title: Halobacterium salinarum NRC-1 growth curve, tiling arrays

status: Public on Jun 25 2009

first: Tie

last: Koide

address: 1441 N 34th street

institute: Institute for Systems Biology

type: Expression profiling by genome tiling array

summary:
Experimentally mapped transcriptome structure of H. salinarum NRC-1 by hybridizing total RNA (including RNA species <200 nt) to genome-wide high-density tiling arrays (60 mer probes with 40 nt overlap between contiguous probes).
H. salinarum NRC-1 presents a number of interesting switches in metabolism during growth due to complex changes in EFs including pH, oxygen, nutrition, etc. While most single perturbations (radiation, oxygen, metals, etc.) affect the expression of only ~10% of all genes (Baliga et al, 2004; Kauret al , 2006; Whitehead et al, 2006), the changes during growth resulted in differential regulation of a significantly higher proportion of genes (~63%, 1,518 genes). These conditions enabled the investigation of a wider transcriptional landscape, which includes not only modulation of transcript levels, but also extensive changes in transcriptome structure. We observed altered transcription start sites (TSSs), transcription termination site (TTSs), operon organizations and differential regulation of putative ncRNAs. By integrating hybridization signals with dynamic growth-related changes, we estimated the probability that each tiling array probe was complementary to a transcribed region, mapped locations of putative transcript boundaries and identified 1,574 TSSs and 1,952 TTSs for most genes with some transcriptional variation. In sum, TSSs were assigned to 64% (1,156 singletons and 544 genes in 203 operons) of all annotated genes and TTSs were assigned to 1,114 genes and 202 operons. We were also able to identify 5' and 3' UTRs and revise start sites for 61 genes and 12 operons.

overall_design: H. salinarum NRC-1 growth curve experiments were conducted in CM media, in a water bath incubator at 37oC with agitation of 125 rpm. Reference samples were cultured under standard growth conditions (Baliga and DasSarma, 1999), at mid-log phase (OD600 = ~0.6), as well as all strains used for ChIP-chip experiments (Facciotti et al., 2007). Whole-genome high resolution tiling arrays for H. salinarum NRC-1 were designed with e-Array (Agilent Technologies), using strand specific 60mer probes tiled every 20nt for the main chromosome (NC_002607) and every 21nt for the plasmids pNRC200 (NC_002608) and pNRC100 (NC_001869), consisting a total of 244K probes, including manufacturers’ controls. Microarrays were printed by Agilent technologies and hybridized to total RNA, which was isolated using mirVana miRNA Isolation kit (Ambion) and direct labeled with Alexa547 and Alexa647 dyes (Kreatech) (Baliga et al., 2004). We used direct chemical labeling of RNA (Baliga et al., 2004) to avoid enzymatic labeling artifacts (Perocchi et al., 2007) and enable strand-specific signals for transcribed segments. Hybridization and washing were performed according to array manufacturer’s instructions. Arrays were scanned in ScanArray (Perkin Elmer) and spot-finding was performed using Feature Extraction (Agilent Technologies). Two biological replicates were sampled and dye-flip experiments were conducted for each sample. Resulting intensities were quantile normalized across all experiments. Log ratios were calculated for each probe (growth curve sample/reference). Reference RNA signals were normalized by sequence content using a linear model similar to that of (Johnson et al., 2006). Interactive visualization of the data was performed in the Gaggle Genome Browser (Bare et al., in preparation), available at http://baliga.systemsbiology.net/regulatory_logic/.

last: Reiss

first: Christopher

last: Bare

first: Marc

middle: T

last: Facciotti

first: Amy

middle: K

last: Schmid

first: Min

last: Pan

first: Bruz

last: Marzolf

first: Phu

last: Van

first: Fang-Yin

last: Lo

first: Abhishek

last: Pratap

first: Eric

last: Deutsch

first: Amelia

last: Peterson

first: Dan

last: Martin

first: Nitin

last: Baliga


title: Expression from C. elegans L1 animals

status: Public on Jan 01 2010

city: Bethesda

first: Michael

last: Krause

state: MD

address: 5 Center Drive

department: LMB/NIDDK

country: USA

institute: NIH

summary:
Nutrient-driven O-GlcNAcylation of key components of the transcription machinery may epigenetically modulate gene expression in metazoans. Knockouts of the O-GlcNAc cycling enzymes in C. elegans are viable and fertile, allowing a global analysis of the impact of GlcNAcylation.
Whole genome transcriptional profiling of the O-GlcNAc cycling mutants confirmed dramatic deregulation of genes in these key pathways. As predicted, the O-GlcNAc cycling mutants show phenotypically altered lifespan and susceptibility to UV stress.

overall_design: L1 larvae were synchronized by starvation for two days after hatching in sterile buffer.  Wild type and mutant animals were collected and total RNA isolated for gene expression analysis

first: John

last: Hanover


title: Gene expression analysis of HPV-immortalized keratinocytes

status: Public on Apr 22 2009

city: Jerusalem

first: Alexander

last: Levitzki

address: Givat Ram

department: Department of Biological Chemistry

country: Israel

institute: The Hebrew University of Jerusalem

summary: To identify early processes in carcinogenesis, we used an in vitro model, based on the initiating event in cervical cancer, human papillomavirus (HPV) transformation of keratinocytes. We compared gene expression in primary keratinocytes (K) and HPV16-transformed keratinocytes from early (E) and late (L) passages, and from benzo[a]pyrene treated L cells (BP). The transformed cells exhibit similar transcriptional changes to clinical cervical carcinoma. We revealed a contraction in expression of the apoptotic network during HF1 cell transformation, which affected the ability of L and BP cells to execute apoptosis, but did not lead to resistance to apoptotic stimuli. The contraction in the apoptotic machinery during the process of transformation was accompanied by a switch from apoptosis to necrosis in response to CDDP. The shrinkage of the pro- and anti-apoptotic networks appears to be part of a general contraction in the number of genes transcribed in L and BP cells. We also identified a large group of genes with induced expression, which are involved in cell metabolism and cell cycle, suggesting increased investment of the transformed cell in cellular proliferation. We hypothesize that the decrease in expression of many diverse pathways, including the pro- and anti-apoptotic networks, cuts the energy requirements for cell maintenance, allowing energy to be diverted towards rapid cell proliferation. This study supports the hypothesis that the process of cancer transformation may be accompanied by a shift from apoptosis to necrosis.

overall_design: We isolated mRNA from three independent cultures each of Keratinocytes and HPV16-immortalized keratinocytes : E, L and BP cells, grown under basal conditions. cDNA was prepared and hybridized to the Human Genome U133A Array (Affymetrix).

first: Nataly

last: Kravchenko-Balasha

first: Sarit

last: Mizrachy-Schwartz

first: Shoshana

last: Klein


title: Genes Differentially Expressed as a result of Candida albicans SC5314 biofilms exposure to 10b

status: Public on Dec 10 2009

city: Shanghai

first: Liang

last: Rong-mei

address: Guohe road 325

country: China

institute: smmu

summary: Biomaterial infections are an increasingly alarming problem, and because of their intrinsic recalcitrance to conventional therapy, a new class of antifungal drugs must be explored. 10b, a 2-aminotetralin derivate, was synthesized as a novel chemical structural antifungal agent and exibited strong anti-biofilm activity. To further investigate the action mechanism, we used microarray analysis to investigate the genes expression profiles of C. albicans biofilms treated or untreated with 10b and found 150 genes were differentially expressed. Of them, 69 showed a decrease in expression and 81 showed an increase in expression -10 differentially expressed genes related to biofilm formation, Filamentous or hypha growth. A gene related to specifically hydrolyzing β-1, 3 glucan was significantly increased. 10 down-regulated genes were involved in glycolysis, fermentation and active oxygen scavenging. 15 overexpressed genes were related to the lipid metabolic process. Of them, 13 genes were directly linked to ergosterol biosynthesis including ERG2, ERG6 and ERG11. 10 genes related to translation were over-expressed. Among them, 2 genes involved in negative regulation of transcription were significantly up-regulated.

overall_design: Total RNA from the control SC5314 biofilms and 10b-treated SC5314 biofilms were used to generate target cDNA, and then hybridized to 8k Candida albicans Genome Array Genechips, representing about 7925 characterized Candida albicans genes. Two independent experiments were conducted. Reference strain was control SC5314 biofilms and test strain was SC5314 biofilms treated with 10b.

first: Rongmei

last: Liang


title: PRINCIPAL COMPONENT ANALYSIS FOR EXPERIMENTS

status: Public on Aug 15 2011

city: Akita

first: Tomokazu

last: Konishi

state: Akita

address: Shimoshinjyo Nishi

department: Bioresource Sciences

country: Japan

institute: Akita Prefectural University

type:
Third-party reanalysis
Expression profiling by array

summary:
Although principal component analysis is frequently used in multivariate/ analysis, it has disadvantages when applied to experimental or diagnostic data. First, the identified principal components have poor generality; since the size and directions of the components are dependent on the particular data set, the components are valid only within the set. Second, the method is sensitive to experimental noise and bias between sample groups, since it cannot reflect the design of experiments; rather, it estimates the same weight and independence of all the samples in the matrix. Third, the resulting components are often difficult to interpret. To address these issues, several options were introduced to the methodology. The resulting components were scaled to unify their size unit. Also, the principal axes were identified using training data sets and shared among experiments. This training data reflects the design of experiments, and its preparation allows noise to be reduced and group bias to be removed. The effects of these options were observed in microarray experiments, and showed an improvement in the separation of groups and robustness to noise. Additionally, unknown samples were appropriately classified using pre-arranged axes, and principal axes well reflected the characteristics of groups in the experiments.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series.


title: Whole-Tissue Gene Expression Study of Pancreatic Ductal Adenocarcinoma

status: Public on Jun 13 2009

city: Bucharest

first: Liviu

last: Badea

address: 8-10 Averescu Blvd.

department: Research

country: Romania

institute: ICI

summary: Expression analysis of 36 pancreatic ductal adenocarcinoma tumors and matching normal pancreatic tissue samples from pancreatic cancer patients of the Clinical Institute Fundeni (ICF) using Affymetrix U133 Plus 2.0 whole-genome chips.

overall_design: Pairs of normal and tumor tissue samples were obtained at the time of surgery from resected pancreas of 36 pancreatic cancer patients. Gene expression was analyzed on Affymetrix U133 plus 2.0 whole genome microarrays. For three of the 36 normal-tumor sample pairs we carried out replicate microarray hybridizations in order to gauge the technical measurement errors. We thus performed 78 genechip hybridizations in total. A patient sample pair was excluded from further analysis since one of the samples did not meet the quality controls. The microarray data was subsequently normalized using the RMA algorithm.

first: Irinel

last: Popescu


title: Gene expression profiling of cultured cells from brainstem of spontaneously hypertensive and Wistar Kyoto rats

status: Public on Dec 31 2008

city: São Paulo

first: Eduardo

middle: Moraes

last: Reis

state: SP

address: Av. Prof. Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: University of São Paulo

summary:
Hypertension is a multifactor disease that possibly involves alterations in gene expression in hypertensive relative to normotensive subjects that are largely unknown. In this study we used high-density oligoarrays to compare gene expression profiles in cultured neurons and glia from pons and medulla oblongata of newborn spontaneously hypertensive (SHR) and normotensive Wistar Kyoto (WKY) rats, a widely documented animal model of hypertension. We found 358 genes differentially expressed between SHR and WKY brainstem cells that preferentially map to 24 metabolic/signaling pathways. Some of the pathways and regulated genes identified herein are obviously related to blood pressure regulation; however there are several genes differentially expressed in SHR not yet associated to hypertension or participating in blood pressure regulation. These constitute a rich resource for the identification and characterization of novel genes involved in hypertension development, or associated to phenotypical differences observed in SHR relative to WKI. In conclusion, this study describes for the first time the gene profiling pattern of brainstem cells from SHR and WKY rats, which opens up new possibilities and strategies of investigation and possible therapeutics to hypertension, as well as for the understanding of the brain contribution in this pathology.
Keywords: Gene expression profiling of cultured cells from brainstem of spontaneously hypertensive and normotensive Wistar Kyoto rats

overall_design:
Global measurements of gene expression from normotensive and hypertensive were obtained using the CodeLink Expression Bioarray System (GE Healthcare, UK), which interrogates 34,000 annotated genes and ESTs expressed in the rat genome. Each rat strain was hybridized in three independent biological replicates. Target labeling and hybridization was performed strictly as recommended by the array manufacturer.

