title: longitudinal expression profiling in whole blood of multiple sclerosis patients and controls [MS vs Ctrl Replication dataset]

status: Public on Jun 17 2013

city: San Francisco

first: Sergio

middle: E

last: Baranzini

address: 675 Nelson Rising Lane, Room S-215

department: Neurology

institute: University of California San Francisco

summary:
Multiple sclerosis is the most common autoimmune disease of the central nervous system. Studying whole blood RNA from a cohort of 195 MS patients and 66 healthy controls, we identified gene expression signatures for interferon treatment and disease status by microarray analysis.
Blood was collected at multiple time points (up to 3 for patients, 2 for controls). Patients were either untreated or treated with Interferon. In total, 626 Affymetrix exon arrays were analyzed, split into discovery and replication data sets. This metadata file contains information on all samples processed in the replication data set (n=102) when we compared gene expression in untreated MS patients (n=27) to healthy controls (n=25).

overall_design: The following comparisons were made: untreated MS vs Controls (discovery and replication), untreated vs Interferon treated MS (discovery and replication). For each comparison, respective arrays were processed (background corrected and normalized) together, but seperate from other comparisons. The two time points for controls were averaged. For the first comparison, we report differentially expressed genes at an FDR cutoff of 0.1 at any of the three tested time points in MS patients in the discovery data set. For the second comparison, the FDR cutoff was 0.001. The respective genes were validated in the replication data set when they passed a nominal p-value cutoff of 0.05 at any of the three tested time points.

first: Dorothee

last: Nickles

first: Jorge

last: Oksenberg


title: longitudinal expression profiling in whole blood of multiple sclerosis patients and controls [MS vs Ctrl Discovery dataset]

state: CA

country: USA

summary:
Multiple sclerosis is the most common autoimmune disease of the central nervous system. Studying whole blood RNA from a cohort of 195 MS patients and 66 healthy controls, we identified gene expression signatures for interferon treatment and disease status by microarray analysis.
Blood was collected at multiple time points (up to 3 for patients, 2 for controls). Patients were either untreated or treated with Interferon. In total, 626 Affymetrix exon arrays were analyzed, split into discovery and replication data sets. This metadata file contains information on all samples processed in the discovery data set (n=212) when we compared gene expression in untreated MS patients (n=62) to healthy controls (n=41).

middle: R


title: Longitudinal expression profiling in whole blood of multiple sclerosis patients and controls

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

overall_design: Refer to individual Series


title: longitudinal expression profiling in whole blood of multiple sclerosis patients and controls [IFN_replication dataset]

summary:
Multiple sclerosis is the most common autoimmune disease of the central nervous system. Studying whole blood RNA from a cohort of 195 MS patients and 66 healthy controls, we identified gene expression signatures for interferon treatment and disease status by microarray analysis.
Blood was collected at multiple time points (up to 3 for patients, 2 for controls). Patients were either untreated or treated with Interferon. In total, 626 Affymetrix exon arrays were analyzed, split into discovery and replication data sets. This metadata file contains information on all samples processed in the replication data set (n=183) when we compared gene expression in untreated MS patients (n=27) to IFN treated patients (n=48).


status: Public on May 22 2013

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

summary: An European eel-specific microarray platform was developed to identify genes involved in response to pollutants. A comparative analysis of gene expression was conducted between European eel Anguilla anguilla individuals from lowly-polluted Wijmeers pond at Uitbergen (Belgium), highly-polluted Hazewinkel pond at Willebroek (Belgium), extremely-polluted Dessel-Schotel canal  at the locations of Schotel (Belgium) and low polluted Bolsena lake (Italy) environments.

overall_design: A comparative analysis of gene expression was conducted between European eel Anguilla anguilla individuals from lowly-polluted Wijmeers pond at Uitbergen (Belgium), highly-polluted Hazewinkel pond at Willebroek (Belgium), extremely-polluted Dessel-Schotel canal  at the locations of Schotel (Belgium) and low polluted Bolsena lake (Italy) environments. Gene expression profiling was performed using an European eel-specific oligo-DNA microarray (GPL15124) of 14,913 probes based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Milan

last: Massimo

first: Pujolar

last: Marti

first: Zane

last: Lorenzo


title: The genomic and transcriptomic dynamics of treatment-naïve epithelial ovarian cancer

status: Public on Jun 05 2013

city: Utrecht

first: Wigard

last: Kloosterman

address: Universiteitsweg 100

country: Netherlands

institute: University Medical Center Utrecht

summary: We reveal three-dimensional patterns of tumour growth by exploiting the unique metastasizing patterns of treatment naïve stage IIIC/IV epithelial ovarian cancer. We performed topographic mapping of structural genomic rearrangements, coding mutations, copy number changes and RNA expression in biopsies derived from 27 primary and metastatic sites across three patients. Based on somatic genomic changes, we performed sample clustering and obtained unique insight in natural tumour growth and spread. Based on extensive multi-level profiling, our data highlight the diverse modes of epithelial ovarian cancer development before applying selective pressure from therapy.

overall_design: We performed SNP array analysis on tumor biopsies from 3 patients (P1, P2, P3) with advanced stage ovarian cancer. This submission includes SNP data for 26 tumor biopsies and 5 normal tissue samples.

