

city: detroit

first: naimei

last: tang

state: mi

address: 110 E warren ave

department: internal medicine

institute: wanye state university

summary: Bisbenzimides, or Hoechst 33258 (H258), and its derivative Hoechst 33342 (H342) are archetypal molecules for designing minor groove binders, and widely used as tools for staining DNA and analyzing side population cells. They are supravital DNA minor groove binders with AT selectivity. H342 and H258 share similar biological effects based on the similarity of their chemical structures, but also have their unique biological effects. For example, H342, but not H258, is a potent apoptotic inducer and both H342 and H258 can induce transgene overexpression in in vitro studies. However, the molecular mechanisms by which Hoechst dyes induce apoptosis and enhance transgene overexpression are unclear. The purpose of the present study is to determine the molecular mechanisms underlying different biological effects between H342 and H258.

overall_design: H2373 treated with H258 or H342

first: Naimei

last: Tang

first: Xinbo

last: Zhang


title: affy_syringae_malaga_athaliana-Role of different proteases in plant defence

status: Public on Apr 20 2011

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

summary:
affy_syringae_malaga_athaliana - affy_syringae_malaga_athaliana - - Pseudomonas syringae is a plant pathogenic bacterium that relies on a type III secretion system (T3SS) to cause disease in susceptible hosts and to trigger defence in resistant plants. The T3SS translocates effector proteins directly inside the plant cell. Some P. syringae pathovars translocate the effector HopZ1a, which is recognized in Arabidopsis, triggering the hypersensitive response (HR). This resistance does not depend on the usual defence pathways involved in resistance against other avirulence effectors, so it would be very helpful to know the transcriptomic events that take place in the context of a hypersensitive response triggered by HopZ1a. ULP genes codifies for plant SUMO-proteases. Recent studies by our group revealed that they could be involved in plant defense against microorganisms.-- We infiltrated Arabidopsis thaliana ecotype Columbia wild type with 10mM MgCl2 (as mock inoculation), the virulent pathogen Pseudomonas syringae pv. tomato (Pto), Pto expressing the effector HopZ1a and Pto expressing a HopZ1a derivative carrying a point mutation in a residue essential for the cystein-protease activity. We also grew ulp1c/ulp1d mutant plants to analyze them either without treatment or inoculated with MgCl2 (as mock) and Pto wt.

Keywords: gene knock out,normal vs antisens mutant comparison

overall_design: 24 arrays - ATH1

first: Stephanie

last: Huguet

first: Alberto

last: Macho

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Genes regulated by Nkx2-3 in human intestinal microvascular endothelial cells

status: Public on Apr 15 2011

city: hershey

first: wei

last: yu

address: 500 university drive

institute: pennsylvania state university

summary: Nkx2-3 is associated with inflammatory bowel disease (IBD). Nkx2-3 is expressed in microvascular endothelial cells and the muscuularis mucosa of the gastrointestinal tract. Human intestinal microvascular cells (HIMEC) are actively involved in the pathogenesis of IBD and IBD-associated microvascular dysfunction. To understand the cellular function of Nkx2-3 and its potential role underlying IBD pathogenesis, we investigated the genes regulated by Nkx2-3 in HIMEC usin cDNA microarray.

overall_design: 2 HIMEC lines (21B and 432) are used in thi study. For each HIMEC lines, either si-Nkx2-3 or contro vector was transfected 2 times to get biological replicates.

first: Wei

last: Yu

first: John

last: Hegarty

first: Gail

last: West

first: Xi

last: Chen


title: Nociceptor differentiation from pluripotent cells

status: Public on Apr 01 2011

first: Stuart

middle: M

last: Chambers

address: 1270 York Ave

institute: Sloan-Kettering Institute

summary: Here we performed the first combinatorial small molecule screen for the rapid conversion of hPSCs into postmitotic neurons. We identified a combination of five small molecule pathway inhibitors sufficient to yield neurons at > 75% efficiency within 10 days of differentiation in the absence of any recombinant growth factors. The resulting human neurons express canonical markers of nociceptive sensory fate.