CodeLink Expression Analysis software (GE Healthcare) was used to extract background-subtracted spot intensities from microarray images. Measurements that were bellow the intensity of negative controls plus 2 standard deviations were excluded. Only genes with valid measurements in all three biological replicates of normotensive or hypertensive animals were further analyzed. To make experiments comparable, intensity data from different hybridizations were normalized by the quantile method

middle: M

first: Merari

middle: R

last: Ferrari


title: Halobacterium salinarum NRC-1 total RNA hybridization of TFBd overexpression versus Reference sample

city: Seattle

first: Tie

last: Koide

state: WA

summary: Total RNA hybridizations of Halobacterium salinarum NRC-1 total RNA versus a strain overexpressing TFBd were compared to verify the transcriptome landscape changes. Comparison with TFBd binding sites localized using ChIP-chip data and MeDiChI algorithm (Reiss et al, 2008) allowed observation that TF-binding in the middle of coding sequences can also result in transcription initiation or termination internal to a single annotated protein-coding gene.

overall_design: Total RNA sample of plasmid based expression of Cmyc tagged transcription factor TFBd grown in standard growth media with mevinolin.

first: Marc

last: Facciotti

first: Min

last: Pan

first: David

middle: J

last: Reiss

middle: S


title: Musashi 2 regulates normal hematopoiesis and accelerates leukemogenesis

status: Public on Jul 21 2010

city: Cambridge

first: Fatima

last: Al-Shahrour

state: MA

address: 7 Cambridge Center

department: Cancer program

institute: Broad Institute of MIT and Harvard

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Primary Human Bronchial Epithelial Cells (HBEs) Stimulated with IL-22 and IL-17

status: Public on Jan 23 2008

city: Pittsburgh

first: Shean

last: Aujla

state: PA

address: 3460 Fifth Ave

department: Division of Pulmonary Medicine, Allergy and Immunology

institute: Children's Hospital of Pittsburgh

summary:
Primary HBE cells were stimulated with IL-22 and IL-17, and gene expression was studied using an Affymetrix platform microarray, in order to investigate which genes may be upregulated or downregulated in response to these cytokines.  Of particular interest was the host defense genes such as antimicrobial peptides, which have been shown to be upregulated by IL-22 and IL-17 in skin keratinocytes.
Keywords: cytokine effect

overall_design:
There were 4 conditions to this study (media, IL-22, IL-17 and IL-22+17) and there were 3 biological replicates of each condition.
Gene expression study using one timepoint of 24 hours after stimulating these primary cells with the above conditions

first: Jay

last: Kolls


title: Human dermal lymphatic endothelial cells stimulated with VEGF-A or VEGF-C for 1h, 4h, 8h and 24h

status: Public on Jul 25 2008

city: Zurich

middle: Woo

last: Shin

state: Zurich

address: Wolfgang-Paulistrasse 10; HCI H394

department: Institute of Pharmaceutical Sciences

country: Switzerland

institute: ETH Zurich

summary:
Lymphatic vessel growth and activation, mediated by vascular endothelial growth factor- (VEGF)-C and/or VEGF-A, play an important role in metastatic cancer spread and in chronic inflammation. We aimed to comprehensively identify downstream molecular targets induced by VEGF-A or VEGF-C in lymphatic endothelium. To this end, we treated human dermal lymphatic endothelial cells (LEC) with VEGF-A or VEGF-C for up to 24 hours, followed by a time-series transcriptional profiling using gene microarray technology. We identified a number of genes - many of them not previously known to be involved in lymphangiogenesis - that clustered either as early response genes, transiently induced genes or progressively induced genes. Endothelial specific molecule-1 (ESM-1) was one of the genes that were most potently induced by both VEGF-A and VEGF-C.
Keywords: Time course, growth factor comparison

overall_design: Overnight serum starved human primary dermal microvascular lymphatic endothelial cells (LEC; passage 5-7) were stimulated with either VEGF-A or VEGF-C for 24 hours, 8 hours, 4 hours and 1 hour. Total RNA from all samples were isolated using TriZol at time point zero (control reference point). Treatments were performed at three independent times (triplicates) for each growth factor and at each time point (except the control reference time point), total of 27 samples and labeled and hybridized using the AB1700 microarray platform.

first: Reto

last: Huggenberger

first: Michael

last: Detmar


title: Prevalence of transcription promoters within archaeal operons and coding sequences

type: Genome binding/occupancy profiling by array

type: Genome binding/occupancy profiling by genome tiling array

summary:
Despite knowledge of complex prokaryotic transcription mechanisms, generalized rules, such as the simplified organization of genes into operons with well-defined promoters and terminators, have played a significant role in systems analysis of regulatory logic in both bacteria and archaea. Here, we have investigated the prevalence of alternate regulatory mechanisms through genome-wide characterization of transcript structures of ~64% of all genes including putative non-coding RNAs in Halobacterium salinarum NRC-1. Our integrative analysis of transcriptome dynamics and protein-DNA interaction datasets revealed widespread environment-dependent modulation of operon architectures, transcription initiation and termination inside coding sequences, and extensive overlap in 3' ends of transcripts for many convergently transcribed genes. A significant fraction of these alternate transcriptional events correlate to binding locations of 11 transcription factors and regulators (TFs) inside operons and annotated genes - events usually considered spurious or non-functional. With experimental validation, we illustrate the prevalence of overlapping genomic signals in archaeal transcription, casting doubt on the general perception of rigid boundaries between coding sequences and regulatory elements

This SuperSeries is composed of the SubSeries listed below.


title: Female and Male Mice from the MRL/lpr and Non-Obese Diabetic (NOD) Strains.

status: Public on Feb 01 2009

city: Boston

middle: A

last: Sullivan

address: 20 Staniford Street

institute: Schepens Eye Research Institute

summary:
The Effect of Sex on Lacrimal Gland Gene Expression in the MRL/lpr and Non-obese Diabetic Mouse Models of SjšgrenÕs Syndrome
Keywords: Female vs Male Lacrimal Gland Gene Expression.

overall_design: Female and male lacrimal glands were harvested each mouse strain . Tissues were pooled into 3 biological replicates and were hybridized to separate microarrays.  Each cRNA prep was hybridized to a GE Healthcare/Amersham Biosciences CodeLink UniSet Mouse 20K I Bioarray and a Affymetrix GeneChip Mouse Expression Array 430A.

first: S

last: Richards

first: R

middle: V

last: Jensen

first: D


title: Systems biology of gene expression of bladder papilloma cells modulated by a malignant-derived extracellular matrix

status: Public on Jun 10 2008

city: Oklahoma City

first: Robert

middle: Evan

last: Hurst

state: OK

address: 920 S. L. Young Blvd

department: Urology

institute: Oklahoma University Health Sciences Center

summary:
This study was undertaken to identify how gene expression of the RT4 bladder papilloma cells respond to extracellular matrics (ECM) Matrigel. Gene expression profile of RT4 cells grown on Plastic was compared with expression profiles of RT4 cells grown on Matriges over 12 hours-9 days timecourse. Total 5881 hypervariable (HV) genes were found to vary significantly over the time points, indicating a response to matrix change. Correlational clustering showed these HV genes fell into distinct families, predominantly genes which became highly expressed on ECM. Another cluster show genes expressed at 12 hours after grown on Matrigel and third cluster show genes whose expression decreased below noise level on Matrigel. This indicate that processes responsible for cell adaptation to ECM happen within first 12 hours and the second cluster form last response of those active processes. Over 1-9 days of cell grows on Matrigel those genes are constantly expressed. Cell signaling and cellular growth and proliferation accounted for major functions for those genes. G-protein signaling, immune response and NF-kB signaling accounted for most dramatically affected canonical pathways. Genes sharing similar ontologies also share several overrepresented transcription regulatory elements confirmed by independent experiment on Panomics platform.Thus, rapid response for ECM orchestrated by several transcription factors was observed. Identified canonical pathways indicate possible targets for manipulating cell phenotype on ECM.
Keywords: extracellular matrix, gene expression, RT4, Matrigel, microarray, time course

overall_design: Three dimensional gel cultures with Matrigel were performed by layering 0.8 mls of ice cold Matrigel onto polyethylene terephthalate membranes of 6-well cell culture inserts (Falcon, Becton-Dickinson Labware, Franklin Lakes, NJ). Gels were solidified at 37º C.  RT4 cells were trypsinized, brought up on 20 mls McCoys media with 10% Fetal Calf Serum (FCS).  Cells were centrifuged  then brought up in McCoys media with 10% FCS to a concentration of 500,000 cells/250µl.   250µl added on top of each solidified matrigel disc and 2mls of McCoys with 10% FCS layered underneath each culture insert. Cells were maintained for 10 days and media replenished underneath the insert twice a week.  Cells were harvested at 12 hrs, 24hrs, 2 days, 3 days, 4days, 6 days, 7 days, 8 days, and 9 days of growth in culture using Matrisperse (Falcon, Becton-Dickinson Labware, Franklin Lakes, NJ) and RNA collected. Data were normalized as was described previously in Dozmorov I et al., Nucleic Acids Res. 2004 Oct 28;32(19). In general, intensities were converted to expression and normalized to low-expressed genes, which provide possible technical noise level. The arrays are then adjusted to each other by robust linear regression and this Log10 transformed data presented for each sample. Group of low-expressed genes is  selected by normal distribution fitting. This group provides internal standard of measurement noise (ISMN). Genes above 5SD from mean of ISMN were selected as expressed

first: Mikhail

middle: G

last: Dozmorov

first: Kimberly

middle: D

last: Kyker

first: Ricardo

last: Saban

first: Igor

middle: B

last: Centola

middle: E


title: Simvastatin attenuates lung vascular leak and inflammation in a murine model of radiation-induced lung injury