first: Marlous

last: Hoogstraat

first: Mirjam

last: de Pagter

first: Geert

last: Cirkel

first: Markus

middle: J

last: van Roosmalen

first: Tim

last: Harkins

first: Karen

last: Duran

first: Jennifer

last: Kreeftmeijer

first: Ivo

last: Renkens

first: Els

middle: P

last: Witteveen

first: Clarence

last: Lee

first: Isaac

last: Nijman

first: Tanisha

last: Guy

first: Ruben

last: van 't Slot

first: Trudy

last: Jonges

first: Martijn

last: Lolkema

first: Marco

last: Koudijs

first: Ronald

last: Zweemer

first: Emile

last: Voest

first: Edwin

last: Cuppen


title: Mycobacterium tuberculosis microarray to screen anti-tuberculosis compounds

status: Public on Apr 24 2013

city: Singapore

first: Ahmad Nazri

last: Mohamed Naim

address: 60 Biopolis Street, Genome, #02-01

department: Infectious disease

country: Singapore

institute: Genome institute of Singapore

summary: Feature reduction of microarray data from mycobacteria treated with a variety of various clinical and investigational drugs

overall_design: We are using feature reduction to demonstrate that subsets of biomarker genes representative of the whole genome are sufficient for MOA classification and deconvolution in a medium-throughput microfluidic format ultimately leading to a cost effective and rapid tool for routine antibacterial drug-discovery programs.

first: Paul

last: Murima

first: Paola

last: Florez de Sessions

first: Vivian

last: Lim

first: Ahmad

middle: N

last: Naim

first: Bifani

last: Pablo

first: Helena

middle: I

last: Boshoff

first: Thomas

last: Dick

first: Martin

last: Hibberd

first: Mark

last: Schreiber

first: Srinivasa

last: Rao


title: Large inverted duplications form via a hairpin mechanism

status: Public on Apr 03 2013

city: Atlanta

first: Karen

last: Hermetz

state: GA

address: 1518 Clifton Rd

department: Human Genetics

institute: Emory University School of Medicine

summary: Inverted duplications are a common type of copy number variation (CNV) in germline and somatic genomes. Large duplications that include many genes can lead to both neurodevelopmental phenotypes in children and gene amplifications in tumors. There are several models for inverted duplication formation, most of which include a dicentric chromosome intermediate followed by breakage-fusion-bridge (BFB) cycles, but the mechanisms that give rise to the inverted dicentric chromosome in most inverted duplications remain unknown. Here we have combined high-resolution array CGH, custom sequence capture, next-generation sequencing, and long-range PCR to analyze the breakpoints of 50 nonrecurrent inverted duplications in patients with intellectual disability, autism, and congenital anomalies. Sequence analysis of breakpoint junctions reveals a normal-copy disomic spacer between inverted and non-inverted copies of the duplication. Further, short inverted repeats are present at the boundary of the disomic spacer and the inverted duplication. These data support a mechanism of inverted duplication formation whereby a chromosome with a double-strand break intrastrand pairs with itself to form a “hairpin” intermediate that, after DNA replication, produces a dicentric inverted chromosome with a disomic spacer corresponding to the site of the hairpin. We also find evidence of short insertions and inversions at inverted duplication junctions, consistent with a DNA replication-based CNV mechanism. This process can give rise to inverted duplications adjacent to terminal deletions, inverted duplications juxtaposed to translocations, and inverted duplication ring chromosomes

overall_design: High resolution array CGH; two-color experiment, clinical patient vs. normal control gDNA; sex mis-matched

first: Katie

last: Rudd


title: Temporal Concordance between Apical and Transcriptional Points-of-Departure for Chemical Risk Assessment

status: Public on Apr 22 2013

city: RTP

first: Longlong

last: Yang

state: NC

address: 6 Davis Dr.

institute: CIIT Centers for Health Research

summary: The number of legacy chemicals without toxicity reference values combined with the rate of new chemical development are overwhelming the capacity of the traditional risk assessment paradigm.  More efficient approaches are needed to quantitatively estimate chemical risks.  In this study, rats were dosed orally with multiple doses of six chemicals for 5 days, 2, 4, and 13 weeks.  Target organs were analyzed for traditional histological and organ weight changes and transcriptional changes using microarrays.  Histological and organ weight changes in this study and the tumor incidences in the original cancer bioassays were analyzed using benchmark dose (BMD) methods to identify noncancer and cancer points-of-departure. The dose-response changes in gene expression were also analyzed using BMD methods and the responses grouped based on signaling pathways.  A comparison of transcriptional BMD values for the most sensitive pathway with BMD values for the noncancer and cancer apical endpoints showed a high degree of correlation at all time points.  When the analysis included data from an earlier study with 8 additional chemicals, transcriptional BMD values for the most sensitive pathway were significantly correlated with noncancer (r = 0.827, p = 0.0031) and cancer-related (r = 0.940, p = 0.0002) BMD values at 13 weeks.  The average ratio of apical-to-transcriptional BMD values was less than two suggesting that for the current chemicals, transcriptional perturbation did not occur at significantly lower doses than apical responses. Based on our results, we propose a practical framework for application of transcriptomic data to chemical risk assessment.