overall_design: Two treatments (LSB and 3i) at days 2,3,5,7,9, and 15, in triplicate

first: Lorenz

last: Studer


title: Enhancer-like function for long non-coding RNAs in human

status: Public on Apr 12 2011

first: Ulf

middle: Andersson

last: Ørom

address: Ihnestrasse 63-73

department: OWL

institute: Max Planck Institute for Molecular Genetics

type:
Expression profiling by array
Non-coding RNA profiling by array


title: Quantitative transcriptomic analysis of abscisic acid-induced and reactive oxygen species-dependent expression changes and proteomic profiling in Arabidopsis suspension cells

status: Public on Apr 07 2011

city: La Jolla

first: Maik

last: Boehmer

address: 9500 Gilman Dr 0116

institute: University of Caifornia, San Diego

summary: Early rapid changes in response to the phytohormone abscisic acid (ABA) have been observed at the transcript level, but little is known how these transcript changes translate to changes in protein abundance under the same conditions. Here we have performed a global quantitative analysis of transcript and protein changes in Arabidopsis suspension cells in response to ABA using microarrays and quantitative proteomics. In summary, 3494 transcripts and 50 proteins were significantly regulated by ABA over a treatment period of 20–24 h. Abscisic acid also caused a rapid and strong increase in production of extracellular reactive oxygen species (ROS) with an average half-rise time of 33 sec. A subset of ABA-regulated transcripts were differentially regulated in the presence of the ROS scavenger dimethylthiourea (DMTU) as compared with ABA alone, suggesting a role for ROS in the regulation of these ABA-induced genes. Transcript changes showed an overall poor correlation to protein changes (r = 0.66). Only a subset of genes was regulated at the transcript and protein level, including known ABA marker genes. We furthermore identified ABA regulation of proteins that function in a branch of glucosinolate catabolism previously not associated with ABA signaling. The discovery of genes that were differentially regulated at the transcript and at the protein level emphasizes the strength of our combined approach. In summary, our dataset not only expands previous studies on gene and protein regulation in response to ABA, but rather uncovers unique aspects of the ABA regulon and gives rise to additional mechanisms regulated by ABA.

overall_design: Experimental Goals: 1. Identification of the set of genes that is regulated by Abscisic acid (ABA) in T87 suspension cells. 2. Test the effect of the H2O2 scavenger Dimethylthiourea (DMTU) on gene activation by ABA 3. Comaprison of changes in transcript and protein abundance in response to ABA

first: Julian

last: Schroeder


title: Impact of IRF1 on transcriptome changes in Huh-7 human hepatoma cells and STAT1-deficient human fibroblasts

first: Charles

last: Rice

address: 1230 York Ave

department: Virology and Infectious Disease

summary: IRF1, and interferon-induced transcription factor, was found to have antiviral activity against a range of viruses when overexpressed. To determine which genes are associated with expression of IRF1, gene expression analysis was carried out in two different cell line expressing IRF1. The results show that more than 100 genes, many of which overlap with type I interferon-stimulated genes, are induced more than 3-fold by IRF1. A majority of the genes were induced in both cell types, while some genes were highly induced in a cell type-specific manner.

overall_design: To investigate the impact of IRF1 overexpression on the transriptome of two target cell lines, cells were transduced with a lentiviral vector expressing IRF1 or Firefly luciferase (Fluc) as a control. Total mRNA was harvested 48 h post-transduction and processed for Illumina BeadArray analysis. Skin fibroblast cell line described in Dupuis, S. et al., Impaired response to interferon-alpha/beta and lethal viral disease in human STAT1 deficiency. Nat Genet 33 (3), 388 (2003)

last: Schoggins


title: Gene expression profile of IGROV1 cells after treatment of saline or CpG-ODN

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori


title: Gene expression profile of IGROV1 cells after in vitro treatment with CpG-ODN

summary: CpG-ODN is a potent immuno-stimulatory molecule. In order to exclude a direct effect of murine CpG-ODN on IGROV1 human ovarian cancer cell line a gene expression experiment was performed.