status: Public on Mar 02 2009

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

summary:
Background: Microvascular injury and increased vascular leakage are prominent features of the radiation-induced lung injury (RILI) which follows cancer–associated thoracic irradiation. The mechanisms of RILI are incompletely understood and therapeutic strategies to limit RILI are currently unavailable. We established a murine model of radiation pneumonitis in order to assess mechanism-based therapies for RILI-induced inflammation and vascular barrier dysfunction. Based on prior studies, we investigated the therapeutic potential of simvastatin as a vascular barrier protective agent in RILI.
Methods: C57BL6/J mice receiving single dose exposure to 18, 20, 22, or 25 Gy, (n=10/group) were temporally assessed (4-12 weeks) for cellular and biochemical indices of injury present in both bronchoalveolar lavage (BAL) and lung tissues (cytokines, tyrosine nitrosylated proteins, leukocytes, extravasation of Evans blue dye or EBD, BAL albumin, histology). In specific experiments, irradiated mice (25Gy) received simvastatin (10 mg/kg) via intraperitoneal injection three times a week (pre and post irradiation) for 2- 6 weeks post irradiation.
Results. Acute RILI evolved in a dose- and time-dependent fashion. Mice irradiated with 25Gy exhibited modest increases in BAL leukocytes but significant increases in BAL IL-6 (p=0.03) and TNF-a (p=0.01) at 4 weeks compared to controls. Increases in BAL nitrotyrosine content peaked at 6 weeks (p=0.03) and was accompanied by marked nitrotyrosine immunostaining in lung tissues. Indices of increase lung vascular permeability such as EBD extravasation, BAL protein and BAL albumin significantly increased over time beginning at 6 weeks (p>0.002 all) with histological evidence of severe edema formation and airway inflammation. Simvastatin- treated irradiated mice were noted to exhibit marked attenuation of vascular leak with significantly decreased BAL protein (p=0.01) and inflammatory cell infiltration (50% reduction).
Conclusion: Simvastatin is a potentially important therapeutic strategy to limit RILI and may influence radiation associated morbidity and mortality.
We used microarrays to detail the global programme of gene expression induced by radiation in Wild type and the protection of SIMVA

overall_design: animals were treated by Vehical, Radiation (25Gy), SIMVA(10mg/kg), or both.

first: Biji

last: Mathew

first: Jeffrey

last: Jacobson

first: Lilianna

last: Moreno-Vinasco

first: Yves

last: Lussier

first: Ralph

first: Joe

last: Garcia


title: Focal gains of VEGFA and molecular classification of hepatocellular carcinoma

status: Public on Jun 22 2008

city: Chapel Hill

first: Derek

last: Chiang

state: NC

address: UNC Lineberger Cancer Center, 450 West Drive, CB #7295

department: Department of Genetics

institute: University of North Carolina

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

summary:
The data are derived from anonymized patient samples for which demographic information is not provided

This SuperSeries is composed of the SubSeries listed below.

middle: Y

first: Augusto

last: Villanueva

first: Yujin

last: Hoshida

first: Judit

last: Peix

first: Philippa

last: Newell

first: Beatriz

last: Minguez

first: Amanda

last: Cozza

first: Diana

last: Donovan

first: Swan

middle: N

last: Thung

first: Manel

last: Sole

first: Victoria

last: Tovar

first: Clara

last: Alsinet

first: Alex

last: Ramos

first: Jordi

last: Barretina

first: Sasan

last: Roayaie

first: Myron

last: Schwartz

first: Vesna

last: Najfeld

last: Bruix

first: Vincenzo

last: Mazzaferro

first: Azra

middle: H

last: Ligon

first: Samuel

last: Waxman

first: Scott

last: Friedman

first: William

last: Sellers

first: Matthew

last: Meyerson

first: Josep

last: Llovet


title: Non-demented individuals with intermediate Alzheimer's neuropathologies - neuronal expression (6 regions)

status: Public on Dec 05 2007

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
Layer II stellate neurons (entorhinal cortex) and layer III cortical neurons (hippocampus CA1, middle temporal gyrus, posterior cingulate, superior frontal gyrus, primary visual cortex) were gene expression profiled.  Brain regions are from non-demented individuals with intermediate Alzheimer's disease neuropathologies
Keywords: neuronal gene expression profiling

overall_design: ~500 neurons were selected from each of 6 brain regions.  Total RNA was isolated from each batch of neurons, double round amplified, and hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays.


title: Gene expression profiling of 91 hepatocellular carcinomas with hepatitis C virus etiology

first: Derek

last: Chiang

summary:
To characterize the genetic alterations that instigate hepatitis C virus-induced hepatocellular carcinoma (HCC), we conducted an integrative genomic analysis of 103 HCCs.  Most tumors harbored 1q gain, 8q gain or 8p loss, with occasional alterations in 13 additional chromosome arms.  In addition to amplifications at 11q13 in 6 tumors, 4 tumors harbored focal gains at 6p21 incorporating VEGFA, which were confirmed in 4 of 113 HCC in an independent validation set.  Strikingly, this locus overlapped with copy gains in 4 of 371 lung adenocarcinomas.  Overexpression of VEGFA via 6p21 gain suggested a cell-nonautonomous mechanism of oncogene activation.  Hierarchical clustering of gene expression among 91 tumors identified 5 classes, including ‘Wnt-CTNNB1’, ‘proliferation’ and ‘interferon-related’ gene classes.  We also discovered a novel class defined by polysomy of chromosome 7, gains of which were associated with early tumor recurrence after resection.  These findings reveal key alterations in HCC pathogenesis and implicate potential therapeutic targets.
Keywords: disease state analysis

overall_design: 91 hepatocellular carcinomas were obtained at the time of surgical resection or orthotopic transplantation.

first: Augusto

last: Villanueva

first: Yujin

last: Hoshida

first: Judit

last: Peix

first: Philippa

last: Newell

first: Beatriz

last: Minguez

first: Amanda

last: Cozza

first: Diana

last: Donovan

first: Swan

last: Thung

last: Sole


title: Gene expression profiles of head and neck squamous cell carcinoma (HNSCC)

status: Public on Nov 24 2007

city: Chiba

first: Satoya

last: Shimizu

address: 1-8-1 Inohana, Chuo-ku

institute: Chiba university

summary:
Distant metastasis is a major factor associated with poor prognosis in head and neck squamous cell carcinoma (HNSCC), but little is known of its molecular mechanisms. New markers that predict clinical outcome, in particular the ability of primary tumors to develop metastatic tumors, are urgently needed. Here, we identified neurotensin, highly expressed in HNSCCs in comparison with normal tissues, as an invasion-promoting factor in HNSCC by using microarray analysis of clinical samples. Indeed, neurotensin overexpression associated with lymph node metastasis of neck, and tumors exhibiting neurotensin overexpression had a poor distant metastasis-free survival rate. In HNSCC cells which expressed neurotensin receptor 1 (NTSR1), neurotensin promoted cellular invasion, migration, and induction of matrix metalloproteinases transcripts. Disruption of NTSR1 signaling by silencing RNA caused the reversion of the invasion of HNSCC cells. By further microarray analysis using neurotensin-treated cells, neurotensin caused increased expression of genes implicated in tumor progression and metastasis including cell growth, migration, invasion, adhesion, angiogenesis, and apoptosis. Our findings have revealed a critical role of neurotensin/NTSR1 for invasion and migration in the metastatic process of HNSCC. This study raises the possibility that neurotensin/NTSR1 could be used as a possible predictive marker and a molecular therapeutic target in the antimetastatic strategies of HNSCC.
Keywords: Identification of a novel therapeutic target for head and neck squamous cell carcinomas

overall_design: A total of 21 primary HNSCC samples were obtained from patients who underwent tumor resection at Chiba University Hospital (Chiba, Japan). 21 samples of normal-appearing mucosa at the margin of the surgical resection several centimeters from the tumor were also collected and designated histologically normal mucosa. 21 HNSCCs and paired normal tissues were used for microarray experiment. The clinicopathological grade was classified according to the criteria of the Japan Society for Head and Neck Cancer. The Ethics Committee of Chiba University approved our study, and informed consent was obtained from all patients for use of their tissue samples and clinical data. Tissue samples were immediately snap frozen in liquid nitrogen and stored at -80°C until use.


title: Transcriptome Survey of Malaria Parasite Liver Stages

status: Public on Jan 07 2008

first: Stefan

middle: H. I.

last: Kappe

address: 307 Westlake Ave N, Suite 500

institute: Seattle Biomedical Research Institute

summary:
To facilitate pre-eythrocytic malaria vaccine and drug target identification, a comprehensive transcriptome analysis of the parasites liver stages (LS) was undertaken. Green fluorescent protein-tagged Plasmodium yoelii (PyGFP) was used to isolate LS-infected hepatocytes from the rodent host. Genome-wide LS gene expression was profiled and compared to other parasite life cycle stages. The analysis reveals ~2000 genes active during LS development.
Keywords: Stage comparison, time course

overall_design:
1. The study profiled gene expressions in samples from 7 stages of malaria parasite P. yoelii life cycle:
a. ooSpz: Sporozoites from infected A. stephensi mosquitoes midguts (harvested 10 days after mosquito feeding)
b. sgSpz: Sporozoites infected A. stephensi mosquitoes salivary glands (harvested 15 days after mosquito feeding)
c. LS24: Isolated liver stage infected hepatocytes 24 hrs after in vivo infection
d. LS40: Isolated liver stage infected hepatocytes 40 hrs after in vivo infection
e. LS50: Isolated liver stage infected hepatocytes 50 hrs after in vivo infection
f. Schz: Purified erythrocytic schizonts
g. BS: mixed erythrocytic stages when parasitemia was at 5-10%
2. Samples from Liver stage parasites and Sporozoites were mainly compared to samples from mixed erythrocytic and/or schizont stage parasites with various technical replicates, including dye swaps in some comparisons.

first: Alice

last: Tarun

first: Xinxia

last: Peng

first: Ronald

middle: F

last: Dumpit

first: Hilda

last: Silva-Rivera

first: Lawrence

middle: W

last: Bergman


title: SKOV-3TR

status: Public on Oct 31 2007

first: Ahmed

middle: Ashour

last: Ahmed

address: Robinson Way

department: Oncology, University of Cambridge

country: United Kingdom

institute: Cancer Research UK Cambridge Research Institute

summary:
Human paclitaxel-resistant (SKOV-3TR) ovarian cancer cell line and the
parent SKOV-3 cell line were grown in RPMI medium containing 10% fetal
calf serum. The experiment was done to compare the expression
differences between the parent SKOV-3 cell line and the derived SKOV-3TR
cell line.

Cells were plated in T75 flasks. They were cultured until they were
80% confluent and harvested by trypsinization followed by pelleting of
the cells. All RNA isolation was accomplished with the Tri-Reagent
(SIgma) and purified using the Qiagen RNeasy Mini Kit reagents. The
RNA (50 ug) was annealed with a random hexamer primer, and
reverse-transcribed into cDNA with Powerscript (Clontech) reverse
transcriptase for 2h at 42 degrees in the presence of amino-allyl
dUTP.

The cDNA from SKOV-3 RNA and SKOV-3TR RNA was covalently coupled
separately with Cy3 and Cy5 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0. The Cy3 and Cy5 labelled cDNAs were
combined and purified with a QIAquick PCR purification kit and
hybridized to the microarray using the Hybrite chamber (Vysis).