overall_design: Four to five week-old rats were exposed in dose-response and for multiple durations to 6 chemicals. The chemicals were 1,2,4-tribromobenzene (CAS No. 615-54-3), 2,3,4,6-tetrachlorophenol (CAS No. 58-90-2), bromobenzene (CAS No. 108-86-1), 4,4'-methylenebis(N,N-dimethyl)benzenamine (CAS No. 101-61-1), hydrazobenzene (CAS No. 122-66-7), N-nitrosodiphenylamine (CAS No. 86-30-6). For  1,2,4-tribromobenzene and 2,3,4,6-tetrachlorophenol,  male Sprague Dawley (Rat/Crl:CD(SD)) rats were used.  For bromobenzene and hydroazobenzene, male F344/DuCrl rats were used. For 4,4'-methylenebis(N,N-dimethyl)benzenamine and N-nitrosodiphenylamine, female F344/DuCrl rats were used. The exposure durations were 5 days, 2 weeks, 4 weeks, and 13 weeks.  The dose and route of exposure are provided with the individual sample annotations. With each chemical treatment, a matched vehicle control group was run concurrently with the exposure.  Gavage exposures were administered 7 days per week and feed exposures were provided 7 days per week. At the appropriate time point, animals were euthanized with a lethal intraperitoneal injection of sodium pentobarbital. For the liver, slices from each of the lobes were mixed together and used for microarray analysis.  For the thyroid, the gland was transversely sectioned and the bottom portion was used for microarray analysis.  For the bladder, the organ was longitudinally bisected, a slice was removed for histology and the remainder of the organ was minced and used for microarray analysis.  Microarrays were run on five rats per dose per time point.


title: Transcriptional profiling of HCC vs. Normal liver and Pericancer vs. Normal liver.

status: Public on Mar 14 2013

city: Shanghai

first: Lin

last: Wei

address: No.25/Ln.2200, Xie Tu Road

country: China

institute: Shanghai Cancer Institute

summary: Hepatocellular carcinoma (HCC) is one of the most malignant and lethal cancers in the world. Its complex process of molecular pathogenesis indicates that HCC is caused by multiple etiological factors and involves multiple types of genes during its development and progression. In the current study, we performed a microarray analysis on the mRNA transcriptome of HCC (C), peri-cancerous liver (P) and normal liver (N) tissues. After integrating these results with information from the Gene Ontology and KEGG Pathway databases, we analyzed the potential interactions between different genes and constructed an interaction network, and identified the regulator, mediator and effector genes in this interaction network.

overall_design: Three types of tissues: 49 pairs of homogenous human primary hepatocellular carcinoma (Cancer, C) and pericancer liver tissues (Pericancer, P), 10 normal liver tissues (Normal, N). Three-condition experiment, HCC vs. Normal and Pericancer vs. Normal.

first: Baofeng

last: Lian

first: Yuannv

last: Zhang

first: Wei

last: Li

first: Jianren

last: Gu

first: Lu

last: Xie

first: Xianghuo

last: He


title: Loss-of-function of MYO5B induces epithelial cell scattering in enterocytes

city: Innsbruck

first: Daniel

last: Bindreither

state: Tirol

address: Innrain 82

department: Division of Molecular Pathophysiology

country: Austria

institute: Medical University Innsbruck

summary: A non-functional myosin Vb motor in duodenal enterocytes results in disruption of epithelial cell polarity characterized by complete loss of microvilli and mislocalization of apical brush border proteins in the cytoplasm which finally cause a devastating disease in neonates with severe malabsorption defects accompanied by protracted diarrhea during infancy, classified as microvillus inclusion disease (MVID). The exact mechanisms how loss-of-function of MYO5B induces polarity loss are not completely understood in MVID pathogenesis. Obtaining better insights in cell polarity defects caused by loss of MYO5B, we performed microarray- in combination with protein expression-analysis in an inducible CaCo2 MYO5B RNAi cell system. Surprisingly, in MYO5B-depleted CaCo2 cells, CDH1 coding for the cell adhesion protein E-Cadherin and important for cell adhesion and therefore maintenance of cell polarity, was significantly downregulated. Interestingly, mesenchymal cell markers, specifically Vimentin and N-Cadherin, physiologically not expressed in differentiated epithelium, were  upregulated and accompanied by increased phospho-c-jun levels in the nucleus. Importantly phospho-c-jun was also found in nuclei of duodenal enterocytes in MVID patients, indicating loss of MYO5B induces epithelial cell scattering in enterocytes.

overall_design: 3 Myosin 5B KD versus 3 control samples

first: Cornelia

last: Thoeni

first: Georg

middle: F

last: Vogel

first: Johannes

last: Rainer

first: Pornpimol

last: Charoentong

first: Zlatko

last: Trajanoski

first: Stephan

last: Geley

first: Silvia

last: Lechner

first: Kristian

last: Pfaller

first: Michael

middle: W

last: Hess

last: Müller

first: Andreas

last: Janecke

first: Ernest

last: Cutz

first: Lukas

middle: A

last: Huber


title: Profiling of copy-number variation between DNA isolation from different tissues of BN and ACI rats

status: Public on Mar 21 2013

first: Victor

last: Guryev

address: Uppsalalaan 8

institute: Hubrecht Institute

type: Genome variation profiling by genome tiling array

summary: We used Nimblegen HD aCGH to detect DNA recovery from different tissue samples

overall_design: Comparison of DNA isolated from different tissues of BN and ACI rats in dye-swap setup

first: Sebastiaan

last: van Heesch

first: James

last: Shull


title: Structural polymorphism in the promoter of pfmrp2 confers tolerance to mefloquine and chloroquine in Plasmodium falciparum [CGH]