overall_design: The ovarian cancer cell line IGROV-1 was obtained from the ATCC (Rockville, MD). Cells were routinely maintained in RPMI medium 1640 (Sigma, St. Louis, MO) supplemented with 10% FCS (Sigma) and 2 mM glutamine (Cambrex, East Rutherford, NJ). Cells were maintained at 37°C in a water-saturated atmosphere of 5% CO2 in air. 1x106 IGROV-1 cells were seeded in 6-well plates and, after seeding, cells were treated with 10uM of CpG-ODN in culture medium [phosphorothioated ODN1826 (5’-TCCATGACGTTCCTGACGTT-3’), TriLink Biotechnologies (San Diego, CA, USA)] for 24 hours. At the end of treatment, cells were collected and RNA extracted.

first: L

first: A

last: Balsari

first: M

last: Sommariva


title: Mesothelioma tumor gene expression profiles

first: Yupu

last: Liang

summary: Malignant pleural mesotheliomas (MPMs) often show CDKN2A and NF2 inactivation but other highly recurrent mutations have not been described. To identify additional driver genes, we used an integrated genomic analysis of 53 MPM tumor samples to guide a focused sequencing effort that uncovered somatic inactivating mutations in BAP1 in 23% of MPM. The BAP1 nuclear deubiquitinase is known to target histones (together with ASXL1 as a Polycomb repressor subunit) and the HCF1 transcriptional co-factor, and we show that BAP1 knockdown in MPM cell lines affects E2F and Polycomb target genes. These findings implicate transcriptional deregulation in the pathogenesis of MPM.

overall_design: Total RNA from 53 pleural mesothelioma tumors was extracted and hybridized to Affymetrix gene expression arrays to compile a set of gene expression profiling data for this disease.

first: Marc

last: Ladanyi

first: Matthew

last: Bott


title: IGROV1 gene expression analysis after in vivo locoregional treatment with CpG-ODN

summary: Toll-like receptor 9 synthetic agonist oligodeoxynucleotides expressing CpG motifs are currently evaluated for their anti-tumor activity, mainly in association with DNA-damaging drugs. Microarray expression analyses of genes implicates in DNA repair on tumor cells from mice treated with CpG-OD, revealed a down-regulation in tumor cells. These findings provide the first time evidence that immune cells upon TLR9 engagement can sensitize cancer cells to DNA damaging chemotherapy.

overall_design: IGROV-1 human ovarian carcinoma cells were adapted to growth  intraperitoneally (i.p.) and maintained by serial i.p. passages of ascitic cells into healthy mice as described. Mice were injected i.p. with 2.5 x 106 ascitic cells in 0.2 ml of saline and treated starting 10-11 days later, when mice showed evident and established ascites, with CpG-ODN [phosphorothioated ODN1826 (5’-TCCATGACGTTCCTGACGTT-3’), TriLink Biotechnologies (San Diego, CA, USA)]. delivered i.p. at a dose of 20 µg/mouse for 3 consecutive days or 1 time, control mice received saline (4 mice/group). 24 hours after the last treatment with saline or CpG-ODN, ascites-bearing mice were sacrificed by cervical dislocation. Tumor cells adhered to peritoneal wall were collected and extraction immediately frozen in liquid nitrogen until RNA extraction.


title: Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max

city: Oak Ridge

first: David

last: Weston

state: TN

department: Environmental Sciences Division

institute: David Weston

sample_organism:
Populus trichocarpa
Arabidopsis thaliana
Glycine max


title: Comprehensive gene expression analysis of human embryonic stem cell during differentiation into neural cells

city: Tehran

first: Vahid

last: Hajihoseini

state: Tehran

address: Banihashem st, resalat ave

department: Systems Biology

country: Iran

institute: Royan Institute

summary: In this research we have done a comprehensive transcripteome analysis of hESC differentiation at three different stages: early neural differentiation, neural ectoderm, and mature neurons. We detected and validated time-dependent gene expression patterns and represented that the gene expression patterns exhibit early ESC differentiation. Pathway analysis revealed dynamic expression patterns of members of several signaling pathways.