Fluorescent array images were collected for both Cy3 and Cy5 with a
ScanArray 4000 (Perkin Elmer) at a resolution of 10 um at maximum
laser power and photo-multiplier tube voltage of 50 to
60%. Segmentation was performed using the histogram method of the
QuantArray (Perkin Elmer) package. Data was transformed into log base
2 expression ratios and normalized using scaled loess normalization.
Keywords: repeat sample

first: James

last: Brenton


title: Pre-treatment expression data from patients recruited to the paclitaxel arm of the CTCR-OV01 study

status: Public on Oct 30 2007

summary:
All patients with suspected ovarian cancer (Raised CA 125 and a complex pelvic mass in a perimenopausal woman) were radiologically staged using CT scan and a chest x-ray. Patients with evidence of intra-abdominal metastasis and/or malignant pleural effusion were approached for entry to the study. Tissue biopsy was obtained either under radiological control (core needle biopsy) or via laparoscopic surgery (punch biopsy). Patients with histologicaly confirmed epithelial ovarian cancer were randomized to receive either three cycles of carboplatin (AUC 7) or paclitaxel (175 mg/m2).

Following data filtering, only 3426 genes were retained for further downstream analysis (see 'Data_after_filtering.txt' at the foot of this record).  For data filtering details, please see the 'Data processing' field in any of the associated Sample records.
Keywords: Prospective Randomized trial

overall_design: Patients with suspected ovarian cancer had a biopsy obtained before the start of treatment. Each sample was divided into two; one for histological confirmation and the other was immediately frozen for RNA extraction.


title: Salmonella Typhiumurium LT2, wild type versus aroD mutant.

status: Public on Oct 24 2007

city: Brno

first: Magdalena

last: Crhanova

address: Hudcova 70

department: Bacteriology

country: Czech Republic

institute: Veterinary research institute

summary:
Transcriptional analysis of aroD mutant strain compared to an isogenic wild type strain Salmonella Typhimurium.
Keywords: Genetic modification.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Three independent biological replicates.

first: Ivan

last: Rychlik


title: The complete genome sequence and analysis of the human pathogen Arcobacter butzleri.

status: Public on Aug 15 2007

city: Albany

first: Craig

middle: T

last: Parker

state: CA

address: 800 Buchanan St

department: PSM

institute: USDA ARS

summary:
Background:
The human pathogen Arcobacter butzleri is a member of the epsilon subdivision of the Proteobacteria and a close taxonomic relative of other established pathogens, such as Campylobacter jejuni and Helicobacter pylori. Here we present the complete genome sequence of the human clinical isolate, A. butzleri strain RM4018.
Results:
Arcobacter butzleri is a member of the Campylobacteraceae, but the majority of its proteome is most similar to those of Thiomicrospira denitrificans and Wolinella succinogenes, both members of the Helicobacteraceae. In addition, many of the genes and pathways described here, e.g. those involved in signal transduction and sulfur metabolism, have been identified previously within the epsilon subdivision only in T. denitrificans and/or W. succinogenes, or are unique to the subdivision. The analyses indicated also that a large proportion of the A. butzleri genome is devoted to growth and survival under diverse environmental conditions, with a large number of respiration-associated proteins, signal transduction and chemotaxis proteins and proteins involved in DNA repair and adaptation. To investigate the genomic diversity of A. butzleri strains, we constructed an A. butzleri DNA microarray comprising 2238 genes from strain RM4018. Comparative genomic indexing analysis of 12 additional A. butzleri strains identified both the core genes of A. butzleri and intraspecies hypervariable regions, where < 70% of the genes were present in at least two strains.
Conclusion:
The presence of environmentally-associated pathways and loci, as well as genes associated with virulence indicates that this free-living, water-borne organism A. butzleri can be classified rightfully as an emerging pathogen.
Keywords: comparative genomic hybridization

sample_organism:
Aliarcobacter butzleri
Aliarcobacter butzleri RM4018

overall_design: The genomic diversity of 13 A. butzleri strains from a both human and animals was examined by microarray-based comparative genomic indexing (CGI) analysis.  The CGI analysis allowed the assessment of CDS content for each A. butzleri strain relative to the A. butzleri DNA microarray, which comprises 2238 CDS from strain RM4018.  Genomic DNA from strain RM4018 was used as a reference DNA and competitively hybridized with genomic DNA from each of the A. butzleri strains. We used the GENCOM software to assign the CDS as present, absent or multicopy for each A. butzleri strain.

first: William

last: Miller

first: Marc

last: Rubenfield

first: George

middle: L

last: Mendz

middle: M

last: Wösten

first: David

last: Ussery

first: John

last: Stolz

first: Guilin

last: Wang

first: Joel

last: Malek

first: Andrea

last: Rogosin

first: Larry

last: Stanker

first: Robert

last: Mandrell


title: Gene expression profiling of CEBPA double and single mutant and CEBPA wild type AML.

status: Public on Jan 21 2009

city: Houston

first: Roel

last: Verhaak

state: TX

address: 1400 Pressler St

department: Bioinformatics and Comp Bio

institute: MD Anderson Cancer Center

summary:
Mutations in CCAAT/enhancer binding protein alpha (CEBPA) are seen in 5-14% of acute myeloid leukemia (AML) and have been associated with a favorable clinical outcome. Most AMLs with CEBPA mutations simultaneously carry two mutations (CEBPAdouble-mut), usually biallelic, while single heterozygous mutations (CEBPAsingle-mut) are less frequently seen. Using denaturing high performance liquid chromatography and nucleotide sequencing we identified among a cohort of 598 newly diagnosed AMLs a subset of 41 CEBPA mutant cases, i.e. 28 CEBPAdouble-mut and 13 CEBPAsingle-mut cases. CEBPAdouble-mut associated with a unique gene expression profile as well as favorable overall and event-free survival, retained in multivariable analysis that included cytogenetic risk, FLT3-ITD and NPM1 mutation, white blood cell count and age. In contrast, CEBPAsingle-mut AMLs did not express a discriminating signature and could not be distinguished from wild type cases as regards clinical outcome. These results demonstrate significant underlying heterogeneity within CEBPA mutation positive AML with prognostic relevance.

Keywords: Gene expression profiling by arrays

overall_design: Gene expression profiling of 524 cases of de novo AML. Comparisons of cases with double and single CEBPA mutations versus those with wild type CEBPA.

first: Ruud

last: Delwel

first: Bas

middle: J

last: Wouters


title: Expression data from the abdominal aorta and abdominal aortic aneurysm

status: Public on Jul 26 2007

city: Detroit

first: Gerard

last: Tromp

state: MI

address: 3309 Scott Hall, 540 East Canfield Ave

department: Center for Molecular Medicine and Genetics

institute: Wayne State University School of Medicine

summary:
Global gene expression information that can be used to identify pathways
involved in the pathophysiology of disease.
We used microarrays to identify which genes are expressed in either the
abdominal aorta (control) or in abdominal aortic aneurysms (case), and also
which genes may be differential between the two tissue states.
Keywords: Characterization of expression in both diseased and non-diseased abdominal aortas.

overall_design:
Abdominal aortas and abdominal aortic aneurysms were obtained from
either autopsy within 24 hours of death (control tissue) or surgical
prooceedures (aneurysms). RNA was isolated and run on two platforms
either as pools or as the individual samples contributing to the pools.

first: Helena

last: Kuivaniemi

first: Guy

last: Lenk

first: Shantel

last: Weinsheimer


title: Genetic changes in the evolution of multidrug resistance for cultured human ovarian cancer cells

status: Public on Aug 24 2007

city: Vancouver

first: T

last: Buys

state: BC

address: 675 W.10th Avenue

department: Cancer Genetics and Developmental Biology

country: Canada

institute: British Columbia Cancer Research Centre

summary:
Gene expression profiles were assessed for vincristine-sensitive parental ovarian tumor cell line (SKOV3) and its highly vincristine-resistant derivative (SKVCR 2.0)
Keywords: vincristine, drug resistance, ovarian, SKOV3, MDR

overall_design: Duplicate gene expression microarray experiments were undertaken for each of SKOV3 and SKVCR 2.0.  Comparative analysis between these two groups defined genes activated in vincristine resistance

first: Timon

middle: P

first: Raj

last: Chari

first: Eric

last: Lee

first: May

last: Zhang

first: Calum

last: MacAulay

first: Stephen

last: Lam

first: Wan

first: Victor

last: Ling


title: Expression data from 43 Ovarian tumors

status: Public on May 31 2007

city: Atlanta

first: Nathan

middle: J.

last: Bowen

state: GA

address: 223 James P Brawley Drive

department: Center for Cancer Research and Therapeutic Development

institute: Clark Atlanta University

summary:
Gene expression profiles of malignant carcinomas surgically removed from ovarian cancer patients pre-treated with chemotherapy (neo-adjuvant) prior to surgery group into two distinct clusters. One group clusters with carcinomas from patients not pre-treated with chemotherapy prior to surgery (C-L) while the other clusters with non-malignant adenomas (A-L).
Although the C-L cluster is preferentially associated with p53 loss-of-function (LOF) mutations, the C-L cluster cancer patients display a more favorable clinical response to chemotherapy as evidenced by enhanced long-term survivorships.
Keywords: Patient Tumor Samples

overall_design: A set of 43 ovarian tumors was obtained from the Ovarian Cancer Institute (Atlanta).  Tissue was collected at the time of surgery and preserved in RNAlater (Ambion, Austin, TX) within one minute of collection.  Labeled probe was hybridized to the Affymetrix HG-U95Av2 arrays.

first: Carlos

middle: S

last: Moreno

first: John

last: McDonald


title: A Highly Sensitive and Specific System for Large-scale Gene Expression Profiling

status: Public on Jun 01 2007

city: Shanghai

first: Guohong

last: Hu

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health

summary:
Gene expression profiling of very few or even single cells is of particular interest in many applications. However, detection of a large number of mRNA sequences from a small number of cells is limited by the sensitivity of available methods. High-throughput multiplex reverse transcription followed by PCR amplification (RT-PCR) has much to offer to these studies due to its inherent sensitivity, efficiency and cost-effectiveness. A multiplex RT-PCR based high-throughput gene profiling system is described in this communication. With this system >1000 different mRNA species can be amplified in a single tube to a detectable amount. By using specially designed PCR primers, the long-standing low specificity problem associated with high-throughput gene expression profiling has been solved. Amplified sequences are then resolved by microarray with probes that only hybridize to sequences amplified from mRNA. The method is so sensitive that mRNA in single cells can be reliably detected. Differentially expressed genes identified with the high-throughput approach in the breast cancer cell line, MCF-7, and its drug resistant variant, MCF-7/AdrR, could be validated by a different method. The approach may greatly facilitate the analysis of combinatorial expression of known genes in any cells in many important applications with a limited amount of RNA.
Keywords: drug resistence

overall_design: To establish the microarray system, duplicates of 100 MCF7/AdrR cells were hybridized to test the stablity of the array. Comparative analysis of MCF7 and MCF7/AdrR cells were preformed and the results were validated through individual gene analysis. RNA from single cells were hybridized to the array to test the sensitivity of the system.