status: Public on Feb 07 2013

first: Sachel

last: Mok

address: 60 Nanyang Drive

institute: Nanyang Technological University

summary: Drug resistance in Plasmodium falciparum remains a challenge for the malaria eradication programs around the world. With the emergence of artemisinin resistance, the efficacy of the partner drugs in the artemisinin combination therapies (ACT) that include quinoline based drugs is becoming critical. So far only few resistance markers have been identified and verified from which only two ABC transmembrane transporters namely PfMDR1 and PfCRT have been experimentally verified. Another P. falciparum ABC transporter, the multidrug resistance-associated protein (PfMRP2) represents an additional possible factor of drug resistance in P. falciparum. In this study, we identify a parasite clone that is derived from the 3D7 P. falciparum strain and which shows increased resistance to chloroquine and mefloquine through the trophozoite and schizont stages. We demonstrate that the resistance phenotype is caused by a 4.1 kb deletion in the 5’ upstream region of the pfmrp2 gene that leads to an alteration in the pfmrp2 transcription that result in increased levels of PfMRP2 protein. These results also suggest the importance of putative promoter elements in regulation of gene expression during the P. falciparum intra-erythrocytic developmental cycle and the potential of such genetic polymorphisms to underlie drug resistance phenotypes. Presented here are the data from microarray-based genome-wide transcriptomic and genomic studies of the drug-sensitive and drug-resistant 3D7 clones 11C/wt and 6A/mut.

overall_design: 2 P. falciparum lab clones derived from 3D7 strain were harvested during the intra-erythrocytic cycle for genomic DNA. gDNA were extracted by phenol chloroform. Synthesis of labelled target DNA was carried out as previously described: Bozdech, Z., M. Llinas, B. L. Pulliam, E. D. Wong, J. Zhu & J. L. DeRisi, (2003) The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 1: E5, and used in comparative genomic microarray hybridizations (CGH).

first: Zbynek

last: Bozdech


title: Global expression analyses of yeast cells harboring specific members of the cytosolic Hsp70-Ssa family

status: Public on Dec 31 2012

city: Kamakura

first: Satoko

last: Takizawa

state: Kanagawa

address: 6-10-1 Tebiro

department: New Frontiers Research Laboratories

country: Japan

institute: TORAY Industries, Inc.

summary:
Yeast DNA microarray was used to assess and compare the global expression profile of strains harboring different family members of the major cytosolic Hsp70 family. Viability of a yeast strain deleted for all genes encoding members of the Hsp70-Ssa family (Ssa1/2/3/4) was maintained by the presence of a single Ssa family member expressed ectopically from a plasmid vector.
The Hsp70-Ssa family constitutes the main source of Hsp70 molecular chaperone activity in the yeast cell. A yeast cell must actively express a member of this family to remain viable. Hsp70-Ssa are highly conserved both within yeast and amongst other species. Ssa1 and 2 are 97% identical at amino acid level and 80% identical to Ssa3 and 4. The aim of this study was to attribute specific functions to single Ssa family members by identifying specific genes or gene families whose expression was altered in the presence (or absence) of Ssa family members.

overall_design: Eight independent RNA samples were pooled to represent a single biological sample for expression analysis. For example, the single sample analyzed for cells harboring only Ssa1 is a pooled sample of eight independent RNA extractions. Hybridization was performed for cells harboring either Ssa1, Ssa2, Ssa3 or Ssa4 as the sole cytosolic Hsp70-Ssa family member. Gene expression profiles of Ssa2/3/4 were all compared to Ssa1.

first: Gary

last: Jones

first: Naushaba

last: Hasin

first: Sarah

last: Cusack


title: Sox2 ChIP-chip on human neural stem cell line REN cells

status: Public on Aug 30 2012

city: Seoul

first: jihae

last: Seo

address: 11-1 Daehyun-Dong Seodaemun-Gu

department: Ewha research center for systems biology

country: South Korea

institute: Ewha womans university

type: Genome binding/occupancy profiling by genome tiling array

summary:
Analysis of technical variance of ChIP-on-Chip studies by characterization of SOX2 in neural stem cell.
Keywords: ChIP, SOX2

overall_design: ChIP-on-chip against SOX2

first: Jihae

first: Lee

middle: k

last: eun

first: Jiwon

last: Roh

first: Sanghyuk

last: Lee

first: Jaesang

last: Kim


title: Vibrio vulnificus: Wild type vs. iscR mutant (V. vulnificus iron-sulfur cluster regulator)

status: Public on Feb 27 2013

first: Jonggyu

last: Lim

address: Gwanak 599

institute: Seoul National University

summary: IscR is a novel global regulator potentially contributing to the overall success in survival and pathogenesis of V. vulnificus by coordinating the regulation of various virulence factors. The profiles of transcripts from the V. vulnificus iscR mutant and the parental wild type were compared by using a V. vulnificus whole-genome microarray.

overall_design:
Two-condition experiment: Wild type vs. iscR mutant. Biological replicates: 3 control, 3 mutant strains, independently grown and harvested. One replicate per array.
For transcriptome analysis, the V. vulnificus whole genome TwinChip, manufactured and kindly provided by the 21C Frontier Microbial Genomics and Applications Center (Daejeon, South Korea), was used.

first: Jong

middle: G

first: Sang

middle: H

last: Choi


title: Gene expression profiling of acute drought response in leaf and root of rice

status: Public on Sep 21 2012

city: Yongin

first: Yeon-Ki

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

institute: GreenGene Biotech Inc.