overall_design: The hESC cells were passaged every 7 days using collagenase/dispase and cultured under feeder-free culture conditions on Matrigel in hESC medium. Three biological replicates per time point served as the input to generate biotin-labeled cRNA using a linear amplification kit.

first: Ali

last: Fathi

first: Maryam

last: Hatami

first: Faranak

last: Fattahi

first: Hossein

last: Baharvand

first: Ghasem

last: Salekdeh


title: Gene expression analysis in A549 cells

first: Ulf

last: Ørom

summary: Snai1 or ncRNA-a7 were knocked down in A549 cells using siRNA and the changes in mRNA levels were determined.

overall_design: Comparative analysis of duplicate microarray experiments compared to control transfected cells.

middle: A

first: Ramin

last: Shiekhattar


title: Gene expression profiling of IGROV1 cells after in vitro treatment with ascitic fluid from human ovarian cancer bearing mice

summary: CpG-ODN demonstrated anti-tumor activity in IGROV-1 ascites tumor-bearing mice. To evaluate if soluble molecules present in ascitic fluid, presumably released by innate immune cells via TLR9 stimulation, is directly involved with gene expression modulation a microarray experiment was performed.

overall_design: IGROV-1 human ovarian carcinoma cells were adapted to growth intraperitoneally (i.p.) and maintained by serial i.p. passages of ascitic cells into healthy mice as described. Mice were injected i.p. with 2.5 x 106 ascitic cells in 0.2 ml of saline and treated starting 10-11 days later, when mice showed evident and established ascites, with CpG-ODN [phosphorothioated ODN1826 (5’-TCCATGACGTTCCTGACGTT-3’), TriLink Biotechnologies (San Diego, CA, USA)]. Delivered i.p. at a dose of 20 µg/mouse for 3 consecutive days or 1 time, control mice received saline (3 mice/group). Twenty-four hours after the last treatment with saline or CpG-ODN, ascites-bearing mice were sacrificed by cervical dislocation. Ascitic fluid was collected using a heparinized syringe and the volume recorded. The fluid was transferred to a centrifuge tube maintained on ice. After centrifugation, supernatant was removed and stored at -80°C for in vitro experiments. The ovarian cancer cell line IGROV-1 was obtained from the ATCC (Rockville, MD). Cells were routinely maintained in RPMI medium 1640 (Sigma, St. Louis, MO) supplemented with 10% FCS (Sigma) and 2 mM glutamine (Cambrex, East Rutherford, NJ). Cells were maintained at 37°C in a water-saturated atmosphere of 5% CO2 in air. 1x106 IGROV-1 cells were seeded in 6-well plates and, after seeding, cells were treated with 2 ml of culture medium in the presence of ascites from saline-treated mice or CpG-ODN-treated mice (ratio medium:ascites, 1:1) for 24 hours. At the end of treatment, cells were collected and RNA extracted.


title: Finding direct target genes of VND7

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

summary: The Arabidopsis thaliana NAC domain transcription factor, VASCULAR-RELATED NAC-DOMAIN7 (VND7), acts as a key regulator of xylem vessel differentiation. In order to identify direct target genes of VND7, we performed global transcriptome analysis using Arabidopsis transgenic lines in which VND7 activity could be induced post-translationally. This analysis identified 63 putative direct target genes of VND7, which encode a broad range of proteins, such as transcription factors, IRREGULAR XYLEM proteins and proteolytic enzymes, known to be closely associated with xylem vessel formation. Recombinant VND7 protein binds to several promoter sequences present in candidate direct target genes: specifically, in the promoter of XYLEM CYSTEINE PEPTIDASE1, two distinct regions were demonstrated to be responsible for VND7 binding. We also found that expression of VND7 restores secondary cell wall formation in the fiber cells of inflorescence stems of nst1 nst3 double mutants, as well as expression of NAC SECONDARY WALL THICKENING PROMOTING FACTOR3 (NST3, however, the vessel-type secondary wall deposition was observed only as a result of VND7 expression. These findings indicated that VND7 upregulates, directly and/or indirectly, many genes involved in a wide range of processes in xylem vessel differentiation, and that its target genes are partially different from those of NSTs.