first: Qifeng

last: Yang

first: Gang

last: Yue

first: Marco

middle: A

last: Azaro

first: Hui-Yun

last: Wang

first: Xiangfeng

last: Cui

first: Honghua

last: Li


title: Ribonomic analysis of human Pum1 in HeLa cells

status: Public on May 01 2008

city: Durham

first: Adam

middle: R

last: Morris

address: Box 3020 Research Dr.

department: Molecular Genetics and Microbiology

institute: Duke Uniersity Medical Center

summary:
PUF family proteins are among the best characterized regulatory RNA-binding proteins in non-mammalian species, but relatively little is known about mRNA targets or functions of mammalian PUF proteins.  In this study, we used ribonomic analysis to identify and analyze mRNAs associated with ribonucleoproteins containing an endogenous human PUF protein, Pum1.  Pum1 associated mRNAs were highly enriched for genes encoding proteins that function in transcriptional regulation and cell cycle/proliferation, results consistent with the post-transcriptional RNA regulon model and the proposed ancestral functions of PUF proteins in stem cell biology.  Analysis of 3’UTR sequences of Pum1 associated mRNAs revealed a core Pum1 consensus sequence, UGUAHAUA.  Pum1 knockdown demonstrated that Pum1 enhances decay of associated mRNAs, and re-localization of Pum1 to stress granules suggested that Pum1 functions in repression of translation.  This study is the first in vivo genome-wide mRNA target identification of a mammalian PUF protein and provides direct evidence that human PUF proteins regulate stability of associated mRNAs.  Comparison of Pum1 associated mRNAs to mRNA targets of PUF proteins from S. cerevisiae and Drosophila demonstrates how a well conserved RNA-binding domain and cognate binding sequence have been evolutionarily rewired to regulate the collective expression of different sets of functionally related genes.
Keywords: RIP-chip

overall_design: Pum1 IP, negative IP, and total IP samples were analyzed for each of 3 biological replicates.  Each IP or total RNA sample was run on a separate array versus a common reference sample

first: Neelanjan

last: Mukherjee

first: Jack

middle: D

last: Keene


title: A2B5/OTMP+ rat perineuronal oligodendrocytes

status: Public on Jun 01 2008

city: Bethesda

first: Joe

last: Nielsen

address: 49 Convent Drive BD49,5A75

institute: NIH/NINDS

summary:
Oligodendrocytes are cells from the central nervous system that can be grouped into precursors, myelin-forming, and non-myelinating perineuronal. The function of perineuronal oligodendrocytes is unknown; it was suggested that they can ensheath denuded axons. We tested this hypothesis. Using cell-specific tags, microarray technology and bioinformatics tools to identify gene expression differences between these subpopulations allowed us to capture the genetic signature of perineuronal oligodendrocytes. Here we report that perineuronal oligodendrocytes are configured for a dual role. As perineuronal, they integrate a repertoire of transcripts designed to create a cell with its own physiological agenda. But they maintain a reservoir of untranslated transcripts encoding the major myelin proteins for – we speculate – a pathological eventuality. We posit that the signature molecules PDGFR-αβ, cytokine PDGF-CC, and the transcription factor Pea3 used – among others - to define the non-myelinating phenotype, may be critical for mounting a myelinating programme during demyelination. Harnessing this capability is of therapeutic value for diseases such as multiple sclerosis. This is the first molecular characterization of perineuronal oligodendrocytes.
Keywords: developmental

overall_design: Flow Cytometry was used to isolate A2B5/OTMP+ oligodendrocytes from postnatal day 7 rat brain.  4 bioloical replicates were obtained.  This data can be compared to the previously submitted oligodendrocyte expression data (GSE5940).

first: Sara

last: Szuchet

first: Joseph

first: Gabor

last: Lovas

first: Javier

last: Velasco

first: Dragan

last: Maric

first: Lynn

last: Hudson


title: Comparison of protein expression profiles in NCI-60 cell panel containing nine difererent cancer tissue types.

status: Public on Feb 01 2007

first: Uma

last: Shankavaram

address: 9000 Rockville Pike

department: NCI

institute: NIH

summary:
Because most potential molecular markers and targets are proteins, proteomic profiling is expected to yield more direct answers to functional and pharmacological questions than does transcriptional profiling. To aid in such studies, we have developed a protocol for making reverse-phase protein lysate microarrays with larger numbers of spots than previously feasible. Our first application of these arrays was to profiling of the 60 human cancer cell lines (NCI-60) used by the National Cancer Institute to screen compounds for anticancer activity. Each glass slide microarray included 648 lysate spots representing the NCI-60 cell lines plus controls, each at 10 two-fold serial dilutions to provide a wide dynamic range. Mouse monoclonal antibodies and the catalyzed signal amplification system were used for immunoquantitation.  The signal levels from the >30,000 data points for our first 52 antibodies were analyzed by using P-SCAN and a quantitative dose interpolation method. Clustered image maps revealed biologically interpretable patterns of protein expression. Among the principal early findings from these arrays were two promising pathological markers for distinguishing colon from ovarian adenocarcinomas.  When we compared the patterns of protein expression with those we had obtained for the same genes at the mRNA level by using both cDNA and oligonucleotide arrays, a striking regularity appeared: cell-structure-related proteins almost invariably showed a high correlation between mRNA and protein levels across the NCI-60 cell lines, whereas non-cell-structure-related proteins showed poor correlation.

http://discover.nci.nih.gov/host/2003_profiling_abstract.jsp
Keywords: Cancer cell line comparison.

overall_design: Nine tissue types included in the NCI-60 panel are as follows: Breast, CNS, Colon, Lung, Melanoma, Leukemia, Ovary, Prostate and Renal.  The NCI-60 cell line lysates were analyzed with using 176 antibodies that were prescreened to give highest quality by western blot analysis. Each array contained 64 samples (60 cancer cells and 4 control pool) in 10 serial dilutions.

first: Satoshi

last: Nishizuka

first: Lu

last: Charboneau

last: Young

first: Sylvia

last: Major

first: William

last: Reinhold

first: Mark

last: Waltham

first: Hosein

last: Kouros-Mehr

first: Kimberly

last: Bussey

first: Jae

last: Lee

first: Virginia

last: Espina

first: Peter

last: Munsen

first: Eamnuel

last: Petricoin III

first: Lance

last: Liotta

first: John

last: Weinstein


title: Impact of food-deprivation on mammary transcriptome of lactating goats

status: Public on Feb 21 2007

city: St Genes-Champanelle

first: Christine

last: Leroux

address: Centre INRA de Theix

department: PHASE

country: France

institute: INRA

summary:
Animal nutrition considerably affects milk composition that influences its nutritional quality. Milk component synthesis and secretion by the mammary gland involve expression of a large number of genes whose nutritional regulation remains poorly defined. In this study, we examined the effect of food deprivation (FD) on the expression of 8379 genes in caprine mammary gland using a bovine oligonucleotide microarray. Twelve lactating goats were assigned to 2 groups based on their feeding level (control diet ad libitum vs. 48-h FD). We identified 161 genes whose expression was altered by FD. Most of these genes (88%) were downregulated, suggesting a stress response by the mammary gland. In particular, the decrease in expression of genes involved in milk protein, lactose, and lipid metabolism could contribute together with the shortage of nutrients to the drop in milk protein, lactose, and fat secretion. In addition, this study highlights modification of the expression of at least 14 genes that could be responsible for a slowdown in mammary cell proliferation and differentiation and/or an increase in programmed cell death in response to 48-h FD in goats.
Keywords: Response to nutritional factor

overall_design: 12 slides were performed for a total of 6 independent comparisons: each microarray was co-hybridized with a control goat sample and a food-deprived goat sample; each hybridization was repeated in a dye-swap manner for a total of 4 replicated spots per oligonucleotide (2 intra- and 2 inter-slides).

first: Séverine

last: Ollier

first: Christèle

last: Robert-Granié

first: Laurence

last: Bernard

first: Yves

last: Chilliard


title: Whole Daphnia_20microg/L Cadmium_48hr

status: Public on Dec 07 2007

city: Bloomington

first: Joseph

last: Shaw

state: IN

address: 1315 E. Tenth Street

department: The School of Public and Environmental Affairs

institute: Indiana University

summary:
"Gene response profiles for Daphnia pulex exposed to the environmental stressor cadmium reveals novel crustacean metallothioneins." Joseph.R.Shaw, John.K.Colbourne, Jennifer.C.Davey, Stephen.P.Glaholt, Thomas.H.Hampton, Celia.Y.Chen, Carol.L.Folt, Joshua.W.Hamilton (BMC Genomics 2007).

Genomic research tools such as microarrays are proving to be important resources to study the complex regulation of genes that respond to environmental perturbations. A first generation cDNA microarray was developed for the environmental indicator species Daphnia pulex, to identify genes whose regulation is modulated following exposure to the metal stressor cadmium. Our experiments revealed interesting changes in gene transcription that suggest their biological roles and their potentially toxicological features in responding to this important environmental contaminant.

Our microarray identified genes reported in the literature to be regulated in response to cadmium exposure, suggested functional attributes for genes that share no sequence similarity to proteins in the public databases, and pointed to genes that are likely members of expanded gene families in the Daphnia genome. Genes identified on the microarray also were associated with cadmium induced phenotypes and population-level outcomes that we experimentally determined. A subset of genes regulated in response to cadmium exposure was independently validated using quantitative-realtime (Q-RT)-PCR. These microarray studies led to the discovery of three genes coding for the metal detoxication protein metallothionein (MT). The gene structures and predicted translated sequences of D. pulex MTs clearly place them in this gene family. Yet, they share little homology with previously characterized MTs.