type: Expression profiling by genome tiling array

summary: In this research, an array of 27,448 rice genes was used to elucidate gene expression in air-dried rice seedlings (lead and root) at various periods of treatment times. The analyses show that rice responds to drought stress mainly by down-regulating many biological processes including gene expression and regulation, protein phosphorylation, and cellular metabolism. Among strategies to actively adapt to drought, most significant are inducing protective molecules, which may be differentially regulated based on plant organs.

overall_design:
A total of 20 chips was used for the microarray analysis. Total RNAs were extracted from leaf and root of rice seedlings that had undergone 0-12 hrs acute drought. Experiments were duplicated.
The profiling was conducted with the Rice 3'-Tiling Microarray designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.dna.affrc.go.jp/).

first: Pham

middle: T

last: Thu

first: Joung

middle: S

first: Baek

last: Nahm

first: Yeon

middle: K


title: Zebrafish toxicogenomics and phenotypic analyses reveal molecular insights into bisphenol-A (BPA) early-life exposure toxicity.

status: Public on Jun 01 2012

first: Siew Hong

last: Lam

address: 14 Science Drive 4

department: Biological Sciences

institute: National University of Singapore

summary: In this study, developing zebrafish were exposed to 500-4500 µg/L BPA for 7 days from 3 hours post-fertilization for a microarray experiment to obtain molecular insights into BPA early-life exposure toxicity.

overall_design: We analyzed a total of 18 arrays; five biological replicate arrays for zebrafish treated with 500  µg/L BPA, four biological replicate arrays for zebrafish treated with 1500 µg/L BPA, four biological replicate arrays for zebrafish treated with 4500 µg/L BPA against 5 biological replicate arrays for control fish. A common reference sample was used for both treated and control samples.

first: Siew

first: Hlaing

middle: M

last: Myintzu

first: Choong

middle: Y

last: Ung

first: Sinnakarupan

last: Mathavan

first: Zhiyuan

last: Gong


title: M. smegmatis pruR::Tn611 mutant (MB100pruR)

status: Public on May 01 2012

city: Bronx

first: Michael

last: Berney

state: NY

address: 1301 Morris Park Avenue

department: Department of Microbiology and Immunology

institute: Albert Einstein College of Medicine

summary: Transcriptional profiling of M. smegmatis MB100pruR vs. MB100 (isogenic parent) grown in serumvials on Hartmans de Bont medium supplemented with glycerol and proline

overall_design: Two-condition experiment. Biological replicates: 4 independently grown and harvested. One replicate per array.

first: Gregory

last: Cook


title: Responsive genes upon deletion of the ohkA gene in Streptomyces coelicolor M145

status: Public on Jan 05 2011

first: Yinhua

last: Lu

address: 300 Fenglin Road

department: Institute of Plant physiology and ecology

institute: Shanghai Institutes for Biological Sciences

summary: Transcription profile analysis between the wild-type strain M145 and the ohkA-deletion mutant to determine the overall transcription changes caused by the deletion of orphan histidine kinase gene ohkA in S.coelicolor.

overall_design: Transcription changes between the ohkA mutant and the wild-type strain M145 were performed at three time points, 48,64,88h.

first: Juanmei

last: He

first: Hong

last: Zhu

first: Zhenyu

last: Yu

first: Rui

last: Wang

first: Fujun

last: Dang

first: Weiwen

last: Zhang

first: Sheng

last: Yang

first: Weihong

last: Jiang


title: Mercury toxicity in barley roots

status: Public on May 13 2009

city: Texcoco

first: Marta

middle: Silva

last: Lopes

state: Mexico

address: km 45, carretera Mexico-Veracruz, El Batan, Texcoco

department: wheat physiology

country: Mexico

institute: cimmyt

summary: The effects of mercury (HgCl2) on barley (Hordeum vulgare L.) growth, physiological traits and gene expression profiles were studied. The shoot to root ratio was decreased in the two levels of HgCl2 (500 and 1000 μM) assayed, which was related primarily with decreases in shoot dry weight. Moreover stomatal conductance was limited and leaf carbon isotope discrimination decreased. Therefore water uptake limitations seem to be an important component of barley responses to HgCl2. Evidences for decreased stomatal conductance and water uptake limitations were further confirmed by the over expression of ABA related transcripts and down regulation of an aquaporin in roots. Root dry weight was only affected at 1000 μM HgCl2 and root browning was observed, while several transcripts for lignin biosynthesis were up regulated in HgCl2. Microarray analysis further revealed that growth inhibition in HgCl2 was related to increased expression of genes participating in ethylene biosynthesis and down regulation of several genes participating in DNA synthesis, chromatin structure and cell division, cell wall degradation and modification, oxidative pentose phosphate cycle and nitrogen metabolism pathway. Genes involved in detoxification and defence mechanisms were up regulated including several cytochrome P450s, glucosyltransferases and glutathione-s-transferases and amino acid metabolism participatory genes. It is concluded that barley plants survive in the presence of HgCl2 through several mechanisms that include water uptake limitations, shoot and root growth regulation, increased expression of genes involved in the biosynthesis of several plant protection secondary metabolites and finally through detoxification.