overall_design: Total RNAs of the transgenic plants expressing 35S:VND7-VP16-GR treated with DEX plus CHX and those treated with CHX only were compared.  As a control experiment, transgenic plants harboring empty vector were treated similarly and the total RNAs were compared similarly to identify genes merely induced by DEX treatment itself.

first: Masatoshi

last: Yamaguchi

first: Misato

last: Ohtani

first: Taku

last: Demura


title: Expression profiling MOLT-4 treated with MABL

city: Gotemba

first: Naoshi

last: Fukushima

state: Shizuoka

address: Komakado 1-135

department: Fuji Gotemba labs.

institute: Chugai pharmaceutical co., ltd.

summary: Analysis of MOLT-4 cells at various time points up to 6 hours following treatment with mouse anti-CD47 antibody (MABL) and goat anti-mouse IgG (GAM) as the crosslinker of MABL. MABL induces apoptosis in CD47-positive MOLT-4 cells. Cell death signals via CD47 ligation were analyzed by using Affymetrix Human Genome U133A microarray.

overall_design: MOLT-4 cell line was obtained from the American Type Culture Collection (ATCC) and grown in RPMI1640 medium (SIGMA) with 10% FBS(JBS). It was maintained  at 37 degree C and 5% CO2. Cells were washed with PBS(-) followed by treatment with 10 ug/mL MABL (anti-CD47 antibody) for 0, 0.5, 1, 3 and 6 h. Total RNA was isolated and converted to cDNA using a Superscript Double Stranded cDNA synthesis kit (Invitrogen). Fragmented cDNA was hybridized to Affymetrix Human Genome U133A array and gene expression signals were analyzed. Probes showing >2 or <0.5 fold-change for both replicates compared with the control (geometric mean of 0h replicate signals) were selected at any time.

first: Hideaki

last: Mizuno

first: Yasuko

last: Kinoshita


title: Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max [Arabidopsis]

summary: The heat shock response continues to be layered with additional complexity as interactions and cross-talk among heat shock proteins, the reactive oxygen network and hormonal signaling are discovered. However, comparative analyses exploring variation in each of these processes among species remains relatively unexplored. In controlled environment experiments, photosynthetic response curves were conducted from 22 °C to 42 °C and indicated that temperature optimum of light saturated photosynthesis was greater for Glycine max relative to Arabidopsis thaliana or Populus trichocarpa. Transcript profiles were taken at defined states along the temperature response curves and inferred pathway analysis revealed species-specific variation in the abiotic stress and the minor carbohydrate raffinose/galactinol pathways. A weighted gene co-expression network approach was used to group individual genes into network modules linking biochemical measures of the antioxidant system to leaf-level photosynthesis among P. trichocarpa, G. max and A. thaliana. Network enabled results revealed an expansion in the G. max HSP17 protein family and divergence in the regulation of the antioxidant and heat shock module relative to P. trichocarpa and A. thaliana. These results indicate that although the heat shock response is highly conserved, there is considerable species-specific variation in its regulation.

overall_design: fully expanded leaf samples from 4 randomly collected plants per species were harvested at 4 physiological states as determined from prior gas exchange measurements (growth temperature - baseline, photosynthetic optimum, 20% inhibition of optimum and 30% inhibition of optimum).This resulted in 16 separate samples hybridized to independent microarrays totaling 4 – replicates x 4 physiological states).


title: Classical Hodgkin lymphoma shows epigenetic features of an abortive plasma cellular differentiation: expression of PCM vs. B-cell lines

first: Volkhard

last: Seitz

address: Hindenburgdamm 30

institute: Charité Universitätsmedizin

summary:
Background
Epigenetic changes are involved in the extinction of the B-cell gene expression program of classical Hodgkin lymphoma. However, little is known regarding epigenetic similarities between classical Hodgkin lymphoma and plasma cell myeloma cells, both of which share an extinction of the gene expression program of mature B-cells.