The genomic information obtained from this study represents an important first step in characterizing microarray patterns that may be diagnostic to specific environmental contaminants and give insights into their toxicological mechanisms, while also providing a practical tool for evolutionary, ecological, and toxicological functional gene discovery studies. Advances in Daphnia genomics will enable the further development of this species as a model organism for the environmental sciences.
Keywords: cDNA microarrays, stress response, expressed sequence tags (EST), Daphnia Genomics Consortium, Arthropod, Gene Expression Profiling, Gene Expression Regulation

overall_design: Microarrays were used to discover genes that were differentially expressed following sub-lethal cadmium exposure (LC01; 20microg/L, 48-h) in D. pulex. They utilized RNA isolated from three independent and concurrently replicated exposures of Daphnia to cadmium and control conditions. RNA was applied to three microarrays using a standard, control vs. treated design that included dye swaps.

middle: K

last: Colbourne

first: Jennifer

middle: C

last: Davey

first: Stephen

last: Glaholt

first: Thomas

last: Hampton

first: Celia

middle: Y

last: Chen

first: Carol

last: Folt

first: Joshua

last: Hamilton


title: Parkinson's disease vs. controls, whole blood

status: Public on Dec 30 2006

city: Lyngby

first: Aron

last: Eklund

address: Kemitorvet, Building 208

department: Center for Biological Sequence Analysis

country: Denmark

institute: Technical University of Denmark

summary:
Parkinson’s disease (PD) progresses relentlessly and affects five million people worldwide. Laboratory tests for PD are critically needed for developing treatments designed to slow or prevent progression of the disease. We performed a transcriptome-wide scan in 105 individuals to interrogate the molecular processes perturbed in cellular blood of patients with early-stage PD. The molecular marker here identified is strongly associated with risk of PD in 66 samples of the training set (third tertile cross-validated odds ratio of 5.7 {P for trend 0.005}). It is further validated in 39 independent test samples (third tertile odds ratio of 5.1 {P for trend 0.04}). The genes differentially expressed in patients with PD, or Alzheimer’s or progressive supranuclear palsy offer unique insights into disease-linked processes detectable in peripheral blood. Combining gene expression scans in blood and linked clinical data will facilitate the rapid characterization of candidate biomarkers as demonstrated here with respect to PD.
Keywords: disease state analysis

overall_design: Whole blood expression data from 50 patients with Parkinson's disease,  33 with neurodegenerative diseases other than PD, and 23 healthy controls.

first: Clemens

last: Scherzer


title: Gene Expression Profile Signatures Indicate a Role for Wnt Signaling in Endothelial Commtment From Embryonic Stem Cells

status: Public on May 23 2006

first: Monte

last: Willis

address: 103 Mason Farm Road

department: Pathology & Laboratory Medicine

institute: UNC

summary:
Embryonic stem (ES) cells have the potential to generate a variety of cell
lineages including endothelial cells, blood cells and smooth muscle cells.
flk1-expressing cells derived from ES cells serve as vascular progenitors.
We have used global gene expression analysis in order to establish a
comprehensive list of candidate genes in the developing vasculature during
ES cell differentiation in vitro. A large set of genes, including growth
factors, cell surface molecules, transcriptional factors, and members of
several signal transduction pathways that are known to be involved in
vasculogenesis or angiogenesis, were found to have expression patterns as
expected. Some unknown or functionally uncharacterized genes were
differentially regulated in flk1+ cells compared with flk1 cells,
suggesting possible roles for these genes in vascular commitment.
Particularly, multiple components of the Wnt signaling pathway were
differentially regulated in flk1+ cells, including Wnt proteins, their
receptors, downstream transcriptional factors, and other components
belonging to this pathway. Activation of the Wnt signal was able to expand
vascular progenitor populations whereas suppression of Wnt activity reduced
flk1+ populations. Suppression of Wnt signaling also inhibited the formation
of matured vascular capillary-like structures during late stages of EB
differentiation. These data indicate a requisite and ongoing role for Wnt
activity during vascular development, and the gene expression profiles
identify candidate components of this pathway that participate in vascular
cell differentiation.
Keywords: Time course, development, endothelial cell, angiogenesis, embryonic stem cells, mouse, vasculature, Wnt signaling

overall_design: Flk1 positive and negative cells isolated from murine embryoid bodies were subjected to gene expression profiling at 84 hours, 95 hours and eight days post differentiation using the Agilent mouse development platform.

first: Hong

last: Wang

first: Peter

last: Charles

first: Yaxu

last: Wu

first: Rongqin

last: Ren

first: Jeffry

last: Rubin

first: Charles

last: Perou

first: Victoria

last: Bautch

first: Cam

last: Patterson


title: Genomic signatures of chromosomal instability and osteosarcoma progression detected by high resolution array CGH and interphase FISH

status: Public on Nov 21 2007

city: Toronto

first: Shamini

last: Selvarajah

state: Ontario

address: 555 University Ave

department: Cancer Institute

institute: Hospital for Sick Children

type: Genome variation profiling by genome tiling array

summary:
Background:  Osteosarcoma (OS) tumors and derived cell lines are characterized by complex chromosomal abnormalities.  The availability of molecular genome profiling techniques such as array CGH have markedly enabled the high-resolution genome analysis of tumor genomes, as well as helped elucidate the mechanisms leading to their complexity.  The identification of tumor-specific genomic profiles is currently the focus of many array CGH studies, but there have been no analyses to date documenting the genomic signatures consistent with chromosomal instability mechanisms in OS.    Results:  In this study we utilized high-resolution oligonucleotide array CGH to interrogate recurrent signatures of genomic imbalance in 10 OS tumors that were consistent with the breakage fusion bridge(BFB) mechanism.  Comparative analysis of the tumors showed that they exhibited varying levels of genomic imbalance.  The analysis also highlighted three chromosomal regions (6p21 ~ p22, 8q24 and 17p11.2 ~ p12) that were consistently involved in high level gain or amplification events.  These three regions have been previously shown by us to be not only involved in high-level imbalance in OS-derived cell lines, but also to exhibit similar imbalance profiles consistent with BFB-related events.  Karyotype and dual-color FISH analysis showed that repeated rearrangements of these unstable chromosomes through BFB cycles may create a heterogeneous pattern of copy number alterations.    Conclusions:  This genome-wide analysis is the first to utilize oligonucleotide array CGH and FISH analysis to derive possible genomic signatures of chromosomal instability in OS tumors.  Perpetuation of the BFB cycle will create a heterogeneous pattern of copy number alterations by repeated rearrangement of the unstable tumor genome., thereby generating diverse phenotypes The resulting phenotypic diversity can generate tumors with a propensity for an aggressive disease course.  A better understanding of the underlying mechanisms events leading to tumor development could result in the identification of prognostic markers and therapeutic targets.
Keywords: osteosarcoma, chromosomal instability, gene amplification, breakage-fusion-bridge cycle, oligonucleotide array comparative genomic hybridization

overall_design: 10 OS tumor samples were used; fluor-flip was performed with normal human DNA as control

first: Maisa

last: Yoshimoto


title: Gene expression profiling of 19 cattle tissues reveals unique patterns related to tissue function

status: Public on Mar 24 2006

city: Urbana

first: Mark

middle: Robert

last: Band

state: IL

address: 1201 W. Gregory Dr

department: Biotechnology

institute: University of Illinois

summary:
cDNA microarrays have been shown to be useful for monitoring global gene expression patterns in normal and disease states and in response to various environmental stimuli. In this study we have used a cattle cDNA microarray containing 7653 elements to analyze expression profiles in 19 different cattle tissues. Signal intensities from all tissue sample RNAs were compared to a reference standard RNA created from different tissues and cell lines. Data analysis identified a subset of genes significantly differentially expressed between tissues and the reference standard that were further subdivided according to fold change. Log transformed ratios were normalized using the intensity-based regional Lowess algorithm. A global error model, to account for the dependence of variation on signal intensities, was used to identify lists of genes for effect of tissue on gene expression taking into account an experiment-wise significance of 0.05, using either a Bonferroni correction (663 genes) or Benjamini and Hochberg’s False Discovery Rate (3350 genes). Non-supervised cluster analysis revealed groups of genes common to nerve, muscle, immune or digestive tissues. Discriminant analysis was used to support physiological functional categories and embryonic origin of tissues. Unique profiles were constructed with genes preferentially expressed in specific tissues or tissue groups in order to define gene expression for individual tissues. Global expression along a large collection of tissues revealed tissue specific expression of enzyme isomers and utilization in specific metabolic pathways. A comprehensive matrix of all possible pair-wise comparisons for individual genes among tissues was constructed to further identify genes with tissue-specific behavior and possibly unique function.
Keywords: Comparative Tissue Profiling

overall_design: A reference design was used to compare 19 cattle tissues. All tissues were compared to a universal control consisting of a mix of cattle cell lines. All samples were duplicated with a dye swap.

first: Robin

middle: E

last: Everts

first: Zonglin

last: Liu

first: Dawn

last: Morin

first: Jonathan

middle: U

last: Peled

first: Sandra

last: Rodriguez-Zas

first: Harris

last: Lewin


title: Poor prognosis in cancer is associated with a expression signature of aberrant PTEN tumor suppressor pathway activity

status: Public on Apr 07 2007

city: Lund

first: Lao

middle: H

last: Saal

address: Scheelevägen 2, MV404B2

department: Department of Oncology and Pathology

country: Sweden

institute: Lund University

summary:
Pathway-specific therapy is the future of cancer management. The oncogenic phosphatidylinositol 3-kinase (PI3K) pathway is frequently activated in solid tumors; however, currently, no reliable test for PI3K pathway activation exists for human tumors. Taking advantage of the observation that loss of PTEN, the negative regulator of PI3K, results in robust activation of this pathway, we developed and validated a microarray gene expression signature for immunohistochemistry (IHC)-detectable PTEN loss in breast cancer (BC). The most significant signature gene was PTEN itself, indicating that PTEN mRNA levels are the primary determinant of PTEN protein levels in BC. Some PTEN IHC-positive BCs exhibited the signature of PTEN loss, which was associated to moderately reduced PTEN mRNA levels cooperating with specific types of PIK3CA mutations and/or amplification of HER2. This demonstrates that the signature is more sensitive than PTEN IHC for identifying tumors with pathway activation. In independent data sets of breast, prostate, and bladder carcinoma, prediction of pathway activity by the signature correlated significantly to poor patient outcome. Stathmin, encoded by the signature gene STMN1, was an accurate IHC marker of the signature and had prognostic significance in BC. Stathmin was also pathway-pharmacodynamic in vitro and in vivo. Thus, the signature or its components such as stathmin may be clinically useful tests for stratification of patients for anti-PI3K pathway therapy and monitoring therapeutic efficacy. This study indicates that aberrant PI3K pathway signaling is strongly associated with metastasis and poor survival across carcinoma types, highlighting the enormous potential impact on patient survival that pathway inhibition could achieve.
Keywords: Disease state analysis

overall_design: 105 breast cancer tumor samples were analyzed on 2-color cDNA microarrays using the Stratagene Universal Human Reference RNA as the common reference sample.

last: Johansson

first: Karolina

last: Holm

first: Sofia

last: Gruvberger-Saal

first: Qing-Bai

last: She

first: Matthew

last: Maurer

first: Susan

last: Koujak

first: Adolfo

last: Ferrando

first: Per

last: Malmstrom

first: Lorenzo

last: Memeo

first: Jorma

last: Isola

first: Par-Ola

last: Bendahl

first: Neal

last: Rosen

first: Hanina

last: Hibshoosh

first: Markus

last: Ringner

first: Ake

last: Borg

first: Ramon

last: Parsons


title: Embryonic and adult neural crest stem cells

status: Public on Apr 18 2006

city: Newcastle upon Tyne

first: Maya

last: Sieber-Blum

address: Central Parkway Road

department: Institute of Human Genetics and

institute: Newcastle University

summary:
Cells were isolated from mouse embryonic neural crest stem cells at culture day 2 (NCSC), from day 7 in vitro differentiated progeny (NCP) and day 2 epidermal neural crest stem cells from bulge explants of adult whisker follicles (EPI-NCSC).
Keywords: LongSAGE

first: Yao

middle: F

last: Hu


title: Rat gastric ECL cell transcriptomes: Change of gene expression during 24 hrs fasting

status: Public on Nov 22 2006

city: Los Angeles

first: Nils

middle: Werner Georg

last: Lambrecht

address: 11301 Wilshire Blvd, Bldg.113, Rm.325A

department: Physiology

institute: UCLA

summary:
Gastric ECL cells and parietal (PC) cells in normal conditions and gastric ECL cells after 24 hrs fasting were purified using a combination of counter-flow elutriation, nycodenz gradient and FACS based on acridine orange labeling of histamine containing vesicles (ECL cells) or autofluorescense (PC cells) to homogeneity. cRNA probes from this purified cell suspensions and from mixed gastric homogenates were hybridized to whole rat genome expression oligonucleotide microarrays. We imported each channel separately (normalized intensity of Cy3 labeled samples = gProcessedSignal and of Cy5 labeled samples = rProcessedSignal) from the original Agilent Feature Extraction data files (submitted as raw data) after slide scanning from all slides into a Genespring 7.3 microarray database warehouse. Genespring’s built in statistical module was used to compare all channels to each other. The normalization used was against specific samples (the 5 channels of Gastric mucosal scrapings). Genespring identifies genes differentially expressed in the ECL cell samples and the parietal samples and also calculates the significance of difference (p-value).
Keywords: rat whole genome expression microarray analysis (transcriptome)

overall_design:
ECL cells: free access to food and water (250 gm Sprague Dawley Rat)
PC cells: free access to food and water (250 gm Sprague Dawley Rat)
ECL cells: 24 hrs fasting, free access to water (250 gm Sprague Dawley Rat)
Gastric mucosa scrapes: free access to food and water (250 gm Sprague Dawley Rat)
Fasting gastric mucosa scrapes: 24 hrs fasting, free access to water (250 gm Sprague Dawley Rat)