overall_design: Six samples were analysed including 3 biological replicates of mercury exposed roots and 3 controls (no mercury added to the growing solution)

first: Santiago

last: Iglesia-Turino

first: Anna

last: Febrero

first: Llorenc

last: Cabrera-Bosquet

first: Jordi

last: Bort

first: Jose

middle: L

last: Araus


title: Intrinsic Gene Expression Profiles of Gliomas are a Better Predictor of Survival than Histology

status: Public on Apr 26 2010

city: Rotterdam

first: Pim

last: French

address: Dr Molewaterplein 50

institute: Erasmus MC

summary: Histological classification of gliomas guides treatment decisions. Because of the high interobserver variability, we aimed to improve classification by performing gene expression profiling on a large cohort of glioma samples of all histological subtypes and grades. The seven identified intrinsic molecular subtypes are different from histological subgroups and correlate better to patient survival. Our data indicate that distinct molecular subgroups clearly benefit from treatment. Specific genetic changes (EGFR amplification, IDH1 mutation, 1p/19q LOH) segregate in -and may drive- the distinct molecular subgroups. Our findings were validated on three large independent sample cohorts (TCGA, REMBRANDT, and GSE12907). We provide compelling evidence that expression profiling is a more accurate and objective method to classify gliomas than histology.

overall_design: 276 glioma samples of all histology, 8 control samples

first: Lonneke

last: Gravendeel

first: Mathilde

middle: C

last: Kouwenhoven

first: Olivier

last: Gevaert

first: Johan

middle: J

last: de Rooi

first: Andrew

last: Stubbs

first: J

middle: E

last: Duijm

first: Anneleen

last: Daemen

first: Fonnet

last: Bleeker

first: Linda

middle: B

last: Bralten

first: Nanne

last: Kloosterhof

first: Bart

last: De Moor

first: Peter

last: van der Spek

last: Kros

last: Sillevis Smitt

first: Martin

last: van den Bent


title: Genomic profiling of neoplasms developed in SEC31A-JAK2 expressing mice

status: Public on Jun 19 2010

city: Leuven

first: Julio

last: Finalet

address: Herestraat 49

country: Belgium

institute: KULeuven

summary: The genetics of classical Hodgkin lymphoma (cHL) is poorly understood. The finding of a JAK2-involving t(4;9)(q21;p24) in one case of cHL prompted us to characterize this translocation on a molecular level and to determine the prevalence of JAK2 rearrangements in cHL. We showed that the t(4;9)(q21;p24) leads to a novel SEC31A-JAK2 fusion. Screening of 131 cHL cases identified one additional case with SEC31A-JAK2 and two additional cases with rearrangements involving JAK2. We demonstrated that SEC31A-JAK2 is oncogenic in vitro and acts as a constitutively activated tyrosine kinase that is sensitive to JAK inhibitors. In vivo, SEC31A-JAK2 was found to induce a T-lymphoblastic lymphoma or myeloid hyperplasia in a murine bone marrow transplant model. Altogether, we identified SEC31A-JAK2 as a first aberration characteristic for cHL and provide evidence that JAK2 rearrangements occur in a minority of cHL cases. Given the proven oncogenic potential of this novel fusion, our studies provide new insights into the pathogenesis of cHL and indicate that in at least some cases, constitutive activation of the JAK-STAT pathway is caused by JAK2 rearrangements. The finding that SEC31A-JAK2 responds to JAK inhibitors indicates that patients with cHL and JAK2 rearrangements may benefit from targeted therapies.

overall_design:
Genomic profiling of primary and secondary transplanted mice expressing SEC31A-JAK2 with myeloid hyperplasia and T-lymphoblastic lymphoma

Individual sample against a normal control


title: embryogenesis ws-somatic embryogenesis

city: Evry

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

department: URGV

country: France

institute: INRA

summary: gnp07_regeneome_embryogenesis - embryogenesis ws - Identify genes involved in somatic embryogenesis - To compare embryogenic areas of a callus with undifferenciate area in the same callus

overall_design: 3 dye-swap - tissue comparison

first: M

last: Obellianne

last: Hervé

last: Chupeau

first: Y

first: S

last: Balzergue

last: Martin-Magniette

first: C

last: Pannetier


title: Human ileum epithelium LCMD Project

status: Public on Feb 28 2008

city: Davis

first: Michael

last: George

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

summary:
The small intestinal epithelium mediates vital functions of nutrient absorption and host defense. The spatial organization of the epithelial cells along the crypt-villus axis segregates them into regions of specialized function. However, many of the mechanisms governing intestinal epithelial cell migration and the coordination of interactions with adjacent cells and the extracellular matrix are not fully understood. We have evaluated in vivo gene expression patterns of ileal epithelial cells in healthy human subjects, isolated by laser capture microdissection from either the villus epithelial or crypt cell regions of the small intestinal mucosa. Expression profiles in villus epithelium and Paneth cell lineages were determined by quantitative real-time PCR, DNA microarray, and immunohistochemistry based methods. Relative expression levels of selected epithelial biomarkers were compared between the ileum, jejunum, duodenum, colon, stomach, and esophagus. Previously established biomarkers as well as a novel and distinct set of genes believed to be linked to epithelial cell motility, adhesion, and differentiation were found to be enriched in each of the two corresponding cell populations. Additionally, high baseline expression levels of innate antimicrobials, alpha defensin 5 (HD5) and regenerating islet-derived 3 alpha (Reg3A), were detected exclusively within the small bowel, most notably in the ileum, in comparison to other sites along the gastrointestinal tract. Our findings provide new and important insights regarding the molecular machinery employed by small intestinal epithelial cells to mediate their function and spatial organization in vivo.
Keywords: analysis of epithelial cells from crypt or upper villus regions

overall_design: Surgical specimens of human intestinal mucosa were obtained from 4 individuals undergoing surgery for colon cancer, bowel obstruction, or other non-inflammatory conditions. The samples were fixed overnight in 4% (w/v) paraformaldehyde, dehydrated in a graded alcohol series and paraffin-embedded. At least 500 epithelial cells from the crypt or upper villus regions were then captured by LCMD from unstained 6µm thick sections using a PALM MicroLaser System Total RNA was extracted for microarray-based gene expression analysis.