Design and methods
Global histone H3 acetylation patterns were determined in cell lines derived from classical Hodgkin lymphoma, plasma cell myeloma and B-cell lymphoma by chromatin immunoprecipitation and subsequent hybridization onto promoter tiling arrays. H3K27 trimethylation was analyzed by chromatin immunoprecipitation and real-time DNA-PCR for selected genes. Epigenetic modifications were compared to gene expression data.

Results
B-cell characteristic genes were hypoacetylated in classical Hodgkin lymphoma and plasma cell myeloma cell lines, as demonstrated by comparison of their histone H3 acetylation patterns to those of B-cell lines. However, the number of genes jointly hyperacetylated and expressed in classical Hodgkin lymphoma and plasma cell myeloma cell lines, such as IFR4/MUM1 and RYBP, is limited. Moreover, H3K27 trimethylation for selected B-cell characteristic genes revealed that this additional epigenetic silencing is much more prevalent in classical Hodgkin lymphoma as compared to plasma cell myeloma.

Conclusion
Our epigenetic data support the view that classical Hodgkin lymphoma is characterized by an abortive plasma cell differentiation with a down-regulation of B-cell characteristic genes but without activation of most plasma cell typical genes.

overall_design:
Gene expression analysis of  plasma cell myeloma (PCM) and B-cell lines:
Microarray data of the B-cell line Namalwa that was published previously by our group (GEO accession number GSE8388) was analyzed together with newly generated data for the B-cell lines SU-DHL4 and SU-DHL6 (duplicates) and three PCM cell lines (L363, U266, LP1). For all cell lines, RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A). Microarrays were normalized using RMA, and differential expression was calculated using moderated t-test.

first: Philippe

last: Thomas

first: Karin

last: Zimmermann

first: Ulrike

last: Paul

first: Anke

last: Ehlers

first: Maria

last: Joosten

first: Lora

last: Dimitrova

first: Dido

last: Lenze

last: Sommerfeld

first: Elisabeth

last: Oker

last: Leser

first: Harald

last: Stein

first: Michael

last: Hummel


title: Dihydrotestosterone induced changes in gene expression in primary and immortalized human corneal epithelial cells

status: Public on Mar 31 2011

city: Boston

first: David

last: Sullivan

address: 20 Staniford Street

institute: Schepens Eye Research Institute

summary:
Genome-wide analysis of dihydrotestosterone (DHT) induced changes in gene expression in primary and immortalized human corneal epithelial cells.

Analysis of regulation of primary and immortalized human corneal epithelial cells by dihydrotestosterone at gene expression level. The hypothesis tested in the present study was that the androgen-eye interaction in ocular surface epithelial cells like corneal cells is influenced by androgens through regulation of the expression of multiple genes. Results provide important information of the differential regulation and comparitive analysis of numerous genes in response to dihydrotestosterone incubation in primary and immortalized human corneal epithelial cells.

overall_design: Total RNA was obtained from primary and immortalized human corneal epithelial cells treated for 5 days with 10 nM dihydrotestosterone (n=3) or vehicle (n=3).  The RNA was then used with Illumina HumanHT-12 v3 Expression BeadChips to determine the effect of DHT on gene expression in the primary human corneal cells grown in our laboratory and the immortalized human corneal epithelial cell line developed in Dr. Rheinwald's laboratory [Rheinwald et al. MCB, 22 (14): 5157. (2002)] and charecterized in Dr. Ilene Gibson's laboratory [Gipson et al. IOVS, 44 (6): 2496. (2003)].

first: Payal

last: Khandelwal


title: Skipsey: Fenclorim safening of Arabidopsis

status: Public on Apr 06 2011

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

summary: Wild type Arabidopsis thaliana Col-0 root cultures, were treated with fenclorim or 4-chloro-6-methyl-2-phenylpyrimidine dissolved in acetone to achieve a final concentration of 100uM. The final acetone concentration of 0.1% was replicated in control root cultures. Samples were taken at four and twenty-four hours post addition in biological triplicate. Root cultures were routinely maintained at 25C in the dark.