Three independent cell purifications, total RNA isolations and at least one dye swap per sample set (3).

middle: W

first: Iskandar

last: Yakubov

first: George

last: Sachs


title: IPF versus Control

status: Public on Aug 08 2005

city: Pittsburgh

first: Thomas

last: Richards

institute: University of Pittsburgh

summary:
Archived lung tissues of patients with IPF were obtained from the tissue bank of the Department of Pathology at the University of Pittsburgh. The diagnosis of IPF was confirmed by open lung biopsy. All patients fulfilled the criteria of the American Thoracic Society and European Respiratory Society for the diagnosis of IPF. Normal histology lung tissues resected from patients with lung cancer were used as controls.
Keywords: parallel sample

first: Annie

last: Pardo

first: Kevin

last: Gibson

first: Moises

last: Selman

first: Naftali

last: Kaminski


title: The effects of Lactobacillus plantarum and E. coli on Caco2 human colonocytes genes expression

status: Public on Sep 13 2007

city: Baltimore

first: Pinaki

last: Panigrahi

state: MD

address: 22 South Greene Street, Room N5W68

department: Pediatrics

institute: University of Maryland

summary:
In this study, we examined Caco-2 cell gene expression after infection with E. coli (Ec), Lactobacillus plantarum (Lp) and the combination of the two (mix)
Keywords: Lactobacillus plantarum and E. coli influences on Caco2 cells gene expression

overall_design: Cells were washed in PBS and re-fed with experimental DMEM without serum or antibiotics before the experiments.  Caco-2 cells were infected with E. coli (10 9 CFU/ml at 1:10 multiplicity ratio), and/or L. plantarum (1010 CFU/ml, 1:100 multiplicity ratio), and incubated for 2 hr

first: Gheorghe

middle: T

last: Braileanu

first: Hegang

last: Chen

first: Colin

middle: O

last: Stine


title: Estrogen receptor beta expression is associated with tamoxifen response in ER alpha-negative breast carcinoma

status: Public on Apr 01 2007

city: New York

first: Sofia

last: Gruvberger-Saal

state: NY

address: 1130 St. Nicholas Ave., ICRC 406

department: Institute for Cancer Genetics

institute: Columbia University

summary:
Purpose: Endocrine therapies, such as tamoxifen are commonly given to most patients with estrogen receptor (ER) alpha-positive breast carcinoma but are not indicated for persons with ERalpha-negative cancer. The factors responsible for response to tamoxifen in 5-10% of patients with ERalpha-negative tumors are not clear. The aim of the present study was to elucidate the biology and role of the second ER, ERbeta, in patients treated with adjuvant tamoxifen.
Experimental Design: We investigated ERbeta by immunohistochemistry in 353 stage II primary breast tumors from patients treated with two years adjuvant tamoxifen, and generated gene expression profiles for a representative subset of 88 tumors.
Results: ERbeta was associated with increased survival (distant disease-free survival, P=0.01; overall survival, P=0.22), and in particular within ERalpha-negative patients (P=0.003; P=0.04), but not in the
ERalpha-positive subgroup (P=0.49; P=0.88). Lack of ERbeta conferred early relapse (hazard ratio, 14; 95% CI, 1.8-106; P=0.01) within the ERalpha-negative subgroup even after adjustment for other markers. ERalpha was an independent marker only within the ERbeta-negative tumors (hazard ratio, 0.44; 95% CI, 0.21-0.89; P=0.02). An ERbeta gene expression profile was identified and was markedly different from the ERalpha signature.
Conclusion: Expression of ERbeta is an independent marker for favorable prognosis after adjuvant tamoxifen treatment in ERalpha-negative breast cancer patients, and involves a gene expression program
distinct from ERalpha. These results may be highly clinically significant, because in the U.S. alone, approximately 10,000 women are diagnosed annually with ERalpha-negative/ERbeta-positive breast carcinoma and may benefit from adjuvant tamoxifen.
Keywords: Disease state analysis

overall_design: 88 breast cancer tumor samples were analyzed on 2-color cDNA microarrays containing ~27K reporters with Stratagene Universal Human Reference RNA as the common reference sample.

first: Par-Ola

last: Bendahl

first: Lao

last: Saal

first: Mervi

last: Laakso

first: Cecilia

last: Hegardt

first: Patrik

last: Eden

first: Carsten

last: Peterson

first: Per

last: Malmstrom

first: Jorma

last: Isola

first: Marten

last: Ferno


title: Hepatic transcriptional profiling of juvenile broiler chickens divergently selected for abdominal fatness or leanness

status: Public on Sep 01 2007

city: Newark

first: Larry

middle: Albert

last: Cogburn

state: DE

address: 531 South College Ave.

department: Animal and Food Sciences

institute: University of Delaware

summary:
Chickens divergently selected for either high abdominal fat content (fat genotype) or low abdominal fat content (lean genotype) at SRA-INRA, France were used to profile hepatic gene expression during juvenile development (1 to 11 weeks of age) and to identify differentially expressed genes associated with genotype and age. The fat line (FL) and lean line (LL) chickens are different in various phenotypic and metabolic measurements, including abdominal fatness, plasma glycemia and T3. The FL and LL chickens represent unique models for characterizing biomedical and agricultural traits. The Del-Mar 14K Chicken Integrated Systems microarrays were used for a transcriptional scan in liver during juvenile development using a balanced block hybridization design. Log2-transformed fluorescence intensities were analyzed with a two-stage mixed model. A total of 905 differentially expressed "functional" genes were identified (FDR<0.10). The greatest number of differentially expressed genes (400) was detected at 7 weeks of age. The differentially expressed genes include metabolic enzymes, acute phase proteins, growth factors, immune factors and transcription factors involved in various pathways. Several of the functional genes are also identified as positional candidate genes within QTLs in an F2 population established from an intercross between the FL and LL lines.
Keywords: Divergently selected chickens, fatness, transcriptional profiling, differentially expressed genes

overall_design: A balance block design was used for microarray hybridizations, where half of the birds of each genotype and age were labeled with Alexa Flour 647 (red) and the other half with Alexa Flour 555 (green). Four biological replicates were used for each genotype (FL or LL) at six different ages (1, 3, 5, 7, 9 and 11 wk).

first: Nares

last: Trakooljul

first: Jean

last: Simon


title: Gene expression profile of human lung cell line (A549) treated with 2mM 59cobalt chloride during 30mn, 2h, 4h and 24h

status: Public on Sep 22 2006

city: bagnols sur ceze

first: Bérenguer

last: Frédéric

department: SBTN

institute: CEA/DSV

summary:
The purpose of this work was to identify the potential signatures of cobalt exposure using a toxicogenomic approach. A time course transcriptome analysis was performed on human type II epithelial cell line A549.
Cells were exposed to cobalt at midlog phase ; a medium without FCS containing cobalt (CoCl2, Sigma) or not was added for 30mn, 2h, 4h or 24h. Total RNA was isolated using the Quiagen RNeasy miniprep kit, and then labelled using the FairPlay Microarray Labelling Kit (Stratagene). Amino reactive Cy3- and Cy5- dyes (CyTMDye Post-Labelling Reactive Dye Pack, Amersham) were further chemically coupled to test and control cDNA respectively. After hybridization, microarrays were scanned with GenePix 4000B (Axon Instrument Inc., Forster City, CA). Cy3 and Cy5 fluorescence intensities for the spots were quantified after local subtraction of background noise using Genepix Pro 4.0 software (Axon Instrument Inc.)
Keywords: Time course

overall_design:
30 mn : exposure 1 (2 microarrays) - exposure 2 (4 microarrays)
2h :      exposure 1 (2 microarrays) - exposure 2 (4 microarrays)
4h :      exposure 1 (2 microarrays) - exposure 2 (2 microarrays)
24h:     exposure 1 (4 microarrays) - exposure 2 (6 microarrays) - exposure 3 (4 microarrays)

first: Frédéric

last: Berenguer

first: Véronique

last: Malard

first: Gérard

last: Steinmetz


title: Stomach ECL cell expression analysis

status: Public on Jan 26 2006

first: Nils

last: Lambrecht

summary:
Gene expression analysis of stomach ECL cells and mixed gastric fundic epithelial cells
Keywords: Gastric ECL cells, Subtractive Hybridization, Comparative genomic hybridization

overall_design: Each set of experiments (n = 2) contained dye swap experiment(s).

first: Iskandar

last: Yakubov

first: Cindy

last: Zer

first: George

last: Sachs


title: UV-B induced genes in wild-type Arabidopsis versus mutants uvr8-1 and hy5-1 using Affymetrix ATH1 array

status: Public on Dec 01 2005

city: Glasgow

first: Gareth

last: Jenkins

address: Bower Building

department: Institute of Biomedical and Life Sciences

institute: University of Glasgow

summary:
This experiment tests the effect of physiological dose of UV-B radiation on wild-type and uvr8-1 (UV Resistance Locus 8) and hy5-1 transcription factor mutants of Arabidopsis.
Keywords: strain, stress response

overall_design: The experiment is done using Affymetrix ATH1 array (GPL198). Three biological replicates for wild type and uvr8-1 mutant were subjected to white light and to UV-B light whilst three biological replicates of hy5-1 mutant were subjected to UV-B light only (15 samples in total).

first: Robert

last: Brown

first: Catherine

last: Cloix

first: Jiang

middle: G

last: Huai

first: Eirini

last: Kaiserli

first: Pawel

last: Herzyk

first: Daniel

middle: J

last: Kliebenstein

middle: I


title: Seed development in LEAFY COTYLEDON1 mutants

status: Public on Jan 01 2005

first: Bob

last: Goldberg

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

summary:
Analysis of gene expression in Ws-0 lec1 (LEAFY COTYLEDON1) mutant Arabidopsis thaliana. Developmental stages studied includes 24-Hr post-fertilization, globular stage, cotyledon stage, mature green stage, post-mature green stage, and seedlings.