middle: D

first: Charles

last: Bevins


title: A Gene Expression Phenotype In Lymphocytes From Friedreich’s Ataxia Patients

status: Public on Jul 26 2011

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary:
Gene expression studies in peripheral tissues from patients with neurodegenerative disorders can provide insights into disease pathogenesis, and identify potential biomarkers, an important goal of translational research in neurodegeneration. Friedreich’s Ataxia (FRDA) is a chronic neurodegenerative disease caused by reduced transcription of frataxin, a ubiquitously expressed protein. We studied in vitro lymphocytes from FRDA patients and carriers, in order to identify a peripheral gene expression phenotype. Peripheral biomarkers related to disease status would be extremely valuable for assessing drug efficacy and could provide new pathophysiological insights.
We identified a subset of genes changed in cells from patients with pathological frataxin deficiency and a core set of these genes were confirmed in independent series. Changes in gene expression were related to the mitochondria, lipid metabolism, cell cycle, and DNA repair, consistent with FRDA’s known pathophysiology. We evaluated the in vitro effect of multiple compounds (HDAC inhibitors) on this putative biomarker set, and found that this biochemical phenotype was ameliorated in accordance with drug efficacy.  Frataxin downregulation is associated with robust changes in gene expression in PBMCs, providing pathogenetic insights and a core subset of genes which, if verified in vivo, could be used as a peripheral biomarker.

overall_design: We characterized the gene expression profiles in peripheral blood mononuclear cells (PBMCs) from FRDA patients, compared with controls and related carriers. Cells were studied both before and after in vitro treatment with compounds that increase frataxin levels. Quantitative real-time PCR and additional microarrays were used to confirm a core set of genes in multiple independent series

first: Ryan

last: Burnett

first: Susan

last: Perlman

first: Revital

last: Versano

first: Fuying

last: Gao

first: Heather

last: Plasterer

first: Myriam

last: Rai

first: Francesco

last: Saccá

first: Alessandro

last: Filla

first: David

middle: R

last: Lynch

first: James

last: Rusche

first: Joel

last: Gottesfeld

first: Massimo

last: Pandolfo

first: Daniel

last: Geschwind


title: Timecourse of Enterococcus faecalis infection of HUC cells

status: Public on Jun 10 2007

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 urothelial cells respond to Enterococcus infection over the course of infection. 239 hypervariable (HV) genes were found to vary significantly over the time points, indicating a biological role in infection. Correlational clustering showed these HV genes fell into distinct families indicating a defined sequence of events following infection. Early events (0-1.5 hours post infection) were associated with upregulation of not well-known but bladder-associated genes which represented early immune response, cytoskeleton remodeling  and cell cycle. Up- and downregulated genes at the middle time period (1.5-8 hours post infection) represented a variety of processes, from immune response/suppression, cell cycle/apoptosis to metabolism and cytoskeleton remodeling. Several transcription factors point to multiple pathways activation. At the late time points (8-10 hours post infection) downregulated genes represented major events of cell death, matrix degradation and immune response decline. Confocal microscopy confirms major cell death at these time points. Several events and pathways, like immune response suppression or cytoskeleton remodeling via Wnt/β-catenin and/or Rho/Rac pathway, were identified throughout the time course of HUC infection by Enterococcus. Those may be new targets for preventing and/or cure Enterococcus caused pathology.
Keywords: Enterococcus, time course, microarray, infection, gene expression

overall_design: Immortalized human urothelial cells (HUC from ATCC) were grown into multilayer urothelium mimetic for 7 days in Ham's F-12 medium containing 10% FCS changed every 2 or 3 d. Cells were counted and infected at a multiplicity of infection of 100. RNA was isolated from cells that had been infected for 30, 60, 90 min, 4, 6, 8 and 10 h and expression was measured on a microarray spotted with 22,464 long oligos (~70mers) from the UniGene database. Data was normalized as described in Dozmorov I et al., Nucleic Acids Res. 2004 Oct 28;32(19). Hypervariable genes (239) were clustered and analyzed for presence of common transcription factors, networks and signaling pathways.