overall_design: 18 samples were used in this experiment

first: Mark

last: Skipsey


title: eif3k/WT transcript levels

status: Public on Mar 29 2011

city: Knoxville

first: Albrecht

last: von Arnim

address: M407 Walters Life Sciences Building

department: Biochemistry, Cellular and Molecular Biology

institute: the University of Tennessee

summary: To understand the contribution of the k subunit of eukaryotic transcription factor 3 (eif3k) to the translation of specific mRNAs, we compared the polysome loading states and overall transcript levels of wild type Arabidopsis and the eif3k T-DNA insertion mutant by Affymetrix arrays.

overall_design: We analyzed the transcript levels of wild type Arabidopsis and the eif3k mutant using the Arabidopsis Affymetrix ATH1 array. Data from 3 biological replicates were collected.

first: Byung-Hoon

last: Kim


title: Gene expression changes in wild type, tga2tga3tga5tga6, and sid2-2 plants after treatment with the safeners mefenpyr and isoxadifen

status: Public on Mar 27 2011

city: Freising

first: Carina

last: Behringer

address: Emil-Ramann-Str. 4

department: Institute of plant systems biology

institute: TU München

summary: Comparison of gene expression changes in safener- or BF-treated wild type (Col0) or mutants (tga2tga3tga5tga6, sid2-2) of the salicylic acid signaling pathway.

overall_design: Measurements of three biological samples were prepared for each genotype.

first: Andreas

last: Schaller

first: Klaus

last: Bartsch


title: eif3k/WT polysome loading

overall_design: We analyzed the polysome loading states of wild type Arabidopsis and the eif3k mutant using the Arabidopsis Affymetrix ATH1 array. Data from 3 biological replicates were collected.


title: eif3k/WT polysome loading and transcript levels

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

overall_design: Refer to individual Series


title: Gene Expression Profiles in Early Stages Uterine Serous Carcinomas in comparison to G3 and G1 Endometrioid Adenocarcinoma

city: buffalo

first: Dan

last: Wang

address: Elm & Carlton Streets

institute: RPCI

summary: The goal of this study was to identify differentially expressed genes (DEG) between uterine serouscarcinoma (USC) vs. early stages high/low grade endometrioid adenocarcinoma (EAC).

overall_design: Gene expression profiles of 33 cancer samples were analyzed (EAC-G1=11, EAC-G3=11, USC-G3=11) using the human genome wide illumina bead microarrays.

first: Paulette

last: Mhawech-Fauceglia

first: Joshua

last: Kesterson

first: Susanna

last: syriac

first: Kimberly

last: Clark

first: Peter

last: Frederick

first: Shashikant

last: Lele

first: Song

last: Liu


title: Arabidopsis seedlings collected during hypocotyl elongation and hypocotyl stasis

city: Davis

first: Julin

middle: N

last: Maloof

address: One Shields Ave

department: Plant Biology

institute: University of California, Davis

summary: The hypocotyl of Arabidopsis seedlings shows rhythmic periods of elongation.  The patterns of elongation are controlled by a combination of internal factors, such as the circadian clock, and external factors such as light.  In a previous study we had found that two transcription factors, PIF4 and PIF5 are important integrators of clock and light signals for the control of elongation.  Here we use microarrays to find genes that are correlated with elongation and that are controlled by PIF4 and/or PIF5.

overall_design: Arabidopsis seedlings grown under short day conditions for three days were transferred to SD/3 conditions (160 min light: 320 min dark cycles) from the dawn of the fourth day.  Seedlings were then collected during periods of hypocotyl elongation and stasis for three days.  There are two types of replication: temporal and independent experiments. For temporal replication, samples collected at the same time of day on subsequent days were used as replicates.  In addition, replicate samples were collected in two independent time courses for most time points. Col and CCA1OX samples from the first time course for time points 280, 1240, 1720, 2680, 3160, and 4120 were originally deposited under GEO Series GSE6906; they have been re-analyzed for this study.  Each sample consists of multiple pooled seedlings.