Microarray Methods: Total RNA was extracted using the Hot Borate Method [Stones et. al. PNAS vol 98 no 20: 11806-11811 (2001)]. Biotinylated cRNA were prepared using the ENZO BioArray High Yield RNA Transcript Labeling Kit (Farmingdale, NY).  cRNA was subsequently hybridized to Affymetrix ATH1 Arabidopsis GeneChips. The scanned array images were analyzed using Affymetrix Microarray Suite 4.0 (MAS 4.0) with a global scaling intensity set at 500.
Keywords: other

first: Brandon

last: Le

first: Anhthu

middle: Q

last: Bui

first: Julie

last: Pelletier

first: Linda

last: Kwong

first: Jack

last: Okamuro

middle: L

last: Fischer

first: Gary

middle: N

last: Drews

first: John

last: Harada

middle: B


title: mouse liver samples

city: Potomac Falls

first: Agnieszka

middle: Maria

last: Lichanska

institute: Tessarae, LLC

summary:
Total RNA was extracted from mouse liver samples using an Ambion RNaqueous RNA extraction kit. Targets were produced using modified Affymetrix procedure from 5ug of total RNA. 3 biological replicates were analysed per each group of animals.
Keywords = growth hormone
Keywords = signaling
Keywords = gene expression
Keywords: other

middle: M

first: Jennifer

last: Rowland

first: Sheryl

last: Maher

last: Kerr

first: Mary

last: White

first: Richard

first: Rohan

middle: D

last: Teasdale

first: Peter

last: Noakes

first: Michael

last: Waters


title: Gene Expression in Iron-Deficient Rat Duodenum

status: Public on Jan 26 2005

city: Tucson

first: James

middle: Forrest

last: Collins

address: PO Box 245073, 1501 N. campbell Ave.

institute: University of Arizona Health Sciences Center

summary:
The effect of iron-deficiency on duodenal gene expression was investigated in rats at different developmental stages.
Keywords: time-course

first: Kris

middle: V

last: Kowdley

first: Fayez

middle: K

last: Ghishan


title: SRBCT

status: Public on Oct 11 2004

city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

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

country: Germany

summary:
Comparison of gene expression profiles between neuroblastoma samples and Ewing family tumor samples. RNA from native tumor samples was processed for DNA-microarray analysis using Affymetrix HG-U133A microarrays. Primary image analysis was performed using MAS 5.0 and data were scaled to an target intesity of 500.
Keywords: ordered

middle: S

first: Christoph

last: Hutter

first: Ingo

last: Neumann

first: Sabine

last: Foja

first: Uwe

middle: E

last: Hattenhorst

first: Gesine

last: Hansen

first: Danny

last: Afar

first: Stefan

last: Burdach


title: Neuroblastoma cell lines

summary:
Gene expression analysis of cell lines initially established as neuroblastoma cell lines. Cells were harvested and processed for DNA-microarray analysis using Affymetrix HG-U133A microarrays. Primary image analysis was performed using MAS 5.0 and data were scaled to an target intesity of 500.
Keywords: other

overall_design: RNA was extracted from established cell lines and subjected to microarray analysis


title: IRE1 and XBP-1 effects on the Drosophila unfolded protein response

status: Public on May 20 2006

city: San Francisco

first: Julie

last: Hollien

address: 1700 Fourth Street

department: Cell and Molecular Pharmacology

institute: UCSF

summary:
The unfolded protein response (UPR) allows the endoplasmic reticulum (ER) to recover from the accumulation of misfolded proteins, in part by increasing its folding capacity. IRE1 promotes this remodeling by detecting misfolded ER proteins and activating a transcription factor, XBP-1, through endonucleolytic cleavage of its mRNA. We found that IRE1 independently mediated the rapid degradation of a specific subset of mRNAs. The arrays deposited here show the effects of depletion of IRE1 and XBP-1 on UPR induction in S2 cells. We have characterized the IRE1-dependent repressive branch of this response.
Keywords: stress response, RNAi, DTT

overall_design: We knocked down IRE1, XBP-1, or neither (control) in S2 cells using RNAi, and then induced the UPR with DTT, a reducing agent that disrupts disulphide-linked folding. Each experiment was done in triplicate. Each sample (varying RNAi and -/+ DTT) was hybridized to a single spotted array along with a reference sample, which was the same for all arrays.

first: Jonathan

last: Weissman


title: Saccharomyces cerevisiae Sko1-HA strain MAP37, W303-1A background

status: Public on Sep 21 2005

city: Boston

first: Francis

last: Gibbons

state: MA

address: 250 Longwood Ave

department: BCMP (Biological Chemistry and Molecular Pharamcology)

institute: Harvard Medical School

summary:
These three replicates were analyzed in "Genomewide identification of Sko1 target promoters reveals a regulatory network that operates in response to osmotic stress in Saccharomyces cerevisiae.
", by Proft M, Gibbons FD, Copeland M, Roth FP, Struhl K; published in Eukaryot Cell. 2005 Aug;4(8):1343-52.

A new analysis algorithm for Chip-chip data ('Chipper') is described in Genome Biology. Manuscript entitled "Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization." by FD Gibbons, M Proft, K Struhl, and FP Roth. Accepted, no publication date as yet.
Keywords: ChIP-chip

overall_design:
Design is as in original platform submission. Caveat with this dataset is that the data have been filtered to remove intergenic regions deemed unreliable. Thus for 7200 intergenic regions originally spotted on the chip, only about 3500 are included in each replicate, and it's not the same 3500 for each. Overall about 6000 intergenic regions are covered between all three replicates.

Original images have been lost, so re-analysis to generate data for all intergenic regions is no longer possible.

first: Markus

last: Proft

first: Matthew

last: Copeland

first: Frederick

middle: P

last: Roth

first: Kevin

last: Struhl


title: Expression profiling of liver tissue from C57BL6 x DBA strain

status: Public on Nov 25 2004

city: Seattle

first: Stephen

middle: W

last: Edwards

state: WA

department: Research Genetics

institute: Rosetta Inpharmatics (Merck & Co.)

summary:
Expression profiling of liver tissue from 111 F2 female mice resulting from a cross between C57BL/6J and DBA/2J inbred mouse strains.
Mice were feed a chow diet for 12 months followed by 4 months on an atherogenic high-fat, high-cholesterol diet.
Parental and F2 mice were killed at 16 months of age.  The livers were removed immediately and flash frozen for expression profiling.
See Schadt, et al., Nature , Vol 422(6929):297-302 for details.
Keywords = Genetics of Gene Expression
Keywords = mouse
Keywords = C57BL6
Keywords = DBA
Keywords: repeat sample

first: Eric

last: Schadt

first: Stephanie

middle: A

last: Monks

last: Milligan

first: John

middle: R

last: Lamb

first: Peter

last: Linsley

first: Mao

last: Mao

first: Roland

last: Stoughton

middle: H

last: Friend


title: Characterization of Mycobacterium smegmatis SigF regulon

status: Public on Aug 20 2010

city: Lucknow

first: Bhupendra

middle: Narain

last: Singh

state: U P

address: M G Marg

department: Microbiology

country: India

institute: Central Drug Research Institute

summary: Mycobacterium smegmatis SigF is a group III sigma factor. Its ortholog in M. tuberculosis is reported to have role in regulation and function of cell wall components. In present study we have created an M. smegmatis ΔsigF mutant by allele exchange method. M. smegmatis sigF mutant shows non pigmented phenotype and is more sensitive to hydrogen peroxide generated oxidative stress. DNA microarray analysis of M. smegmatis wild type and ΔsigF mutant suggests that SigF in this species controls the expression of several energy and central intermediary metabolism genes along with regulation of carotenoid biosynthesis.

overall_design: Gene expression patterns of M.smegmatis wild type and ΔsigF mutant strains were compared at two growth stages i.e. log (OD600 ~1.4) and stationary (OD600 ~3.0). M. smegmatis strains were grown in DifcoTM MiddleBrook 7H9 broth base (BD Biosciences, Sparks, MD, USA) with 0.2% glycerol (v/v) and 0.05% Tween-80 (Sigma-Aldrich, St Louis, MO, USA) supplemented with 10% albumen dextrose catalase (BD Biosciences) (v/v) at 37 0C with continuous shaking. Total RNA was isolated using Trizole (Invitrogen) method and labelled with cyanine 3 (Cy3) as per Agilent 1-color labelling protocol (Version 5.5, February 2007). Six hundred nanograms of each Cy3 labelled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were performed using Gene Expression Hybridization kit (Agilent Technologies). Hybridization was carried out in Agilent’s Surehyb Chambers at 65 0C for 16 h. The hybridized slides were washed using Agilent Gene Expression wash buffers and scanned using the Agilent Microarray Scanner G Model G2565BA at 5 micron resolution. Feature extracted data was analysed using GeneSpring GX v 7.3.1 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended one color Per Chip and Per Gene Data Transformation. Set measurements less than 0.01 to 0.01 per chip, normalize to 50th percentile per gene, and normalize to specific samples.

first: Anirudh


title: Gene Copy Number Aberrations are Associated with Survival in Histological Subgroups of Non-Small Cell Lung Cancer (copy number data)

status: Public on Nov 01 2011

city: Uppsala

first: Anders

last: Isaksson

address: Akademiska sjukhuset ing61 3tr

institute: Uppsala University

summary:
Hypothesis: Non-small cell lung cancer (NSCLC) is characterized by a multitude of genetic aberrations with unknown clinical impact. In this study, we aimed to identify gene copy number changes that correlate with clinical outcome in NSCLC. To maximize the chance to identify clinically relevant events, we applied a strategy involving two prognostically extreme patient groups.

Results: Genetic aberrations were strongly associated with tumor histology. In adenocarcinoma (n=50), gene copy number gains on chromosome 8q21-q24.3 (177 genes) were more frequent in long-term survivors. In squamous cell carcinoma (n=28), gains on chromosome 14q23.1-24.3 (133 genes) were associated with shorter survival, whereas losses in a neighboring region, 14q31.1-32.33 (110 genes), correlated with favorable outcome. In accordance with copy number gains and losses, mRNA expression levels of corresponding genes were increased or decreased, respectively.

Conclusion: Comprehensive tumor profiling permits the integration of genomic, histologic and clinical data. We identified gene copy number gains and losses, with corresponding changes in mRNA levels, that were associated with prognosis in adenocarcinoma and squamous cell carcinoma of the lung.

overall_design: Short-term (<20 months; n=53) and long-term survivors (>58 months;n=47) were selected from a clinically well-characterized NSCLC patient cohort with available fresh-frozen tumor specimens. The samples were analyzed using high-resolution SNP-array technology. The molecular data was combined with information on clinical parameters.

first: Patrick

last: Micke

first: Lars

last: Holmberg

first: Karolina

last: Edlund

first: Hanna

last: Göransson

first: Simon

last: Ekman

first: Michael

last: Bergqvist

first: Lena

last: Scheibenflug

first: Kristina

last: Lamberg

first: Gunnar

last: Myrdal

last: Berglund

first: Mats

last: Lambe

first: Fredrik

last: Nyberg

first: Andrew

last: Thomas

first: Johan

last: Botling