first: Mikhail

last: Dozmorov

first: Kimberly

last: Kyker

first: Rikardo

last: Saban

first: Nathan

last: Shankar

first: Arto

last: Baghdayan

last: Centola


title: SALL4 ChIP-chip using NimbleGen HG18 RefSeq Promoter tiling array (2.7kb)

status: Public on May 17 2008

city: Las Vegas

first: Yupo

last: Ma

state: NV

address: 1 Breakthrough Way

institute: Nevada Cancer Institute

summary:
Increasing studies suggest that SALL4 may play vital roles in leukemogenesis. We have used chromatin immunoprecipitation followed by microarray hybridization as a screening tool to determine potential genes that may account for the role SALL4 plays in leukemogenesis. Analysis of SALL4 binding sites reveals that genes involved in cell death, cancer, DNA replication/repair, and cell cycle were highly enriched (p<0.05). These genes include 38 important apoptosis-inducing genes (TNF, TP53, PTEN, CARD9, CARD11, CYCS, LTA) and apoptosis-inhibiting genes (Bmi-1, BCL2, XIAP, DAD1, TEGT). Real-time PCR has shown that expression levels of these genes changed significantly after SALL4 knockdown, which ubiquitously led to cell apoptosis. Flow cytometry revealed that reduction of SALL4 expression in NB4 and other leukemia cell lines dramatically increased caspase-3, Annexin V, and DNA fragmentation activity.  Bromodeoxyuridine-incorporation assays showed decreased numbers of S phase cells and increased numbers of G1- and G2- phase cells indicating reduced DNA synthesis, consistent with results from cell proliferation assays.  In addition, NB4 cells that express low levels of SALL4 have significantly decreased tumorigenecity in immunodeficient mice.  Our studies provide a foundation in the development of leukemia stem cell-specific therapy by targeting SALL4.
Keywords: ChIP-chip

overall_design:
The global targets of SALL4 were determined using a NimbleGen promoter tiling array (2.7kb, information below) in the human cell line NB4.  Because SALL4 is thought to play a significant role in leukemogenesis we focused primarily on genes involved in apoptosis and only used the ChIP-chip array as a screening tool to identify potential genes that may bind these genes.  Upon identification and verification of apoptosis genes bound by SALL4 we utilized functional assays to determine the effect of SALL4 on these genes.  In addition, gene expression profiling was used to determine pathways functionally altered by Sall4 reduction.

Source: UCSC
Build: HG18
Probe Length: 50-75mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
Recommended Storage: Store arrays desiccated at room temperature.

Promoter tiling from 2200bp upstream and 500bp downstream of the transcription start site for RefSeq genes.

first: Jianchang

last: Yang

first: Li

last: Chai

first: Chong

last: Gao

first: Taylor

last: Fowles

first: Zaida

last: Alipio

first: Hien

last: Dang

first: Louis

last: Fink

last: Ward


title: Sulfate_Pyruvate_Desulfovibrio_G20

status: Public on Apr 25 2010

city: Raleigh

first: Stan

last: Martin

address: 1404 Crete Dr.

institute: Science Apps, L3C

summary: In order to genetically determine the essential components of electron flow during respiration of sulfate by the anaerobe Desulfovibrio desulfuricans G20, a growth mode independent of sulfate is needed. However, a mutant of the G20 strain, I2, lacking the abundant type-1 tetraheme cytochrome c3 (TpI-c3), was found to be altered in growth with  sulfate. Here we report that I2 does not reduce sulfate with electrons from pyruvate. In contrast, in the absence of sulfate, fermentative growth of I2 on pyruvate actually yielded slightly greater cellular protein than G20. When provided lactate with sulfate or when fermenting pyruvate, I2 produced more hydrogen and accumulated little if any succinate. G20 grows by fumarate dismutation and accumulates the theoretical 2:1 ratio of the end products, succinate and acetate, respectively. In contrast, I2 did not grow on fumarate alone. We inferred that TpI-c3 might be required for transfer of electrons to the membrane-bound fumarate reductase or for establishing a redox environment needed to trigger synthesis of the enzymes for succinate production. Microarray and proteomic analyses of gene and protein expression in I2 compared with G20 were consistent with increases in those enzymes predicted to be necessary for the generation of end products measured. These results support a role for the periplasmic TpI-c3 in electron flow from pyruvate to sulfate and in establishing conditions for enzyme production for fumarate dismutation. In addition, evidence for the simultaneous operation of respiratory electron flow and substrate-level phosphorylation was obtained from end product analysis.

overall_design: Strains I2 and G20 of Desulfovibrio desulfuricans were grown in different media. Four biological replicates of G20 on lactate media, and two biological replicates of G20 on Pyruvate media were compared with three replicates of I2 on lactate media and two replicates of I2 on pyruvate media.


title: embryogenesis col0-somatic embryogenesis

first: Delphine

last: Gey

summary: gnp07_regeneome_embryogenesis - embryogenesis col0 - Identify genes involved in somatic embryogenesis - compare embryogenic areas of a callus with undifferenciate area in the same callus

overall_design: 4 dye-swap - tissue comparison

first: M

last: Obellianne

first: J

last: Hervé

last: Chupeau

first: Y

first: S

last: Balzergue

last: Martin-Magniette

first: C

last: Pannetier


title: time course uranyl nitrate response-Transcriptomic analysis of uranyl response in Arabidopsis thaliana

status: Public on Jun 17 2008

first: Frederique

last: Bitton

address: 2 rue Gaston Cremieux

summary:
cea06-01_uranyl_nitrate - time course uranyl nitrate response - Dynamic analyses of transcriptomic response to urany l nitrate - Plants are grown on sand and transfert in hydroponic culture during 2 days and then expose or not to 50uM uranyl nitrate at pH 4.5 in water or only to water at pH 4.5. Roots and leaves were collected independently after 2h, 6h and 30h of treament.

Keywords: organ comparison,time course,treated vs untreated comparison

overall_design: 20 dye-swap - CATMA arrays

first: Jean-Pierre

middle: P

last: Renou

first: Nathalie

last: Leonhardt

first: Veronique

last: Hugouvieux

first: Marie-Laure