first: Kazunari

last: Nozue

first: Stacey

last: Harmer


title: ZNF703 overexpression and/or knockdown in the breast cancer cell line MCF-7

city: Cambridge

first: Suraj

last: Menon

address: Li Ka Shing Center, Robinson Way

institute: Cambridge Research Institute, Cancer Research UK

summary: The telomeric amplicon at 8p12 is common in ER+ breast cancers. Array-CGH and expression analyses of 1172 tumors revealed ZNF703/Zeppo1 was the single gene within the minimal amplicon and was amplified predominantly in the Luminal B subtype. Amplification was shown to correlate with increased gene and protein expression and was associated with a distinct expression signature and poor outcome. In the luminal MCF-7 cell line manipulation of ZNF703 expression altered transcription of genes also present within the primary tumor signature, including TGFBR2 (whose promoter was bound by ZNF703). Overexpression of ZNF703 rendered MCF-7 cells insensitive to TGFβ-induced suppression of mammosphere formation. Forced overexpression of ZNF703 in normal human breast epithelial cells enhanced the frequency of in vitro colony-forming cells from luminal progenitors. Together these data strongly point to ZNF703/Zeppo1 as a novel oncogene in Luminal B breast cancer.

overall_design: MCF-7 breast cancer cell line was infected with ZNF703 overexpression (ZNF703) or control (HIV) virus and following GFP sorting of infected cells, were transfected with control siRNA (siC) or siRNA against endogenous ZNF703 (siZNF), resulting in four different conditions: siC_HIV, siC_ZNF, siZNF_HIV and siZNF-ZNF. RNA for each condition was harvested from triplicate plates.

first: Daniel

last: Holland

first: Carlos

last: Caldas


title: Polyglutamine Atrophin provokes neurodegeneration in Drosophila

status: Public on Mar 01 2011

city: London

first: Eric

last: Blanc

address: New Hunt's House

department: MRC Centre for Developmental Neurobiology

institute: King's College London

summary:
Dentatorubral-pallidoluysian Atrophy (DRPLA) is a human polyQ disease caused by the expansion of a CAG strech in the atrophin-1 (at-1) gene. In all vertebrates, a second atrophin gene (at-2) is present and it encodes a related protein void of polyQ tracks. In D.melanogaster there is one conserved Atrophin (Atro) gene, ubiquitously expressed, which contains all functional domains of vertebrate Atrophins, including two polyQ stretches. To understand to what extent transcriptional alterations cause neurodegeneration and are linked to the normal functions of Atrophin, we performed a genome wide transcriptional profiling in our Drosophila models, focusing on primary events that precede neurodegeneration.
We have found that polyQ Atro downregulates fat, which protects from neurodegeneration and Atrophin toxicity trhough the Hippo kinase cascade.

overall_design: Neurodegeneration progression caused by poly glutamine expansions of the Atro gene is measured by mRNA expression profiles in 4 D.melanogaster genotypes: in wild-type animals (controls), animals constitutively expressing the wild-type Atro transgene, animals constitutively expressing the polyQ expanded Atro transgenes A66QC and A75QN. The expressions of the Atro genes are under a GMR-Gal4 driver repressed by a Gal80 universal repressor sensitive to temperature. When flies are raised at 18 C, the transgenes are not expressed, but their expression is switched on when they are shifted to the ageing protocol at 29 C at time point day 0. The neurodegeneration is assessed after 2 and 14 days post-high-temperature shift.

first: Manolis

last: Fanto


title: NB4 cell line treatment with WEB-2170

status: Public on Mar 22 2011

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

institute: Centre for Regenerative Medicine

summary: This study reports the ability of WEB-2170, an antagonist of platelet-activating-factor receptor, to induce apoptosis in human acute myelogenous leukemia (AML) cells.

overall_design: Action mechanisms of WEB-2170 were first investigated in promyelocytic NB4 cells by DNA microarray profiling followed by morphologic, cytofluorimetric and biological analyses which were then extended to other AML cell lines including KG1, NB4-MR4, THP1 and U937, and, eventually, to blasts from patients with different AML subtypes (M0-M5).